"uuid","repository link","title","author","contributor","publication year","abstract","subject topic","language","publication type","publisher","isbn","issn","patent","patent status","bibliographic note","access restriction","embargo date","faculty","department","research group","programme","project","coordinates"
"uuid:fe50979a-2553-453b-8cf7-c9757453ff19","http://resolver.tudelft.nl/uuid:fe50979a-2553-453b-8cf7-c9757453ff19","Engineering ssRNA tile filaments for (dis)assembly and membrane binding","De Franceschi, N. (TU Delft BN/Cees Dekker Lab); Hoogenberg, B. (TU Delft BN/Cees Dekker Lab); Katan, A.J. (TU Delft QN/Afdelingsbureau); Dekker, C. (TU Delft BN/Cees Dekker Lab)","","2024","Cytoskeletal protein filaments such as actin and microtubules confer mechanical support to cells and facilitate many cellular functions such as motility and division. Recent years have witnessed the development of a variety of molecular scaffolds that mimic such filaments. Indeed, filaments that are programmable and compatible with biological systems may prove useful in studying or substituting such proteins. Here, we explore the use of ssRNA tiles to build and modify filaments in vitro. We engineer a number of functionalities that are crucial to the function of natural proteins filaments into the ssRNA tiles, including the abilities to assemble or disassemble filaments, to tune the filament stiffness, to induce membrane binding, and to bind proteins. This work paves the way for building dynamic cytoskeleton-mimicking systems made out of rationally designed ssRNA tiles that can be transcribed in natural or synthetic cells.","","en","journal article","","","","","","","","","","","BN/Cees Dekker Lab","","",""
"uuid:e731427f-24d4-4e2d-a24a-4dc46ebf7972","http://resolver.tudelft.nl/uuid:e731427f-24d4-4e2d-a24a-4dc46ebf7972","Construction and application of an algebraic dual basis and the Fine-Scale Greens’ Function for computing projections and reconstructing unresolved scales","Shrestha, S. (TU Delft Aerodynamics; Universidad Politécnica de Madrid); Dekker, J. (TU Delft Numerical Analysis); Gerritsma, M.I. (TU Delft Aerodynamics); Hulshoff, S.J. (TU Delft Aerodynamics); Akkerman, I. (TU Delft Ship Hydromechanics and Structures)","","2024","In this paper, we build on the work of Hughes and Sangalli (2007) dealing with the explicit computation of the Fine-Scale Greens’ function. The original approach chooses a set of functionals associated with a projector to compute the Fine-Scale Greens’ function. The construction of these functionals, however, does not generalise to arbitrary projections, higher dimensions, or Spectral Element methods. We propose to generalise the construction of the required functionals by using dual functions. These dual functions can be directly derived from the chosen projector and are explicitly computable. We show how to find the dual functions for both the L2 and the H01 projections. We then go on to demonstrate that the Fine-Scale Greens’ functions constructed with the dual basis functions consistently reproduce the unresolved scales removed by the projector. The methodology is tested using one-dimensional Poisson and advection–diffusion problems, as well as a two-dimensional Poisson problem. We present the computed components of the Fine-Scale Greens’ function, and the Fine-Scale Greens’ function itself. These results show that the method works for arbitrary projections, in arbitrary dimensions. Moreover, the methodology can be applied to any Finite/Spectral Element or Isogeometric framework.","(Fine-Scale) Greens’ function; Advection–diffusion equation; Duality; Poisson equation; Projection; Variational multiscale","en","journal article","","","","","","","","","","","Aerodynamics","","",""
"uuid:e9a46f61-c1f3-49b1-b9e4-de5633921265","http://resolver.tudelft.nl/uuid:e9a46f61-c1f3-49b1-b9e4-de5633921265","Connecting the dots: key insights on ParB for chromosome segregation from single-molecule studies","Tišma, M. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Kaljević, Jovana (John Innes Centre); Gruber, Stephan (University of Lausanne); Le, Tung B.K. (John Innes Centre); Dekker, C. (TU Delft BN/Cees Dekker Lab)","","2024","Bacterial cells require DNA segregation machinery to properly distribute a genome to both daughter cells upon division. The most common system involved in chromosome and plasmid segregation in bacteria is the ParABS system. A core protein of this system - partition protein B (ParB) - regulates chromosome organization and chromosome segregation during the bacterial cell cycle. Over the past decades, research has greatly advanced our knowledge of the ParABS system. However, many intricate details of the mechanism of ParB proteins were only recently uncovered using in vitro single-molecule techniques. These approaches allowed the exploration of ParB proteins in precisely controlled environments, free from the complexities of the cellular milieu. This review covers the early developments of this field but emphasizes recent advances in our knowledge of the mechanistic understanding of ParB proteins as revealed by in vitro single-molecule methods. Furthermore, we provide an outlook on future endeavors in investigating ParB, ParB-like proteins, and their interaction partners.","atomic force microscopy; magnetic tweezers; optical tweezers; ParABS system; ParB; single-molecule studies","en","review","","","","","","","","","","","BN/Cees Dekker Lab","","",""
"uuid:8884bec9-7326-436a-8723-86870fb14c87","http://resolver.tudelft.nl/uuid:8884bec9-7326-436a-8723-86870fb14c87","Single-molecule visualization of twin-supercoiled domains generated during transcription","Janissen, R. (TU Delft BN/Bionanoscience); Barth, R. (TU Delft BN/Cees Dekker Lab); Polinder, M.L. (TU Delft BN/Cees Dekker Lab); van der Torre, J. (TU Delft BN/Cees Dekker Lab); Dekker, C. (TU Delft BN/Cees Dekker Lab)","","2024","Transcription-coupled supercoiling of DNA is a key factor in chromosome compaction and the regulation of genetic processes in all domains of life. It has become common knowledge that, during transcription, the DNA-dependent RNA polymerase (RNAP) induces positive supercoiling ahead of it (downstream) and negative supercoils in its wake (upstream), as rotation of RNAP around the DNA axis upon tracking its helical groove gets constrained due to drag on its RNA transcript. Here, we experimentally validate this so-called twin-supercoiled-domain model with in vitro real-time visualization at the single-molecule scale. Upon binding to the promoter site on a supercoiled DNA molecule, RNAP merges all DNA supercoils into one large pinned plectoneme with RNAP residing at its apex. Transcription by RNAP in real time demonstrates that up- and downstream supercoils are generated simultaneously and in equal portions, in agreement with the twin-supercoiled-domain model. Experiments carried out in the presence of RNases A and H, revealed that an additional viscous drag of the RNA transcript is not necessary for the RNAP to induce supercoils. The latter results contrast the current consensus and simulations on the origin of the twin-supercoiled domains, pointing at an additional mechanistic cause underlying supercoil generation by RNAP in transcription.","","en","journal article","","","","","","","","","","BN/Bionanoscience","BN/Cees Dekker Lab","","",""
"uuid:1ad5a3ec-6216-4a4a-8963-333493f3f680","http://resolver.tudelft.nl/uuid:1ad5a3ec-6216-4a4a-8963-333493f3f680","Author Correction: Testing pseudotopological and nontopological models for SMC-driven DNA loop extrusion against roadblock-traversal experiments (Scientific Reports, (2023), 13, 1, (8100), 10.1038/s41598-023-35359-2)","Barth, R. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Pradhan, B. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Kim, E. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Davidson, Iain F. (Research Institute of Molecular Pathology, Vienna); van der Torre, J. (TU Delft BN/Cees Dekker Lab); Peters, Jan‑Michael ‑M (Research Institute of Molecular Pathology, Vienna); Dekker, C. (TU Delft BN/Cees Dekker Lab)","","2023","Correction to: Scientific Reports, published online 19 May 2023 The original version of this Article contained an error in Figure 1b-1, where the fore- and background order of the strands “DNA” (in black) and “Brn1 Kleisin” (in green), were switched. The original Figure 1 and accompanying legend appear below. (Figure presented.) Description of the mechanism postulated by Shaltiel et al. for roadblock passage into an extruded loop on the DNA and a potential nontopological model. (a) The steps through the proposed DNA loop extrusion cycle are commented in more detail in steps 1–6 within the figure. Adapted from Ref.11. (b) Potential nontopological model which is closely analogous to the pseudotopological model, but with a slight variation in the DNA-SMC topology which allows particle bypass. The original Article has been corrected.","","en","journal article","","","","","","author correction DOI 10.1038/s41598-023-35359-2","","","","","BN/Cees Dekker Lab","","",""
"uuid:36b66022-b1b9-4da5-b8b8-27320ec8b946","http://resolver.tudelft.nl/uuid:36b66022-b1b9-4da5-b8b8-27320ec8b946","Modeling and Characterization of Pre-Charged Collapse-Mode CMUTs","Saccher, M. (TU Delft Electronic Components, Technology and Materials); Kawasaki, S. (TU Delft Electronic Components, Technology and Materials); Klootwijk, Johan (Philips Research); van Schaijk, Rob (Philips Engineering Solutions); Dekker, R. (TU Delft Electronic Components, Technology and Materials; Philips Engineering Solutions)","","2023","Recently, the applications of ultrasound transducers expanded from high-end diagnostic tools to point of care diagnostic devices and wireless power receivers for implantable devices. These new applications additionally require that the transducer technology must comply to biocompatibility and manufacturing scalability. In this respect, Capacitive Micromachined Ultrasound Transducers (CMUTs) have a strong advantage compared to the conventional PZT based transducers. However, current CMUTs require a large DC bias voltage for their operation, which limits the miniaturizability of these devices. In this study, we propose a pre-charged collapse-mode CMUT for immersive applications that can operate without an external bias by means of a charge trapping Al2O3 layer embedded in the dielectrics between the top and bottom electrodes. The built-in charge layer was analytically modeled and four layer stack combinations were investigated and characterized. The measurement results of the CMUTs were then used to fit the model and to quantify the amount and type of trapped charge. It was found that these devices polarize due to the ferroelectric-like behavior of the Al2O3, and the amount of charge stored in the charge-trapping layer was estimated to be approximately 0.02 C/m2. Their acoustic performance shows a transmit and receive sensitivity of 8.8 kPa/V and 13.1 V/MPa respectively. In addition, we show that increasing the charging temperature, the charging duration, and the charging voltage results in a higher amount of stored charge. Finally, results of ALT tests showed that these devices have a lifetime of more than 2.5 years at body temperature.","Ultrasonic imaging; Transducers; Electrodes; Performance evaluation; Biomembranes; Sensitivity; Electrostatics; CMUT; zero-bias CMUTs; collapse-mode CMUTs; ultrasound transducer","en","journal article","","","","","","","","","","","Electronic Components, Technology and Materials","","",""
"uuid:e74abb2e-16a9-4573-8906-521fb6543f33","http://resolver.tudelft.nl/uuid:e74abb2e-16a9-4573-8906-521fb6543f33","Nanopores as versatile single-molecule tools: From DNA turbines to protein sequencing","Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft)","","2023","","","en","journal article","","","","","","Green Open Access added to TU Delft Institutional Repository ‘You share, we take care!’ – Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.","","2023-08-10","","","BN/Cees Dekker Lab","","",""
"uuid:7a88d8da-6d4a-4798-a6ec-fc147519a30d","http://resolver.tudelft.nl/uuid:7a88d8da-6d4a-4798-a6ec-fc147519a30d","Optimizing single-molecule experimental approaches for the study of complex protein assemblies on DNA","Dekker, N.H. (TU Delft BN/Nynke Dekker Lab; Kavli institute of nanoscience Delft)","","2023","","","en","journal article","","","","","","Green Open Access added to TU Delft Institutional Repository ‘You share, we take care!’ – Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.","","2023-08-10","","","BN/Nynke Dekker Lab","","",""
"uuid:2c301c79-3b16-448e-991b-97ffec7546dd","http://resolver.tudelft.nl/uuid:2c301c79-3b16-448e-991b-97ffec7546dd","A new setup to study the influence of plant growth on the consolidation of dredged cohesive sediment","Barciela Rial, M. (TU Delft Environmental Fluid Mechanics; HAN University of Applied Sciences); Saaltink, Remon M. (Universiteit Utrecht; ARCADIS Nederland); van Kessel, Thijs (Deltares); Chassagne, C. (TU Delft Environmental Fluid Mechanics); Dekker, Stefan C. (Universiteit Utrecht; Open Universiteit, Heerlen); de Boer, Hugo J. (Universiteit Utrecht); Griffioen, Jasper (Universiteit Utrecht; TNO); Wassen, Martin J. (HAN University of Applied Sciences); Winterwerp, J.C. (TU Delft Environmental Fluid Mechanics)","","2023","Dredged cohesive sediment is progressively being used for wetland construction. However, little is known about the effect of plant growth during the self-weight consolidation of this sediment. In order to check the feasibility of such a study, a new experimental setup has been constructed. As an example, the effect of Phragmites australis on the consolidation and drainage of dredged sediment from Lake Markermeer, the Netherlands was investigated. The changes in pore water pressures at 10 cm depth intervals during a 129-day period in a column with and without plants were measured, while the water level was fixed at a constant level. Water loss via evaporation and plant transpiration was measured using Mariotte bottles and the photosynthetic processes — including plant transpiration — were measured with a LI-COR photosynthesis system. The results show that several processes initiated by Phragmites australis interfere with the physical processes involved in sediment drainage and consolidation. Phragmites australis effectively altered the pore pressure gradient via water extraction, especially between 40 and 60 cm from the bottom of the column. In this zone, daily cycles in pore pressures were observed which could directly be linked to the diurnal cycle of stomatal gas exchange. On average, water loss via evaporation and transpiration of leaves of Phragmites australis amounted to 3.9 mm day−1, whereas evaporation of bare soil amounted on average to 0.6 mm day−1. The depth-averaged hydraulic conductivity increased on average by 40% in presence of Phragmites australis. This pilot experiment confirms that the pressures sensors coupled with the new set-up enable to study pore pressure development over time and to link the effect of plant growth with alterations in water pressures profiles. A more systematic study with this set-up will in the future enable to quantify the effects of plant growth on consolidation.","consolidation; wetland; dredged sediment; plant growth; pore pressure; cohesive; drainage","en","journal article","","","","","","","","","","","Environmental Fluid Mechanics","","",""
"uuid:9371e760-5c94-4b8c-9912-db2d12963000","http://resolver.tudelft.nl/uuid:9371e760-5c94-4b8c-9912-db2d12963000","CAF-1 deposits newly synthesized histones during DNA replication using distinct mechanisms on the leading and lagging strands","Rouillon, Clément (University Medical Center Utrecht); Eckhardt, Bruna V. (University Medical Center Utrecht); Kollenstart, Leonie (University of Copenhagen); Gruss, Fabian (University Medical Center Utrecht); Verkennis, Alexander E.E. (University Medical Center Utrecht); Rondeel, Inge (University Medical Center Utrecht); van Laar, T. (TU Delft BN/Nynke Dekker Lab; Kavli institute of nanoscience Delft); Albanese, Pascal (Universiteit Utrecht); Dekker, N.H. (TU Delft BN/Nynke Dekker Lab; Kavli institute of nanoscience Delft)","","2023","During every cell cycle, both the genome and the associated chromatin must be accurately replicated. Chromatin Assembly Factor-1 (CAF-1) is a key regulator of chromatin replication, but how CAF-1 functions in relation to the DNA replication machinery is unknown. Here, we reveal that this crosstalk differs between the leading and lagging strand at replication forks. Using biochemical reconstitutions, we show that DNA and histones promote CAF-1 recruitment to its binding partner PCNA and reveal that two CAF-1 complexes are required for efficient nucleosome assembly under these conditions. Remarkably, in the context of the replisome, CAF-1 competes with the leading strand DNA polymerase epsilon (Polϵ) for PCNA binding. However, CAF-1 does not affect the activity of the lagging strand DNA polymerase Delta (Polδ). Yet, in cells, CAF-1 deposits newly synthesized histones equally on both daughter strands. Thus, on the leading strand, chromatin assembly by CAF-1 cannot occur simultaneously to DNA synthesis, while on the lagging strand these processes may be coupled. We propose that these differences may facilitate distinct parental histone recycling mechanisms and accommodate the inherent asymmetry of DNA replication.","","en","journal article","","","","","","","","","","","BN/Nynke Dekker Lab","","",""
"uuid:cee547a9-ce7d-4646-bf23-d664e0b19eda","http://resolver.tudelft.nl/uuid:cee547a9-ce7d-4646-bf23-d664e0b19eda","An Ultrasonically Powered System Using an AlN PMUT Receiver for Delivering Instantaneous mW-Range DC Power to Biomedical Implants","Rashidi, A. (TU Delft Bio-Electronics); Saccher, M. (TU Delft Electronic Components, Technology and Materials); Karuthedath, Cyril Baby (VTT Technical Research Center of Finland); Sebastian, Abhilash Thanniyil (VTT Technical Research Center of Finland); Savoia, Alessandro Stuart (University of Roma Tre); Lavigne, Frederik (Cyient); Stubbe, Frederic (Cyient); Dekker, R. (TU Delft Electronic Components, Technology and Materials; Philips); Giagka, Vasiliki (TU Delft Bio-Electronics; Fraunhofer Institute for Reliability and Microintegration IZM)","","2023","Aluminum Nitride (AlN) Piezoelectric Micromachined Ultrasonic Transducers (PMUTs) are gaining interest for biomedical implant power due to biocompatibility and lowtemperature processing. However, due to the low piezoelectric coefficient of AlN PMUTs, storage capacitors are often used to accumulate ultrasonic power transferred over an extended time. The accumulated energy is then used to power a DC load, which leads to a long start-up time, and insufficient duty cycle for some applications. We present an ultrasonically powered system for biomedical implants capable of delivering mW-range instantaneous power to DC loads, without pre-storing it. The system features a 25 mm2 AlN PMUT, an inductive matching network, and an application-specific power management integrated circuit(ASIC). For an acoustic intensity of 360 mW/cm2 at the surface of the PMUT, an open-circuit voltage of 1.11 V and an aperture efficiency of 30.5 % are measured. Furthermore, by connecting a series-matching inductor to the PMUT, the highest-reported power delivered to the load (PDL) of 6.4 mW is measured over an optimal load of 7.6 Ω. Finally, together with the ASIC and at the intensity of 108 mW/cm2, our system delivers 1.04 mW DC power to a 3.3 kΩ load, which is over two orders of magnitude higher than the previously reported average DC power for AlN PMUTs.","ultrasonic powering; AlN PMUT; matching network; power management; implants","en","conference paper","IEEE","","","","","Green Open Access added to TU Delft Institutional Repository 'You share, we take care!' - Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.","","2024-05-07","","","Bio-Electronics","","",""
"uuid:c3cad0fb-9174-49f0-b02b-767ba61a4fab","http://resolver.tudelft.nl/uuid:c3cad0fb-9174-49f0-b02b-767ba61a4fab","A Comparative Study of Si3N4 and Al2O3 as Dielectric Materials for Pre-Charged Collapse-Mode CMUTs","Saccher, M. (TU Delft Electronic Components, Technology and Materials); Schaijk, Rob van (Philips); Kawasaki, Shinnosuke (TNO); Klootwijk, Johan H. (Philips); Rashidi, A. (TU Delft Bio-Electronics); Giagka, Vasiliki (TU Delft Bio-Electronics; Fraunhofer Institute for Reliability and Microintegration IZM); Savoia, Alessandro Stuart (University of Roma Tre); Dekker, R. (TU Delft Electronic Components, Technology and Materials; Philips)","","2023","Capacitive Micromachined Ultrasound Transducers (CMUTs) have many advantages compared to other ultrasonic transducer technologies, especially for implantable devices. However, they require a high bias voltage for efficient operation. To eliminate the need for an external bias voltage, a charge storage layer can be embedded in the dielectric. This study aims to compare the performance of Si 3 N 4 and Al 2 O 3 when used as a charge storage layer. By measuring the shift in the C-V curve, Si 3 N 4 exhibits a larger shift than Al 2 O 3 , indicating a better charge-trapping capability. When using the pre-charged CMUTs as power receivers, the Si 3 N 4 version harvested up to 80 mW -only a few mW more than the Al 2 O 3 - with an efficiency of about 50 %. Accelerated Lifetime Tests predict a lifetime of about 7.8 and 1.2 years for Si 3 N 4 and Al 2 O 3 respectively.","pre-charged CMUT; Capacitive Micromachined Ultrasound Transducer; zero-bias transducers; ultrasonic power transfer","en","conference paper","IEEE","","","","","Green Open Access added to TU Delft Institutional Repository 'You share, we take care!' - Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.","","2024-05-07","","","Electronic Components, Technology and Materials","","",""
"uuid:e7d89c7a-794d-42f1-af01-4819700e61b0","http://resolver.tudelft.nl/uuid:e7d89c7a-794d-42f1-af01-4819700e61b0","Phase Distribution Efficiency of cm-Scale Ultrasonically Powered Receivers","Saccher, M. (TU Delft Electronic Components, Technology and Materials); Rashidi, A. (TU Delft Bio-Electronics); Savoia, Alessandro Stuart (University of Roma Tre); Giagka, Vasiliki (TU Delft Bio-Electronics; Fraunhofer Institute for Reliability and Microintegration IZM); Dekker, R. (TU Delft Electronic Components, Technology and Materials; Philips)","","2023","In the domain of ultrasonically powered biomedical implants, there is an increasing interest in cm-scale ultrasonic receivers (RX). However, when a single-element transducer is used as the RX transducer, an uneven phase distribution across the RX area can significantly reduce the harvestable power. In this paper, we investigate the impact of lateral and angular misalignment on the acoustic field phase distribution across the RX surface. We show that, for a single-element RX transducer, lateral misalignment has minimal effect on the harvestable power, whereas even small angular misalignments can cause a considerable reduction, especially for larger RX sizes. We present a potential solution that consists of subdividing a large RX transducer (e.g. 20 × 20mm2) into smaller elements, which significantly improves power transfer efficiency by taking advantage of the smaller phase variation across the surface of each element. The trade-offs between achieving a minimum acceptable power transfer efficiency and managing the increased complexity in packaging and matching circuitry are also discussed.","phase distribution efficiency; ultrasonic receivers; ultrasound power transfer; receiver partitioning","en","conference paper","IEEE","","","","","Green Open Access added to TU Delft Institutional Repository 'You share, we take care!' - Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.","","2024-05-07","","","Electronic Components, Technology and Materials","","",""
"uuid:2bc020a9-c5a4-49e4-aa74-615dba20d234","http://resolver.tudelft.nl/uuid:2bc020a9-c5a4-49e4-aa74-615dba20d234","Dynamic ParB–DNA interactions initiate and maintain a partition condensate for bacterial chromosome segregation","Tišma, M. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Janissen, R. (TU Delft BN/Bionanoscience; Kavli institute of nanoscience Delft); Antar, Hammam (University of Lausanne); Martin Gonzalez, A. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Barth, R. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Beekman, T.G.T. (Student TU Delft); van der Torre, J. (TU Delft BN/Cees Dekker Lab); Michieletto, Davide (University of Edinburgh); Gruber, Stephan (University of Lausanne); Dekker, C. (TU Delft BN/Cees Dekker Lab)","","2023","In most bacteria, chromosome segregation is driven by the ParABS system where the CTPase protein ParB loads at the parS site to trigger the formation of a large partition complex. Here, we present in vitro studies of the partition complex for Bacillus subtilis ParB, using single-molecule fluorescence microscopy and AFM imaging to show that transient ParB–ParB bridges are essential for forming DNA condensates. Molecular Dynamics simulations confirm that condensation occurs abruptly at a critical concentration of ParB and show that multimerization is a prerequisite for forming the partition complex. Magnetic tweezer force spectroscopy on mutant ParB proteins demonstrates that CTP hydrolysis at the N-terminal domain is essential for DNA condensation. Finally, we show that transcribing RNA polymerases can steadily traverse the ParB–DNA partition complex. These findings uncover how ParB forms a stable yet dynamic partition complex for chromosome segregation that induces DNA condensation and segregation while enabling replication and transcription.","OA-Fund TU Delft","en","journal article","","","","","","","","","","BN/Bionanoscience","BN/Cees Dekker Lab","","",""
"uuid:51720a5b-07db-43b9-b303-dd3c78f81082","http://resolver.tudelft.nl/uuid:51720a5b-07db-43b9-b303-dd3c78f81082","Aeropropulsive Performance Modelling of Over-The-Wing Propulsion at Incidence","Dekker, H.N.J. (Royal Netherlands Aerospace Centre NLR); Tuinstra, M (Royal Netherlands Aerospace Centre NLR); Baars, W.J. (TU Delft Aerodynamics); Scarano, F. (TU Delft Aerodynamics); Ragni, D. (TU Delft Wind Energy)","","2023","A semi-emperical model is developed, able to capture the aeropropulsive performance characteristics of Over-The-Wing propellers at incidence. The model is based on an hypothesis on the interactions of the propeller- and wing-induced flow fields. Effects of these interactions on the both the thrust and lift are written in a form in which the dominant design parameters appear explicitly. Both the flow hypothesis and model results are validated using experimental data of a single Over-The-Wing propeller. It is shown that for moderate angles of attack, the propulsive thrust is reduced by the wing’s circulation. For angles of attack greater than the stall angle of the isolated wing, thrust is increased by the ingestion of low momentum flow. The propeller is not able to delay stall but induces flow over the wing, which is returned as reduced pressure over the suction side. The model predictions closely match the experimental results for thrust, but integral loading measurements of the wing are required to validate the lift predictions.","","en","conference paper","American Institute of Aeronautics and Astronautics Inc. (AIAA)","","","","","","","","","","Aerodynamics","","",""
"uuid:a9e8251a-65d8-47ca-a441-feb690175770","http://resolver.tudelft.nl/uuid:a9e8251a-65d8-47ca-a441-feb690175770","Automated cell counting for Trypan blue-stained cell cultures using machine learning","Kuijpers, L.C. (TU Delft BN/Nynke Dekker Lab; Intravacc B.V.); van Veen, E.N.W. (TU Delft BN/Nynke Dekker Lab); Van der Pol, Leo (Intravacc B.V.); Dekker, N.H. (TU Delft BN/Nynke Dekker Lab)","","2023","Cell counting is a vital practice in the maintenance and manipulation of cell cultures. It is a crucial aspect of assessing cell viability and determining proliferation rates, which are integral to maintaining the health and functionality of a culture. Additionally, it is critical for establishing the time of infection in bioreactors and monitoring cell culture response to targeted infection over time. However, when cell counting is performed manually, the time involved can become substantial, particularly when multiple cultures need to be handled in parallel. Automated cell counters, which enable significant time reduction, are commercially available but remain relatively expensive. Here, we present a machine learning (ML) model based on YOLOv4 that is able to perform cell counts with a high accuracy (>95%) for Trypan blue-stained insect cells. Images of two distinctly different cell lines, Trichoplusia ni (High FiveTM; Hi5 cells) and Spodoptera frugiperda (Sf9), were used for training, validation, and testing of the model. The ML model yielded F1 scores of 0.97 and 0.96 for alive and dead cells, respectively, which represents a substantially improved performance over that of other cell counters. Furthermore, the ML model is versatile, as an F1 score of 0.96 was also obtained on images of Trypan blue-stained human embryonic kidney (HEK) cells that the model had not been trained on. Our implementation of the ML model comes with a straightforward user interface and can image in batches, which makes it highly suitable for the evaluation of multiple parallel cultures (e.g. in Design of Experiments). Overall, this approach for accurate classification of cells provides a fast, bias-free alternative to manual counting.","","en","journal article","","","","","","","","","","","BN/Nynke Dekker Lab","","",""
"uuid:9b2bbe3b-a8c2-423d-8977-176b9a0b6b86","http://resolver.tudelft.nl/uuid:9b2bbe3b-a8c2-423d-8977-176b9a0b6b86","Ultrasound Imaging with Pre-charged Collapse-Mode CMUTs","Kawasaki, S. (TNO); Saccher, M. (TU Delft Electronic Components, Technology and Materials); de Wijs, Willem-Jan (Philips); van den Brand, Jeroen (TNO); Dekker, R. (TU Delft Electronic Components, Technology and Materials; Philips)","","2023","Capacitive micromachined ultrasonic transducers (CMUTs) with a built-in charge layer are known as a pre-charged CMUT. In our prior work, we have shown how to model and characterize the charges inside the pre-charged collapse-mode CMUT and conducted life-time test that showed that the charges trapped inside the dielectric were stable in the order of years [1]. However, our prior work focused on the use of pre-charged collapse-mode CMUTs as a way to achieve ultrasound power reception, which does not require the CMUT to be actively driven. In this work, for the first time we use pre-charged collapse-mode CMUTs with an Al2O3 charge-trapping layer to create a B-mode ultrasound image. Thus, this work shows the first example that pre-charged collapse-mode CMUTs can fully operate with only an AC voltage.","CMUT; pre-charged CMUT; wearable ultrasound","en","conference paper","IEEE","","","","","Green Open Access added to TU Delft Institutional Repository 'You share, we take care!' - Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.","","2024-05-07","","","Electronic Components, Technology and Materials","","",""
"uuid:1ba0d52e-a233-4d54-b8ec-4700ecee5997","http://resolver.tudelft.nl/uuid:1ba0d52e-a233-4d54-b8ec-4700ecee5997","Looping the Genome with SMC Complexes","Kim, Eugene (Max Planck Insitute of Biophysics, Frankfurt); Barth, R. (TU Delft BN/Cees Dekker Lab); Dekker, C. (TU Delft BN/Cees Dekker Lab)","","2023","SMC (structural maintenance of chromosomes) protein complexes are an evolutionarily conserved family of motor proteins that hold sister chromatids together and fold genomes throughout the cell cycle by DNA loop extrusion. These complexes play a key role in a variety of functions in the packaging and regulation of chromosomes, and they have been intensely studied in recent years. Despite their importance, the detailed molecular mechanism for DNA loop extrusion by SMC complexes remains unresolved. Here, we describe the roles of SMCs in chromosome biology and particularly review in vitro single-molecule studies that have recently advanced our understanding of SMC proteins. We describe the mechanistic biophysical aspects of loop extrusion that govern genome organization and its consequences.","DNA loop extrusion; genome organization; single-molecule studies; SMC complexes","en","review","","","","","","","","","","","BN/Cees Dekker Lab","","",""
"uuid:7fc47989-1d98-40b1-ba87-3bd189025859","http://resolver.tudelft.nl/uuid:7fc47989-1d98-40b1-ba87-3bd189025859","How do molecular motors fold the genome?","Dekker, C. (TU Delft BN/Cees Dekker Lab); Haering, Christian H. (Julius-Maximilians University); Peters, Jan Michael (Campus-Vienna-Biocenter 1); Rowland, B.D. (TU Delft BN/Benjamin Rowland Lab; Netherlands Cancer Institute)","","2023","A potential mechanism of DNA loop extrusion by molecular motors is discussed.","","en","journal article","","","","","","Green Open Access added to TU Delft Institutional Repository ‘You share, we take care!’ – Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.","","2024-05-10","","","BN/Cees Dekker Lab","","",""
"uuid:53e8ba52-452a-4951-b3f3-c284f105dff0","http://resolver.tudelft.nl/uuid:53e8ba52-452a-4951-b3f3-c284f105dff0","DAIS: The Delft Database of EEG Recordings of Dutch Articulated and Imagined Speech","Dekker, Bo (Student TU Delft); Schouten, A.C. (TU Delft Biomechanical Engineering); Scharenborg, O.E. (TU Delft Multimedia Computing)","","2023","Silent speech interfaces could enable people who lost the ability to use their voice or gestures to communicate with the external world, e.g., through decoding the person’s brain signals when imagining speech. Only a few and small databases exist that allow for the development and training of brain computer interfaces (BCIs) that can decode imagined speech from recorded brain signals. Here, we present an open database consisting of electroencephalography (EEG) and speech data from 20 participants recorded during the covert (imagined) and actual articulation of 15 Dutch prompts. A validation speaker-independent classification experiment using a ResNet-50 model with spatial-spectral-temporal features extracted from the EEG signals obtained an average accuracy of 70.6% for the classification of rest vs. covert vs. articulated speech trials. This and observed structural differences in the EEG signals between covert and articulated speech demonstrate that the EEG signals in the three classes contain discriminative information.","Brain computer interfaces; covert (imagined) speech; , electroencephalography (EEG); ResNet","en","conference paper","IEEE","","","","","Green Open Access added to TU Delft Institutional Repository 'You share, we take care!' - Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.","","2023-11-05","","Biomechanical Engineering","Multimedia Computing","","",""
"uuid:37e3d82e-2bc7-4b92-bad0-320d931af6a8","http://resolver.tudelft.nl/uuid:37e3d82e-2bc7-4b92-bad0-320d931af6a8","Directing Min protein patterns with advective bulk flow","Meindlhumer, S. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Brauns, Fridtjof (Ludwig Maximilians University); Finžgar, Jernej Rudi (Ludwig Maximilians University); Kerssemakers, J.W.J. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Frey, Erwin (Ludwig Maximilians University; Max Planck School Matter to Life, Munich)","","2023","The Min proteins constitute the best-studied model system for pattern formation in cell biology. We theoretically predict and experimentally show that the propagation direction of in vitro Min protein patterns can be controlled by a hydrodynamic flow of the bulk solution. We find downstream propagation of Min wave patterns for low MinE:MinD concentration ratios, upstream propagation for large ratios, but multistability of both propagation directions in between. Whereas downstream propagation can be described by a minimal model that disregards MinE conformational switching, upstream propagation can be reproduced by a reduced switch model, where increased MinD bulk concentrations on the upstream side promote protein attachment. Our study demonstrates that a differential flow, where bulk flow advects protein concentrations in the bulk, but not on the surface, can control surface-pattern propagation. This suggests that flow can be used to probe molecular features and to constrain mathematical models for pattern-forming systems.","","en","journal article","","","","","","","","","","","BN/Cees Dekker Lab","","",""
"uuid:8f682970-d1c9-4bd0-af34-a4b92cff1957","http://resolver.tudelft.nl/uuid:8f682970-d1c9-4bd0-af34-a4b92cff1957","Partial and complete replanning of an intermodal logistic system under disruptions","Akyüz, M. Hakan (Erasmus Universiteit Rotterdam); Dekker, Rommert (Erasmus Universiteit Rotterdam); Sharif Azadeh, S. (TU Delft Transport and Planning)","","2023","The exclusive and excessive use of long-distance road transportation is not suitable way to reduce the negative environmental impacts of logistics systems. Intermodal transport, combining road with other transport modes, has the potential to reduce both operating costs and carbon footprints. One of the reasons for the low share of intermodal transport is its requirement for the coordination of scheduled transport services that can result in reducing reliability in case of disruptions due to the arrival of new shipment orders, fluctuations in shipment quantities, delays, and service cancellations within the network. This calls for reliable and efficient algorithms to replan the shipments’ distribution. In this paper, the replanning problem is formulated as a path-based multi-commodity network flows. We provide two different network topologies, one of which is based on a time–space network, while the other embeds time aspect in a highly scalable alternative structure to large transportation networks. We propose a column generation method whose pricing sub-problems are presented as resource constrained shortest path problem solved via a tailored label-correcting algorithm. We look at the pros and cons of complete and partial replanning in case of disruption and provide managerial insights for intermodal networks. An extensive set of computational experiments is presented on realistic instances being generated with the consultation of our industrial partners for a logistic network including railways, waterways, and roads. The promising outcomes validate the efficiency of the proposed approach that can be easily adjusted to real-time intermodal logistic replanning.","Column generation; Disruptions; Multi-commodity network flow; Replanning intermodal transportation","en","journal article","","","","","","","","","","","Transport and Planning","","",""
"uuid:a82db596-c4d8-4a33-8f62-3dd51b302e2d","http://resolver.tudelft.nl/uuid:a82db596-c4d8-4a33-8f62-3dd51b302e2d","The archaeal Cdv cell division system","Blanch Jover, A. (TU Delft BN/Cees Dekker Lab); Dekker, C. (TU Delft BN/Cees Dekker Lab)","","2023","The Cdv system is the protein machinery that performs cell division and other membrane-deforming processes in a subset of archaea. Evolutionarily, the system is closely related to the eukaryotic ESCRT machinery, with which it shares many structural and functional similarities. Since its first description 15 years ago, the understanding of the Cdv system progressed rather slowly, but recent discoveries sparked renewed interest and insights. The emerging physical picture appears to be that CdvA acts as a membrane anchor, CdvB as a scaffold that localizes division to the mid-cell position, CdvB1 and CvdB2 as the actual constriction machinery, and CdvC as the ATPase that detaches Cdv proteins from the membrane. This paper provides a comprehensive overview of the research done on Cdv and explains how this relatively understudied machinery acts to perform its cell-division function. Understanding of the Cdv system helps to better grasp the biophysics and evolution of archaea, and furthermore provides new opportunities for the bottom-up building of a divisome for synthetic cells.","archaea; Cdv System; Cell division; ESCRT-III; synthetic cells","en","review","","","","","","Green Open Access added to TU Delft Institutional Repository ‘You share, we take care!’ – Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.","","2023-12-01","","","BN/Cees Dekker Lab","","",""
"uuid:aaf7472e-a5a4-49a7-9e4e-c772e9d26e12","http://resolver.tudelft.nl/uuid:aaf7472e-a5a4-49a7-9e4e-c772e9d26e12","MukBEF-dependent chromosomal organization in widened Escherichia coli","Japaridze, A. (TU Delft Dynamics of Micro and Nano Systems; TU Delft BN/Bionanoscience; Kavli institute of nanoscience Delft); van Wee, R.G. (TU Delft BN/Chirlmin Joo Lab; Kavli institute of nanoscience Delft); Gogou, C. (TU Delft BN/Dimphna Meijer Lab; Kavli institute of nanoscience Delft); Kerssemakers, J.W.J. (TU Delft BN/Cees Dekker Lab; TU Delft BN/Bionanoscience; Kavli institute of nanoscience Delft); van den Berg, D.F. (TU Delft BN/Stan Brouns Lab); Dekker, C. (TU Delft BN/Cees Dekker Lab; TU Delft BN/Bionanoscience; Kavli institute of nanoscience Delft)","","2023","The bacterial chromosome is spatially organized through protein-mediated compaction, supercoiling, and cell-boundary confinement. Structural Maintenance of Chromosomes (SMC) complexes are a major class of chromosome-organizing proteins present throughout all domains of life. Here, we study the role of the Escherichia coli SMC complex MukBEF in chromosome architecture and segregation. Using quantitative live-cell imaging of shape-manipulated cells, we show that MukBEF is crucial to preserve the toroidal topology of the Escherichia coli chromosome and that it is non-uniformly distributed along the chromosome: it prefers locations toward the origin and away from the terminus of replication, and it is unevenly distributed over the origin of replication along the two chromosome arms. Using an ATP hydrolysis-deficient MukB mutant, we confirm that MukBEF translocation along the chromosome is ATP-dependent, in contrast to its loading onto DNA. MukBEF and MatP are furthermore found to be essential for sister chromosome decatenation. We propose a model that explains how MukBEF, MatP, and their interacting partners organize the chromosome and contribute to sister segregation. The combination of bacterial cell-shape modification and quantitative fluorescence microscopy paves way to investigating chromosome-organization factors in vivo.","chromosome segregation; E. coli; MatP; MukBEF; nucleoid architecture; SMC","en","journal article","","","","","","","","","","BN/Bionanoscience","Dynamics of Micro and Nano Systems","","",""
"uuid:9fd37e6d-a9a6-465b-b43f-e01f4cead794","http://resolver.tudelft.nl/uuid:9fd37e6d-a9a6-465b-b43f-e01f4cead794","Principles and best practices of optimizing a micromirror-based multicolor TIRF microscopy system","Mc Cluskey, K.A. (TU Delft BN/Nynke Dekker Lab); Dekker, N.H. (TU Delft BN/Nynke Dekker Lab)","","2023","TIRF (Total Internal Reflection Fluorescence) microscopy is a powerful tool for measuring the intra- and intermolecular dynamics of fluorescently-labeled single molecules. As TIRF measurements move to more complex biological systems with more fluorescent probes, the multi-band-pass dichroic that separates excitation from emission becomes limiting for the microscope's detection efficiency. To avoid this, multicolor colocalization-based experiments can employ “micromirror” (mm)TIRF, which replaces the dichroic with two 45°-angled rod mirrors that control the TIR excitation beam(s). Whereas a dichroic spectrally separates excitation and emission wavelengths, the micromirrors act to spatially separate the excitation beams from the collected emission photons within the objective lens itself. Comprehensive control of the TIR beam in mmTIRF can yield excellent signal to noise, and hence data quality, but at the price of increased optical complexity. Here, we introduce the theory behind these additional optical components and provide practical advice from our experience on the best way to set up, align, optimize, and maintain a mmTIRF instrument. We also demonstrate the practical effects of small misalignments to illustrate both the optimized signal quality and the degree of accuracy required to achieve it. We hope that this guide increases the accessibility of this type of instrumentation and helps researchers use it to produce data of the highest quality possible.","(co)Localization microscopy; CoSMoS; Micromirror; Single-molecule fluorescence microscopy; TIRF","en","journal article","","","","","","","","","","","BN/Nynke Dekker Lab","","",""
"uuid:8a5844c1-360e-41bd-8d05-b5cbb7c5a3ad","http://resolver.tudelft.nl/uuid:8a5844c1-360e-41bd-8d05-b5cbb7c5a3ad","CTCF is a DNA-tension-dependent barrier to cohesin-mediated loop extrusion","Davidson, Iain F. (Research Institute of Molecular Pathology, Vienna); Barth, R. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Zaczek, Maciej (Research Institute of Molecular Pathology, Vienna); van der Torre, J. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Tang, Wen (Research Institute of Molecular Pathology, Vienna); Nagasaka, Kota (Research Institute of Molecular Pathology, Vienna); Janissen, R. (TU Delft BN/Bionanoscience; Kavli institute of nanoscience Delft); Kerssemakers, J.W.J. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Wutz, Gordana (Research Institute of Molecular Pathology, Vienna); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Peters, Jan Michael (Research Institute of Molecular Pathology, Vienna)","","2023","In eukaryotes, genomic DNA is extruded into loops by cohesin1. By restraining this process, the DNA-binding protein CCCTC-binding factor (CTCF) generates topologically associating domains (TADs)2,3 that have important roles in gene regulation and recombination during development and disease1,4–7. How CTCF establishes TAD boundaries and to what extent these are permeable to cohesin is unclear8. Here, to address these questions, we visualize interactions of single CTCF and cohesin molecules on DNA in vitro. We show that CTCF is sufficient to block diffusing cohesin, possibly reflecting how cohesive cohesin accumulates at TAD boundaries, and is also sufficient to block loop-extruding cohesin, reflecting how CTCF establishes TAD boundaries. CTCF functions asymmetrically, as predicted; however, CTCF is dependent on DNA tension. Moreover, CTCF regulates cohesin’s loop-extrusion activity by changing its direction and by inducing loop shrinkage. Our data indicate that CTCF is not, as previously assumed, simply a barrier to cohesin-mediated loop extrusion but is an active regulator of this process, whereby the permeability of TAD boundaries can be modulated by DNA tension. These results reveal mechanistic principles of how CTCF controls loop extrusion and genome architecture.","","en","journal article","","","","","","","","","","BN/Bionanoscience","BN/Cees Dekker Lab","","",""
"uuid:5e9d801f-8f3b-4651-8cb4-95f38a9d7e57","http://resolver.tudelft.nl/uuid:5e9d801f-8f3b-4651-8cb4-95f38a9d7e57","Single-Molecule Structure and Topology of Kinetoplast DNA Networks","He, P. (TU Delft BN/Cees Dekker Lab; Southeast University; Kavli institute of nanoscience Delft); Katan, A.J. (TU Delft QN/Afdelingsbureau; Kavli institute of nanoscience Delft); Tubiana, Luca (Università di Trento; University of Vienna); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Michieletto, Davide (University of Edinburgh)","","2023","Kinetoplast DNA (kDNA) is a two-dimensional Olympic-ring-like network of mutually linked DNA minicircles found in certain parasites called trypanosomes. Understanding the self-assembly and replication of this structure are not only major open questions in biology but can also inform the design of synthetic topological materials. Here, we report the first high-resolution, single-molecule study of kDNA network topology using AFM and steered molecular dynamics simulations. We map out the DNA density within the network and the distribution of linking number and valence of the minicircles. We also characterize the DNA hubs that surround the network and show that they cause a buckling transition akin to that of a 2D elastic thermal sheet in the bulk. Intriguingly, we observe a broad distribution of density and valence of the minicircles, indicating heterogeneous network structure and individualism of different kDNA structures. Finally, we estimate the 2D Young modulus of the network to be orders of magnitude smaller than that of other 2D materials. Our findings explain outstanding questions in the field and offer single-molecule insights into the properties of a unique topological material.","","en","journal article","","","","","","","","","","","BN/Cees Dekker Lab","","",""
"uuid:558e0b18-ced1-411d-b8e0-dd2783a9a3f2","http://resolver.tudelft.nl/uuid:558e0b18-ced1-411d-b8e0-dd2783a9a3f2","Correction: Aeropropulsive Performance Modelling of Over-The-Wing Propulsion at Incidence","Dekker, H.N.J. (TU Delft Wind Energy); Tuinstra, Marthijn (Royal Netherlands Aerospace Centre NLR); Baars, W.J. (TU Delft Aerodynamics); Scarano, F. (TU Delft Aerodynamics); Ragni, D. (TU Delft Wind Energy)","","2023","","","en","conference paper","","","","","","","","","","","Wind Energy","","",""
"uuid:fd58024b-d0d6-4800-9c71-9d84b49d3206","http://resolver.tudelft.nl/uuid:fd58024b-d0d6-4800-9c71-9d84b49d3206","Zero-Mode Waveguide Nanowells for Single-Molecule Detection in Living Cells","Yang, Sora (University Medical Center Utrecht; Koninklijke Nederlandse Akademie van Wetenschappen (KNAW)); Klughammer, N. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Barth, A. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Tanenbaum, M. (TU Delft BN/Bionanoscience; University Medical Center Utrecht; Koninklijke Nederlandse Akademie van Wetenschappen (KNAW)); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft)","","2023","Single-molecule fluorescence imaging experiments generally require sub-nanomolar protein concentrations to isolate single protein molecules, which makes such experiments challenging in live cells due to high intracellular protein concentrations. Here, we show that single-molecule observations can be achieved in live cells through a drastic reduction in the observation volume using overmilled zero-mode waveguides (ZMWs- subwavelength-size holes in a metal film). Overmilling of the ZMW in a palladium film creates a nanowell of tunable size in the glass layer below the aperture, which cells can penetrate. We present a thorough theoretical and experimental characterization of the optical properties of these nanowells over a wide range of ZMW diameters and overmilling depths, showing an excellent signal confinement and a 5-fold fluorescence enhancement of fluorescent molecules inside nanowells. ZMW nanowells facilitate live-cell imaging as cells form stable protrusions into the nanowells. Importantly, the nanowells greatly reduce the cytoplasmic background fluorescence, enabling the detection of individual membrane-bound fluorophores in the presence of high cytoplasmic expression levels, which could not be achieved with TIRF microscopy. Zero-mode waveguide nanowells thus provide great potential to study individual proteins in living cells.","fluorescence correlation spectroscopy; fluorescence enhancement; fluorescence microscopy; live-cell imaging; palladium; single-molecule fluorescence; zero-mode waveguide","en","journal article","","","","","","","","","","BN/Bionanoscience","BN/Cees Dekker Lab","","",""
"uuid:a9346733-a82d-4692-972f-4ac966078db0","http://resolver.tudelft.nl/uuid:a9346733-a82d-4692-972f-4ac966078db0","Supercoiling-dependent DNA binding: quantitative modeling and applications to bulk and single-molecule experiments","Kolbeck, Pauline J. (Universiteit Utrecht; Ludwig Maximilians University); Tišma, M. (TU Delft BN/Cees Dekker Lab); Analikwu, B.T. (TU Delft BN/Cees Dekker Lab); Vanderlinden, Willem (Ludwig Maximilians University); Dekker, C. (TU Delft BN/Cees Dekker Lab); Lipfert, Jan (Ludwig Maximilians University; Universiteit Utrecht)","","2023","DNA stores our genetic information and is ubiquitous in applications, where it interacts with binding partners ranging from small molecules to large macromolecular complexes. Binding is modulated by mechanical strains in the molecule and can change local DNA structure. Frequently, DNA occurs in closed topological forms where topology and supercoiling add a global constraint to the interplay of binding-induced deformations and strain-modulated binding. Here, we present a quantitative model with a straight-forward numerical implementation of how the global constraints introduced by DNA topology modulate binding. We focus on fluorescent intercalators, which unwind DNA and enable direct quantification via fluorescence detection. Our model correctly describes bulk experiments using plasmids with different starting topologies, different intercalators, and over a broad range of intercalator and DNA concentrations. We demonstrate and quantitatively model supercoiling-dependent binding in a single-molecule assay, where we directly observe the different intercalator densities going from supercoiled to nicked DNA. The single-molecule assay provides direct access to binding kinetics and DNA supercoil dynamics. Our model has broad implications for the detection and quantification of DNA, including the use of psoralen for UV-induced DNA crosslinking to quantify torsional tension in vivo, and for the modulation of DNA binding in cellular contexts.","","en","journal article","","","","","","","","","","","BN/Cees Dekker Lab","","",""
"uuid:deac6a5d-c41b-4642-86e8-f9c8317b011f","http://resolver.tudelft.nl/uuid:deac6a5d-c41b-4642-86e8-f9c8317b011f","Nucleotide binding halts diffusion of the eukaryotic replicative helicase during activation","Ramirez Montero, D.F. (TU Delft BN/Nynke Dekker Lab; Kavli institute of nanoscience Delft); Sanchez González, H. (TU Delft BN/Nynke Dekker Lab; Kavli institute of nanoscience Delft); van Veen, E.N.W. (TU Delft BN/Nynke Dekker Lab; TU Delft BN/Bionanoscience; Kavli institute of nanoscience Delft); van Laar, T. (TU Delft BN/Nynke Dekker Lab; Kavli institute of nanoscience Delft); Solano Hermosilla, B.P. (TU Delft BN/Nynke Dekker Lab; Kavli institute of nanoscience Delft); Diffley, John F.X. (Francis Crick Institute); Dekker, N.H. (TU Delft BN/Nynke Dekker Lab; Kavli institute of nanoscience Delft)","","2023","The eukaryotic replicative helicase CMG centrally orchestrates the replisome and leads the way at the front of replication forks. Understanding the motion of CMG on the DNA is therefore key to our understanding of DNA replication. In vivo, CMG is assembled and activated through a cell-cycle-regulated mechanism involving 36 polypeptides that has been reconstituted from purified proteins in ensemble biochemical studies. Conversely, single-molecule studies of CMG motion have thus far relied on pre-formed CMG assembled through an unknown mechanism upon overexpression of individual constituents. Here, we report the activation of CMG fully reconstituted from purified yeast proteins and the quantification of its motion at the single-molecule level. We observe that CMG can move on DNA in two ways: by unidirectional translocation and by diffusion. We demonstrate that CMG preferentially exhibits unidirectional translocation in the presence of ATP, whereas it preferentially exhibits diffusive motion in the absence of ATP. We also demonstrate that nucleotide binding halts diffusive CMG independently of DNA melting. Taken together, our findings support a mechanism by which nucleotide binding allows newly assembled CMG to engage with the DNA within its central channel, halting its diffusion and facilitating the initial DNA melting required to initiate DNA replication.","","en","journal article","","","","","","","","","","BN/Bionanoscience","BN/Nynke Dekker Lab","","",""
"uuid:6328df2c-be3e-4db5-b373-8d552f786fee","http://resolver.tudelft.nl/uuid:6328df2c-be3e-4db5-b373-8d552f786fee","A chromatinized origin reduces the mobility of ORC and MCM through interactions and spatial constraint","Sanchez González, H. (TU Delft BN/Nynke Dekker Lab; Kavli institute of nanoscience Delft); Liu, Z. (TU Delft BN/Nynke Dekker Lab; Kavli institute of nanoscience Delft); van Veen, E.N.W. (TU Delft BN/Nynke Dekker Lab; Kavli institute of nanoscience Delft); van Laar, T. (TU Delft BN/Nynke Dekker Lab; Kavli institute of nanoscience Delft); Diffley, John F.X. (Francis Crick Institute); Dekker, N.H. (TU Delft BN/Nynke Dekker Lab; Kavli institute of nanoscience Delft)","","2023","Chromatin replication involves the assembly and activity of the replisome within the nucleosomal landscape. At the core of the replisome is the Mcm2-7 complex (MCM), which is loaded onto DNA after binding to the Origin Recognition Complex (ORC). In yeast, ORC is a dynamic protein that diffuses rapidly along DNA, unless halted by origin recognition sequences. However, less is known about the dynamics of ORC proteins in the presence of nucleosomes and attendant consequences for MCM loading. To address this, we harnessed an in vitro single-molecule approach to interrogate a chromatinized origin of replication. We find that ORC binds the origin of replication with similar efficiency independently of whether the origin is chromatinized, despite ORC mobility being reduced by the presence of nucleosomes. Recruitment of MCM also proceeds efficiently on a chromatinized origin, but subsequent movement of MCM away from the origin is severely constrained. These findings suggest that chromatinized origins in yeast are essential for the local retention of MCM, which may facilitate subsequent assembly of the replisome.","","en","journal article","","","","","","","","","","","BN/Nynke Dekker Lab","","",""
"uuid:0cfc15e2-ead8-4ebe-ae28-d10a09d6a76f","http://resolver.tudelft.nl/uuid:0cfc15e2-ead8-4ebe-ae28-d10a09d6a76f","Unsteady flow behaviour of multi-rotors in ground proximity","Dekker, H.N.J. (TU Delft Wind Energy; National Aerospace Laboratory - Netherlands); Baars, W.J. (TU Delft Aerodynamics); Scarano, F. (TU Delft Aerodynamics); Tuinstra, Marthijn (National Aerospace Laboratory - Netherlands); Ragni, D. (TU Delft Wind Energy)","","2023","The unsteady flow behaviour of two side-by-side rotors in ground proximity is experimentally investigated. The rotors induce a velocity distribution interacting with the ground causing the radial expansion of the rotor wakes. In between the rotors, an interaction of the two wakes takes place, resulting in an upward flow similar to a fountain. Two types of flow topologies are examined and correspond to two different stand-off heights between the rotors and the ground: the first one where the height of the fountain remains below the rotor disks, and a second one where it emerges above, being re-ingested. The fountain unsteadiness is shown to increase when re-ingestion takes place, determining a location switch from one rotor disk to the other, multiple times during acquisition. Consequently, variable inflow conditions are imposed on each of the two rotors. The fountain dynamics is observed at a frequency that is about two orders of magnitude lower than the blade passing frequency. The dominant characteristic time scale is linked to the flow recirculation path, relating this to system parameters of thrust and ground stand-off height. The flow field is analysed using proper orthogonal decomposition, in which coupled modes are identified. Results from the modal analysis are used to formulate a simple dynamic flow model of the re-ingestion switching cycle.","Aerodynamics; Experimental aerodynamics; Ground proximity; Multi-rotor; Unsteady fountain flow","en","journal article","","","","","","","","","","","Wind Energy","","",""
"uuid:572005f8-f90c-407a-9fe2-93f38a4d60e5","http://resolver.tudelft.nl/uuid:572005f8-f90c-407a-9fe2-93f38a4d60e5","A DNA turbine powered by a transmembrane potential across a nanopore","Shi, X. (TU Delft BN/Cees Dekker Lab; Katholieke Universiteit Leuven; Kavli institute of nanoscience Delft); Pumm, Anna Katharina (Technische Universität München); Maffeo, Christopher (University of Illinois at Urbana-Champaign); Kohler, Fabian (Technische Universität München); Feigl, Elija (Technische Universität München); Zhao, W. (TU Delft RST/Storage of Electrochemical Energy; Kavli institute of nanoscience Delft); Verschueren, D.V. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Golestanian, Ramin (Max Planck Institute for Dynamics and Self-Organisation; University of Oxford); Aksimentiev, Aleksei (University of Illinois at Urbana-Champaign); Dietz, Hendrik (Technische Universität München); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft)","","2023","Rotary motors play key roles in energy transduction, from macroscale windmills to nanoscale turbines such as ATP synthase in cells. Despite our abilities to construct engines at many scales, developing functional synthetic turbines at the nanoscale has remained challenging. Here, we experimentally demonstrate rationally designed nanoscale DNA origami turbines with three chiral blades. These DNA nanoturbines are 24–27 nm in height and diameter and can utilize transmembrane electrochemical potentials across nanopores to drive DNA bundles into sustained unidirectional rotations of up to 10 revolutions s−1. The rotation direction is set by the designed chirality of the turbine. All-atom molecular dynamics simulations show how hydrodynamic flows drive this turbine. At high salt concentrations, the rotation direction of turbines with the same chirality is reversed, which is explained by a change in the anisotropy of the electrophoretic mobility. Our artificial turbines operate autonomously in physiological conditions, converting energy from naturally abundant electrochemical potentials into mechanical work. The results open new possibilities for engineering active robotics at the nanoscale.","","en","journal article","","","","","","","","","","","BN/Cees Dekker Lab","","",""
"uuid:53a7d176-6e40-4fe6-88de-1d4e10ba5eed","http://resolver.tudelft.nl/uuid:53a7d176-6e40-4fe6-88de-1d4e10ba5eed","Microwell-enhanced optical rapid antibiotic susceptibility testing of single bacteria","Roslon, I.E. (TU Delft Dynamics of Micro and Nano Systems; SoundCell B.V.); Japaridze, A. (TU Delft Dynamics of Micro and Nano Systems; SoundCell B.V.); Rodenhuis, Stef (Student TU Delft); Hamoen, Lieke (Student TU Delft); Ghatkesar, M.K. (TU Delft Micro and Nano Engineering); Steeneken, P.G. (TU Delft Dynamics of Micro and Nano Systems); Dekker, C. (TU Delft BN/Cees Dekker Lab); Alijani, F. (TU Delft Dynamics of Micro and Nano Systems)","","2023","Bacteria that are resistant to antibiotics present an increasing burden on healthcare. To address this emerging crisis, novel rapid antibiotic susceptibility testing (AST) methods are eagerly needed. Here, we present an optical AST technique that can determine the bacterial viability within 1 h down to a resolution of single bacteria. The method is based on measuring intensity fluctuations of a reflected laser focused on a bacterium in reflective microwells. Using numerical simulations, we show that both refraction and absorption of light by the bacterium contribute to the observed signal. By administering antibiotics that kill the bacteria, we show that the variance of the detected fluctuations vanishes within 1 h, indicating the potential of this technique for rapid sensing of bacterial antibiotic susceptibility. We envisage the use of this method for massively parallelizable AST tests and fast detection of drug-resistant pathogens.","Medical Microbiology; Microbiology","en","journal article","","","","","","","","","","","Dynamics of Micro and Nano Systems","","",""
"uuid:41a872d7-d65a-401f-9ef4-aa10844327eb","http://resolver.tudelft.nl/uuid:41a872d7-d65a-401f-9ef4-aa10844327eb","De novo fabrication of custom-sequence plasmids for the synthesis of long DNA constructs with extrahelical features","Ramirez Montero, D.F. (TU Delft BN/Nynke Dekker Lab; Kavli institute of nanoscience Delft); Liu, Z. (TU Delft BN/Nynke Dekker Lab; Kavli institute of nanoscience Delft); Dekker, N.H. (TU Delft BN/Nynke Dekker Lab; Kavli institute of nanoscience Delft)","","2023","DNA constructs for single-molecule experiments often require specific sequences and/or extrahelical/noncanonical structures to study DNA-processing mechanisms. The precise introduction of such structures requires extensive control of the sequence of the initial DNA substrate. A commonly used substrate in the synthesis of DNA constructs is plasmid DNA. Nevertheless, the controlled introduction of specific sequences and extrahelical/noncanonical structures into plasmids often requires several rounds of cloning on pre-existing plasmids whose sequence one cannot fully control. Here, we describe a simple and efficient way to synthesize 10.1-kb plasmids de novo using synthetic gBlocks that provides full control of the sequence. Using these plasmids, we developed a 1.5-day protocol to assemble 10.1-kb linear DNA constructs with end and internal modifications. As a proof of principle, we synthesize two different DNA constructs with biotinylated ends and one or two internal 3′ single-stranded DNA flaps, characterize them using single-molecule force and fluorescence spectroscopy, and functionally validate them by showing that the eukaryotic replicative helicase Cdc45/Mcm2-7/GINS (CMG) binds the 3′ single-stranded DNA flap and translocates in the expected direction. We anticipate that our approach can be used to synthesize custom-sequence DNA constructs for a variety of force and fluorescence single-molecule spectroscopy experiments to interrogate DNA replication, DNA repair, and transcription.","","en","journal article","","","","","","Green Open Access added to TU Delft Institutional Repository ‘You share, we take care!’ – Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.","","2024-05-14","","","BN/Nynke Dekker Lab","","",""
"uuid:46da84a0-473b-4720-b7e3-f54336f2ff5a","http://resolver.tudelft.nl/uuid:46da84a0-473b-4720-b7e3-f54336f2ff5a","Dynamin A as a one-component division machinery for synthetic cells","De Franceschi, N. (TU Delft BN/Cees Dekker Lab; Polish Academy of Sciences; Kavli institute of nanoscience Delft); Barth, R. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Meindlhumer, S. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Fragasso, A. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft)","","2023","Membrane abscission, the final cut of the last connection between emerging daughter cells, is an indispensable event in the last stage of cell division and in other cellular processes such as endocytosis, virus release or bacterial sporulation. However, its mechanism remains poorly understood, impeding its application as a cell-division machinery for synthetic cells. Here we use fluorescence microscopy and fluorescence recovery after photobleaching measurements to study the in vitro reconstitution of the bacterial protein dynamin A inside liposomes. Upon external reshaping of the liposomes into dumbbells, dynamin A self-assembles at the membrane neck, resulting in membrane hemi-scission and even full scission. Dynamin A proteins constitute a simple one-component division machinery capable of splitting dumbbell-shaped liposomes, marking an important step towards building a synthetic cell.","","en","journal article","","","","","","Green Open Access added to TU Delft Institutional Repository 'You share, we take care!' - Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.","","2024-04-05","","","BN/Cees Dekker Lab","","",""
"uuid:21750af7-55de-4dda-be73-d5dcbbe6fbee","http://resolver.tudelft.nl/uuid:21750af7-55de-4dda-be73-d5dcbbe6fbee","Identifying energy model fingerprints in mitigation scenarios","Dekker, Mark M. (Netherlands Environmental Assessment Agency; Universiteit Utrecht); Daioglou, Vassilis (Netherlands Environmental Assessment Agency; Universiteit Utrecht); Pietzcker, Robert (Potsdam Institute for Climate Impact Research); Rodrigues, Renato (Potsdam Institute for Climate Impact Research); de Boer, Harmen Sytze (Netherlands Environmental Assessment Agency); Dalla Longa, Francesco (TNO Energy and Materials Transition); Drouet, Laurent (Fondazione Centro Euro-Mediterraneo sui Cambiamenti Climatici); Emmerling, Johannes (Fondazione Centro Euro-Mediterraneo sui Cambiamenti Climatici); Fattahi, Amir (TNO Energy and Materials Transition); Fotiou, Theofano (E3-Modelling); Fragkos, Panagiotis (E3-Modelling); Fricko, Oliver (International Institute for Applied Systems Analysis, Laxenburg); Gusheva, E. (TU Delft Energie and Industrie); Harmsen, Mathijs (Netherlands Environmental Assessment Agency; Universiteit Utrecht); Huppmann, Daniel (International Institute for Applied Systems Analysis, Laxenburg); Kannavou, Maria (E3-Modelling); Krey, Volker (International Institute for Applied Systems Analysis, Laxenburg); Lombardi, F. (TU Delft Energie and Industrie); Luderer, Gunnar (Potsdam Institute for Climate Impact Research; Technical University of Berlin); Pfenninger, Stefan (TU Delft Energie and Industrie); Tsiropoulos, Ioannis (E3-Modelling); Zakeri, Behnam (International Institute for Applied Systems Analysis, Laxenburg); van der Zwaan, Bob (TNO Energy and Materials Transition; Universiteit van Amsterdam; Johns Hopkins University School of Advanced International Studies, Bologna); Usher, Will (KTH Royal Institute of Technology); van Vuuren, Detlef (Netherlands Environmental Assessment Agency; Universiteit Utrecht)","","2023","Energy models are used to study emissions mitigation pathways, such as those compatible with the Paris Agreement goals. These models vary in structure, objectives, parameterization and level of detail, yielding differences in the computed energy and climate policy scenarios. To study model differences, diagnostic indicators are common practice in many academic fields, for example, in the physical climate sciences. However, they have not yet been applied systematically in mitigation literature, beyond addressing individual model dimensions. Here we address this gap by quantifying energy model typology along five dimensions: responsiveness, mitigation strategies, energy supply, energy demand and mitigation costs and effort, each expressed through several diagnostic indicators. The framework is applied to a diagnostic experiment with eight energy models in which we explore ten scenarios focusing on Europe. Comparing indicators to the ensemble yields comprehensive ‘energy model fingerprints’, which describe systematic model behaviour and contextualize model differences for future multi-model comparison studies.","","en","journal article","","","","","","","","","","","Energie and Industrie","","",""
"uuid:9539c468-9e56-4683-a1e2-6fa528298d70","http://resolver.tudelft.nl/uuid:9539c468-9e56-4683-a1e2-6fa528298d70","Electrostatic control of the proximity effect in the bulk of semiconductor-superconductor hybrids","van Loo, N. (TU Delft QRD/Kouwenhoven Lab; TU Delft QuTech Advanced Research Centre; Eindhoven University of Technology; Kavli institute of nanoscience Delft); Mazur, G.P. (TU Delft QRD/Wimmer Group; TU Delft QuTech Advanced Research Centre; Kavli institute of nanoscience Delft); Dvir, T. (TU Delft QRD/Kouwenhoven Lab; TU Delft QuTech Advanced Research Centre; Kavli institute of nanoscience Delft); Wang, Guanzhong (TU Delft QRD/Wimmer Group; TU Delft QuTech Advanced Research Centre; Kavli institute of nanoscience Delft); Dekker, R.C. (TU Delft QN/Steele Lab; TU Delft QuTech Advanced Research Centre; Kavli institute of nanoscience Delft); Lemang, M.F. (TU Delft QN/Afdelingsbureau; TU Delft QuTech Advanced Research Centre; Kavli institute of nanoscience Delft); Sfiligoj, C. (TU Delft BUS/Quantum Delft; TU Delft QuTech Advanced Research Centre; Kavli institute of nanoscience Delft); Bordin, A. (TU Delft QRD/Kouwenhoven Lab; TU Delft QuTech Advanced Research Centre; Kavli institute of nanoscience Delft); van Driel, D. (TU Delft QRD/Kouwenhoven Lab; TU Delft QuTech Advanced Research Centre; Kavli institute of nanoscience Delft); Kouwenhoven, Leo P. (TU Delft QN/Kouwenhoven Lab; Kavli institute of nanoscience Delft)","","2023","The proximity effect in semiconductor-superconductor nanowires is expected to generate an induced gap in the semiconductor. The magnitude of this induced gap, together with the semiconductor properties like spin-orbit coupling and g-factor, depends on the coupling between the materials. It is predicted that this coupling can be adjusted through the use of electric fields. We study this phenomenon in InSb/Al/Pt hybrids using nonlocal spectroscopy. We show that these hybrids can be tuned such that the semiconductor and superconductor are strongly coupled. In this case, the induced gap is similar to the superconducting gap in the Al/Pt shell and closes only at high magnetic fields. In contrast, the coupling can be suppressed which leads to a strong reduction of the induced gap and critical magnetic field. At the crossover between the strong-coupling and weak-coupling regimes, we observe the closing and reopening of the induced gap in the bulk of a nanowire. Contrary to expectations, it is not accompanied by the formation of zero-bias peaks in the local conductance spectra. As a result, this cannot be attributed conclusively to the anticipated topological phase transition and we discuss possible alternative explanations.","","en","journal article","","","","","","","","","","","QRD/Kouwenhoven Lab","","",""
"uuid:68d24b7f-ad4a-49b8-abff-108f576a1db7","http://resolver.tudelft.nl/uuid:68d24b7f-ad4a-49b8-abff-108f576a1db7","Three-dimensional localization microscopy with increased axial precision through TIRF angle modulation","Fan, D. (TU Delft Team Carlas Smith); Cnossen, J.P. (TU Delft Team Carlas Smith); Hung, S. (TU Delft Team Carlas Smith); Kromm, D. (TU Delft Support Delft Center for Systems and Control); Dekker, N.H. (TU Delft BN/Nynke Dekker Lab); Verbiest, G.J. (TU Delft Dynamics of Micro and Nano Systems); Smith, C.S. (TU Delft Team Carlas Smith)","","2023","To better understand the interactions between biological molecules, a high optical resolution in all three dimensions is crucial. The intrinsically lower axial resolution of microscopes however, is a limiting factor in fluorescence imaging, correspondingly in fluorescence based single molecule localization microscopy (SMLM). Here, we present a method to improve the axial localization precision in SMLM by combining point-spread-function engineering with total internal reflection fluorescence (TIRF) fields with decay lengths that vary within the on-time of a fluorophore. Such time-varying illumination field intensity allows one to extract additional axial location information from the emitted photons. With this time varying illumination approach, we show that axial localization is improved two-fold over TIRF-based SMLM using astigmatic PSFs. We calculate theoretical resolution gains for various imaging conditions via the Cramér Rao Lower Bound (CRLB), a commonly used metric to compute the best attainable localization precision in SMLM.","PSF engineering; Single molecule localization microscopy; Super-resolution microscopy; TIRF microscopy; Total internal reflection fluorescence","en","journal article","","","","","","","","","","","Team Carlas Smith","","",""
"uuid:bcd05848-9b2b-4097-a87c-16f5d9496e96","http://resolver.tudelft.nl/uuid:bcd05848-9b2b-4097-a87c-16f5d9496e96","Testing pseudotopological and nontopological models for SMC-driven DNA loop extrusion against roadblock-traversal experiments","Barth, R. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Pradhan, B. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Kim, E. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Davidson, Iain F. (Research Institute of Molecular Pathology, Vienna); van der Torre, J. (TU Delft BN/Cees Dekker Lab); Peters, Jan Michael (Research Institute of Molecular Pathology, Vienna); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft)","","2023","DNA loop extrusion by structural-maintenance-of-chromosome (SMC) complexes has emerged as a primary organizing principle for chromosomes. The mechanism by which SMC motor proteins extrude DNA loops is still unresolved and much debated. The ring-like structure of SMC complexes prompted multiple models where the extruded DNA is topologically or pseudotopologically entrapped within the ring during loop extrusion. However, recent experiments showed the passage of roadblocks much bigger than the SMC ring size, suggesting a nontopological mechanism. Recently, attempts were made to reconcile the observed passage of large roadblocks with a pseudotopological mechanism. Here we examine the predictions of these pseudotopological models and find that they are not consistent with new experimental data on SMC roadblock encounters. Particularly, these models predict the formation of two loops and that roadblocks will reside near the stem of the loop upon encounter—both in contrast to experimental observations. Overall, the experimental data reinforce the notion of a nontopological mechanism for extrusion of DNA.","","en","journal article","","","","","","","","","","","BN/Cees Dekker Lab","","",""
"uuid:123505ce-8577-45f0-8b08-dae626231525","http://resolver.tudelft.nl/uuid:123505ce-8577-45f0-8b08-dae626231525","Detection of phosphorylation post-translational modifications along single peptides with nanopores","Nova, I.C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Ritmejeris, J. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Brinkerhoff, H.D. (TU Delft BN/Cees Dekker Lab; University of Washington; Kavli institute of nanoscience Delft); Koenig, T.J.R. (TU Delft BN/Bionanoscience; TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Gundlach, Jens H. (University of Washington); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft)","","2023","Current methods to detect post-translational modifications of proteins, such as phosphate groups, cannot measure single molecules or differentiate between closely spaced phosphorylation sites. We detect post-translational modifications at the single-molecule level on immunopeptide sequences with cancer-associated phosphate variants by controllably drawing the peptide through the sensing region of a nanopore. We discriminate peptide sequences with one or two closely spaced phosphates with 95% accuracy for individual reads of single molecules.","","en","journal article","","","","","","Green Open Access added to TU Delft Institutional Repository ‘You share, we take care!’ – Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.","","2023-12-29","","BN/Bionanoscience","BN/Cees Dekker Lab","","",""
"uuid:3670ec8a-5a12-4e4e-80ed-df5d52f0bb3d","http://resolver.tudelft.nl/uuid:3670ec8a-5a12-4e4e-80ed-df5d52f0bb3d","Diameter Dependence of Transport through Nuclear Pore Complex Mimics Studied Using Optical Nanopores","Klughammer, N. (TU Delft BN/Cees Dekker Lab); Barth, A. (TU Delft BN/Cees Dekker Lab); Dekker, Maurice (University Medical Center Groningen); Fragasso, A. (TU Delft BN/Cees Dekker Lab; TU Delft BN/Bionanoscience); Onck, Patrick R. (University Medical Center Groningen)","","2023","The nuclear pore complex (NPC) regulates the selective transport of large biomolecules through the nuclear envelope. As a model system for nuclear transport, we construct NPC mimics by functionalizing the pore walls of freestanding palladium zero-mode waveguides with the FG-nucleoporin Nsp1. This approach enables the measurement of single-molecule translocations through individual pores using optical detection. We probe the selectivity of Nsp1-coated pores by quantitatively comparing the translocation rates of the nuclear transport receptor Kap95 to the inert probe BSA over a wide range of pore sizes from 35 nm to 160 nm. Pores below 55 ± 5 nm show significant selectivity that gradually decreases for larger pores. This finding is corroborated by coarse-grained molecular-dynamics simulations of the Nsp1 mesh within the pore, which suggest that leakage of BSA occurs by diffusion through transient openings within the dynamic mesh. Furthermore, we experimentally observe a modulation of the BSA permeation when varying the concentration of Kap95. The results demonstrate the potential of single-molecule fluorescence measurements on biomimetic NPCs to elucidate the principles of nuclear transport.","","en","journal article","","","","","","","","","","BN/Bionanoscience","BN/Cees Dekker Lab","","",""
"uuid:6bc5af25-aaf5-41bc-9708-db555b3933bb","http://resolver.tudelft.nl/uuid:6bc5af25-aaf5-41bc-9708-db555b3933bb","Opto-electronic feedback control of membrane potential for real-time control of action potentials","Ördög, Balázs (Leiden University Medical Center); De Coster, Tim (Leiden University Medical Center); Dekker, Sven O. (Leiden University Medical Center); Bart, Cindy I. (Leiden University Medical Center); Zhang, Juan (Leiden University Medical Center); Boink, Gerard J.J. (Universiteit van Amsterdam); Bax, Wilhelmina H. (Leiden University Medical Center); Deng, Shanliang (TU Delft Electronic Components, Technology and Materials; Leiden University Medical Center); den Ouden, B.L. (TU Delft Electronic Components, Technology and Materials); de Vries, Antoine A.F. (Leiden University Medical Center); Pijnappels, Daniël A. (Leiden University Medical Center)","","2023","To unlock new research possibilities by acquiring control of action potential (AP) morphologies in excitable cells, we developed an opto-electronic feedback loop-based system integrating cellular electrophysiology, real-time computing, and optogenetic approaches and applied it to monolayers of heart muscle cells. This allowed accurate restoration and preservation of cardiac AP morphologies in the presence of electrical perturbations of different origin in an unsupervised, self-regulatory manner, without any prior knowledge of the disturbance. Moreover, arbitrary AP waveforms could be enforced onto these cells. Collectively, these results set the stage for the refinement and application of opto-electronic control systems to enable in-depth investigation into the regulatory role of membrane potential in health and disease.","action potential; membrane potential; cellular electrophysiology; feedback loop; real-time computing; optogenetics; Closed-loop control; system integration; heart muscle cells","en","journal article","","","","","","","","","","","Electronic Components, Technology and Materials","","",""
"uuid:e92cbc11-2a04-4b66-bff8-c021a4260347","http://resolver.tudelft.nl/uuid:e92cbc11-2a04-4b66-bff8-c021a4260347","Healthy computer working","Dekker, M.C. (TU Delft Applied Ergonomics and Design)","Vink, P. (promotor); Molenbroek, J.F.M. (copromotor); Delft University of Technology (degree granting institution)","2022","Repetitive Strain Injuries (RSI), also known as Work-Related Upper Limb Disorders (WRULD), surged in the early years of this millennium due to computer work. In this thesis, the magnitude, causes and consequences of this phenomenon for the student population of the Faculty of Industrial Design Engineering (IDE) at the Delft University of Technology (TU Delft) are investigated and described. Longitudinal surveys on RSI amongst IDE students over a 15-year period (2000-2014) show the trend in prevalence and severity of the complaints. From the year 2000 to the present, a multidisciplinary RSI prevention group is active to create awareness, provide information and practical sessions. The organised prevention activities and their scientific basis are introduced and discussed. Furthermore, ideas for products and product-service systems, aimed at preventing or reducing RSI and based on medical insights and understanding of RSI risk factors, are presented. These ideas, developed in IDE master graduation projects and one from industry, are evaluated in user tests and physiological experiments with potential users.
The knowledge and insights gained in this thesis are not only valuable for design students to realise healthy computer working, but also for other educational and professional computer workers.","RSI; WRULD; students; design; prevention; Intervention","en","doctoral thesis","","978-94-6421-758-2","","","","","","","","","Applied Ergonomics and Design","","",""
"uuid:4de4f0ea-08f8-4cf6-88a4-f8e9606c76a1","http://resolver.tudelft.nl/uuid:4de4f0ea-08f8-4cf6-88a4-f8e9606c76a1","A Microfluidic Cancer-on-Chip Platform Predicts Drug Response Using Organotypic Tumor Slice Culture","Chakrabarty, Sanjiban (Erasmus MC; Manipal School of Life Sciences); Quiros Solano, W.F. (TU Delft Electronic Components, Technology and Materials); Kuijten, Maayke M.P. (Erasmus MC); Haspels, Ben (Erasmus MC); Mallya, Sandeep (Manipal School of Life Sciences); van de Stolpe, Anja (Philips Research); Odijk, Hanny (Erasmus MC); van Weerden, Wytske M. (Erasmus MC); Dekker, R. (TU Delft Electronic Components, Technology and Materials; Philips Research)","","2022","Optimal treatment of cancer requires diagnostic methods to facilitate therapy choice and prevent ineffective treatments. Direct assessment of therapy response in viable tumor specimens could fill this diagnostic gap. Therefore, we designed a microfluidic platform for assessment of patient treatment response using tumor tissue slices under precisely controlled growth conditions. The optimized Cancer-on-Chip (CoC) platform maintained viability and sustained proliferation of breast and prostate tumor slices for 7 days. No major changes in tissue morphology or gene expression patterns were observed within this time frame, suggesting that the CoC system provides a reliable and effective way to probe intrinsic chemotherapeutic sensitivity of tumors. The customized CoC platform accurately predicted cisplatin and apalutamide treatment response in breast and prostate tumor xenograft models, respectively. The culture period for breast cancer could be extended up to 14 days without major changes in tissue morphology and viability. These culture characteristics enable assessment of treatment outcomes and open possibilities for detailed mechanistic studies. SIGNIFICANCE: The Cancer-on-Chip platform with a 6-well plate design incorporating silicon-based microfluidics can enable optimal patient-specific treatment strategies through parallel culture of multiple tumor slices and diagnostic assays using primary tumor material.","","en","journal article","","","","","","","","","","","Electronic Components, Technology and Materials","","",""
"uuid:df4e36ee-2da6-40da-9ac0-49b476451ff4","http://resolver.tudelft.nl/uuid:df4e36ee-2da6-40da-9ac0-49b476451ff4","Bulk Acoustic Wave Based Mocrfluidic Particle Sorting with Capacitive Micromachined Ultrasonic Transducers","Kawasaki, S. (TU Delft Electronic Components, Technology and Materials); Yeh, Jia-Jun (Student TU Delft); Saccher, M. (TU Delft Electronic Components, Technology and Materials); Li, Jian (Student TU Delft); Dekker, R. (Philips Research)","","2022","The main limitation of acoustic particle separation for microfluidic application is its low sorting efficiency. This is due to the weak coupling of surface acoustic waves (SAWs) into the microchannel. In this work, we demonstrate bulk acoustic wave (BAW) particle sorting using capacitive micromachined ultrasonic transducers (CMUTs) for the first time. A collapsed mode CMUT was driven in air to generate acoustic pressure within the silicon substrate in the in-plane direction of the silicon die. This acoustic pressure was coupled into a water droplet, positioned at the side of the CMUT die, and measured with an optical hydrophone. By using a beam steering approach, the ultrasound generated from 32 CMUT elements were added in-phase to generate a maximum peak-to-peak pressure of 0.9 MPa. Using this pressure, 10 µm latex beads were sorted almost instantaneously.","CMUT; Microfluidic particle sorting; Acoustic particle sorting; bulk acoustic wave","en","conference paper","IEEE","","","","","Green Open Access added to TU Delft Institutional Repository 'You share, we take care!' - Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.","","2022-08-11","","","Electronic Components, Technology and Materials","","",""
"uuid:5a3583d1-78cc-42d4-a103-1a30f9f1f989","http://resolver.tudelft.nl/uuid:5a3583d1-78cc-42d4-a103-1a30f9f1f989","Condensin extrudes DNA loops in steps up to hundreds of base pairs that are generated by ATP binding events","Ryu, J.K. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Rah, S.H. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Janissen, R. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Kerssemakers, J.W.J. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Bonato, Andrea (University of Edinburgh); Michieletto, Davide (University of Edinburgh); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft)","","2022","The condensin SMC protein complex organizes chromosomal structure by extruding loops of DNA. Its ATP-dependent motor mechanism remains unclear but likely involves steps associated with large conformational changes within the ∼50 nm protein complex. Here, using high-resolution magnetic tweezers, we resolve single steps in the loop extrusion process by individual yeast condensins. The measured median step sizes range between 20-40 nm at forces of 1.0-0.2 pN, respectively, comparable with the holocomplex size. These large steps show that, strikingly, condensin typically reels in DNA in very sizeable amounts with ∼200 bp on average per single extrusion step at low force, and occasionally even much larger, exceeding 500 bp per step. Using Molecular Dynamics simulations, we demonstrate that this is due to the structural flexibility of the DNA polymer at these low forces. Using ATP-binding-impaired and ATP-hydrolysis-deficient mutants, we find that ATP binding is the primary step-generating stage underlying DNA loop extrusion. We discuss our findings in terms of a scrunching model where a stepwise DNA loop extrusion is generated by an ATP-binding-induced engagement of the hinge and the globular domain of the SMC complex.","","en","journal article","","","","","","","","","","","BN/Cees Dekker Lab","","",""
"uuid:dfdeb7da-6405-4adc-8a79-3ff7d82af230","http://resolver.tudelft.nl/uuid:dfdeb7da-6405-4adc-8a79-3ff7d82af230","Focused ultrasound neuromodulation on a multiwell MEA","Saccher, M. (TU Delft Electronic Components, Technology and Materials); Kawasaki, S. (TU Delft Electronic Components, Technology and Materials); Proietti Onori, Martina (Erasmus MC); van Woerden, Geeske M. (Erasmus MC); Giagka, Vasiliki (TU Delft Bio-Electronics; Fraunhofer Institute for Reliability and Microintegration IZM); Dekker, R. (TU Delft Electronic Components, Technology and Materials; Philips Research)","","2022","Background
Microelectrode arrays (MEA) enable the measurement and stimulation of the electrical activity of cultured cells. The integration of other neuromodulation methods will significantly enhance the application range of MEAs to study their effects on neurons. A neuromodulation method that is recently gaining more attention is focused ultrasound neuromodulation (FUS), which has the potential to treat neurological disorders reversibly and precisely.
Methods
In this work, we present the integration of a focused ultrasound delivery system with a multiwell MEA plate.
Results
The ultrasound delivery system was characterised by ultrasound pressure measurements, and the integration with the MEA plate was modelled with finite-element simulations of acoustic field parameters. The results of the simulations were validated with experimental visualisation of the ultrasound field with Schlieren imaging. In addition, the system was tested on a murine primary hippocampal neuron culture, showing that ultrasound can influence the activity of the neurons.
Conclusions
Our system was demonstrated to be suitable for studying the effect of focused ultrasound on neuronal cultures. The system allows reproducible experiments across the wells due to its robustness and simplicity of operation.","OA-Fund TU Delft","en","journal article","","","","","","","","","","","Electronic Components, Technology and Materials","","",""
"uuid:78d8b7b9-1d1f-434e-a22a-98f15d52eb33","http://resolver.tudelft.nl/uuid:78d8b7b9-1d1f-434e-a22a-98f15d52eb33","Respiratory reoxidation of NADH is a key contributor to high oxygen requirements of oxygen-limited cultures of Ogataea parapolymorpha","Dekker, W.J.C. (TU Delft BT/Industriele Microbiologie); Jürgens, H. (TU Delft BT/Industriele Microbiologie); Ortiz Merino, R.A. (TU Delft BT/Industriele Microbiologie); Mooiman, C. (TU Delft BT/Bioprocess Engineering); van den Berg, Remon (Student TU Delft); Kaljouw, Astrid (Student TU Delft); Mans, R. (TU Delft BT/Industriele Microbiologie); Pronk, J.T. (TU Delft BT/Biotechnologie)","","2022","While thermotolerance is an attractive trait for yeasts used in industrial ethanol production, oxygen requirements of known thermotolerant species are incompatible with process requirements. Analysis of oxygen-sufficient and oxygen-limited chemostat cultures of the facultatively fermentative, thermotolerant species Ogataea parapolymorpha showed its minimum oxygen requirements to be an order of magnitude larger than those reported for the thermotolerant yeast Kluyveromyces marxianus. High oxygen requirements of O. parapolymorpha coincided with a near absence of glycerol, a key NADH/NAD+ redox-cofactor-balancing product in many other yeasts, in oxygen-limited cultures. Genome analysis indicated absence of orthologs of the Saccharomyces cerevisiae glycerol-3-phosphate-phosphatase genes GPP1 and GPP2. Co-feeding of acetoin, whose conversion to 2,3-butanediol enables reoxidation of cytosolic NADH, supported a 2.5-fold increase of the biomass concentration in oxygen-limited cultures. An O. parapolymorpha strain in which key genes involved in mitochondrial reoxidation of NADH were inactivated did produce glycerol, but transcriptome analysis did not reveal a clear candidate for a responsible phosphatase. Expression of S. cerevisiae GPD2, which encodes NAD+-dependent glycerol-3-phosphate dehydrogenase, and GPP1 supported increased glycerol production by oxygen-limited chemostat cultures of O. parapolymorpha. These results identify dependence on respiration for NADH reoxidation as a key contributor to unexpectedly high oxygen requirements of O. parapolymorpha.","Ogataea parapolymorpha; anaerobic growth; Custers effect; genome sequence; glycerol metabolism; thermotolerance","en","journal article","","","","","","","","","","BT/Biotechnologie","BT/Industriele Microbiologie","","",""
"uuid:d7a4b319-ea9a-416c-8290-f635d8fb8571","http://resolver.tudelft.nl/uuid:d7a4b319-ea9a-416c-8290-f635d8fb8571","Goal Conflicts, Classical Management and Constructivism: How Operators Get Things Done","Boskeljon-Horst, Leonie (Koninklijke Luchtmacht); J. de Boer, Robert (SDO University of Applied Sciences); Sillem, S. (TU Delft Values Technology and Innovation); Dekker, Sidney W. A. (Griffith University)","","2022","In this study we identify the differences in goal realisation when applying two conflicting paradigms regarding rule perception and management. We gathered more than 30 scenarios where goal conflicts were apparent in a military operational unit. We found that operators repetitively utilized certain routines in executing their tasks in an effort to realize several conflicting goals. These routines were not originally intended nor designed into the rules and not explicitly included in documentation. They were not necessarily at odds with the literal wording and/or the intent of rules and regulations, although we did find examples of this. Our data showed that local ingenuity was created innovatively within the frame of existing rules or kept invisible to those outside the unit. The routines were introduced and passed on informally, and we found no evidence of testing for the introduction of new risks, no migration into the knowledge base of the organisation, and no dissemination as new best practices. An explanation for this phenomenon was found in the fact that the military organisation was applying a top-down, classical, rational approach to rules. In contrast, the routines were generated by adopting a constructivist view of rules as dynamic, local, situated constructions with operators as experts. The results of this study suggest that organisations are more effective in solving goal conflicts and creating transparency on local ingenuity if they adopt a constructivist paradigm instead of, or together with, a classical paradigm.","local ingenuity; goal conflicts; goal attainment; rule management; safety; productivity; expertise","en","journal article","","","","","","","","","","Values Technology and Innovation","","","",""
"uuid:341cc67e-dd19-472a-984a-ebe29279d009","http://resolver.tudelft.nl/uuid:341cc67e-dd19-472a-984a-ebe29279d009","ParB proteins can bypass DNA-bound roadblocks via dimer-dimer recruitment","Tišma, M. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Panoukidou, Maria (University of Edinburgh); Antar, Hammam (University of Lausanne); Soh, Young Min (University of Lausanne); Barth, R. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Pradhan, B. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Barth, A. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); van der Torre, J. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft)","","2022","The ParABS system is essential for prokaryotic chromosome segregation. After loading at parS on the genome, ParB (partition protein B) proteins rapidly redistribute to distances of ~15 kilobases from the loading site. It has remained puzzling how this large-distance spreading can occur along DNA loaded with hundreds of proteins. Using in vitro single-molecule fluorescence imaging, we show that ParB from Bacillus subtilis can load onto DNA distantly of parS, as loaded ParB molecules themselves are found to be able to recruit additional ParB proteins from bulk. Notably, this recruitment can occur in cis but also in trans, where, at low tensions within the DNA, newly recruited ParB can bypass roadblocks as it gets loaded to spatially proximal but genomically distant DNA regions. The data are supported by molecular dynamics simulations, which show that cooperative ParB-ParB recruitment can enhance spreading. ParS-independent recruitment explains how ParB can cover substantial genomic distance during chromosome segregation, which is vital for the bacterial cell cycle.","","en","journal article","","","","","","","","","","","BN/Cees Dekker Lab","","",""
"uuid:49d66213-e8c8-4045-8562-70c750030017","http://resolver.tudelft.nl/uuid:49d66213-e8c8-4045-8562-70c750030017","Bridging scales in a multiscale pattern-forming system","Würthner, Laeschkir (Ludwig Maximilians University); Brauns, Fridtjof (Ludwig Maximilians University); Pawlik, G. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Halatek, Jacob (Ludwig Maximilians University; Oxford BioMedica, Oxford); Kerssemakers, J.W.J. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Frey, Erwin (Ludwig Maximilians University; Max Planck School Matter to Life, Munich)","","2022","Self-organized pattern formation is vital for many biological processes. Reaction-diffusion models have advanced our understanding of how biological systems develop spatial structures, starting from homogeneity. However, biological processes inherently involve multiple spatial and temporal scales and transition from one pattern to another over time, rather than progressing from homogeneity to a pattern. To deal with such multiscale systems, coarse-graining methods are needed that allow the dynamics to be reduced to the relevant degrees of freedom at large scales, but without losing information about the patterns at small scales. Here, we present a semiphenomenological approach which exploits mass conservation in pattern formation, and enables reconstruction of information about patterns from the large-scale dynamics. The basic idea is to partition the domain into distinct regions (coarse grain) and determine instantaneous dispersion relations in each region, which ultimately inform about local pattern-forming instabilities. We illustrate our approach by studying the Min system, a paradigmatic model for protein pattern formation. By performing simulations, we first show that the Min system produces multiscale patterns in a spatially heterogeneous geometry. This prediction is confirmed experimentally by in vitro reconstitution of the Min system. Using a recently developed theoretical framework for mass-conserving reaction-diffusion systems, we show that the spatiotemporal evolution of the total protein densities on large scales reliably predicts the pattern-forming dynamics. Our approach provides an alternative and versatile theoretical framework for complex systems where analytical coarse-graining methods are not applicable, and can, in principle, be applied to a wide range of systems with an underlying conservation law.","in vitro Min system; multiscale systems; pattern formation; reaction–diffusion dynamics; reduced dynamics","en","journal article","","","","","","","","","","","BN/Cees Dekker Lab","","",""
"uuid:89c96d13-47a7-46ce-a0c2-f259e86a3642","http://resolver.tudelft.nl/uuid:89c96d13-47a7-46ce-a0c2-f259e86a3642","The associations of knee extensor muscle steadiness with maximal voluntary torque and physical function in patients with knee osteoarthritis","Satam, Anuja P. (Reade Centre for Rehabilitation and Rheumatology); van der Leeden, Marike (Vrije Universiteit Amsterdam; Reade Centre for Rehabilitation and Rheumatology); de Zwart, Arjan (Reade Centre for Rehabilitation and Rheumatology); Verberne, Simon (Reade Centre for Rehabilitation and Rheumatology); Schrijvers, Jim C. (Vrije Universiteit Amsterdam); Hall, Michelle (University of Melbourne); Dekker, Joost (Vrije Universiteit Amsterdam); Lems, Willem F. (Vrije Universiteit Amsterdam; Reade Centre for Rehabilitation and Rheumatology); Harlaar, J. (TU Delft Biomechatronics & Human-Machine Control; Erasmus MC); van der Esch, Martin (Hogeschool van Amsterdam; Reade Centre for Rehabilitation and Rheumatology)","","2022","Background: Muscle weakness is characteristic of knee osteoarthritis. Muscle steadiness may be an important adjunct to knee muscle strength in improving physical function in knee osteoarthritis. However, the role of muscle steadiness is uncertain. Aims: To determine the associations of knee extensor muscle steadiness with maximal voluntary torque and physical function in patients with knee osteoarthritis. Methods: Baseline data from 177 patients in a randomized clinical trial were used. Isokinetic knee extension torque was processed into maximal voluntary torque [Nm]. Muscle steadiness was expressed as the coefficient of variance [%] and as peak power frequency [Hz]. Physical function was assessed using the Western Ontario and McMaster Universities Osteoarthritis Index, the Get-Up-and-Go and Stair-climb tests. Associations were determined using regression analyses and adjusted for confounders. Findings: Lower muscle steadiness (i.e., higher coefficient of variance and peak power frequency) was associated with lower maximal voluntary torque (B = − 7.38, [−10.8, −3.95], R2 = 0.10 and B = −14.71, [−28.29, −1.13], R2 = 0.03, respectively). Higher coefficient of variance was associated with lower self-reported physical function (B = 1.14, [0.11,2.17], R2 = 0.03) and remained significant after adjusting for potential confounders. Peak power frequency was not associated with physical function. Interpretation: Low muscle steadiness was weakly associated with low muscle strength and poorer self-reported physical function. Muscle steadiness and muscle strength seem to be different attributes of muscle function. There is no convincing evidence that muscle steadiness is an important adjunct in studying physical function in patients with knee osteoarthritis.","Knee osteoarthritis; Muscle steadiness; Muscle torque; Physical function","en","journal article","","","","","","Green Open Access added to TU Delft Institutional Repository 'You share, we take care!' - Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.","","2023-02-12","","","Biomechatronics & Human-Machine Control","","",""
"uuid:52bceb73-9b62-45da-aec5-f6a8c3cfd514","http://resolver.tudelft.nl/uuid:52bceb73-9b62-45da-aec5-f6a8c3cfd514","Quantitative analysis of surface wave patterns of Min proteins","Meindlhumer, S. (TU Delft BN/Cees Dekker Lab); Kerssemakers, J.W.J. (TU Delft BN/Cees Dekker Lab); Dekker, C. (TU Delft BN/Cees Dekker Lab)","","2022","The Min protein system is arguably the best-studied model system for biological pattern formation. It exhibits pole-to-pole oscillations in E. coli bacteria as well as a variety of surface wave patterns in in vitro reconstitutions. Such Min surface wave patterns pose particular challenges to quantification as they are typically only semi-periodic and non-stationary. Here, we present a methodology for quantitatively analysing such Min patterns, aiming for reproducibility, user-independence, and easy usage. After introducing pattern-feature definitions and image-processing concepts, we present an analysis pipeline where we use autocorrelation analysis to extract global parameters such as the average spatial wavelength and oscillation period. Subsequently, we describe a method that uses flow-field analysis to extract local properties such as the wave propagation velocity. We provide descriptions on how to practically implement these quantification tools and provide Python code that can directly be used to perform analysis of Min patterns.","min proteins; pattern formation; image analysis; surface protein waves; quantification; python","en","journal article","","","","","","","","","","","BN/Cees Dekker Lab","","",""
"uuid:f0f0d085-291a-4d71-8f23-62bfe12ed03f","http://resolver.tudelft.nl/uuid:f0f0d085-291a-4d71-8f23-62bfe12ed03f","A capacity index to replace flawed incident-based metrics for worker safety","Dekker, S.W.A. (TU Delft Control & Simulation; Griffith University); Tooma, Michael (Clyde & Co)","","2022","The shortcomings of incident-based metrics for worker safety such as total recordable incident frequency rate (TRIFR) are well documented. In particular, a low TRIFR is no assurance against legal liability. There is considerable overlap between the literature on safety as the presence of capacities to make things go well, and jurisprudence in labour and workplace safety law on employer due diligence. In this article, the authors propose an index that merges the two, measuring the capacities to acquire and maintain safety knowledge, to understand the nature of operations, to resource for safety, to respond to risks, to demonstrate engagement and compliance, and for assurance.","capacity index; legal compliance; occupational accident; occupational injury; occupational safety; safety management; TRIFR","en","journal article","","","","","","Green Open Access added to TU Delft Institutional Repository ‘You share, we take care!’ – Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.","","2023-07-01","","","Control & Simulation","","",""
"uuid:2ad4a243-4824-4d43-98b4-9a55dc672c85","http://resolver.tudelft.nl/uuid:2ad4a243-4824-4d43-98b4-9a55dc672c85","‘Ladder’-based safety culture assessments inversely predict safety outcomes","Boskeljon-Horst, L. (Royal Netherlands Air Force Headquarters); Sillem, S. (TU Delft Values Technology and Innovation); Dekker, S.W.A. (Griffith University)","","2022","There is little empirical evidence on the predictive value of safety culture assessments (SCAs) in relation to how accident-prone an organisation might be. Recently, Antonsen not just demonstrated how a quantitative SCA mispredicted future safety outcomes, but actually showed an inverse relationship between the assessment and subsequent critical incident investigation findings. To add to our understanding, this article presents research on whether a SCA has a predictive capacity for safety outcomes. Like in Antonsen's research, an opportunity emerged when a helicopter taxiing accident, resulting in a rotor strike occurred for a helicopter squadron that had just undergone a SCA. The assessment used ‘culture ladder’ rubrics for its findings, which allowed us to look for specific features in the subsequent independent accident investigation (in which the researchers were not involved). As with Antonsen's findings, our research shows that a ‘ladder’-based assessment has little predictive value. Any predictive value it has is in the inverse of the assessment findings. For instance, where the SCA showed that the safety culture was very mature regarding finding a balance between safety and the mission at hand or the breaking of rules, the accident investigation pointed these out as the causes of the accident.","predictive value; safety; safety culture assessment; safety culture ladder; safety outcome","en","journal article","","","","","","Green Open Access added to TU Delft Institutional Repository ‘You share, we take care!’ – Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.","","2023-07-01","","Values Technology and Innovation","","","",""
"uuid:e675faf3-0112-4a65-bea6-e6d3471f85be","http://resolver.tudelft.nl/uuid:e675faf3-0112-4a65-bea6-e6d3471f85be","Repentance as Rebuke: Betrayal and Moral Injury in Safety Engineering","Dekker, S.W.A. (TU Delft Control & Simulation; Griffith University); Layson, Mark D. (Charles Sturt University); Woods, David D. (Ohio State University)","","2022","Following other contributions about the MAX accidents to this journal, this paper explores the role of betrayal and moral injury in safety engineering related to the U.S. federal regulator’s role in approving the Boeing 737MAX—a plane involved in two crashes that together killed 346 people. It discusses the tension between humility and hubris when engineers are faced with complex systems that create ambiguity, uncertain judgements, and equivocal test results from unstructured situations. It considers the relationship between moral injury, principled outrage and rebuke when the technology ends up involved in disasters. It examines the corporate backdrop against which calls for enhanced employee voice are typically made, and argues that when engineers need to rely on various protections and moral inducements to ‘speak up,’ then the ethical essence of engineering—skepticism, testing, checking, and questioning—has already failed.","Accident; Betrayal; Boeing 737MAX; Engineering ethics; Federal Aviation Administration; Moral injury","en","journal article","","","","","","","","","","","Control & Simulation","","",""
"uuid:f44f527b-8e45-447c-a905-8791d3c09f52","http://resolver.tudelft.nl/uuid:f44f527b-8e45-447c-a905-8791d3c09f52","Managing Knowledge for Future-proof Tunnels in the Netherlands","de Haas, K. (Centrum Ondergronds Bouwen (COB)); Berkhout, B (Centrum Ondergronds Bouwen (COB); Witteveen+Bos); Dekker, H.R.E. (Rijkswaterstaat); Broere, W. (TU Delft Geo-engineering)","Hededal, Ole (editor)","2022","Determining the scope of (structural) renovation of aging tunnels is a complicated task and modular renovation is becoming increasingly necessary. The COB Tunnel Programme aims at developing the knowledge necessary to renovate these tunnels in a modular fashion, to reduce hindrance as much as possible. Part of this program is the development of a Structural Health Analysis (SHA) for collecting data on the condition of the civil structure of tunnels, which will give tunnel owners insight in the need for research on structural parts of the tunnel, refurbishment and the risks for the tunnel performance in the future. As a lot of knowledge will be gathered and generated, structurally securing of this knowledge is also necessary. To meet this need, the tunnel program also started development of a knowledge management system. This paper describes the aims of the knowledge management system in relation to the overall tunnel program, as well as the tools and methods devised to gather all necessary information for tunnels constructed several decades ago, where not all required information is readily available in digital form, or even in paper archives.","Immersed tunnels; Renovation; Maintenance and Operation; Knowledge Management; Structural Health Assessment","en","conference paper","","","","","","","","","","","Geo-engineering","","",""
"uuid:6180ca9e-e6f1-4260-b422-2dc3312a5c07","http://resolver.tudelft.nl/uuid:6180ca9e-e6f1-4260-b422-2dc3312a5c07","25.8 Gb/s Submillimeter Optical Data Link Module for Smart Catheters","Li, J. (TU Delft Electronic Components, Technology and Materials); Li, Chenhui (Eindhoven University of Technology); Henneken, Vincent (Philips Research); Louwerse, Marcus (Philips Innovation Services); Van Rens, Jeannet (Philips Research); Dijkstra, Paul (Philips Innovation Services); Raz, Oded (Eindhoven University of Technology); Dekker, R. (TU Delft Electronic Components, Technology and Materials; Philips Research)","","2022","The digitization of smart catheters will dramatically increase the demand for reliable and high data transmission in the distal tips. Optical fiber is a good candidate to provide high-speed data transmission. However, the extremely small size of the smart catheter tip, with less than a few millimeters in diameter, hampers the integration of optical fiber connections in the catheter tip. Our work presents a stand-alone optical data link module (ODLM) with a dimension of 240 μm × 280 μm × 420 μm for use in a 1 mm diameter intravascular ultrasound (IVUS) smart catheter. The fabrication of the ODLM is based on the Flex-to-Rigid (F2R) integration technology. In the ODLM, the flexible interconnects reroute the electrical contacts of the flip-chipped vertical-cavity sur-face-emitting laser (VCSEL) to the side of the device. This design enables the ODLM to be mounted on a flex-PCB and fit into a 200-300 μm gap in the IVUS catheter tip. An optical fiber that runs parallel to the catheter shaft is self-aligned to a commercially available VCSEL by inserting it into the through-silicon hole (TSH) of the ODLM. Clear eye diagrams prove the stand-alone ODLM can transmit 25.8 Gb/s, 231-1 Pseudo-Random Binary Sequence (PRBS) when driven through a high-speed bias-tee. The BER test indicates that error-free operation can be achieved at an optical output of around -4 dBm.","Catheters; Contacts; Flex-to-Rigid; Microassembly; Microfabrication; Optical device fabrication; Optical fibers; Optical interconnections; Optical transmitters; Silicon; Smart catheters; Vertical cavity surface emitting lasers","en","journal article","","","","","","","","","","","Electronic Components, Technology and Materials","","",""
"uuid:f32a8335-4be9-4b95-a7a8-905e86be82b2","http://resolver.tudelft.nl/uuid:f32a8335-4be9-4b95-a7a8-905e86be82b2","High-resolution imaging of bacterial spatial organization with vertical cell imaging by nanostructured immobilization (VerCINI)","Whitley, K.D. (TU Delft BN/Cees Dekker Lab; Newcastle University; Kavli institute of nanoscience Delft); Middlemiss, Stuart (Newcastle University); Jukes, Calum (Newcastle University); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Holden, Séamus (Newcastle University)","","2022","Light microscopy is indispensable for analysis of bacterial spatial organization, yet the sizes and shapes of bacterial cells pose unique challenges to imaging. Bacterial cells are not much larger than the diffraction limit of visible light, and many species have cylindrical shapes and so lie flat on microscope coverslips, yielding low-resolution images when observing their short axes. In this protocol, we describe a pair of recently developed methods named VerCINI (vertical cell imaging by nanostructured immobilization) and µVerCINI (microfluidic VerCINI) that greatly increase spatial resolution and image quality for microscopy of the short axes of bacteria. The concept behind both methods is that cells are imaged while confined vertically inside cell traps made from a nanofabricated mold. The mold is a patterned silicon wafer produced in a cleanroom facility using electron-beam lithography and deep reactive ion etching, which takes ~3 h for fabrication and ~12 h for surface passivation. After obtaining a mold, the entire process of making cell traps, imaging cells and processing images can take ~2–12 h, depending on the experiment. VerCINI and µVerCINI are ideal for imaging any process along the short axes of bacterial cells, as they provide high-resolution images without any special requirements for fluorophores or imaging modalities, and can readily be combined with other imaging methods (e.g., STORM). VerCINI can easily be incorporated into existing projects by researchers with expertise in bacteriology and microscopy. Nanofabrication can be either done in-house, requiring specialist facilities, or outsourced based on this protocol.","","en","review","","","","","","","","2022-07-31","","","BN/Cees Dekker Lab","","",""
"uuid:3d7bff96-e838-4ba2-a10e-36ef47fe5bc3","http://resolver.tudelft.nl/uuid:3d7bff96-e838-4ba2-a10e-36ef47fe5bc3","The archaeal division protein CdvB1 assembles into polymers that are depolymerized by CdvC","Blanch Jover, A. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); De Franceschi, N. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Fenel, Daphna (Université Grenoble Alpes); Weissenhorn, Winfried (Université Grenoble Alpes); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft)","","2022","The Cdv proteins constitute the cell division system of the Crenarchaea, a machinery closely related to the ESCRT system of eukaryotes. Using a combination of TEM imaging and biochemical assays, we here present an in vitro study of Metallosphaera sedula CdvB1, the Cdv protein that is believed to play a major role in the constricting ring that drives cell division in the Crenarchaea. We show that CdvB1 self-assembles into filaments that are depolymerized by the Vps4-homolog ATPase CdvC. Furthermore, we find that CdvB1 binds to negatively charged lipid membranes and can be detached from the membrane by the action of CdvC. Our findings provide novel insight into one of the main components of the archaeal cell division machinery.","Archaea; Cdv system; CdvB1; cell division; ESCRT-III","en","journal article","","","","","","","","","","","BN/Cees Dekker Lab","","",""
"uuid:cc34249f-db98-4743-83ad-e8d7a119dd6a","http://resolver.tudelft.nl/uuid:cc34249f-db98-4743-83ad-e8d7a119dd6a","Probing nanomotion of single bacteria with graphene drums","Roslon, I.E. (TU Delft Dynamics of Micro and Nano Systems); Japaridze, A. (TU Delft Dynamics of Micro and Nano Systems); Steeneken, P.G. (TU Delft Dynamics of Micro and Nano Systems; TU Delft QN/Steeneken Lab); Dekker, C. (TU Delft BN/Cees Dekker Lab); Alijani, F. (TU Delft Dynamics of Micro and Nano Systems)","","2022","Motion is a key characteristic of every form of life1. Even at the microscale, it has been reported that colonies of bacteria can generate nanomotion on mechanical cantilevers2, but the origin of these nanoscale vibrations has remained unresolved3,4. Here, we present a new technique using drums made of ultrathin bilayer graphene, where the nanomotion of single bacteria can be measured in its aqueous growth environment. A single Escherichia coli cell is found to generate random oscillations with amplitudes of up to 60 nm, exerting forces of up to 6 nN to its environment. Using mutant strains that differ by single gene deletions that affect motility, we are able to pinpoint the bacterial flagella as the main source of nanomotion. By real-time tracing of changes in nanomotion on administering antibiotics, we demonstrate that graphene drums can perform antibiotic susceptibility testing with single-cell sensitivity. These findings deepen our understanding of processes underlying cellular dynamics, and pave the way towards high-throughput and parallelized rapid screening of the effectiveness of antibiotics in bacterial infections with graphene devices.","","en","journal article","","","","","","Green Open Access added to TU Delft Institutional Repository 'You share, we take care!' - Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.","","2023-07-01","","","Dynamics of Micro and Nano Systems","","",""
"uuid:2c769412-ec1d-4303-bc8b-d72191e0259e","http://resolver.tudelft.nl/uuid:2c769412-ec1d-4303-bc8b-d72191e0259e","pmTR database: Population matched (pm) germline allelic variants of T-cell receptor (TR) loci","Dekker, J.J. (TU Delft Pattern Recognition and Bioinformatics; Leiden University Medical Center; University of Applied Sciences Leiden); van Dongen, Jacques J.M. (Leiden University Medical Center); Reinders, M.J.T. (TU Delft Pattern Recognition and Bioinformatics; Leiden University Medical Center; Delft Bioinformatics Lab); Khatri, Indu (Leiden University Medical Center)","","2022","The IMGT database profiles the TR germline alleles for all four TR loci (TRA, TRB, TRG and TRD), however, it does not comprise of the information regarding population specificity and allelic frequencies of these germline alleles. The specificity of allelic variants to different human populations can, however, be a rich source of information when studying the genetic basis of population-specific immune responses in disease and in vaccination. Therefore, we meticulously identified true germline alleles enriched with complete TR allele sequences and their frequencies across 26 different human populations, profiled by “1000 Genomes data”. We identified 205 TRAV, 249 TRBV, 16 TRGV and 5 TRDV germline alleles supported by at least four haplotypes. The diversity of germline allelic variants in the TR loci is the highest in Africans, while the majority of the Non-African alleles are specific to the Asian populations, suggesting a diverse profile of TR germline alleles in different human populations. Interestingly, the alleles in the IMGT database are frequent and common across all five super-populations. We believe that this new set of germline TR sequences represents a valuable new resource which we have made available through the new population-matched TR (pmTR) database, accessible via https://pmtrig.lumc.nl/.","","en","journal article","","","","","","","","","","","Pattern Recognition and Bioinformatics","","",""
"uuid:a5f4b947-34e2-492b-92f8-ae62b9fefa19","http://resolver.tudelft.nl/uuid:a5f4b947-34e2-492b-92f8-ae62b9fefa19","Sustained unidirectional rotation of a self-organized DNA rotor on a nanopore","Shi, X. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Pumm, Anna Katharina (Technische Universität München); Isensee, Jonas (Max Planck Institute for Dynamics and Self-Organization); Zhao, W. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Verschueren, D.V. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Martin Gonzalez, A. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Golestanian, Ramin (University of Oxford; Max Planck Institute for Dynamics and Self-Organization); Dietz, Hendrik (Technische Universität München); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft)","","2022","Flow-driven rotary motors such as windmills and water wheels drive functional processes in human society. Although examples of such rotary motors also feature prominently in cell biology, their synthetic construction at the nanoscale has remained challenging. Here we demonstrate flow-driven rotary motion of a self-organized DNA nanostructure that is docked onto a nanopore in a thin solid-state membrane. An elastic DNA bundle self-assembles into a chiral conformation upon phoretic docking onto the solid-state nanopore, and subsequently displays a sustained unidirectional rotary motion of up to 20 rev s−1. The rotors harness energy from a nanoscale water and ion flow that is generated by a static chemical or electrochemical potential gradient in the nanopore, which are established through a salt gradient or applied voltage, respectively. These artificial nanoengines self-organize and operate autonomously in physiological conditions, suggesting ways to constructing energy-transducing motors at nanoscale interfaces.","","en","journal article","","","","","","","","2023-02-04","","","BN/Cees Dekker Lab","","",""
"uuid:bc75866f-7d2b-4560-a7ed-4b5600b639ec","http://resolver.tudelft.nl/uuid:bc75866f-7d2b-4560-a7ed-4b5600b639ec","Verification, validation, and parameter study of a computational model for corrosion pit growth adopting the level-set method. Part II: Stress corrosion","Fayezioghani, A. (TU Delft Applied Mechanics); Dekker, R. (TNO); Sluys, Lambertus J. (TU Delft Materials- Mechanics- Management & Design)","","2022","Structural components in corrosive environments such as pipelines, bridges, aircrafts, and turbines are imposed to stress corrosion. A stress corrosion model for pit growth should a) accurately consider the electrochemistry of the corrosion process, b) properly deal with the moving interface between solid and electrolyte, and c) effectively incorporates the synergism between corrosion and mechanical field at the interface. In Part II, the influence of mechanical loading is added to the approach described in Part I. Part II investigates the model's capabilities of simulating stress corrosion via a set of numerical examples of corrosion pitting which include experimental validation and uncertainty quantification of model parameters and properties.","Finite element method; Level-set method; Moving boundary problem; Stress corrosion; Uncertainty quantification; Validation","en","journal article","","","","","","","","","","Materials- Mechanics- Management & Design","Applied Mechanics","","",""
"uuid:fceff6b0-cc87-4e2b-acd4-daf986153b3a","http://resolver.tudelft.nl/uuid:fceff6b0-cc87-4e2b-acd4-daf986153b3a","CENP-B-mediated DNA loops regulate activity and stability of human centromeres","Chardon, Florian (PSL Research University); Japaridze, A. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Witt, Hannes (Vrije Universiteit Amsterdam); Velikovsky, Leonid (PSL Research University); Chakraborty, Camellia (PSL Research University); Wilhelm, Therese (PSL Research University); Dumont, Marie (PSL Research University); Yang, W.W.W. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft)","","2022","Chromosome inheritance depends on centromeres, epigenetically specified regions of chromosomes. While conventional human centromeres are known to be built of long tandem DNA repeats, much of their architecture remains unknown. Using single-molecule techniques such as AFM, nanopores, and optical tweezers, we find that human centromeric DNA exhibits complex DNA folds such as local hairpins. Upon binding to a specific sequence within centromeric regions, the DNA-binding protein CENP-B compacts centromeres by forming pronounced DNA loops between the repeats, which favor inter-chromosomal centromere compaction and clustering. This DNA-loop-mediated organization of centromeric chromatin participates in maintaining centromere position and integrity upon microtubule pulling during mitosis. Our findings emphasize the importance of DNA topology in centromeric regulation and stability.","AFM microscopy; CENP; centromere; chromosomes; DNA breaks; DNA compaction; DNA topology; genome stability; optical tweezers; secondary structures","en","journal article","","","","","","Green Open Access added to TU Delft Institutional Repository ‘You share, we take care!’ – Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.","","2023-07-01","","","BN/Cees Dekker Lab","","",""
"uuid:5450fed3-58ea-4cbc-929f-b61868c34977","http://resolver.tudelft.nl/uuid:5450fed3-58ea-4cbc-929f-b61868c34977","Nanopore-based technologies beyond DNA sequencing","Ying, Yi Lun (Nanjing University); Hu, Zheng Li (Nanjing University); Zhang, Shengli (Rijksuniversiteit Groningen); Qing, Yujia (University of Oxford); Fragasso, A. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Maglia, Giovanni (Rijksuniversiteit Groningen); Meller, Amit (Technion); Bayley, Hagan (University of Oxford); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Long, Yi Tao (Nanjing University)","","2022","Inspired by the biological processes of molecular recognition and transportation across membranes, nanopore techniques have evolved in recent decades as ultrasensitive analytical tools for individual molecules. In particular, nanopore-based single-molecule DNA/RNA sequencing has advanced genomic and transcriptomic research due to the portability, lower costs and long reads of these methods. Nanopore applications, however, extend far beyond nucleic acid sequencing. In this Review, we present an overview of the broad applications of nanopores in molecular sensing and sequencing, chemical catalysis and biophysical characterization. We highlight the prospects of applying nanopores for single-protein analysis and sequencing, single-molecule covalent chemistry, clinical sensing applications for single-molecule liquid biopsy, and the use of synthetic biomimetic nanopores as experimental models for natural systems. We suggest that nanopore technologies will continue to be explored to address a number of scientific challenges as control over pore design improves.","","en","review","","","","","","Green Open Access added to TU Delft Institutional Repository ‘You share, we take care!’ – Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.","","2023-07-01","","","BN/Cees Dekker Lab","","",""
"uuid:40a6da94-63e6-495a-a9f1-205d995331cf","http://resolver.tudelft.nl/uuid:40a6da94-63e6-495a-a9f1-205d995331cf","Characterizing single-molecule dynamics of viral RNA-dependent RNA polymerases with multiplexed magnetic tweezers","Kuijpers, L.C. (TU Delft BN/Nynke Dekker Lab); van Laar, T. (TU Delft BN/Nynke Dekker Lab); Janissen, R. (TU Delft BN/Cees Dekker Lab); Dekker, N.H. (TU Delft BN/Nynke Dekker Lab)","","2022","Multiplexed single-molecule magnetic tweezers (MT) have recently been employed to probe the RNA synthesis dynamics of RNA-dependent RNA polymerases (RdRp). Here, we present a protocol for simultaneously probing the RNA synthesis dynamics of hundreds of single polymerases with MT. We describe the preparation of a dsRNA construct for probing single RdRp kinetics. We then detail the measurement of RdRp RNA synthesis kinetics using MT. The protocol is suitable for high-throughput probing of RdRp-targeting antiviral compounds for mechanistic function and efficacy. For complete details on the use and execution of this protocol, please refer to Janissen et al. (2021).","Biophysics; Microbiology; Molecular biology; Molecular/Chemical probes; Single-molecule assays","en","journal article","","","","","","","","","","","BN/Nynke Dekker Lab","","",""
"uuid:19a5fba0-34cf-448b-9902-1aaf713e612e","http://resolver.tudelft.nl/uuid:19a5fba0-34cf-448b-9902-1aaf713e612e","Transport receptor occupancy in nuclear pore complex mimics","Fragasso, A. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); de Vries, Hendrik W. (Rijksuniversiteit Groningen); Andersson, John (Chalmers University of Technology); van der Sluis, E.O. (TU Delft BN/Marileen Dogterom Lab; Kavli institute of nanoscience Delft); van der Giessen, Erik (Rijksuniversiteit Groningen); Onck, Patrick R. (Rijksuniversiteit Groningen); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft)","","2022","Nuclear pore complexes (NPCs) regulate all molecular transport between the nucleus and the cytoplasm in eukaryotic cells. Intrinsically disordered Phe-Gly nucleoporins (FG-Nups) line the central conduit of NPCs to impart a selective barrier where large proteins are excluded unless bound to a transport receptor (karyopherin; Kap). Here, we assess “Kap-centric” NPC models, which postulate that Kaps participate in establishing the selective barrier. We combine biomimetic nanopores, formed by tethering Nsp1 to the inner wall of a solid-state nanopore, with coarse-grained modeling to show that yeast Kap95 exhibits two populations in Nsp1-coated pores: one population that is transported across the pore in milliseconds, and a second population that is stably assembled within the FG mesh of the pore. Ionic current measurements show a conductance decrease for increasing Kap concentrations and noise data indicate an increase in rigidity of the FG-mesh. Modeling reveals an accumulation of Kap95 near the pore wall, yielding a conductance decrease. We find that Kaps only mildly affect the conformation of the Nsp1 mesh and that, even at high concentrations, Kaps only bind at most 8% of the FG-motifs in the nanopore, indicating that Kap95 occupancy is limited by steric constraints rather than by depletion of available FG-motifs. Our data provide an alternative explanation of the origin of bimodal NPC binding of Kaps, where a stable population of Kaps binds avidly to the NPC periphery, while fast transport proceeds via a central FG-rich channel through lower affinity interactions between Kaps and the cohesive domains of Nsp1. [Figure not available: see fulltext.]","biomimetics; coarse-grained modeling; intrinsically disordered proteins; karyopherins; molecular dynamics; nanopores; nuclear pore complex; nuclear transport receptors","en","journal article","","","","","","","","","","","BN/Cees Dekker Lab","","",""
"uuid:d3966710-06e9-4ba1-a350-9cace425facb","http://resolver.tudelft.nl/uuid:d3966710-06e9-4ba1-a350-9cace425facb","Aerodynamic Interactions of Side-by-Side Rotors in Ground Proximity","Dekker, H.N.J. (TU Delft Wind Energy); Ragni, D. (TU Delft Wind Energy); Baars, W.J. (TU Delft Aerodynamics); Scarano, F. (TU Delft Aerodynamics); Tuinstra, Marthijn (Royal Netherlands Aerospace Centre NLR)","","2022","An experimental investigation is conducted to study the aerodynamic behavior of a two-rotor system in ground proximity. The counter-rotating rotors are placed side-by-side in the hovering condition. The time-averaged and unsteady flow behavior is studied when the rotor-to-rotor lateral distance and the distance between the rotors and the ground are varied. The experiments are performed using three-dimensional large-scale volumetric velocimetry with helium-filled soap bubbles as tracers, tracked by the particle motion analysis technique “Shake-The-Box.” The mean velocity field reveals the wake deflection due to the ground plane and the formation of toroidal-shape regions of separated flow below each rotor. The interaction of the wall jets formed by slipstream deflection results in a separation line with the flow emerging from the wall in a fountain-like pattern. Regimes of flow re-ingestion occur when the rotors are sufficiently far apart. The flowfield exhibits the tendency toward asymmetric states, during which the fountain flow column and the domain of re-ingestion shift closer to one of the rotors. A generic classification of flow regimes is proposed in relation to the behavior of two rotors in ground effect.","","en","journal article","","","","","","","","","","","Wind Energy","","",""
"uuid:7697bcc1-fe9c-4b8a-a6e1-f2a93c99683d","http://resolver.tudelft.nl/uuid:7697bcc1-fe9c-4b8a-a6e1-f2a93c99683d","Condensin-driven loop extrusion on supercoiled DNA","Kim, E. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Martin Gonzalez, A. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Pradhan, B. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); van der Torre, J. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft)","","2022","Condensin, a structural maintenance of chromosomes (SMC) complex, has been shown to be a molecular motor protein that organizes chromosomes by extruding loops of DNA. In cells, such loop extrusion is challenged by many potential conflicts, for example, the torsional stresses that are generated by other DNA-processing enzymes. It has so far remained unclear how DNA supercoiling affects loop extrusion. Here, we use time-lapse single-molecule imaging to study condensin-driven DNA loop extrusion on supercoiled DNA. We find that condensin binding and DNA looping are stimulated by positively supercoiled DNA, and condensin preferentially binds near the tips of supercoiled plectonemes. Upon loop extrusion, condensin collects nearby plectonemes into a single supercoiled loop that is highly stable. Atomic force microscopy imaging shows that condensin generates supercoils in the presence of ATP. Our findings provide insight into the topology-regulated loading and formation of supercoiled loops by SMC complexes and clarify the interplay of loop extrusion and supercoiling.","","en","journal article","","","","","","Green Open Access added to TU Delft Institutional Repository 'You share, we take care!' - Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.","","2023-07-01","","","BN/Cees Dekker Lab","","",""
"uuid:8bf995b4-ad08-4e36-963d-7be4b193222e","http://resolver.tudelft.nl/uuid:8bf995b4-ad08-4e36-963d-7be4b193222e","Spin-Mixing Enhanced Proximity Effect in Aluminum-Based Superconductor–Semiconductor Hybrids","Mazur, G.P. (TU Delft QRD/Kouwenhoven Lab; Kavli institute of nanoscience Delft); van Loo, N. (TU Delft QRD/Kouwenhoven Lab; Kavli institute of nanoscience Delft); Wang, J. (TU Delft QRD/Kouwenhoven Lab; Kavli institute of nanoscience Delft); Dvir, T. (TU Delft QRD/Kouwenhoven Lab; Kavli institute of nanoscience Delft); Wang, Guanzhong (TU Delft QRD/Kouwenhoven Lab; Kavli institute of nanoscience Delft); Korneychuk, S. (Kavli institute of nanoscience Delft); Borsoi, F. (TU Delft QCD/Veldhorst Lab; Kavli institute of nanoscience Delft); Dekker, R.C. (TU Delft QN/Steele Lab; Kavli institute of nanoscience Delft); Badawy, G.H.A. (Eindhoven University of Technology); Vinke, Peter (Student TU Delft; Kavli institute of nanoscience Delft); Quintero Perez, M. (TNO); Heedt, S. (TU Delft BUS/Quantum Delft; Kavli institute of nanoscience Delft); Kouwenhoven, Leo P. (TU Delft QN/Kouwenhoven Lab; Kavli institute of nanoscience Delft)","","2022","In superconducting quantum circuits, aluminum is one of the most widely used materials. It is currently also the superconductor of choice for the development of topological qubits. However, aluminum-based devices suffer from poor magnetic field compatibility. Herein, this limitation is resolved by showing that adatoms of heavy elements (e.g., platinum) increase the critical field of thin aluminum films by more than a factor of two. Using tunnel junctions, it is shown that the increased field resilience originates from spin-orbit scattering introduced by Pt. This property is exploited in the context of the superconducting proximity effect in semiconductor–superconductor hybrids, where it is shown that InSb nanowires strongly coupled to Al/Pt films can maintain superconductivity up to 7 T. The two-electron charging effect is shown to be robust against the presence of heavy adatoms. Additionally, non-local spectroscopy is used in a three-terminal geometry to probe the bulk of hybrid devices, showing that it remains free of sub-gap states. Finally, it is demonstrated that proximitized semiconductor states maintain their ability to Zeeman-split in an applied magnetic field. Combined with the chemical stability and well-known fabrication routes of aluminum, Al/Pt emerges as the natural successor to Al-based systems and is a compelling alternative to other superconductors, whenever high-field resilience is required.","aluminum; high-magnetic-field; nanowires; superconductivity","en","journal article","","","","","","","","","","","QRD/Kouwenhoven Lab","","",""
"uuid:554bbfe8-02be-4527-96d3-e70b979d1b98","http://resolver.tudelft.nl/uuid:554bbfe8-02be-4527-96d3-e70b979d1b98","SMC complexes can traverse physical roadblocks bigger than their ring size","Pradhan, B. (TU Delft BN/Cees Dekker Lab; TU Delft BN/Bionanoscience; Kavli institute of nanoscience Delft); Barth, R. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Kim, E. (TU Delft BN/Cees Dekker Lab; TU Delft BN/Bionanoscience; Kavli institute of nanoscience Delft); van Laar, T. (TU Delft BN/Nynke Dekker Lab; Kavli institute of nanoscience Delft); Yang, W.W.W. (TU Delft BN/Cees Dekker Lab; TU Delft BN/Bionanoscience; Kavli institute of nanoscience Delft); Ryu, J.K. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); van der Torre, J. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Peters, Jan Michael (Research Institute of Molecular Pathology, Vienna); Dekker, C. (TU Delft BN/Cees Dekker Lab; TU Delft BN/Bionanoscience; Kavli institute of nanoscience Delft)","","2022","Ring-shaped structural maintenance of chromosomes (SMC) complexes like condensin and cohesin extrude loops of DNA. It remains, however, unclear how they can extrude DNA loops in chromatin that is bound with proteins. Here, we use in vitro single-molecule visualization to show that nucleosomes, RNA polymerase, and dCas9 pose virtually no barrier to loop extrusion by yeast condensin. We find that even DNA-bound nanoparticles as large as 200 nm, much bigger than the SMC ring size, also translocate into DNA loops during extrusion by condensin and cohesin. This even occurs for a single-chain version of cohesin in which the ring-forming subunits are covalently linked and cannot open to entrap DNA. The data show that SMC-driven loop extrusion has surprisingly little difficulty in accommodating large roadblocks into the loop. The findings also show that the extruded DNA does not pass through the SMC ring (pseudo)topologically, hence pointing to a nontopological mechanism for DNA loop extrusion.","cohesin; condensin; CP: Molecular biology; dCas9; DNA loop extrusion; mechanism; nucleosomes; RNA polymerase; roadblocks; SMC; topology","en","journal article","","","","","","","","","","BN/Bionanoscience","BN/Cees Dekker Lab","","",""
"uuid:eeeb096c-2f7f-40c7-becd-28c064fcdce2","http://resolver.tudelft.nl/uuid:eeeb096c-2f7f-40c7-becd-28c064fcdce2","Orientation-Locked DNA Origami for Stable Trapping of Small Proteins in the Nanopore Electro-Osmotic Trap","Wen, C. (TU Delft BN/Cees Dekker Lab; Wageningen University & Research; Kavli institute of nanoscience Delft); Bertosin, E. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Shi, X. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Schmid, Sonja (Wageningen University & Research)","","2022","Nanopores are versatile single-molecule sensors offering a simple label-free readout with great sensitivity. We recently introduced the nanopore electro-osmotic trap (NEOtrap) which can trap and sense single unmodified proteins for long times. The trapping is achieved by the electro-osmotic flow (EOF) generated from a DNA-origami sphere docked onto the pore, but thermal fluctuations of the origami limited the trapping of small proteins. Here, we use site-specific cholesterol functionalization of the origami sphere to firmly link it to the lipid-coated nanopore. We can lock the origami in either a vertical or horizontal orientation which strongly modulates the EOF. The optimized EOF greatly enhances the trapping capacity, yielding reduced noise, reduced measurement heterogeneity, an increased capture rate, and 100-fold extended observation times. We demonstrate the trapping of a variety of single proteins, including small ones down to 14 kDa. The cholesterol functionalization significantly expands the application range of the NEOtrap technology.","DNA origami; electro-osmotic flow; label-free protein trapping; nanopore electro-osmotic trap (NEOtrap); single-molecule detection","en","journal article","","","","","","","","","","","BN/Cees Dekker Lab","","",""
"uuid:5f83a2d2-6109-4143-8cfc-469155a65fe9","http://resolver.tudelft.nl/uuid:5f83a2d2-6109-4143-8cfc-469155a65fe9","Extracting and characterizing protein-free megabase-pair DNA for in vitro experiments","Holub, M. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Birnie, A.T.F. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Japaridze, A. (TU Delft Dynamics of Micro and Nano Systems; Kavli institute of nanoscience Delft); van der Torre, J. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Ridder, Maxime den (Student TU Delft); de Ram, C. (TU Delft BT/Environmental Biotechnology); Pabst, Martin (TU Delft BT/Environmental Biotechnology); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft)","","2022","Chromosome structure and function is studied using various cell-based methods as well as with a range of in vitro single-molecule techniques on short DNA substrates. Here, we present a method to obtain megabase-pair-length deproteinated DNA for in vitro studies. We isolated chromosomes from bacterial cells and enzymatically digested the native proteins. Mass spectrometry indicated that 97%–100% of DNA-binding proteins are removed from the sample. Fluorescence microscopy analysis showed an increase in the radius of gyration of the DNA polymers, while the DNA length remained megabase-pair sized. In proof-of-concept experiments using these deproteinated long DNA molecules, we observed DNA compaction upon adding the DNA-binding protein Fis or PEG crowding agents and showed that it is possible to track the motion of a fluorescently labeled DNA locus. These results indicate the practical feasibility of a “genome-in-a-box” approach to study chromosome organization from the bottom up.","bottom-up biology; chromosome organization; CP: Molecular biology; DNA; DNA-binding proteins; fluorescence imaging; genome; mass spectrometry","en","journal article","","","","","","","","","","","BN/Cees Dekker Lab","","",""
"uuid:4ac40d0f-5942-4ea6-9a8b-ce2ba78ef5a4","http://resolver.tudelft.nl/uuid:4ac40d0f-5942-4ea6-9a8b-ce2ba78ef5a4","Time-efficient low power time/phase-reversal beamforming for the tracking of ultrasound implantable devices","Saccher, M. (TU Delft Electronic Components, Technology and Materials); Lolla, Sai Sandeep (Student TU Delft); Kawasaki, S. (TU Delft Electronic Components, Technology and Materials); Dekker, R. (Philips Engineering Solutions)","","2022","Ultrasound (US) has recently gained attention for powering and communication with implantable devices due to its short wavelength and low attenuation. However, beam mis-alignments cause a sharp decrease in the amount of transferred power and quality of communication. This work investigates a telemetry protocol that relies on the difference in the phase of the received backscattered signal to precisely focus the US on the implantable device and track it over time. The interrogation signal is generated by a linear phased array probe, and the receiver is a pre-charged collapse-mode Capacitive Micromachined Ultrasound Transducer (CMUT) connected to a load modulation circuit. Using the time/phase reversal tracking algorithm, the RX was located within 300 ms after the first modulation was detected. The ability of the algorithm to track the RX while it is moving was also tested, showing that it can reliably track it up to a speed of 1 mm/s.","Backscattering; Capacitive Micromachined Ultrasound Transducers; CMUT; Tracking","en","conference paper","IEEE","","","","","Green Open Access added to TU Delft Institutional Repository 'You share, we take care!' - Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.","","2023-06-01","","","Electronic Components, Technology and Materials","","",""
"uuid:8f6da54a-8f62-4cbe-9742-5eafb4be24d6","http://resolver.tudelft.nl/uuid:8f6da54a-8f62-4cbe-9742-5eafb4be24d6","Verification, validation, and parameter study of a computational model for corrosion pit growth adopting the level-set method.: Part I: Corrosion","Fayezioghani, A. (TU Delft Applied Mechanics); Dekker, R. (DIANA FEA); Sluys, Lambertus J. (TU Delft Materials- Mechanics- Management & Design)","","2022","Corrosion is a phenomenon observed in structural components in corrosive environments such as pipelines, bridges, aircrafts, turbines, etc. The computational model of corrosion should enjoy two features: a) accurately considering the electrochemistry of corrosion and b) properly dealing with the moving interface between solid and electrolyte. There are several approaches to model corrosion such as using FEM with mesh refinement algorithms, combining FEM and level-set method, employing finite volume methods, adopting peridynamic formulation, and utilizing phase field models. Because of its accuracy, lower computational cost, and robust dealing with multiple pit merging, the model which combines FEM with level-set method is selected to be more extensively assessed in this paper. Part I focuses on demonstrating the model's capabilities of simulating pitting corrosion through a set of numerical examples which include numerical solution verification, experimental validation, and uncertainty quantification of model parameters and properties.","Corrosion; Finite element method; Level-set method; Moving boundary problem; Uncertainty quantification; Validation","en","journal article","","","","","","","","","","Materials- Mechanics- Management & Design","Applied Mechanics","","",""
"uuid:71f1e555-f5b6-4f54-bdc9-e81247b8d873","http://resolver.tudelft.nl/uuid:71f1e555-f5b6-4f54-bdc9-e81247b8d873","High-throughput single-molecule experiments reveal heterogeneity, state switching, and three interconnected pause states in transcription","Janissen, R. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Eslami Mossallam, B. (TU Delft BN/Martin Depken Lab; Kavli institute of nanoscience Delft); Artsimovitch, Irina (Ohio State University); Depken, S.M. (TU Delft BN/Bionanoscience; Kavli institute of nanoscience Delft); Dekker, N.H. (TU Delft BN/Nynke Dekker Lab; Kavli institute of nanoscience Delft)","","2022","Pausing by bacterial RNA polymerase (RNAp) is vital in the recruitment of regulatory factors, RNA folding, and coupled translation. While backtracking and intra-structural isomerization have been proposed to trigger pausing, our mechanistic understanding of backtrack-associated pauses and catalytic recovery remains incomplete. Using high-throughput magnetic tweezers, we examine the Escherichia coli RNAp transcription dynamics over a wide range of forces and NTP concentrations. Dwell-time analysis and stochastic modeling identify, in addition to a short-lived elemental pause, two distinct long-lived backtrack pause states differing in recovery rates. We identify two stochastic sources of transcription heterogeneity: alterations in short-pause frequency that underlies elongation-rate switching, and variations in RNA cleavage rates in long-lived backtrack states. Together with effects of force and Gre factors, we demonstrate that recovery from deep backtracks is governed by intrinsic RNA cleavage rather than diffusional Brownian dynamics. We introduce a consensus mechanistic model that unifies our findings with prior models.","backtracking; Brownian diffusion; CP: Molecular biology; RNA cleavage; RNA polymerase; single molecule; state switching; transcription; transcription heterogeneity; transcription kinetics","en","journal article","","","","","","","","","","BN/Bionanoscience","BN/Cees Dekker Lab","","",""
"uuid:44c790b8-a042-4f4e-9714-1aebc3e68fb5","http://resolver.tudelft.nl/uuid:44c790b8-a042-4f4e-9714-1aebc3e68fb5","CRISPR-dCas9 based DNA detection scheme for diagnostics in resource-limited settings","Bengtson, M.L. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Bharadwaj, M. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Franch, O. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); van der Torre, J. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Meerdink, V.E.E. (TU Delft Science Centre & Programmering; Kavli institute of nanoscience Delft); Schallig, Henk (Amsterdam UMC); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft)","","2022","Nucleic-acid detection is crucial for basic research as well as for applications in medicine such as diagnostics. In resource-limited settings, however, most DNA-detection diagnostic schemes are inapplicable since they rely on expensive machinery, electricity, and trained personnel. Here, we present an isothermal DNA detection scheme for the diagnosis of pathogenic DNA in resource-limited settings. DNA was extracted from urine and blood samples using two different instrument-free methods, and amplified using Recombinase Polymerase Amplification with a sensitivity of <10 copies of DNA within 15 minutes. Target DNA was bound by dCas9/sgRNA that was labelled with a DNA oligomer to subsequently induce Rolling Circle Amplification. This second amplification step produced many copies of a G-quadruplex DNA structure that facilitates a colorimetric readout that is visible to the naked eye. This isothermal DNA-detection scheme can be performed at temperatures between 20-45 °C. As an example of the applicability of the approach, we isothermally (23 °C) detected DNA from a parasite causing visceral leishmaniasis that was spiked into buffer and resulted in a sensitivity of at least 1 zeptomole. For proof of principle, DNA spiked into blood was coupled to the CRISPR-dCas9-based detection scheme yielding a colorimetric readout visible to the naked eye. Given the versatility of the guide-RNA programmability of targets, we envision that this DNA detection scheme can be adapted to detect any DNA with minimal means, which facilitates applications such as point-of-care diagnostics in resource-limited settings.","","en","journal article","","","","","","","","","","","BN/Cees Dekker Lab","","",""
"uuid:56c488a8-873c-4f43-886d-197deed7f94e","http://resolver.tudelft.nl/uuid:56c488a8-873c-4f43-886d-197deed7f94e","Global correction of optical distortions in multicolor single-molecule microscopy using Zernike polynomial gradients","Mc Cluskey, K.A. (TU Delft BN/Nynke Dekker Lab; Kavli institute of nanoscience Delft); van Veen, E.N.W. (TU Delft BN/Nynke Dekker Lab; Kavli institute of nanoscience Delft); Cnossen, J.P. (TU Delft Team Carlas Smith); Wesselink, W.J. (TU Delft BN/Nynke Dekker Lab; Kavli institute of nanoscience Delft); Asscher, F.M. (TU Delft BN/Nynke Dekker Lab); Smith, C.S. (TU Delft Team Carlas Smith; TU Delft ImPhys/Computational Imaging; TU Delft Delft Center for Systems and Control); Dekker, N.H. (TU Delft BN/Nynke Dekker Lab; Kavli institute of nanoscience Delft)","","2021","Accurate image alignment is critical in multicolor single-molecule fluorescence microscopy. Global alignment using affine transformations leaves residual errors due to the nonlinearity of the distortions, which decreases the effective field of view. Subsequent local refinement demands either large amounts of reference data and processing time or specialized imaging techniques like active stabilization. Here, we present a global alignment method, S/T polynomial decomposition, that uses sums of Zernike polynomial gradients to decompose the distortion between two images, correcting both linear and nonlinear distortions simultaneously. With minimal reference data, we gain diagnostic information about the distortion and achieve a colocalization accuracy comparable to local registration methods across the entire field of view.","","en","journal article","","","","","","","","","","Delft Center for Systems and Control","BN/Nynke Dekker Lab","","",""
"uuid:da88e4d8-035b-4e69-806c-6909411d19b3","http://resolver.tudelft.nl/uuid:da88e4d8-035b-4e69-806c-6909411d19b3","Numerical modelling of fatigue crack propagation and stress-assisted pitting corrosion","Dekker, R. (TU Delft Applied Mechanics)","Sluys, Lambertus J. (promotor); Maljaars, Johan (promotor); van der Meer, F.P. (copromotor); Delft University of Technology (degree granting institution)","2021","The world is currently in a severe man-made climate crisis, creating the need for using renewable energy sources such as offshore wind farms. Offshore wind turbines do not take up any valuable space on land and can use the greater wind resource at sea. The downside is, however, that they are exposed to a much harsher environment at sea, which could result in more failures and also lead to a smaller accessibility window for maintenance and repair. The structural components of offshore wind turbines are subjected to a corrosive environment and are exposed to cyclic loads that come in the form of wind and waves, which can cause significant corrosion and fatigue damage. Having accurate numerical models that can capture the physics of these damage processes could help reducing uncertainties on the structural performance of these components and therefore improve the position of offshore wind energy as a competitive renewable energy source. In this thesis, two such models are developed","","en","doctoral thesis","","978-94-6361-598-3","","","","","","","","","Applied Mechanics","","",""
"uuid:fd04588a-842b-4851-959e-4f1d24fd0bc3","http://resolver.tudelft.nl/uuid:fd04588a-842b-4851-959e-4f1d24fd0bc3","Identification and elimination of biosynthetic oxygen requirements in yeasts","Dekker, W.J.C. (TU Delft BT/Industriele Microbiologie)","Pronk, J.T. (promotor); Mans, R. (copromotor); Delft University of Technology (degree granting institution)","2021","Saccharomyces cerevisiae is a natural producer of ethanol and industrial strains can produce ethanol at high volumetric rates and near-theoretical yields. In addition to its fast fermentative metabolism, its GRAS (generally recognized as safe) status, ease of genetic engineering, tolerance to low pH and high ethanol concentrations contribute to the popularity of S. cerevisiae as an industrial platform organism. Ethanolic fermentation is, however, not unique to S. cerevisiae. Other facultatively fermentative yeast species share many performance characteristics with S. cerevisiae and may even hold additional advantages for industrial application. However, they typically lack one key distinctive phenotype of S. cerevisiae: its capability to grow fast in the absence of oxygen on simple media with minimal addition of vitamins and anaerobic growth factors. This characteristic is essential for industrial application, as aeration of large bioreactors is expensive and near-theoretical yields of fermentation products can only be achieved in the absence of respiratory dissimilation of sugars.","","en","doctoral thesis","","978-94-6423-422-0","","","","","","","","","BT/Industriele Microbiologie","","",""
"uuid:8d31363e-1576-466b-87ae-b692a6c05ab6","http://resolver.tudelft.nl/uuid:8d31363e-1576-466b-87ae-b692a6c05ab6","Multiple rereads of single proteins at single-amino acid resolution using nanopores","Brinkerhoff, H.D. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Kang, A.S.W. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Liu, Jingqian (University of Illinois at Urbana-Champaign); Aksimentiev, Aleksei (University of Illinois at Urbana-Champaign); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft)","","2021","A proteomics tool capable of identifying single proteins would be important for cell biology research and applications. Here, we demonstrate a nanopore-based single-molecule peptide reader sensitive to single-amino acid substitutions within individual peptides. A DNA-peptide conjugate was pulled through the biological nanopore MspA by the DNA helicase Hel308. Reading the ion current signal through the nanopore enabled discrimination of single-amino acid substitutions in single reads. Molecular dynamics simulations showed these signals to result from size exclusion and pore binding. We also demonstrate the capability to ""rewind"" peptide reads, obtaining numerous independent reads of the same molecule, yielding an error rate of <10-6 in single amino acid variant identification. These proof-of-concept experiments constitute a promising basis for the development of a singlemolecule protein fingerprinting and analysis technology.","","en","journal article","","","","","","","","","","","BN/Cees Dekker Lab","","",""
"uuid:9a4f95d1-fa28-475f-abdc-4196359541ef","http://resolver.tudelft.nl/uuid:9a4f95d1-fa28-475f-abdc-4196359541ef","Cavity‐box soi: Advanced silicon substrate with pre‐patterned box for monolithic mems fabrication","Kluba, M.M. (TU Delft EKL Processing); Li, J. (TU Delft Electronic Components, Technology and Materials); Parkkinen, Katja (Research and Development, Technology, Okmetic Oy, Vantaa); Louwerse, Marcus (Philips Research); Snijder, Jaap (Philips Research); Dekker, R. (TU Delft Electronic Components, Technology and Materials; Philips Research)","","2021","Several Silicon on Insulator (SOI) wafer manufacturers are now offering products with customer‐defined cavities etched in the handle wafer, which significantly simplifies the fabrication of MEMS devices such as pressure sensors. This paper presents a novel cavity buried oxide (BOX) SOI substrate (cavity‐BOX) that contains a patterned BOX layer. The patterned BOX can form a buried microchannels network, or serve as a stop layer and a buried hard‐etch mask, to accurately pattern the device layer while etching it from the backside of the wafer using the cleanroom microfab-rication compatible tools and methods. The use of the cavity‐BOX as a buried hard‐etch mask is demonstrated by applying it for the fabrication of a deep brain stimulation (DBS) demonstrator. The demonstrator consists of a large flexible area and precisely defined 80 μm‐thick silicon islands wrapped into a 1.4 mm diameter cylinder. With cavity‐BOX, the process of thinning and separating the silicon islands was largely simplified and became more robust. This test case illustrates how cavity‐BOX wafers can advance the fabrication of various MEMS devices, especially those with complex geometry and added functionality, by enabling more design freedom and easing the optimization of the fabrication process.","Buried hard‐etch mask; Cavity‐BOX; Cavity‐SOI; DBS; Flex to Rigid (F2R); Foldable devices; MEMS; Miniaturization; Patterned BOX; SOI substrate","en","journal article","","","","","","","","","","","EKL Processing","","",""
"uuid:fced91bc-6d69-45f2-abad-4d9b781b9ef6","http://resolver.tudelft.nl/uuid:fced91bc-6d69-45f2-abad-4d9b781b9ef6","A microwatt telemetry protocol for targeting deep implants","Kawasaki, S. (TU Delft Electronic Components, Technology and Materials); Subramaniam, Indulakshmi (Student TU Delft); Saccher, M. (TU Delft Electronic Components, Technology and Materials); Dekker, R. (TU Delft Electronic Components, Technology and Materials)","","2021","Implantable medical devices are becoming smaller and more deeply implanted in the human body for various applications (i.e., neurostimulation, drug delivery, bone fracture monitoring). Therefore, an efficient ultrasound power transfer link is needed to charge these devices. However, this is challenging because each ultrasound transducer has limited angular sensitivity. This work proposes a low-power telemetry protocol that can reliably feedback the power sent to the implant with backscattered ultrasound. The protocol works by sending two consecutive interrogation signals and connecting a circuit on the receiver that modulates only one of the two signals. The modulated signal can be decoded with an external ultrasound probe. In this work, the circuit was built, verified, and compared with simulation results. It was shown that the telemetry protocol could accurately localize the receiving ultrasound element at sub-mm precision at a 10 cm depth.","pre-charged CMUT; backscattering; ultrasound power transfer; implantable medical device","en","conference paper","IEEE","","","","","Green Open Access added to TU Delft Institutional Repository ‘You share, we take care!’ – Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.","","2022-05-16","","","Electronic Components, Technology and Materials","","",""
"uuid:c5ce6b54-4fbe-4863-b64a-a87a102986af","http://resolver.tudelft.nl/uuid:c5ce6b54-4fbe-4863-b64a-a87a102986af","The long-term reliability of pre-charged CMUTs for the powering of deep implanted devices","Saccher, M. (TU Delft Electronic Components, Technology and Materials); Kawasaki, S. (TU Delft Electronic Components, Technology and Materials); Dekker, R. (Philips Research)","","2021","Recently, focused ultrasound has been proposed to power deeply implanted medical devices. Almost exclusively, lead zirconate titanate (PZT) transducers are used to convert acoustic energy into electrical energy. Unfortunately, these lead containing devices cannot be hermetically encapsulated since that would block the ultrasound. We propose the use of biocompatible Capacitive Micromachined Ultrasonic Transducer (CMUT) elements to replace traditional PZT transducers. In addition, to eliminate the external bias voltage, we introduced a charge trapping Al2O3 layer inside the CMUT to create a built-in bias voltage. These devices can be pre-charged and used as a receiver for US power. In this work, the viability of charged CMUTs to power deep implants was explored by investigating the effect of the charging parameters and by performing Accelerated Lifetime Tests (ALT). The estimated lifetime at body temperature ranges between 2.5 to 3.5 years at body temperature, which significantly depends on the charging parameters.","capacitive micromachined ultrasound transducers; pre-charged CMUT; zero-bias transducers; ultrasound power transfer; accelerated lifetime test","en","conference paper","IEEE","","","","","Green Open Access added to TU Delft Institutional Repository ‘You share, we take care!’ – Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.","","2022-05-16","","","Electronic Components, Technology and Materials","","",""
"uuid:ffc520c8-bc8f-439d-89cd-a907a98dfd01","http://resolver.tudelft.nl/uuid:ffc520c8-bc8f-439d-89cd-a907a98dfd01","Improving the experience of patients in contact isolation by human-centered design: A proof of concept study using patient journey mapping","Dekker, Mireille (Vrije Universiteit Amsterdam); de Koning, Judith PM (Student TU Delft); Melles, M. (TU Delft Applied Ergonomics and Design; Vrije Universiteit Amsterdam); Sonneveld, M.H. (TU Delft Applied Ergonomics and Design); van Mansfeld, Rosa (Vrije Universiteit Amsterdam); Jongerden, Irene P (Vrije Universiteit Amsterdam)","","2021","Background: Patient information provision about isolation measures is often not standardized. Moreover, it is unclear what information patients and informal caregivers need to optimize their knowledge and actual experience of contact isolation. We explored opportunities for improving the experience of patients in contact isolation from a human-centered design perspective.
Method: We used patient journey mapping and created patient personas based on observations and interviews with patients and health care workers from a hematology, surgery and acute admission ward of a Dutch university hospital.
Result: Patients differed in their experience of contact isolation; three personas were identified. The first liked being in contact isolation, the second had to get used to the measures, the third experienced contact isolation as overwhelming. Patients experienced a lack in structured and tailored information about contact isolation. Nurses confirmed this lack of structure and reported their need for clear instructions on how to inform patients and their informal caregivers and what information to provide at which point in time. By using a human-centered design approach, we created a first draft of an interactive information path for patients, informal care givers and health care workers.
Conclusion: To improve the patient experience in contact isolation, patient information could be structured throughout the patient journey. Information should emphasize the shared responsibility of isolation between patient, health care workers and informal caregivers.","Human-centered design; Design thinking; Infection control guidelines; Infection prevention and control","en","journal article","","","","","","","","","","","Applied Ergonomics and Design","","",""
"uuid:8416cc2e-86ac-4bb4-9be6-c46fa6de888f","http://resolver.tudelft.nl/uuid:8416cc2e-86ac-4bb4-9be6-c46fa6de888f","Infection prevention as a shared responsibility - improving the patient experience during contact isolation","de Koning, Judith (Student TU Delft); Dekker, Mireille (Amsterdam UMC); Jongerden, Irene (Amsterdam UMC); Melles, M. (TU Delft Applied Ergonomics and Design; Amsterdam UMC)","","2021","","","en","poster","","","","","","","","","","","Applied Ergonomics and Design","","",""
"uuid:c1241deb-b2a1-4f87-bd12-3d60c24b6228","http://resolver.tudelft.nl/uuid:c1241deb-b2a1-4f87-bd12-3d60c24b6228","Developments in work-related upper limb disorders (WRULD) amongst Dutch university students from 2004 to 2014","Dekker, M.C. (TU Delft Applied Ergonomics and Design); van Egmond, R. (TU Delft Human Information Communication Design); Molenbroek, J.F.M. (TU Delft Applied Ergonomics and Design); Vink, P. (TU Delft Materials and Manufacturing)","","2021","BACKGROUND: Former studies on work-related upper limb disorders (WRULD) within university education report substantial prevalence rates. In this study, developments in WRULD amongst students in the period 2004-2014 were investigated. Our findings can be a benchmark for future studies, in particular when there are major societal changes as in the case of the COVID-19 pandemic. OBJECTIVE: Differences in time (academic year), how long students have been studying (year of studying), relations with computer time and societal changes were points of interest. METHODS: 2254 students (average age 20.0 years) responded to a questionnaire on WRULD. Students experiencing complaints were further questioned about the severity of complaints and associated body locations. RESULTS: The average percentage of students experiencing complaints was 57%. The highest prevalence rates and severity scores were found in the first and last recorded academic years. The neck, shoulder, back and wrist were most often indicated. The prevalence of complaints raised from the 1st (49%) to the 4th (75%) year of studying. Two seriousness measures showed highest scores in the 5th/6th/7th year of studying. Relations were found between both the prevalence and seriousness of complaints with reported computer time. CONCLUSIONS: After an initial decreasing trend from the academic year 2006/2007 to 2010/2011 there was an increase in WRULD amongst students from 2010/2011 to 2013/2014. Limiting financial and study time factors may have played a role. Structural attention for WRULD prevention and risk factors seems to be effective in reducing prevalence and severity of WRULD. This seems to be even more necessary due to recent COVID-related changes in the students' lives.","COVID-19; MSD; prevalence; RSI; seriousness","en","journal article","","","","","","Green Open Access added to TU Delft Institutional Repository ‘You share, we take care!’ – Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.","","2021-12-24","","","Applied Ergonomics and Design","","",""
"uuid:ad8f1e80-d7d7-4d8e-8dfb-d7ed1129d9b1","http://resolver.tudelft.nl/uuid:ad8f1e80-d7d7-4d8e-8dfb-d7ed1129d9b1","Microelectromechanical Organs-on-Chip","Mastrangeli, Massimo (TU Delft Electronic Components, Technology and Materials); Aydogmus, H. (TU Delft Electronic Components, Technology and Materials); Dostanic, M. (TU Delft Electronic Components, Technology and Materials); Motreuil-Ragot, P.A. (TU Delft Electronic Components, Technology and Materials); Revyn, N. (TU Delft Electronic Components, Technology and Materials); de Wagenaar, B. (TU Delft Electronic Components, Technology and Materials); Dekker, R. (TU Delft Electronic Components, Technology and Materials); Sarro, Pasqualina M (TU Delft Electronic Components, Technology and Materials)","","2021","Stemming from the convergence of tissue engineering and microfluidics, organ-on-chip (OoC) technology can reproduce in vivo-like dynamic microphysiological environments for tissues in vitro. The possibility afforded by OoC devices of realistic recapitulation of tissue and organ (patho)physiology may hold the key to bridge the current translational gap in drug development, and possibly foster personalized medicine. Here we underline the biotechnological convergence at the root of OoC technology, and outline research tracks under development in our group at TU Delft along two main directions: fabrication of innovative microelectromechanical OoC devices, integrating stimulation and sensing of tissue activity, and their embedding within advanced platforms for pre-clinical research. We conclude with remarks on the role of open technology platforms for the broader establishment of OoC technology in pre-clinical research and drug development.","Actuators; microelectrode arrays; microfabrication; open technology platforms; organ-on-chip; sensors; tissues","en","conference paper","IEEE","","","","","Green Open Access added to TU Delft Institutional Repository ‘You share, we take care!’ – Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.","","2022-02-06","","","Electronic Components, Technology and Materials","","",""
"uuid:de7af2e9-3f31-4cfc-a5e6-21c13d32e7fe","http://resolver.tudelft.nl/uuid:de7af2e9-3f31-4cfc-a5e6-21c13d32e7fe","Pre-charged collapse-mode capacitive micromachined ultrasonic transducer (CMUT) for broadband ultrasound power transfer","Kawasaki, S. (TU Delft Electronic Components, Technology and Materials); Westhoek, Y. (Student TU Delft); Subramaniam, I. (Student TU Delft); Saccher, M. (TU Delft Electronic Components, Technology and Materials); Dekker, R. (TU Delft Electronic Components, Technology and Materials; Philips Research)","","2021","Using ultrasound to power deeply implanted biomedical devices is a promising technique due to its low attenuation in body tissue and its short wavelength that allows precise focusing of the energy. Ultrasound energy harvesting conventionally has been done using lead zirconate titanate (PZT) ultrasound transducers, which uses the piezoelectric effect to convert mechanical vibration to an electrical voltage. However, PZT is typically bulky, and is not bio-compatible, and cannot be monolithically integrated with application-specific integrated circuits (ASIC). In this work, a pre-charged collapse-mode capacitive micromachined ultrasonic transducer (CMUT) was fabricated to harvest ultrasound energy. The pre-charged CMUT has a high power transfer efficiency over a wide bandwidth at optimal loading conditions; 43% at 2.15 MHz and 47% at 5.85 MHz. For the last 1.4 years, the device has been in collapse-mode, and it is still functional without any additional charging. This device will enable the development of smaller implantable biomedical devices in the future.","Capacitive micromachined ultrasonic transducer; Pre-charged CMUT; Ultrasound power transfer; Zero-bias transducers","en","conference paper","IEEE","","","","","Green Open Access added to TU Delft Institutional Repository ‘You share, we take care!’ – Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.","","2021-11-29","","","Electronic Components, Technology and Materials","","",""
"uuid:36b19a8a-6b8b-40ab-98e8-2ef73d5a639d","http://resolver.tudelft.nl/uuid:36b19a8a-6b8b-40ab-98e8-2ef73d5a639d","Diagnosing point-of-care diagnostics for neglected tropical diseases","Bharadwaj, M. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Bengtson, M.L. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Golverdingen, Mirte (Student TU Delft); Waling, Loulotte (Kavli institute of nanoscience Delft; Student TU Delft); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft)","","2021","Inadequate and nonintegrated diagnostics are the Achilles' heel of global efforts to monitor, control, and eradicate neglected tropical diseases (NTDs). While treatment is often available, NTDs are endemic among marginalized populations, due to the unavailability or inadequacy of diagnostic tests that cause empirical misdiagnoses. The need of the hour is early diagnosis at the point-of-care (PoC) of NTD patients. Here, we review the status quo of PoC diagnostic tests and practices for all of the 24 NTDs identified in the World Health Organization's (WHO) 2021-2030 roadmap, based on their different diagnostic requirements. We discuss the capabilities and shortcomings of current diagnostic tests, identify diagnostic needs, and formulate prerequisites of relevant PoC tests. Next to technical requirements, we stress the importance of availability and awareness programs for establishing PoC tests that fit endemic resource-limited settings. Better understanding of NTD diagnostics will pave the path for setting realistic goals for healthcare in areas with minimal resources, thereby alleviating the global healthcare burden.","","en","review","","","","","","","","","","","BN/Cees Dekker Lab","","",""
"uuid:b166b69a-141f-4892-bd80-a6fb8334c840","http://resolver.tudelft.nl/uuid:b166b69a-141f-4892-bd80-a6fb8334c840","Critical parameters and procedures for anaerobic cultivation of yeasts in bioreactors and anaerobic chambers","Mooiman, C. (TU Delft BT/Bioprocess Engineering); Bouwknegt, J. (TU Delft BT/Industriele Microbiologie); Dekker, W.J.C. (TU Delft BT/Industriele Microbiologie); Wiersma, S.J. (TU Delft BT/Industriele Microbiologie); Ortiz Merino, R.A. (TU Delft BT/Industriele Microbiologie); de Hulster, A.F. (TU Delft BT/Industriele Microbiologie); Pronk, J.T. (TU Delft BT/Biotechnologie)","","2021","All known facultatively fermentative yeasts require molecular oxygen for growth. Only in a small number of yeast species, these requirements can be circumvented by supplementation of known anaerobic growth factors such as nicotinate, sterols and unsaturated fatty acids. Biosynthetic oxygen requirements of yeasts are typically small and, unless extensive precautions are taken to minimize inadvertent entry of trace amounts of oxygen, easily go unnoticed in small-scale laboratory cultivation systems. This paper discusses critical points in the design of anaerobic yeast cultivation experiments in anaerobic chambers and laboratory bioreactors. Serial transfer or continuous cultivation to dilute growth factors present in anaerobically pre-grown inocula, systematic inclusion of control strains and minimizing the impact of oxygen diffusion through tubing are identified as key elements in experimental design. Basic protocols are presented for anaerobic-chamber and bioreactor experiments.","anaerobic; cultivation; nonconventional yeast; oxygen requirements; saccharomyces","en","journal article","","","","","","","","","","BT/Biotechnologie","BT/Bioprocess Engineering","","",""
"uuid:cecbbe89-0136-4fc7-a400-3be87ef3037c","http://resolver.tudelft.nl/uuid:cecbbe89-0136-4fc7-a400-3be87ef3037c","Identification of Oxygen-Independent Pathways for Pyridine Nucleotide and Coenzyme A Synthesis in Anaerobic Fungi by Expression of Candidate Genes in Yeast","Perli, T. (TU Delft BT/Industriele Microbiologie); Vos, A.M. (TU Delft BT/Industriele Microbiologie); Bouwknegt, J. (TU Delft BT/Industriele Microbiologie); Dekker, W.J.C. (TU Delft BT/Industriele Microbiologie); Wiersma, S.J. (TU Delft BT/Industriele Microbiologie); Mooiman, C. (TU Delft BT/Bioprocess Engineering); Ortiz Merino, R.A. (TU Delft BT/Industriele Microbiologie); Daran, J.G. (TU Delft BT/Industriele Microbiologie); Pronk, J.T. (TU Delft BT/Biotechnologie)","","2021","Neocallimastigomycetes are unique examples of strictly anaerobic eukaryotes. This study investigates how these anaerobic fungi bypass reactions involved in synthesis of pyridine nucleotide cofactors and coenzyme A that, in canonical fungal pathways, require molecular oxygen. Analysis of Neocallimastigomycetes proteomes identified a candidate L-aspartate-decarboxylase (AdcA) and L-aspartate oxidase (NadB) and quinolinate synthase (NadA), constituting putative oxygen-independent bypasses for coenzyme A synthesis and pyridine nucleotide cofactor synthesis. The corresponding gene sequences indicated acquisition by ancient horizontal gene transfer (HGT) events involving bacterial donors. To test whether these enzymes suffice to bypass corresponding oxygen-requiring reactions, they were introduced into fms1∆ and bna2∆ Saccharomyces cerevisiae strains. Expression of nadA and nadB from Piromyces finnis and adcA from Neocallimastix californiae conferred cofactor prototrophy under aerobic and anaerobic conditions. This study simulates how HGT can drive eukaryotic adaptation to anaerobiosis and provides a basis for elimination of auxotrophic requirements in anaerobic industrial applications of yeasts and fungi. IMPORTANCE NAD (NAD +) and coenzyme A (CoA) are central metabolic cofactors whose canonical biosynthesis pathways in fungi require oxygen. Anaerobic gut fungi of the Neocallimastigomycota phylum are unique eukaryotic organisms that adapted to anoxic environments. Analysis of Neocallimastigomycota genomes revealed that these fungi might have developed oxygen-independent biosynthetic pathways for NAD + and CoA biosynthesis, likely acquired through horizontal gene transfer (HGT) from prokaryotic donors. We confirmed functionality of these putative pathways under anaerobic conditions by heterologous expression in the yeast Saccharomyces cerevisiae. This approach, combined with sequence comparison, offers experimental insight on whether HGT events were required and/or sufficient for acquiring new traits. Moreover, our results demonstrate an engineering strategy for enabling S. cerevisiae to grow anaerobically in the absence of the precursor molecules pantothenate and nicotinate, thereby contributing to alleviate oxygen requirements and to move closer to prototrophic anaerobic growth of this industrially relevant yeast.","Anaerobes; Biotechnology; Fungi; Neocallimastigomycetes; Nicotinic acid; Oxygen requirement; Pantothenate; Saccharomyces cerevisiae; Vitamin biosynthesis","en","journal article","","","","","","","","","","BT/Biotechnologie","BT/Industriele Microbiologie","","",""
"uuid:a5d9b2ca-4a1d-47ef-82eb-4dfb9e81a8b0","http://resolver.tudelft.nl/uuid:a5d9b2ca-4a1d-47ef-82eb-4dfb9e81a8b0","Simultaneous orientation and 3D localization microscopy with a Vortex point spread function","Hulleman, C.N. (TU Delft ImPhys/Computational Imaging); Thorsen, R.Ø. (TU Delft ImPhys/Computational Imaging); Kim, E. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft; Max Planck Insitute of Biophysics, Frankfurt); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Stallinga, S. (TU Delft ImPhys/Imaging Physics); Rieger, B. (TU Delft ImPhys/Computational Imaging)","","2021","Estimating the orientation and 3D position of rotationally constrained emitters with localization microscopy typically requires polarization splitting or a large engineered Point Spread Function (PSF). Here we utilize a compact modified PSF for single molecule emitter imaging to estimate simultaneously the 3D position, dipole orientation, and degree of rotational constraint from a single 2D image. We use an affordable and commonly available phase plate, normally used for STED microscopy in the excitation light path, to alter the PSF in the emission light path. This resulting Vortex PSF does not require polarization splitting and has a compact PSF size, making it easy to implement and combine with localization microscopy techniques. In addition to a vectorial PSF fitting routine we calibrate for field-dependent aberrations which enables orientation and position estimation within 30% of the Cramér-Rao bound limit over a 66 μm field of view. We demonstrate this technique on reorienting single molecules adhered to the cover slip, λ-DNA with DNA intercalators using binding-activated localization microscopy, and we reveal periodicity on intertwined structures on supercoiled DNA.","OA-Fund TU Delft","en","journal article","","","","","","","","","","ImPhys/Imaging Physics","ImPhys/Computational Imaging","","",""
"uuid:ea4c94a7-66a3-40b7-b39e-91ac8c2f2392","http://resolver.tudelft.nl/uuid:ea4c94a7-66a3-40b7-b39e-91ac8c2f2392","A designer FG-Nup that reconstitutes the selective transport barrier of the nuclear pore complex","Fragasso, A. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); de Vries, Hendrik W. (Rijksuniversiteit Groningen); Andersson, John (Chalmers University of Technology); van der Sluis, E.O. (TU Delft BN/Technici en Analisten; Kavli institute of nanoscience Delft); van der Giessen, Erik (Rijksuniversiteit Groningen); Dahlin, Andreas (Chalmers University of Technology); Onck, Patrick R. (Rijksuniversiteit Groningen); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft)","","2021","Nuclear Pore Complexes (NPCs) regulate bidirectional transport between the nucleus and the cytoplasm. Intrinsically disordered FG-Nups line the NPC lumen and form a selective barrier, where transport of most proteins is inhibited whereas specific transporter proteins freely pass. The mechanism underlying selective transport through the NPC is still debated. Here, we reconstitute the selective behaviour of the NPC bottom-up by introducing a rationally designed artificial FG-Nup that mimics natural Nups. Using QCM-D, we measure selective binding of the artificial FG-Nup brushes to the transport receptor Kap95 over cytosolic proteins such as BSA. Solid-state nanopores with the artificial FG-Nups lining their inner walls support fast translocation of Kap95 while blocking BSA, thus demonstrating selectivity. Coarse-grained molecular dynamics simulations highlight the formation of a selective meshwork with densities comparable to native NPCs. Our findings show that simple design rules can recapitulate the selective behaviour of native FG-Nups and demonstrate that no specific spacer sequence nor a spatial segregation of different FG-motif types are needed to create selective NPCs.","","en","journal article","","","","","","","","","","","BN/Cees Dekker Lab","","",""
"uuid:c6e140f2-1877-4714-963b-b7cb4baa1743","http://resolver.tudelft.nl/uuid:c6e140f2-1877-4714-963b-b7cb4baa1743","Monolithic integration of a smart temperature sensor on a modular silicon-based organ-on-a-chip device","Martins Da Ponte, R. (TU Delft Bio-Electronics); Gaio, N. (TU Delft Electronic Components, Technology and Materials; BIOND Solutions B.V.); van Zeijl, H.W. (TU Delft Electronic Components, Technology and Materials); Vollebregt, S. (TU Delft Electronic Components, Technology and Materials); Dijkstra, Paul (Philips Innovation Services); Dekker, R. (TU Delft Electronic Components, Technology and Materials; Philips Research); Serdijn, W.A. (TU Delft Bio-Electronics); Giagka, Vasiliki (TU Delft Bio-Electronics; Fraunhofer Institute for Reliability and Microintegration IZM)","","2021","One of the many applications of organ-on-a-chip (OOC) technology is the study of biological processes in human induced pluripotent stem cells (iPSCs) during pharmacological drug screening. It is of paramount importance to construct OOCs equipped with highly compact in situ sensors that can accurately monitor, in real time, the extracellular fluid environment and anticipate any vital physiological changes of the culture. In this paper, we report the co-fabrication of a CMOS smart sensor on the same substrate as our silicon-based OOC for real-time in situ temperature measurement of the cell culture. The proposed CMOS circuit is developed to provide the first monolithically integrated in situ smart temperature-sensing system on a micromachined silicon-based OOC device. Measurement results on wafer reveal a resolution of less than ±0.2 °C and a nonlinearity error of less than 0.05% across a temperature range from 30 to 40 °C. The sensor's time response is more than 10 times faster than the time constant of the convection-cooling mechanism found for a medium containing 0.4 ml of PBS solution. All in all, this work is the first step towards realizing OOCs with seamless integrated CMOS-based sensors capable to measure, in real time, multiple physical quantities found in cell culture experiments. It is expected that the use of commercial foundry CMOS processes may enable OOCs with very large scale of multi-sensing integration and actuation in a closed-loop system manner.","CMOS monolithic integration; MEMS; MEMS-electronics co-fabrication; Organs-on-a-chip; Smart temperature sensor; Time-mode domain signal processing","en","journal article","","","","","","","","","","","Bio-Electronics","","",""
"uuid:cebd7423-e6fa-468e-b332-91bc75abaca1","http://resolver.tudelft.nl/uuid:cebd7423-e6fa-468e-b332-91bc75abaca1","FIB-milled plasmonic nanoapertures allow for long trapping times of individual proteins","Yang, W.W.W. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); van Dijk, M.C. (TU Delft Student Development; Kavli institute of nanoscience Delft); Primavera, Christian (Kavli institute of nanoscience Delft; Student TU Delft); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft)","","2021","We have developed a fabrication methodology for label-free optical trapping of individual nanobeads and proteins in inverted-bowtie-shaped plasmonic gold nanopores. Arrays of these nanoapertures can be reliably produced using focused ion beam (FIB) milling with gap sizes of 10–20 nm, single-nanometer variation, and with a remarkable stability that allows for repeated use. We employ an optical readout where the presence of the protein entering the trap is marked by an increase in the transmission of light through the nanoaperture from the shift of the plasmonic resonance. In addition, the optical trapping force of the plasmonic nanopores allows 20-nm polystyrene beads and proteins, such as beta-amylase and Heat Shock Protein (HSP90), to be trapped for very long times (approximately minutes). On demand, we can release the trapped molecule for another protein to be interrogated. Our work opens up new routes to acquire information on the conformation and dynamics of individual proteins.","Biophysical chemistry; Materials science; Physical chemistry; Protein","en","journal article","","","","","","","","","","","BN/Cees Dekker Lab","","",""
"uuid:a732ed03-62cd-4fb8-bee0-f7282a0db681","http://resolver.tudelft.nl/uuid:a732ed03-62cd-4fb8-bee0-f7282a0db681","Induced intra- and intermolecular template switching as a therapeutic mechanism against RNA viruses","Janissen, R. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Woodman, Andrew (The Pennsylvania State University); Shengjuler, Djoshkun (Institut Pasteur, Paris); Vallet, Thomas (Institut Pasteur, Paris); Lee, Kuo Ming (Chang Gung University); Kuijpers, L.C. (TU Delft BN/Nynke Dekker Lab); Moustafa, Ibrahim M. (The Pennsylvania State University); Fitzgerald, Fiona (The Pennsylvania State University); Dekker, N.H. (TU Delft BN/Nynke Dekker Lab; Kavli institute of nanoscience Delft)","","2021","Viral RNA-dependent RNA polymerases (RdRps) are a target for broad-spectrum antiviral therapeutic agents. Recently, we demonstrated that incorporation of the T-1106 triphosphate, a pyrazine-carboxamide ribonucleotide, into nascent RNA increases pausing and backtracking by the poliovirus RdRp. Here, by monitoring enterovirus A-71 RdRp dynamics during RNA synthesis using magnetic tweezers, we identify the “backtracked” state as an intermediate used by the RdRp for copy-back RNA synthesis and homologous recombination. Cell-based assays and RNA sequencing (RNA-seq) experiments further demonstrate that the pyrazine-carboxamide ribonucleotide stimulates these processes during infection. These results suggest that pyrazine-carboxamide ribonucleotides do not induce lethal mutagenesis or chain termination but function by promoting template switching and formation of defective viral genomes. We conclude that RdRp-catalyzed intra- and intermolecular template switching can be induced by pyrazine-carboxamide ribonucleotides, defining an additional mechanistic class of antiviral ribonucleotides with potential for broad-spectrum activity.","backtracking; copy-back RNA synthesis; enterovirus A71; favipiravir; poliovirus; pyrazine-carboxamide analogue; recombination; RNA-dependent RNA polymerase; T-1106; template switching","en","journal article","","","","","","Accepted Author Manuscript","","2022-11-04","","","BN/Cees Dekker Lab","","",""
"uuid:6c16fcfe-55a6-48b8-a638-2383fc0a1cd0","http://resolver.tudelft.nl/uuid:6c16fcfe-55a6-48b8-a638-2383fc0a1cd0","Schlieren visualization of focused ultrasound beam steering for spatially specific stimulation of the vagus nerve","Kawasaki, S. (TU Delft Electronic Components, Technology and Materials); Dijkema, E. (Student TU Delft); Saccher, M. (TU Delft Electronic Components, Technology and Materials); Giagka, Vasiliki (TU Delft Bio-Electronics; Fraunhofer Institute for Reliability and Microintegration IZM); Schleipen, J.J.H.B. (Philips Research); Dekker, R. (Philips Research)","","2021","In the bioelectronic medicine field, vagus nerve stimulation (VNS) is a promising technique that is expected to treat numerous inflammatory conditions, in addition to the currently FDA approved treatment for epilepsy, depression and obesity [1]. However, current VNS techniques are still limited in the spatial resolution that they can achieve, which limits its therapeutic effect and induces side effects such as coughing, headache and throat pain. In our prior work, we presented a curved ultrasound (US) transducer array with a diameter of 2 mm and with 112 miniature US transducer elements, small enough to be wrapped around the vagus nerve for precise ultrasound nerve stimulation [2]. Due to the curved alignment of the US transducers with 48 of the elements simultaneously excited, the emitted US was naturally focused at the center of the curvature. Building on this work, we employ a beam steering technique to move the focal spot to arbitrary locations within the focal plane of the transducer array. The beam steering was controlled through an in-house built US driver system and was visualized using a pulsed laser schlieren system. The propagation of the US pulse in water was imaged and recorded. This method was found to be a rapid and effective means of visualizing the US propagation.","","en","conference paper","IEEE","","","","","Green Open Access added to TU Delft Institutional Repository ‘You share, we take care!’ – Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.","","2021-12-01","","","Electronic Components, Technology and Materials","","",""
"uuid:ac0665c1-ce46-443f-b861-ee52a86584bd","http://resolver.tudelft.nl/uuid:ac0665c1-ce46-443f-b861-ee52a86584bd","The emerging landscape of single-molecule protein sequencing technologies","Bohländer, P.R. (TU Delft ChemE/Advanced Soft Matter); Filius, M. (TU Delft BN/Chirlmin Joo Lab; Kavli institute of nanoscience Delft); van Kooten, Xander F. (Technion); Pomorski, A.K. (TU Delft BN/Chirlmin Joo Lab; Kavli institute of nanoscience Delft); Schmid, S. (Wageningen University & Research); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Eelkema, R. (TU Delft ChemE/Advanced Soft Matter); Kim, S.H. (TU Delft BN/Chirlmin Joo Lab; Kavli institute of nanoscience Delft); Joo, C. (TU Delft BN/Chirlmin Joo Lab; Kavli institute of nanoscience Delft)","","2021","Single-cell profiling methods have had a profound impact on the understanding of cellular heterogeneity. While genomes and transcriptomes can be explored at the single-cell level, single-cell profiling of proteomes is not yet established. Here we describe new single-molecule protein sequencing and identification technologies alongside innovations in mass spectrometry that will eventually enable broad sequence coverage in single-cell profiling. These technologies will in turn facilitate biological discovery and open new avenues for ultrasensitive disease diagnostics.","","en","review","","","","","","Accepted Author Manuscript","","2021-12-07","","","ChemE/Advanced Soft Matter","","",""
"uuid:bef0ec56-a628-458f-a4cc-f6d8bcc48311","http://resolver.tudelft.nl/uuid:bef0ec56-a628-458f-a4cc-f6d8bcc48311","Mechanisms for Chromosome Segregation in Bacteria","Gogou, C. (TU Delft BN/Dimphna Meijer Lab; Kavli institute of nanoscience Delft); Japaridze, A. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft)","","2021","The process of DNA segregation, the redistribution of newly replicated genomic material to daughter cells, is a crucial step in the life cycle of all living systems. Here, we review DNA segregation in bacteria which evolved a variety of mechanisms for partitioning newly replicated DNA. Bacterial species such as Caulobacter crescentus and Bacillus subtilis contain pushing and pulling mechanisms that exert forces and directionality to mediate the moving of newly synthesized chromosomes to the bacterial poles. Other bacteria such as Escherichia coli lack such active segregation systems, yet exhibit a spontaneous de-mixing of chromosomes due to entropic forces as DNA is being replicated under the confinement of the cell wall. Furthermore, we present a synopsis of the main players that contribute to prokaryotic genome segregation. We finish with emphasizing the importance of bottom-up approaches for the investigation of the various factors that contribute to genome segregation.","bacterial chromosome; chromosome segregation; entropic segregation; ParABS system; prokaryotic segregation mechanisms; structural maintenance of chromosome","en","review","","","","","","","","","","","BN/Dimphna Meijer Lab","","",""
"uuid:aa753cf3-ff43-4bbc-8d52-584903f767c1","http://resolver.tudelft.nl/uuid:aa753cf3-ff43-4bbc-8d52-584903f767c1","Optimized cDICE for Efficient Reconstitution of Biological Systems in Giant Unilamellar Vesicles","Van de Cauter, L. (AMOLF); Fanalista, F. (TU Delft BN/Gijsje Koenderink Lab; Kavli institute of nanoscience Delft); van Buren, L. (TU Delft BN/Gijsje Koenderink Lab; Kavli institute of nanoscience Delft); De Franceschi, N. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Godino, E. (TU Delft BN/Christophe Danelon Lab; Kavli institute of nanoscience Delft); Bouw, Sharon (AMOLF); Danelon, C.J.A. (TU Delft BN/Christophe Danelon Lab; Kavli institute of nanoscience Delft); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Koenderink, G.H. (TU Delft BN/Gijsje Koenderink Lab; Kavli institute of nanoscience Delft); Ganzinger, Kristina A. (AMOLF)","","2021","Giant unilamellar vesicles (GUVs) are often used to mimic biological membranes in reconstitution experiments. They are also widely used in research on synthetic cells, as they provide a mechanically responsive reaction compartment that allows for controlled exchange of reactants with the environment. However, while many methods exist to encapsulate functional biomolecules in GUVs, there is no one-size-fits-all solution and reliable GUV fabrication still remains a major experimental hurdle in the field. Here, we show that defect-free GUVs containing complex biochemical systems can be generated by optimizing a double-emulsion method for GUV formation called continuous droplet interface crossing encapsulation (cDICE). By tightly controlling environmental conditions and tuning the lipid-in-oil dispersion, we show that it is possible to significantly improve the reproducibility of high-quality GUV formation as well as the encapsulation efficiency. We demonstrate efficient encapsulation for a range of biological systems including a minimal actin cytoskeleton, membrane-anchored DNA nanostructures, and a functional PURE (protein synthesis using recombinant elements) system. Our optimized cDICE method displays promising potential to become a standard method in biophysics and bottom-up synthetic biology.","actin cytoskeleton; bottom-up synthetic biology; emulsion transfer; GUVs; in vitro transcription-translation; synthetic cell","en","journal article","","","","","","","","","","","BN/Gijsje Koenderink Lab","","",""
"uuid:3a7cc2fd-869f-4d48-8bad-134da68a5f68","http://resolver.tudelft.nl/uuid:3a7cc2fd-869f-4d48-8bad-134da68a5f68","Reconstitution of Ultrawide DNA Origami Pores in Liposomes for Transmembrane Transport of Macromolecules","Fragasso, A. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); De Franceschi, N. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Stömmer, Pierre (Technische Universität München); van der Sluis, E.O. (TU Delft BN/Technici en Analisten; Kavli institute of nanoscience Delft); Dietz, Hendrik (Technische Universität München); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft)","","2021","Molecular traffic across lipid membranes is a vital process in cell biology that involves specialized biological pores with a great variety of pore diameters, from fractions of a nanometer to >30 nm. Creating artificial membrane pores covering similar size and complexity will aid the understanding of transmembrane molecular transport in cells, while artificial pores are also a necessary ingredient for synthetic cells. Here, we report the construction of DNA origami nanopores that have an inner diameter as large as 30 nm. We developed methods to successfully insert these ultrawide pores into the lipid membrane of giant unilamellar vesicles (GUVs) by administering the pores concomitantly with vesicle formation in an inverted-emulsion cDICE technique. The reconstituted pores permit the transmembrane diffusion of large macromolecules, such as folded proteins, which demonstrates the formation of large membrane-spanning open pores. The pores are size selective, as dextran molecules with a diameter up to 28 nm can traverse the pores, whereas larger dextran molecules are blocked. By FRAP measurements and modeling of the GFP influx rate, we find that up to hundreds of pores can be functionally reconstituted into a single GUV. Our technique bears great potential for applications across different fields from biomimetics, to synthetic biology, to drug delivery.","cDICE; DNA origami; liposomes; nanopores; transmembrane transport","en","journal article","","","","","","","","","","","BN/Cees Dekker Lab","","",""
"uuid:c38e25c7-5a7f-4cc8-a0c6-79b5b847debd","http://resolver.tudelft.nl/uuid:c38e25c7-5a7f-4cc8-a0c6-79b5b847debd","Towards a synthetic cell cycle","Olivi, Lorenzo (Wageningen University & Research); Berger, Mareike (AMOLF); Creyghton, Ramon N.P. (Systems Biophysics; AMOLF); De Franceschi, N. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Mulder, Bela M. (AMOLF); Claassens, Nico J. (Wageningen University & Research); ten Wolde, Pieter Rein (AMOLF); van der Oost, John (Wageningen University & Research)","","2021","Recent developments in synthetic biology may bring the bottom-up generation of a synthetic cell within reach. A key feature of a living synthetic cell is a functional cell cycle, in which DNA replication and segregation as well as cell growth and division are well integrated. Here, we describe different approaches to recreate these processes in a synthetic cell, based on natural systems and/or synthetic alternatives. Although some individual machineries have recently been established, their integration and control in a synthetic cell cycle remain to be addressed. In this Perspective, we discuss potential paths towards an integrated synthetic cell cycle.","","en","review","","","","","","","","","","","BN/Cees Dekker Lab","","",""
"uuid:b4cb7f7d-0c4f-40ba-944c-a4fe9e2d47cc","http://resolver.tudelft.nl/uuid:b4cb7f7d-0c4f-40ba-944c-a4fe9e2d47cc","Engineering the thermotolerant industrial yeast Kluyveromyces marxianus for anaerobic growth","Dekker, W.J.C. (TU Delft BT/Industriele Microbiologie); Ortiz Merino, R.A. (TU Delft BT/Industriele Microbiologie); Kaljouw, Astrid (Student TU Delft); Battjes, Julius (Student TU Delft); Wiering, Frank W. (Student TU Delft); Mooiman, C. (TU Delft BT/Bioprocess Engineering); de la Torre, P. (TU Delft BT/Industriele Microbiologie); Pronk, J.T. (TU Delft BT/Biotechnologie)","","2021","Current large-scale, anaerobic industrial processes for ethanol production from renewable carbohydrates predominantly rely on the mesophilic yeast Saccharomyces cerevisiae. Use of thermotolerant, facultatively fermentative yeasts such as Kluyveromyces marxianus could confer significant economic benefits. However, in contrast to S. cerevisiae, these yeasts cannot grow in the absence of oxygen. Responses of K. marxianus and S. cerevisiae to different oxygen-limitation regimes were analyzed in chemostats. Genome and transcriptome analysis, physiological responses to sterol supplementation and sterol-uptake measurements identified absence of a functional sterol-uptake mechanism as a key factor underlying the oxygen requirement of K. marxianus. Heterologous expression of a squalene-tetrahymanol cyclase enabled oxygen-independent synthesis of the sterol surrogate tetrahymanol in K. marxianus. After a brief adaptation under oxygen-limited conditions, tetrahymanol-expressing K. marxianus strains grew anaerobically on glucose at temperatures of up to 45 °C. These results open up new directions in the development of thermotolerant yeast strains for anaerobic industrial applications.","Anaerobic metabolism; Ergosterol; Ethanol production; Metabolic engineering; Tetrahymanol; Thermotolerance; Yeast biotechnology","en","journal article","","","","","","","","","","BT/Biotechnologie","BT/Industriele Microbiologie","","",""
"uuid:02a52218-9f6b-4c02-8f49-f00ee4e3e728","http://resolver.tudelft.nl/uuid:02a52218-9f6b-4c02-8f49-f00ee4e3e728","Bridging-induced phase separation induced by cohesin SMC protein complexes","Ryu, J.K. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Bouchoux, Céline (Francis Crick Institute); Liu, Hon Wing (Francis Crick Institute); Kim, E. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Minamino, Masashi (Francis Crick Institute); de Groot, Ralph (Kavli institute of nanoscience Delft; Student TU Delft); Katan, A.J. (TU Delft QN/Afdelingsbureau; Kavli institute of nanoscience Delft); Bonato, Andrea (University of Edinburgh); Marenduzzo, Davide (University of Edinburgh); Michieletto, Davide (University of Edinburgh); Uhlmann, Frank (Francis Crick Institute); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft)","","2021","Structural maintenance of chromosome (SMC) protein complexes are able to extrude DNA loops. While loop extrusion constitutes a fundamental building block of chromosomes, other factors may be equally important. Here, we show that yeast cohesin exhibits pronounced clustering on DNA, with all the hallmarks of biomolecular condensation. DNA-cohesin clusters exhibit liquid-like behavior, showing fusion of clusters, rapid fluorescence recovery after photobleaching and exchange of cohesin with the environment. Strikingly, the in vitro clustering is DNA length dependent, as cohesin forms clusters only on DNA exceeding 3 kilo-base pairs. We discuss how bridging-induced phase separation, a previously unobserved type of biological condensation, can explain the DNA-cohesin clustering through DNA-cohesin-DNA bridges. We confirm that, in yeast cells in vivo, a fraction of cohesin associates with chromatin in a manner consistent with bridging-induced phase separation. Biomolecular condensation by SMC proteins constitutes a new basic principle by which SMC complexes direct genome organization.","","en","journal article","","","","","","","","","","","BN/Cees Dekker Lab","","",""
"uuid:8962ea7c-243d-4c15-87cf-a334887c0b53","http://resolver.tudelft.nl/uuid:8962ea7c-243d-4c15-87cf-a334887c0b53","Studying phase separation in confinement","Deshpande, Siddharth (Wageningen University & Research); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft)","","2021","Cells organize their interior through membrane-bound organelles and through membraneless condensates that are formed by liquid–liquid phase separation (LLPS). The complex process of coacervation that is involved in LLPS is challenging to study in living cells. Hence, studying coacervation in cell-mimicking synthetic containers can yield valuable insights. Here, we review recent progress with respect to studying LLPS (particularly coacervation) in artificial compartments, from water-in-oil droplets to membranous liposomes. We describe different strategies to form and control coacervates in microconfinements and to study their physicochemical and biological characteristics. We also describe how coacervation can itself be used in container formation. This review highlights the importance of in vitro coacervate studies for understanding cellular biology and for designing synthetic cells.","Coacervates; Confinement; Droplets; Liposomes; Liquid–liquid phase separation; Microfluidics","en","review","","","","","","","","","","","BN/Cees Dekker Lab","","",""
"uuid:9ceae8c7-ef89-463f-a128-122055fa48e4","http://resolver.tudelft.nl/uuid:9ceae8c7-ef89-463f-a128-122055fa48e4","AutoStepfinder: A fast and automated step detection method for single-molecule analysis","Loeff, L. (TU Delft BN/Chirlmin Joo Lab; Kavli institute of nanoscience Delft); Kerssemakers, J.W.J. (TU Delft BN/Technici en Analisten; Kavli institute of nanoscience Delft); Joo, C. (TU Delft BN/Chirlmin Joo Lab; Kavli institute of nanoscience Delft); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft)","","2021","Single-molecule techniques allow the visualization of the molecular dynamics of nucleic acids and proteins with high spatiotemporal resolution. Valuable kinetic information of biomolecules can be obtained when the discrete states within single-molecule time trajectories are determined. Here, we present a fast, automated, and bias-free step detection method, AutoStepfinder, that determines steps in large datasets without requiring prior knowledge on the noise contributions and location of steps. The analysis is based on a series of partition events that minimize the difference between the data and the fit. A dual-pass strategy determines the optimal fit and allows AutoStepfinder to detect steps of a wide variety of sizes. We demonstrate step detection for a broad variety of experimental traces. The user-friendly interface and the automated detection of AutoStepfinder provides a robust analysis procedure that enables anyone without programming knowledge to generate step fits and informative plots in less than an hour.","AutoStepfinder; biophysics; data analysis; DSML 3: Development/Pre-production: Data science output has been rolled out/validated across multiple domains/problems; fluorescence; magnetic tweezer; nanopore; optical tweezer; single molecule; step detection; Stepfinder","en","journal article","","","","","","","","","","","BN/Chirlmin Joo Lab","","",""
"uuid:56877f27-dfd8-40e9-915a-6e5e41ae5e49","http://resolver.tudelft.nl/uuid:56877f27-dfd8-40e9-915a-6e5e41ae5e49","A cohesive XFEM model for simulating fatigue crack growth under various load conditions","Dekker, R. (TU Delft Applied Mechanics); van der Meer, F.P. (TU Delft Applied Mechanics); Maljaars, J. (Eindhoven University of Technology; TNO); Sluys, Lambertus J. (TU Delft Materials- Mechanics- Management & Design)","","2021","This study presents calibration and validation of a cohesive extended finite element model for fatigue crack propagation in ductile materials. The approach relies on a separation between plasticity around the crack tip and fatigue crack growth at the crack tip such that the influence of plasticity on fatigue driving forces is predicted. This implies that characterization of crack growth requires effective Paris parameters. It is shown that the calibrated model can capture fatigue crack growth behaviour in ductile materials for in-phase and out-of-phase biaxial fatigue loading as well as in-phase biaxial loading with an overload.","Cohesive zone model; Fatigue crack growth; Mixed-mode; Out-of-phase; Overload; XFEM","en","journal article","","","","","","","","","","Materials- Mechanics- Management & Design","Applied Mechanics","","",""
"uuid:1e83a1a7-0b70-4ed5-9c6b-37da10041de7","http://resolver.tudelft.nl/uuid:1e83a1a7-0b70-4ed5-9c6b-37da10041de7","Participatory value evaluation for the evaluation of flood protection schemes","Mouter, N. (TU Delft Transport and Logistics); Koster, Paul (Vrije Universiteit Amsterdam); Dekker, Thijs (University of Leeds)","","2021","Participatory Value Evaluation (PVE) is a new survey method which elicits citizens' preferences over the allocation of public budgets as well as their private income. In a PVE, citizens are asked to choose the best portfolio of projects given a governmental and a private budget constraint. First, this paper aligns PVE with the traditional Kaldor-Hicks welfare economics framework underlying many Cost-Benefit Analyses. Second, this paper positions PVE against other valuation methods. Third, this paper applies the PVE method to evaluate the impacts of projects mitigating flood risks in the Netherlands. This empirical application reveals that Dutch citizens indicate a preference for projects that combine strengthening dikes and give space to the river to flood safely, particularly when such projects positively influence biodiversity and recreational opportunities.","Biodiversity; Cost-benefit analysis; Environmental valuation; Flood protection; Participatory value evaluation; Valuation methods","en","journal article","","","","","","","","","","","Transport and Logistics","","",""
"uuid:ea6e16b7-b1f9-40c9-bafe-a974bdc7de37","http://resolver.tudelft.nl/uuid:ea6e16b7-b1f9-40c9-bafe-a974bdc7de37","Nanopore electro-osmotic trap for the label-free study of single proteins and their conformations","Schmid, S. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft; Wageningen University & Research); Stömmer, Pierre (Technische Universität München); Dietz, Hendrik (Technische Universität München); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft)","","2021","Many strategies have been pursued to trap and monitor single proteins over time to detect the molecular mechanisms of these essential nanomachines. Single-protein sensing with nanopores is particularly attractive because it allows label-free high-bandwidth detection on the basis of ion currents. Here we present the nanopore electro-osmotic trap (NEOtrap) that allows trapping and observing single proteins for hours with submillisecond time resolution. The NEOtrap is formed by docking a DNA-origami sphere onto a passivated solid-state nanopore, which seals off a nanocavity of a user-defined size and creates an electro-osmotic flow that traps nearby particles irrespective of their charge. We demonstrate the NEOtrap’s ability to sensitively distinguish proteins on the basis of size and shape, and discriminate between nucleotide-dependent protein conformations, as exemplified by the chaperone protein Hsp90. Given the experimental simplicity and capacity for label-free single-protein detection over the broad bio-relevant time range, the NEOtrap opens new avenues to study the molecular kinetics underlying protein function.","","en","journal article","","","","","","Accepted Author Manuscript","","2022-03-01","","","BN/Cees Dekker Lab","","",""
"uuid:9a2c6763-cbde-4b0d-98f9-6923228ff869","http://resolver.tudelft.nl/uuid:9a2c6763-cbde-4b0d-98f9-6923228ff869","The NEOtrap – en route with a new single-molecule technique","Schmid, S. (Wageningen University & Research); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft)","","2021","This paper provides a perspective on potential applications of a new single-molecule technique, viz., the nanopore electro-osmotic trap (NEOtrap). This solid-state nanopore-based method uses locally induced electro-osmosis to form a hydrodynamic trap for single molecules. Ionic current recordings allow one to study an unlabeled protein or nanoparticle of arbitrary charge that can be held in the nanopore's most sensitive region for very long times. After motivating the need for improved single-molecule technologies, we sketch various possible technical extensions and combinations of the NEOtrap. We lay out diverse applications in biosensing, enzymology, protein folding, protein dynamics, fingerprinting of proteins, detecting post-translational modifications, and all that at the level of single proteins – illustrating the unique versatility and potential of the NEOtrap.","Nanotechnology; Physical chemistry; Protein","en","review","","","","","","","","","","","BN/Cees Dekker Lab","","",""
"uuid:8c553fc1-3a3a-4254-b565-525ae0cba30b","http://resolver.tudelft.nl/uuid:8c553fc1-3a3a-4254-b565-525ae0cba30b","Nanopores: A versatile tool to study protein Dynamics","Schmid, S. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft; Wageningen University & Research); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft)","","2021","Proteins are the active workhorses in our body. These biomolecules perform all vital cellular functions from DNA replication and general biosynthesis to metabolic signaling and environmental sensing.While static 3D structures are now readily available, observing the functional cycle of proteins-involving conformational changes and interactions-remains very challenging, e.g., due to ensemble averaging. However, time-resolved information is crucial to gain a mechanistic understanding of protein function. Single-molecule techniques such as FRET and force spectroscopies provide answers but can be limited by the required labelling, a narrow time bandwidth, and more. Here, we describe electrical nanopore detection as a tool for probing protein dynamics. With a time bandwidth ranging from microseconds to hours, nanopore experiments cover an exceptionally wide range of timescales that is very relevant for protein function. First, we discuss the working principle of label-free nanopore experiments, various pore designs, instrumentation, and the characteristics of nanopore signals. In the second part, we review a few nanopore experiments that solved research questions in protein science, and we compare nanopores to other single-molecule techniques. We hope to make electrical nanopore sensing more accessible to the biochemical community, and to inspire new creative solutions to resolve a variety of protein dynamics-one molecule at a time.","","en","review","","","","","","Accepted Author Manuscript","","2022-04-16","","","BN/Cees Dekker Lab","","",""
"uuid:718a558c-149f-433d-a482-c3cf25fad032","http://resolver.tudelft.nl/uuid:718a558c-149f-433d-a482-c3cf25fad032","FtsZ treadmilling is essential for Z-ring condensation and septal constriction initiation in Bacillus subtilis cell division","Whitley, K.D. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft; Newcastle University); Jukes, Calum (Newcastle University); Tregidgo, Nicholas (Newcastle University); Karinou, Eleni (Newcastle University); Almada, Pedro (University College London (UCL)); Cesbron, Yann (Newcastle University); Henriques, Ricardo (University College London (UCL); Instituto Gulbenkian de Ciência); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Holden, Séamus (Newcastle University)","","2021","Despite the central role of division in bacterial physiology, how division proteins work together as a nanoscale machine to divide the cell remains poorly understood. Cell division by cell wall synthesis proteins is guided by the cytoskeleton protein FtsZ, which assembles at mid-cell as a dense Z-ring formed of treadmilling filaments. However, although FtsZ treadmilling is essential for cell division, the function of FtsZ treadmilling remains unclear. Here, we systematically resolve the function of FtsZ treadmilling across each stage of division in the Gram-positive model organism Bacillus subtilis using a combination of nanofabrication, advanced microscopy, and microfluidics to measure the division-protein dynamics in live cells with ultrahigh sensitivity. We find that FtsZ treadmilling has two essential functions: mediating condensation of diffuse FtsZ filaments into a dense Z-ring, and initiating constriction by guiding septal cell wall synthesis. After constriction initiation, FtsZ treadmilling has a dispensable function in accelerating septal constriction rate. Our results show that FtsZ treadmilling is critical for assembling and initiating the bacterial cell division machine.","","en","journal article","","","","","","","","","","","BN/Cees Dekker Lab","","",""
"uuid:5513ea77-f0d8-4458-918e-f31493083ec9","http://resolver.tudelft.nl/uuid:5513ea77-f0d8-4458-918e-f31493083ec9","Palladium zero-mode waveguides for optical single-molecule detection with nanopores","Klughammer, N. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Dekker, C. (TU Delft BN/Cees Dekker Lab)","","2021","Holes in metal films do not allow the propagation of light if the wavelength is much larger than the hole diameter, establishing such nanopores as so-called zero-mode waveguides (ZMWs). Molecules, on the other hand, can still pass through these holes. We use this to detect individual fluorophore-labelled molecules as they travel through a ZMW and thereby traverse from the dark region to the illuminated side, upon which they emit fluorescent light. This is beneficial both for background suppression and to prevent premature bleaching. We use palladium as a novel metal-film material for ZMWs, which is advantageous compared to conventionally used metals. We demonstrate that it is possible to simultaneously detect translocations of individual free fluorophores of different colours. Labelled DNA and protein biomolecules can also be detected at the single-molecule level with a high signal-to-noise ratio and at high bandwidth, which opens the door to a variety of single-molecule biophysics studies.","","en","journal article","","","","","","Accepted Author Manuscript","","2022-02-08","","","BN/Cees Dekker Lab","","",""
"uuid:6f0c0b7b-62d4-48f9-bcc7-fdd7ed90998d","http://resolver.tudelft.nl/uuid:6f0c0b7b-62d4-48f9-bcc7-fdd7ed90998d","Genome-in-a-Box: Building a Chromosome from the Bottom up","Birnie, Anthony (Kavli institute of nanoscience Delft; Student TU Delft); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft)","","2021","Chromosome structure and dynamics are essential for life, as the way that our genomes are spatially organized within cells is crucial for gene expression, differentiation, and genome transfer to daughter cells. There is a wide variety of methods available to study chromosomes, ranging from live-cell studies to single-molecule biophysics, which we briefly review. While these technologies have yielded a wealth of data, such studies still leave a significant gap between top-down experiments on live cells and bottom-up in vitro single-molecule studies of DNA-protein interactions. Here, we introduce ""genome-in-a-box""(GenBox) as an alternative in vitro approach to build and study chromosomes, which bridges this gap. The concept is to assemble a chromosome from the bottom up by taking deproteinated genome-sized DNA isolated from live cells and subsequently add purified DNA-organizing elements, followed by encapsulation in cell-sized containers using microfluidics. Grounded in the rationale of synthetic cell research, the approach would enable to experimentally study emergent effects at the global genome level that arise from the collective action of local DNA-structuring elements. We review the various DNA-structuring elements present in nature, from nucleoid-associated proteins and SMC complexes to phase separation and macromolecular crowders. Finally, we discuss how GenBox can contribute to several open questions on chromosome structure and dynamics.","bottom-up biology; chromosome organization; DNA; DNA loop extrusion; DNA-binding proteins; emergent dynamics; minimal genome; phase separation; synthetic cells","en","review","","","","","","","","","","","BN/Cees Dekker Lab","","",""
"uuid:d042ddb6-9120-47a5-bd9b-ae244a81aeb5","http://resolver.tudelft.nl/uuid:d042ddb6-9120-47a5-bd9b-ae244a81aeb5","A level set model for stress-dependent corrosion pit propagation","Dekker, R. (TU Delft Applied Mechanics); van der Meer, F.P. (TU Delft Applied Mechanics); Maljaars, Johan (Eindhoven University of Technology; DIANA FEA); Sluys, Lambertus J. (TU Delft Materials- Mechanics- Management & Design)","","2021","A numerical model for corrosion pit propagation under mechanical loading is presented. The level set method is used for corrosion front tracking and also enables the domain to be split into a solid and a pit domain. In the pit the diffusion of atoms originating from the dissolution process occurring at the pit front is simulated. The model is capable of automatically capturing lacy cover formation due to the inclusion of activation control, diffusion control, and passivation. In the solid static equilibrium is solved to obtain strains and stresses. A parameter, dependent on the signs of the plastic strain increment and the back stress, is introduced to define the influence of plasticity on the corrosion rate. The model is used to study pit growth under electrochemical and mechanical loading. Under activation control combined with an elastic material response, pits propagate faster under constant loading than under cyclic loading. When plastic deformation occurs, cyclic loading can significantly increase the pit growth rate. Increasing the cyclic load frequency results in faster propagation due to kinematic hardening. Under diffusion control, mechanical loading does not influence the pit growth rate, given that the salt layer leading to diffusion control remains intact.","corrosion fatigue; level set method; multiphysics; pitting corrosion","en","journal article","","","","","","","","","","Materials- Mechanics- Management & Design","Applied Mechanics","","",""
"uuid:c24d9ed0-c9e9-4e87-bf44-c2815a468950","http://resolver.tudelft.nl/uuid:c24d9ed0-c9e9-4e87-bf44-c2815a468950","DNA sequence-directed cooperation between nucleoid-associated proteins","Japaridze, A. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Yang, W.W.W. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Nasser, William (INSA Lyon); Muskhelishvili, Georgi (Agricultural University of Georgia, Tbilisi)","","2021","Nucleoid-associated proteins (NAPs) are a class of highly abundant DNA-binding proteins in bacteria and archaea. While both the composition and relative abundance of the NAPs change during the bacterial growth cycle, surprisingly little is known about their crosstalk in mutually binding and stabilizing higher-order nucleoprotein complexes in the bacterial chromosome. Here, we use atomic force microscopy and solid-state nanopores to investigate long-range nucleoprotein structures formed by the binding of two major NAPs, FIS and H-NS, to DNA molecules with distinct binding site arrangements. We find that spatial organization of the protein binding sites can govern the higher-order architecture of the nucleoprotein complexes. Based on sequence arrangement the complexes differed in their global shape and compaction as well as the extent of FIS and H-NS binding. Our observations highlight the important role the DNA sequence plays in driving structural differentiation within the bacterial chromosome.","Organizational Aspects of Cell Biology; Structural Biology","en","journal article","","","","","","","","","","","BN/Cees Dekker Lab","","",""
"uuid:0147cbbb-b175-4b03-a304-78070c21327d","http://resolver.tudelft.nl/uuid:0147cbbb-b175-4b03-a304-78070c21327d","Contrasting the recommendations of participatory value evaluation and cost-benefit analysis in the context of urban mobility investments","Mouter, N. (TU Delft Transport and Logistics); Koster, Paul (Vrije Universiteit Amsterdam); Dekker, Thijs (University of Leeds)","","2021","Participatory Value Evaluation (PVE) is a new method to assess the desirability of government projects. In a PVE, individuals select their preferred portfolio of government projects given a constrained public budget. Individuals’ preferences for (the impacts of) government projects can be determined based on these choices. The obtained preferences can be used to rank government projects in terms of their desirability. Cost-Benefit Analysis (CBA) is an alternative appraisal method used to assess the desirability of government projects. CBA establishes the desirability of public projects through analyzing people's trade-offs between their private income and impacts of public projects. The primary objective of this paper is to investigate whether CBA and PVE lead to different policy recommendations in the context of urban mobility investments. We conducted CBAs and a PVE for 16 urban mobility investment projects and find indicative evidence that projects which focus on improving traffic safety and improvements for cyclists/pedestrians rank higher in the PVE, whereas car projects rank higher in the CBA analysis.","Cost benefit analysis; Participation; Participatory value evaluation; Transport appraisal; Transport planning","en","journal article","","","","","","","","","","","Transport and Logistics","","",""
"uuid:d772a0e9-c8f2-4f95-99bd-4cddceea0bc6","http://resolver.tudelft.nl/uuid:d772a0e9-c8f2-4f95-99bd-4cddceea0bc6","Translocation of DNA through Ultrathin Nanoslits","Yang, W.W.W. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Radha, Boya (The University of Manchester); Choudhary, Adnan (University of Illinois at Urbana-Champaign); You, Yi (The University of Manchester); Mettela, Gangaiah (The University of Manchester); Geim, Andre K. (The University of Manchester); Aksimentiev, Aleksei (University of Illinois at Urbana-Champaign); Keerthi, Ashok (The University of Manchester); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft)","","2021","2D nanoslit devices, where two crystals with atomically flat surfaces are separated by only a few nanometers, have attracted considerable attention because their tunable control over the confinement allows for the discovery of unusual transport behavior of gas, water, and ions. Here, the passage of double-stranded DNA molecules is studied through nanoslits fabricated from exfoliated 2D materials, such as graphene or hexagonal boron nitride, and the DNA polymer behavior is examined in this tight confinement. Two types of events are observed in the ionic current: long current blockades that signal DNA translocation and short spikes where DNA enters the slits but withdraws. DNA translocation events exhibit three distinct phases in their current-blockade traces—loading, translation, and exit. Coarse-grained molecular dynamics simulation allows the different polymer configurations of these phases to be identified. DNA molecules, including folds and knots in their polymer structure, are observed to slide through the slits with near-uniform velocity without noticeable frictional interactions of DNA with the confining graphene surfaces. It is anticipated that this new class of 2D-nanoslit devices will provide unique ways to study polymer physics and enable lab-on-a-chip biotechnology.","2D nanoslits; biopolymers; DNA translocation; graphene; nanofluidics","en","journal article","","","","","","","","","","","BN/Cees Dekker Lab","","",""
"uuid:a560de03-83cd-4d2c-8cda-36f63227b93a","http://resolver.tudelft.nl/uuid:a560de03-83cd-4d2c-8cda-36f63227b93a","Bulk-surface coupling identifies the mechanistic connection between Min-protein patterns in vivo and in vitro","Brauns, Fridtjof (Ludwig Maximilians University); Pawlik, G. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Halatek, Jacob (Microsoft Research New England); Kerssemakers, J.W.J. (TU Delft BN/Technici en Analisten; Kavli institute of nanoscience Delft); Frey, Erwin (Ludwig Maximilians University); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft)","","2021","Self-organisation of Min proteins is responsible for the spatial control of cell division in Escherichia coli, and has been studied both in vivo and in vitro. Intriguingly, the protein patterns observed in these settings differ qualitatively and quantitatively. This puzzling dichotomy has not been resolved to date. Using reconstituted proteins in laterally wide microchambers with a well-controlled height, we experimentally show that the Min protein dynamics on the membrane crucially depend on the micro chamber height due to bulk concentration gradients orthogonal to the membrane. A theoretical analysis shows that in vitro patterns at low microchamber height are driven by the same lateral oscillation mode as pole-to-pole oscillations in vivo. At larger microchamber height, additional vertical oscillation modes set in, marking the transition to a qualitatively different in vitro regime. Our work reveals the qualitatively different mechanisms of mass transport that govern Min protein-patterns for different bulk heights and thus shows that Min patterns in cells are governed by a different mechanism than those in vitro.","","en","journal article","","","","","","","","","","","BN/Cees Dekker Lab","","",""
"uuid:8cf98f09-d71d-487b-9c0a-e8ddd57119d7","http://resolver.tudelft.nl/uuid:8cf98f09-d71d-487b-9c0a-e8ddd57119d7","A next step in disruption management: combining operations research and complexity science","Dekker, Mark M. (Universiteit Utrecht); van Lieshout, Rolf N. (Erasmus Universiteit Rotterdam); Ball, Robin C. (University of Warwick); Bouman, Paul C. (Erasmus Universiteit Rotterdam); Dekker, Stefan C. (Universiteit Utrecht); Dijkstra, Henk A. (Universiteit Utrecht); Goverde, R.M.P. (TU Delft Transport and Planning); Huisman, Dennis (Erasmus Universiteit Rotterdam; N.V. Nederlandse Spoorwegen); Panja, Debabrata (Universiteit Utrecht); Schaafsma, Alfons A.M. (ProRail); van den Akker, Marjan (Universiteit Utrecht)","","2021","Railway systems occasionally get into a state of being out-of-control, meaning that barely any train is running, even though the required resources (infrastructure, rolling stock and crew) are available. Because of the large number of affected resources and the absence of detailed, timely and accurate information, currently existing disruption management techniques cannot be applied in out-of-control situations. Most of the contemporary approaches assume that there is only one single disruption with a known duration, that all information about the resources is available, and that all stakeholders in the operations act as expected. Another limitation is the lack of knowledge about why and how disruptions accumulate and whether this process can be predicted. To tackle these problems, we develop a multidisciplinary framework combining techniques from complexity science and operations research, aiming at reducing the impact of these situations and—if possible—avoiding them. The key elements of this framework are (i) the generation of early warning signals for out-of-control situations, (ii) isolating a specific region such that delay stops propagating, and (iii) the application of decentralized decision making, more suited for information-sparse out-of-control situations.","Complexity science; Operations research; Railway disruption management; Rescheduling","en","journal article","","","","","","","","","","","Transport and Planning","","",""
"uuid:9dbccabe-6a49-4879-beb7-c77bfdc96524","http://resolver.tudelft.nl/uuid:9dbccabe-6a49-4879-beb7-c77bfdc96524","DNA replication origins retain mobile licensing proteins","Sanchez González, H. (TU Delft BN/Nynke Dekker Lab; Kavli institute of nanoscience Delft); Mc Cluskey, K.A. (TU Delft BN/Nynke Dekker Lab; Kavli institute of nanoscience Delft); van Laar, T. (TU Delft BN/Nynke Dekker Lab; Kavli institute of nanoscience Delft); van Veen, E.N.W. (TU Delft BN/Nynke Dekker Lab; Kavli institute of nanoscience Delft); Asscher, F.M. (TU Delft BN/Nynke Dekker Lab; Kavli institute of nanoscience Delft); Solano Hermosilla, B.P. (TU Delft BN/Nynke Dekker Lab; Kavli institute of nanoscience Delft); Diffley, John F.X. (Francis Crick Institute); Dekker, N.H. (TU Delft BN/Nynke Dekker Lab; Kavli institute of nanoscience Delft)","","2021","DNA replication in eukaryotes initiates at many origins distributed across each chromosome. Origins are bound by the origin recognition complex (ORC), which, with Cdc6 and Cdt1, recruits and loads the Mcm2-7 (MCM) helicase as an inactive double hexamer during G1 phase. The replisome assembles at the activated helicase in S phase. Although the outline of replisome assembly is understood, little is known about the dynamics of individual proteins on DNA and how these contribute to proper complex formation. Here we show, using single-molecule optical trapping and confocal microscopy, that yeast ORC is a mobile protein that diffuses rapidly along DNA. Origin recognition halts this search process. Recruitment of MCM molecules in an ORC- and Cdc6-dependent fashion results in slow-moving ORC-MCM intermediates and MCMs that rapidly scan the DNA. Following ATP hydrolysis, salt-stable loading of MCM single and double hexamers was seen, both of which exhibit salt-dependent mobility. Our results demonstrate that effective helicase loading relies on an interplay between protein diffusion and origin recognition, and suggest that MCM is stably loaded onto DNA in multiple forms.","","en","journal article","","","","","","","","","","","BN/Nynke Dekker Lab","","",""
"uuid:ec256520-6c25-497a-8934-1b8eb1f27ddf","http://resolver.tudelft.nl/uuid:ec256520-6c25-497a-8934-1b8eb1f27ddf","Efficacy assessment of newly-designed filtering facemasks during the sars-cov-2 pandemic","Boogaard, Bob (Erasmus MC); Tas, Ali (Leiden University Medical Center); Nijssen, J.P.A. (TU Delft Mechatronic Systems Design); Broeren, F.G.J. (TU Delft Precision and Microsystems Engineering); van den Dobbelsteen, J.J. (TU Delft Medical Instruments & Bio-Inspired Technology); Verhoeven, Vincent (Reinier de Graaf Gasthuis); Pluim, Jip (Reinier de Graaf Gasthuis); Dekker, Sing (Reinier de Graaf Gasthuis); Snijder, Eric J. (Leiden University Medical Center); van Hemert, Martijn J. (Leiden University Medical Center); Herfst, Sander (Erasmus MC)","","2021","The SARS-CoV-2 pandemic resulted in shortages of production and test capacity of FFP2-respirators. Such facemasks are required to be worn by healthcare professionals when performing aerosol-generating procedures on COVID-19 patients. In response to the high demand and short supply, we designed three models of facemasks that are suitable for local production. As these facemasks should meet the requirements of an FFP2-certified facemask, the newly-designed facemasks were tested on the filtration efficiency of the filter material, inward leakage, and breathing resistance with custom-made experimental setups. In these tests, the facemasks were benchmarked against a commercial FFP2 facemask. The filtration efficiency of the facemask’s filter material was also tested with coronavirus-loaded aerosols under physiologically relevant conditions. This multidisciplinary effort resulted in the design and production of facemasks that meet the FFP2 requirements, and which can be produced at local production facilities.","Coronavirus filtration efficiency; Facemask; FFP2; NaCl particle filtration; Respirator","en","journal article","","","","","","","","","","Precision and Microsystems Engineering","Mechatronic Systems Design","","",""
"uuid:65980240-b9b6-4bf1-b434-d1db757e5401","http://resolver.tudelft.nl/uuid:65980240-b9b6-4bf1-b434-d1db757e5401","Privacy-Preserving Data Aggregation with Probabilistic Range Validation","Dekker, Florine W. (TU Delft Cyber Security); Erkin, Z. (TU Delft Cyber Security)","Sako, Kazue (editor); Tippenhauer, Nils Ole (editor)","2021","Privacy-preserving data aggregation protocols have been researched widely, but usually cannot guarantee correctness of the aggregate if users are malicious. These protocols can be extended with zero-knowledge proofs and commitments to work in the malicious model, but this incurs a significant computational cost on the end users, making adoption of these protocols less likely.
We propose a privacy-preserving data aggregation protocol for calculating the sum of user inputs. Our protocol gives the aggregator confidence that all inputs are within a desired range. Instead of zero-knowledge proofs, our protocol relies on a probabilistic hypergraph-based detection algorithm with which the aggregator can quickly pinpoint malicious users. Furthermore, our protocol is robust to user dropouts and, apart from the setup phase, it is non-interactive.","Privacy; Data aggregation; Applied cryptography; Hypergraphs","en","conference paper","Springer Nature","","","","","Green Open Access added to TU Delft Institutional Repository ‘You share, we take care!’ – Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.","","2021-12-09","","","Cyber Security","","",""
"uuid:cebeb915-766a-4e28-b2b8-eecc2214d6ee","http://resolver.tudelft.nl/uuid:cebeb915-766a-4e28-b2b8-eecc2214d6ee","Road Infrastructure Requirements for Improved Performance of Lane Assistance Systems","Reddy, N. (TU Delft Transport and Planning); Farah, H. (TU Delft Transport and Planning); Dekker, Thijs (Provincie Noord-Holland); Huang, Yilin (TU Delft System Engineering); van Arem, B. (TU Delft Transport and Planning)","","2020","There is a pressing need for road authorities to take a proactive role in the deployment of automated vehicles on the existing road network. This requires a comprehensive understanding of the road infrastructure requirements that would lead to safe operation of automated vehicles. In this context, a field test with Lane Departure Warning and Lane Keeping Systems-enabled vehicles was conducted in the province of North Holland, The Netherlands. The performance of these automated systems was evaluated using performance indicators such as Mean Lateral Position and Standard Deviation of Lane Position. In this study, the Systems Theoretic Accident Modelling and Processes (STAMP) model was adopted to understand the relationships between the various components of the “Road System”, which in this study include the road authority, the automated vehicle system, elements of the road infrastructure, and weather conditions. Empirical data from the experiment is used to estimate the relationships between the different components, followed by the assessment of their impact on the performance of the automated vehicles. It was found that visibility conditions have a significant effect on detection performance, which worsens in rainy conditions especially under streetlights. It has been also observed that there is a significant difference in Lane Position between Left Curves and Straight sections, and between lane widths less than 250 cms and those that have larger widths. These findings are combined with the results from the STAMP analysis to formulate a set of road infrastructure requirements that would lead to safe performance of Lane Assistance Systems.","Automated Driving; Lane Assistance Systems; Systems Theory; Systems Theoretic Accident Modeling and Processes (STAMP); Infrastructure effects; Road design","en","poster","","","","","","","","","","","Transport and Planning","","",""
"uuid:f048c853-7e1d-4715-b73d-3b506b274a30","http://resolver.tudelft.nl/uuid:f048c853-7e1d-4715-b73d-3b506b274a30","Sterilization of disposable face masks by means of standardized dry and steam sterilization processes: an alternative in the fight against mask shortages due to COVID-19","de Man, P. (Franciscus Gasthuis & Vlietland); van Straten, Bart (TU Delft Medical Instruments & Bio-Inspired Technology; Van Straten Medical); van den Dobbelsteen, J.J. (TU Delft Medical Instruments & Bio-Inspired Technology); van der Eijk, A. (Leiden University Medical Center); Dekker, S. (Reinier de Graaf Gasthuis); Horeman, T. (TU Delft Medical Instruments & Bio-Inspired Technology); Koeleman, H. (Franciscus Gasthuis & Vlietland)","","2020","","COVID-19; masks; sterilization","en","other","Delft University of Technology","","","","","","","","","","Medical Instruments & Bio-Inspired Technology","","",""
"uuid:1834a774-cf59-4774-be80-1c98535380b5","http://resolver.tudelft.nl/uuid:1834a774-cf59-4774-be80-1c98535380b5","Publisher Correction: The condensin holocomplex cycles dynamically between open and collapsed states (Nature Structural & Molecular Biology, (2020), 27, 12, (1134-1141), 10.1038/s41594-020-0508-3)","Ryu, J.K. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Katan, A.J. (TU Delft QN/Afdelingsbureau; Kavli institute of nanoscience Delft); van der Sluis, E.O. (TU Delft BN/Technici en Analisten; Kavli institute of nanoscience Delft); Wisse, T. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); de Groot, Ralph (Kavli institute of nanoscience Delft; Student TU Delft); Haering, Christian H. (European Molecular Biology Laboratory Heidelberg); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft)","","2020","An amendment to this paper has been published and can be accessed via a link at the top of the paper.","","en","journal article","","","","","","","","","","","BN/Cees Dekker Lab","","",""
"uuid:056d1c01-c0b3-4a3f-96fa-3e62634d6f69","http://resolver.tudelft.nl/uuid:056d1c01-c0b3-4a3f-96fa-3e62634d6f69","pH-Controlled Coacervate-Membrane Interactions within Liposomes","Last, M.G.F. (TU Delft ImPhys/Microscopy Instrumentation & Techniques; Kavli institute of nanoscience Delft); Deshpande, S.R. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft; Wageningen University & Research); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft)","","2020","Membraneless organelles formed by liquid-liquid phase separation are dynamic structures that are employed by cells to spatiotemporally regulate their interior. Indeed, complex coacervation-based phase separation is involved in a multitude of biological tasks ranging from photosynthesis to cell division to chromatin organization, and more. Here, we use an on-chip microfluidic method to control and study the formation of membraneless organelles within liposomes, using pH as the main control parameter. We show that a transmembrane proton flux that is created by a stepwise change in the external pH can readily bring about the coacervation of encapsulated components in a controlled manner. We employ this strategy to induce and study electrostatic as well as hydrophobic interactions between the coacervate and the lipid membrane. Electrostatic interactions using charged lipids efficiently recruit coacervates to the membrane and restrict their movement along the inner leaflet. Hydrophobic interactions via cholesterol-tagged RNA molecules provide even stronger interactions, causing coacervates to wet the membrane and affect the local lipid-membrane structure, reminiscent of coacervate-membrane interactions in cells. The presented technique of pH-triggered coacervation within cell-sized liposomes may find applications in synthetic cells and in studying biologically relevant phase separation reactions in a bottom-up manner.","coacervates; liposomes; liquid−liquid phase separation; membranes; microfluidics","en","journal article","","","","","","","","","","","ImPhys/Microscopy Instrumentation & Techniques","","",""
"uuid:755e06ff-951f-4e20-a22d-0ab47cc2b6b0","http://resolver.tudelft.nl/uuid:755e06ff-951f-4e20-a22d-0ab47cc2b6b0","Direct observation of independently moving replisomes in Escherichia coli","Japaridze, A. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Gogou, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Kerssemakers, J.W.J. (TU Delft BN/Technici en Analisten; Kavli institute of nanoscience Delft); Nguyen, Huyen My (Student TU Delft); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft)","","2020","The replication and transfer of genomic material from a cell to its progeny are vital processes in all living systems. Here we visualize the process of chromosome replication in widened E. coli cells. Monitoring the replication of single chromosomes yields clear examples of replication bubbles that reveal that the two replisomes move independently from the origin to the terminus of replication along each of the two arms of the circular chromosome, providing direct support for the so-called train-track model, and against a factory model for replisomes. The origin of replication duplicates near midcell, initially splitting to random directions and subsequently towards the poles. The probability of successful segregation of chromosomes significantly decreases with increasing cell width, indicating that chromosome confinement by the cell boundary is an important driver of DNA segregation. Our findings resolve long standing questions in bacterial chromosome organization.","","en","journal article","","","","","","","","","","","BN/Cees Dekker Lab","","",""
"uuid:69753852-d305-4289-afb5-6bf0ab4efbfd","http://resolver.tudelft.nl/uuid:69753852-d305-4289-afb5-6bf0ab4efbfd","Interplay between Confinement and Drag Forces Determine the Fate of Amyloid Fibrils","Smith, Kathleen Beth (ETH Zürich); Wehrli, Monika (ETH Zürich); Japaridze, A. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Assenza, Salvatore (ETH Zürich); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Mezzenga, Raffaele (ETH Zürich)","","2020","The fine interplay between the simultaneous stretching and confinement of amyloid fibrils is probed by combining a microcapillary setup with atomic force microscopy. Single-molecule statistics reveal how the stretching of fibrils changed from force to confinement dominated at different length scales. System order, however, is solely ruled by confinement. Coarse-grained simulations support the results and display the potential to tailor system properties by tuning the two effects. These findings may further help shed light on in vivo amyloid fibril growth and transport in highly confined environments such as blood vessels.","","en","journal article","","","","","","","","","","","BN/Cees Dekker Lab","","",""
"uuid:68583842-8b9f-45ae-9cc6-2e79d56ccde3","http://resolver.tudelft.nl/uuid:68583842-8b9f-45ae-9cc6-2e79d56ccde3","Revenue management with two fare classes in synchromodal container transportation","Van Riessen, Bart (Erasmus Universiteit Rotterdam); Mulder, Judith (Erasmus Universiteit Rotterdam); Negenborn, R.R. (TU Delft Transport Engineering and Logistics); Dekker, Rommert (Erasmus Universiteit Rotterdam)","","2020","The cargo fare class mix (CFCM) problem aims to find the optimal fare class mix for a given intermodal transportation network based on known client demands. It is based on a revenue management problem for aviation passengers, the fare class mix problem, but considering intermodal cargo transportation, two major differences apply. Firstly, the CFCM’s premise is that long-term commitments to customers must be provided, such that a customer has a guaranteed daily capacity. Secondly, cargo may be rescheduled or rerouted, as long as the customer’s delivery due date is met. Our goal is to balance revenue maximisation and capacity utilisation by optimally combining two delivery service levels. Therefore, the optimisation problem is to select fare class limits at a tactical level up to which transportation demand will be accepted on a daily basis at the operational level. Any accepted demand that does not fit on the available network capacity during operation, must be transported by truck at increased expenses for the network operator. In this paper, we propose a faster method than the previously proposed solution method for a single corridor network and we provide proofs for the optimality of the result. Using this, we extend the problem to an intermodal network of multiple corridors. We provide numerical results for different settings, in which we compare the baseline of individual corridor optimums with the result of using rerouting. Finally, we apply the methods in a case study for an intermodal transportation network in North-West Europe.","Container transportation; Fare class sizes; Intermodal planning; Revenue management; Synchromodal planning","en","journal article","","","","","","","","","","","Transport Engineering and Logistics","","",""
"uuid:14d51089-742f-40c7-adeb-4422098292d0","http://resolver.tudelft.nl/uuid:14d51089-742f-40c7-adeb-4422098292d0","PDMS-Parylene Adhesion Improvement via Ceramic Interlayers to Strengthen the Encapsulation of Active Neural Implants","Bakhshaee Babaroud, N. (TU Delft Bio-Electronics); Dekker, R. (TU Delft Electronic Components, Technology and Materials); Serdijn, W.A. (TU Delft Bio-Electronics); Giagka, Vasiliki (TU Delft Bio-Electronics; Fraunhofer Institute for Reliability and Microintegration IZM)","","2020","Parylene-C has been used as a substrate and encapsulation material for many implantable medical devices. However, to ensure the flexibility required in some applications, minimize tissue reaction, and protect parylene from degradation in vivo an additional outmost layer of polydimethylsiloxane (PDMS) is desired. In such a scenario, the adhesion of PDMS to parylene is of critical importance to prevent early failure caused by delamination in the harsh environment of the human body. Towards this goal, we propose a method based on creating chemical covalent bonds using intermediate ceramic layers as adhesion promoters between PDMS and parylene.To evaluate our concept, we prepared three different sets of samples with PDMS on parylene without and with oxygen plasma treatment (the most commonly employed method to increase adhesion), and samples with our proposed ceramic intermediate layers of silicon carbide (SiC) and silicon dioxide (SiO2). The samples were soaked in phosphate-buffered saline (PBS) solution at room temperature and were inspected under an optical microscope. To investigate the adhesion property, cross-cut tape tests and peel tests were performed. The results showed a significant improvement of the adhesion and in-soak long-term performance of our proposed encapsulation stack compared with PDMS on parylene and PDMS on plasma-treated parylene. We aim to use the proposed solution to package bare silicon chips on active implants.","","en","conference paper","IEEE","","","","","Accepted author manuscript","","","","","Bio-Electronics","","",""
"uuid:491f7fd1-328a-46bd-b86e-7287cb0071f6","http://resolver.tudelft.nl/uuid:491f7fd1-328a-46bd-b86e-7287cb0071f6","Matching Development of Point-of-Care Diagnostic Tests to the Local Context: A Case Study of Visceral Leishmaniasis in Kenya and Uganda","Bengtson, M.L. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Bharadwaj, M. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); ten Bosch, A.P. (Student TU Delft); Nyakundi, Hellen (University of Nairobi); Matoke-Muhia, Damaris (Kenya Medical Research); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Diehl, J.C. (TU Delft Design for Sustainability)","","2020","The rapid growth of point-of-care (POC) diagnostic tests necessitates a clear vision of when, where, and why a new POC diagnostic test needs to be developed and how it can be used in a way that matches a local health care context. Here, we present an innovative approach toward developing a concept target product profile (CTPP), which is a new mapping tool that helps researchers match a new diagnostic test to a specific local health care context early in the research and development process. As a case study, we focus on the diagnosis of visceral leishmaniasis (VL) in rural resource-limited regions of Kenya and Uganda. Our stepwise approach integrates elements of design thinking and uses a combination of literature reviews and field research for a context analysis of local health care systems and practices. We then use visual thinking in the form of Gigamaps and patient journeys to identify use case scenarios and to present our findings from the field research to key stakeholders. The use case scenarios describe the diagnostic scope of a new POC test based on the feasibility of the new test, the local need, and the contextual fit. For our case study of VL, we identify 2 valuable use case scenarios, namely test-of-cure and screening and confirmation, and we formulate a CTPP. We anticipate that a CTPP will enable researchers to match a new POC diagnostic test during the research and development process to the local health care context in which it will be used.","","en","journal article","","","","","","","","","","","BN/Cees Dekker Lab","","",""
"uuid:3845db1d-20c7-4a74-a547-4c2bde528b18","http://resolver.tudelft.nl/uuid:3845db1d-20c7-4a74-a547-4c2bde528b18","Embedded High-Density Trench Capacitors for Smart Catheters","Li, J. (TU Delft Electronic Components, Technology and Materials); Naaborg, Jeroen (Student TU Delft); Louwerse, Marcus (Philips Innovation Services); Henneken, Vincent (Philips Research); Eugeni, Carlo (Philips Innovation Services); Dekker, R. (TU Delft Electronic Components, Technology and Materials)","","2020","Our work presents embedded high-density oxide-nitride-oxide (ONO) trench capacitors for power supply decoupling in the next generation of smart catheters. These millimeter-scale smart catheters are using a novel integration platform, Flex-to-Rigid (F2R). In the F2R platform, various functional modules are fabricated or assembled on thin silicon islands. They are connected by flexible interconnects and can be folded into arbitrary shapes to facilitate small form-factor integration. Trench decoupling capacitors have the advantage of being integrated into the thin silicon islands of F2R to reduce the parasitic inductances and space consumption. Additionally, their small surface openings can be closed by layer deposition to enable follow-up processes on the closed-up surface. For demonstration, high aspect ratio (1.1:25 and 1.2:30) ONO trench capacitors with total areas of 300x300 µm 2 and 1000x1000 µm 2 are fabricated on planar wafers, and a 700 nm and a 1 µm thick plasma-enhanced chemical vapor deposition (PECVD) SiO2 layers are deposited to test the trench closing process. The F2R compatible ONO trench capacitors have capacitance densities of 6.17 nF/mm 2 and 10.12 nF/mm 2 , combined with breakdown voltages ranging from 28 to 30 V.","Flex-to-Rigid (F2R); HAR (High Aspect Ratio); Intravascular ultrasound (IVUS) catheter; Micro-assembly; Smart catheters; Trench Capacitors","en","conference paper","IEEE","","","","","","","","","","Electronic Components, Technology and Materials","","",""
"uuid:e8cff5e9-c11e-4413-9b08-f01fab43e597","http://resolver.tudelft.nl/uuid:e8cff5e9-c11e-4413-9b08-f01fab43e597","Operational Design Domain Requirements for Improved Performance of Lane Assistance Systems: A Field Test Study in The Netherlands","Reddy, N. (TU Delft Transport and Planning); Farah, H. (TU Delft Transport and Planning); Huang, Yilin (TU Delft System Engineering); Dekker, Thijs (Provincie Noord-Holland); van Arem, B. (TU Delft Transport and Planning)","","2020","There is a pressing need for road authorities to take a proactive role in the deployment of automated vehicles on the existing road network. This requires a comprehensive understanding of the driving environment characteristics that affect the performance of automated vehicles. In this context, a field test with Lane Departure Warning (LDW) and Lane Keeping Systems (LKS)-enabled vehicles was conducted in the Netherlands. Empirical data from the experiment was used to estimate the impact of driving environment components such as weather condition and lane width on the performance of the automated vehicles. Driving at night in the presence of streetlights with rain resulted in least detection performance for both the vehicles as compared to other visibility conditions. As for lane-keeping performance, the LKS positioned the vehicle significantly more to the left of the lane on left-curves than on straight sections. The LKS also positioned the vehicle more left on lanes with a width less than 250 cm than on wider lanes. These findings were translated into levels of service of the Operational Design Domain (ODD). Each level of service corresponded to a performance level of the lane assistance systems, classified as “High”, “Medium”, and “Low”, and defined using indicators.","Automated vehicles; field test; lane assistance systems; operational design domain; performance evaluation; OA-Fund TU Delft","en","journal article","","","","","","","","","","","Transport and Planning","","",""
"uuid:5a6195c2-945b-4c9b-b855-cdf9463f038f","http://resolver.tudelft.nl/uuid:5a6195c2-945b-4c9b-b855-cdf9463f038f","Land of Chabot: A Highway Landscape as a Monument to a Painter","de Wit, S.I. (TU Delft Landscape Architecture); Dekker, Andre (Observatorium)","","2020","In the contemporary metropolitan landscape of Rotterdam, the open landscape spaces that once surrounded the city have been reduced to components in a hybrid field. When the polders were still expansive, with an omnipresent horizon, and big skies, they were depicted extensively by the Dutch landscape painter Henk Chabot (1894-1949). Chabot is the Rotterdam painter of an oeuvre that is associated with angular, realistic expressionism of many layers of paint in hard colours, who painted heavily emphasised skies over poor countryside, or monumental portraits of refugees or farmers. For fifteen years, he lived and worked in a studio by the river Rotte. Now, only a relic of the farmland where he lived remains: an interstice between motorways, recreation parks, and suburbs that seemed to be overlooked in the frenzy of urban planning processes. The reason this interstice still exists is that it has been reserved for a future motorway for the last 30 years, and in the not-so-distant future will become the tunnel entrance for the new A16 motorway. As a left-over space, the terrain seems non-descript. However, it does have the implicit characteristics of a ‘landscape theatre’: introducing the processes and the scale of landscape as self-evident elements of the city, and heralding the open polder landscape twenty minutes away. It borrows its physical boundaries from the Rotte river dyke, the heemtuin (botanical garden) adjacent to the Ommoord apartment blocks, the access road to Ommoord, the industrial estate, and residential area in Terbregge. Such a “borrowed boundary” can be seen as a defining trait of the landscape theatre. The open space that is defined by this borrowed boundary and the central point of the tunnel entrance, is a secluded, self-contained place, removed in time and space, insulated against the everyday reality and, aside from the public realm of streets, squares, and parks, from the hustle and bustle of urban life: a place “outside”.","Land of Chabot; interstitial space; metropolitan garden; highway; landscape theatre","en","journal article","","","","","","","","","","","Landscape Architecture","","",""
"uuid:a2e8f027-1764-4059-9118-195557ca0a52","http://resolver.tudelft.nl/uuid:a2e8f027-1764-4059-9118-195557ca0a52","the Garden in the Landscape Metropolis","de Wit, S.I. (TU Delft Landscape Architecture); Dekker, Andre (Observatorium)","","2020","","","en","contribution to periodical","","","","","","","","","","","Landscape Architecture","","",""
"uuid:e893f4e5-c4ba-447a-a7e9-a70517fbabbb","http://resolver.tudelft.nl/uuid:e893f4e5-c4ba-447a-a7e9-a70517fbabbb","PDMS to Parylene Adhesion Improvement for Encapsulating an Implantable Device","Bakhshaee Babaroud, N. (TU Delft Bio-Electronics); Dekker, R. (TU Delft Electronic Components, Technology and Materials); Serdijn, W.A. (TU Delft Bio-Electronics); Giagka, Vasiliki (TU Delft Bio-Electronics; Fraunhofer Institute for Reliability and Microintegration IZM)","","2020","Parylene-C has been used as a substrate and encapsulation material for many implantable medical devices. However, to ensure the flexibility required in some applications, minimize tissue reaction, and protect parylene from degradation in vivo an additional outmost layer of polydimethylsiloxane (PDMS) is desired. In such a scenario, the adhesion of PDMS to parylene is of critical importance to prevent early failure caused by delamination in the harsh environment of the human body. Towards this goal, we propose a method based on creating chemical covalent bonds using intermediate ceramic layers as adhesion promoters between PDMS and parylene. To evaluate our concept, we prepared three different sets of samples with PDMS on parylene without and with oxygen plasma treatment (the most commonly employed method to increase adhesion), and samples with our proposed ceramic intermediate layers of silicon carbide (SiC) and silicon dioxide (SiO2). The samples were soaked in phosphate-buffered saline (PBS) solution at room temperature and were inspected under an optical microscope. To investigate the adhesion property, cross-cut tape tests and peel tests were performed. The results showed a significant improvement of the adhesion and in-soak long-term performance of our proposed encapsulation stack compared with PDMS on parylene and PDMS on plasmatreated parylene. We aim to use the proposed solution to package bare silicon chips on active implants.","","en","conference paper","","","","","","","","","","","Bio-Electronics","","",""
"uuid:bd246369-2a6d-4c90-a297-d3789f66a319","http://resolver.tudelft.nl/uuid:bd246369-2a6d-4c90-a297-d3789f66a319","DNA-loop extruding condensin complexes can traverse one another","Kim, E. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Kerssemakers, J.W.J. (TU Delft BN/Technici en Analisten; Kavli institute of nanoscience Delft); Shaltiel, Indra A. (European Molecular Biology Laboratory Heidelberg); Haering, Christian H. (European Molecular Biology Laboratory Heidelberg); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft)","","2020","Condensin, a key component of the structure maintenance of chromosome (SMC) protein complexes, has recently been shown to be a motor that extrudes loops of DNA1. It remains unclear, however, how condensin complexes work together to collectively package DNA into chromosomes. Here we use time-lapse single-molecule visualization to study mutual interactions between two DNA-loop-extruding yeast condensins. We find that these motor proteins, which, individually, extrude DNA in one direction only are able to dynamically change each other’s DNA loop sizes, even when far apart. When they are in close proximity, condensin complexes are able to traverse each other and form a loop structure, which we term a Z-loop—three double-stranded DNA helices aligned in parallel with one condensin at each edge. Z-loops can fill gaps left by single loops and can form symmetric dimer motors that pull in DNA from both sides. These findings indicate that condensin may achieve chromosomal compaction using a variety of looping structures.","","en","journal article","","","","","","Accepted Author Manuscript","","2020-09-04","","","BN/Cees Dekker Lab","","",""
"uuid:bd69c4ad-db17-4c80-85cd-5960372bfd02","http://resolver.tudelft.nl/uuid:bd69c4ad-db17-4c80-85cd-5960372bfd02","How deregulation can become overregulation: An empirical study into the growth of internal bureaucracy when governments take a step back","Størkersen, Kristine (Norwegian University of Science and Technology (NTNU)); Thorvaldsen, Trine (SINTEF Ocean); Kongsvik, Trond (Norwegian University of Science and Technology (NTNU)); Dekker, S.W.A. (TU Delft Control & Simulation; Griffith University)","","2020","Over the past decades, government safety management regulation has been driven by deregulation, simplification and organization-level regimes of inspection. So-called functional rule-making requires organizations to implement safety management systems appropriate for their operations. The paradox that seems to have arisen is that overregulation is common in many organizations. Research has found over-proceduralization, safety clutter, bureaucratic overload, and procedures not at the service of safety. To explore the paradoxical relationship between governmental deregulatory measures and organizational overregulation, we analyze empirical data from Norwegian fish farming and coastal transport. The data confirms that practitioners experience a rapidly grown abundance of internal rules and protocols, ill-fitting procedures, and pervasive, exaggerated safety management. We trace three mechanisms that have driven internal overregulation: work auditability; managerial insecurity and liability; and audit practices. These mechanisms show how functional regulation can have unintended consequences when it meets other accountability expectations. Expectations of market doctrine, bureaucratic entrepreneurism and control can lead a company transforming simple governmental regulations into vastly overcomplicated safety management systems. We conclude our study with prescriptions of how this aspect of safety could be done differently.","Bureaucracy; Deregulation; Fish farms; Maritime; Regulation; Safety management","en","journal article","","","","","","","","","","","Control & Simulation","","",""
"uuid:2a0bbbc0-e2d6-4d78-a6bd-f3a13991d7a2","http://resolver.tudelft.nl/uuid:2a0bbbc0-e2d6-4d78-a6bd-f3a13991d7a2","Chromatin fibers stabilize nucleosomes under torsional stress","Kaczmarczyk, A.P. (TU Delft BN/Nynke Dekker Lab; Universiteit Leiden; Kavli institute of nanoscience Delft); Meng, He (Universiteit Leiden); Ordu, O. (TU Delft BN/Nynke Dekker Lab; Kavli institute of nanoscience Delft); Noort, John van (Universiteit Leiden); Dekker, N.H. (TU Delft BN/Nynke Dekker Lab; Kavli institute of nanoscience Delft)","","2020","Torsional stress generated during DNA replication and transcription has been suggested to facilitate nucleosome unwrapping and thereby the progression of polymerases. However, the propagation of twist in condensed chromatin remains yet unresolved. Here, we measure how force and torque impact chromatin fibers with a nucleosome repeat length of 167 and 197. We find that both types of fibers fold into a left-handed superhelix that can be stabilized by positive torsion. We observe that the structural changes induced by twist were reversible, indicating that chromatin has a large degree of elasticity. Our direct measurements of torque confirmed the hypothesis of chromatin fibers as a twist buffer. Using a statistical mechanics-based torsional spring model, we extracted values of the chromatin twist modulus and the linking number per stacked nucleosome that were in good agreement with values measured here experimentally. Overall, our findings indicate that the supercoiling generated by DNA-processing enzymes, predicted by the twin-supercoiled domain model, can be largely accommodated by the higher-order structure of chromatin.","","en","journal article","","","","","","","","","","","BN/Nynke Dekker Lab","","",""
"uuid:a75ec654-df93-4a64-b957-d2e8153c0fc0","http://resolver.tudelft.nl/uuid:a75ec654-df93-4a64-b957-d2e8153c0fc0","Low-Impedance PEDOT:PSS MEA Integrated in a Stretchable Organ-on-Chip Device","Waafi, Affan K. (Student TU Delft); Gaio, N. (TU Delft Electronic Components, Technology and Materials; BIOND Solutions B.V.); Quiros Solano, W.F. (TU Delft Electronic Components, Technology and Materials); Dijkstra, Paul (Philips Innovation Services); Sarro, Pasqualina M (TU Delft Electronic Components, Technology and Materials); Dekker, R. (TU Delft Electronic Components, Technology and Materials; Philips Research)","","2020","We present the first Organ-on-Chip equipped with a low-impedance Poly(3,4-ethylenedioxythiophene) polystyrene sulfonate (PEDOT:PSS) MicroElectrode Array (MEA). The novel device allows simultaneous mechanical stimulation with a stretchable PDMS membrane and electrical monitoring via the PEDOT:PSS MEA of multiple in vitro cell cultures. The surface area enhancement and the morphology of the PEDOT:PSS allows an increase of the charge injection per unit area at the electrode-electrolyte interface, resulting in significantly lower electrochemical impedance of the electrodes. In particular, at 1 kHz the fabricated PEDOT-MEA electrodes show a reduction of the overall impedance up to 99.4 and 93.3 % in comparison with benchmark TiN and Pt electrodes. The superior performance of PEDOT:PSS were also confirmed via Cyclic Voltammetry measurement, in which PEDOT:PSS showed a very large capacitive current, compared with the benchmark electrodes both in the forward and the reverse scans. The obtained results confirm the effectiveness of the proposed PEDOT:PSS coating, and introduce this material in the OOC field. Moreover, the quality and morphology of the fabricated PEDOT:PSS based electrodes were assessed via SEM imaging and Raman spectroscopy.","microelectrode array; Organ-on-chip; PDMS; PEDOT:PSS","en","journal article","","","","","","Green Open Access added to TU Delft Institutional Repository ‘You share, we take care!’ – Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.","","2021-12-06","","","Electronic Components, Technology and Materials","","",""
"uuid:c9fdba61-cf32-42d4-be56-f980219b0347","http://resolver.tudelft.nl/uuid:c9fdba61-cf32-42d4-be56-f980219b0347","Comparing Current Noise in Biological and Solid-State Nanopores","Fragasso, A. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Schmid, S. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft)","","2020","Nanopores bear great potential as single-molecule tools for bioanalytical sensing and sequencing, due to their exceptional sensing capabilities, high-throughput, and low cost. The detection principle relies on detecting small differences in the ionic current as biomolecules traverse the nanopore. A major bottleneck for the further progress of this technology is the noise that is present in the ionic current recordings, because it limits the signal-to-noise ratio (SNR) and thereby the effective time resolution of the experiment. Here, we review the main types of noise at low and high frequencies and discuss the underlying physics. Moreover, we compare biological and solid-state nanopores in terms of the SNR, the important figure of merit, by measuring translocations of a short ssDNA through a selected set of nanopores under typical experimental conditions. We find that SiNx solid-state nanopores provide the highest SNR, due to the large currents at which they can be operated and the relatively low noise at high frequencies. However, the real game-changer for many applications is a controlled slowdown of the translocation speed, which for MspA was shown to increase the SNR > 160-fold. Finally, we discuss practical approaches for lowering the noise for optimal experimental performance and further development of the nanopore technology.","biological nanopores; biosensors; DNA sequencing; ion current noise; signal-to-noise ratio; single-molecule detection; solid-state nanopores; translocation","en","review","","","","","","","","","","","BN/Cees Dekker Lab","","",""
"uuid:45472647-4f76-4955-8732-123c0921db7a","http://resolver.tudelft.nl/uuid:45472647-4f76-4955-8732-123c0921db7a","A Mechanically Tunable Quantum Dot in a Graphene Break Junction","Caneva, S. (TU Delft BN/Cees Dekker Lab; TU Delft Dynamics of Micro and Nano Systems; TU Delft QN/van der Zant Lab; Kavli institute of nanoscience Delft); Hermans, Matthijs (Kavli institute of nanoscience Delft; Student TU Delft); Lee, M. (TU Delft QN/Steeneken Lab; Kavli institute of nanoscience Delft); García-Fuente, Amador (Universidad de Oviedo); Watanabe, Kenji (National Institute for Materials Science); Taniguchi, Takashi (National Institute for Materials Science); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Ferrer, Jaime (Universidad de Oviedo); van der Zant, H.S.J. (TU Delft QN/van der Zant Lab; Kavli institute of nanoscience Delft); Gehring, P. (TU Delft QN/van der Zant Lab; Kavli institute of nanoscience Delft)","","2020","Graphene quantum dots (QDs) are intensively studied as platforms for the next generation of quantum electronic devices. Fine tuning of the transport properties in monolayer graphene QDs, in particular with respect to the independent modulation of the tunnel barrier transparencies, remains challenging and is typically addressed using electrostatic gating. We investigate charge transport in back-gated graphene mechanical break junctions and reveal Coulomb blockade physics characteristic of a single, high-quality QD when a nanogap is opened in a graphene constriction. By mechanically controlling the distance across the newly formed graphene nanogap, we achieve reversible tunability of the tunnel coupling to the drain electrode by 5 orders of magnitude, while keeping the source-QD tunnel coupling constant. The break junction device can therefore become a powerful platform to study the physical parameters that are crucial to the development of future graphene-based devices, including energy converters and quantum calorimeters.","graphene; mechanical break junction; quantum dot (QD); tunnel coupling","en","journal article","","","","","","","","","","","BN/Cees Dekker Lab","","",""
"uuid:da8d78fc-4ade-4d7e-9cda-93fe57af435b","http://resolver.tudelft.nl/uuid:da8d78fc-4ade-4d7e-9cda-93fe57af435b","Adsorption of Aromatics in MFI-Type Zeolites: Experiments and Framework Flexibility in Monte Carlo Simulations","Caro Ortiz, S.A. (TU Delft Engineering Thermodynamics); Zuidema, Erik (Shell Global Solutions B.V.); Dekker, Desmond (Shell Global Solutions International B.V.); Rigutto, Marcello (Shell Global Solutions International B.V.); Dubbeldam, D. (TU Delft Engineering Thermodynamics; Universiteit van Amsterdam); Vlugt, T.J.H. (TU Delft Engineering Thermodynamics)","","2020","Computer simulations of adsorption of aromatics in zeolites are typically performed using rigid zeolite frameworks. However, adsorption isotherms for aromatics are very sensitive to small differences in the atomic positions of the zeolite (Chem. Phys. Lett., 1999, 308, 155-159). This article studies the effect of framework flexibility on the adsorption of aromatics in MFI-type zeolites computed by grand-canonical Monte Carlo simulations. New experimental data of adsorption of ethylbenzene in a MFI-type zeolite at 353 K is presented. The adsorption of n-heptane, ethylbenzene, and xylene isomers is computed in three MFI-type zeolite structures. It is observed that the intraframework interactions in flexible framework models induce small but important changes in the atom positions of the zeolite and hence in the adsorption isotherms. Framework flexibility is differently ""rigid"": flexible force fields produce a zeolite structure that vibrates around a new equilibrium configuration with limited capacity to accommodate to a bulky guest molecule. The vibration of the zeolite atoms only plays a role at high loadings, and the adsorption is mainly dependent on the average positions of the atoms. The simulations show that models for framework flexibility should not be blindly applied to zeolites and a general reconsideration of the parametrization schemes for such models is needed.","","en","journal article","","","","","","","","","","","Engineering Thermodynamics","","",""
"uuid:d7a000b9-68f8-440d-a4c0-c03238d53706","http://resolver.tudelft.nl/uuid:d7a000b9-68f8-440d-a4c0-c03238d53706","Versatile Multilayer Metamaterial Nanoparticles with Tailored Optical Constants for Force and Torque Transduction","Tang, Y. (TU Delft ImPhys/Optics); Ha, S. (TU Delft BN/Nynke Dekker Lab; Kavli institute of nanoscience Delft); Begou, Thomas (Aix Marseille Université); Lumeau, Julien (Aix Marseille Université); Urbach, Paul (TU Delft ImPhys/Optics); Dekker, N.H. (TU Delft BN/Nynke Dekker Lab; Kavli institute of nanoscience Delft); Adam, A.J.L. (TU Delft ImPhys/Optics)","","2020","The ability to apply force and torque directly to micro- and nanoscale particles in optical traps has a wide range of applications. While full control of both force and torque in three dimensions has been realized using top-down fabrication of rod-shaped particles composed of birefringent crystalline materials, widespread usage of such particles is limited as the optical constants of the predominant birefringent materials (quartz SiO2 and rutile TiO2) preclude coverage of the full application space of optical trapping. Here, we show that multilayer metamaterial nanoparticles provide access to a wide range of optical constants that can be specifically tuned for each application. Selecting the material pair Nb2O5/SiO2 from the library of amorphous dielectrics as our metamaterial, we show that its refractive index and birefringence can be designed by adapting the ratio of layer thicknesses. Using a robust top-down fabrication process, we show that uniformly sized, free-floating Nb2O5/SiO2 particles with high birefringence at moderate refractive index are obtained at high yield. Using an optical torque wrench, we show that these particles function as joint force and torque transducers while maintaining excellent stability in aqueous solutions and can be controllably optimized for particular physical characteristics such as maximal torque transfer or rapid response time. We expect that such customizable birefringent metamaterial nanoparticles whose properties surpass those of conventional crystalline particles will provide a means to unleash the full potential of optical trapping applications.","dielectric multilayers; force spectroscopy; metamaterials; nanoparticles; optical trapping; torque spectroscopy","en","journal article","","","","","","","","","","","ImPhys/Optics","","",""
"uuid:d392bceb-4b6e-4c51-9949-6b212600b233","http://resolver.tudelft.nl/uuid:d392bceb-4b6e-4c51-9949-6b212600b233","Hormones in speed-dating: The role of testosterone and cortisol in attraction","van der Meij, Leander (Eindhoven University of Technology); Demetriou, A.M. (TU Delft Multimedia Computing); Tulin, Marina (Universiteit van Amsterdam); Méndez, Ileana (Vrije Universiteit Amsterdam); Dekker, Peter (Vrije Universiteit Amsterdam); Pronk, Tila (Tilburg University)","","2019","There is evidence that testosterone and cortisol levels are related to the attraction of a romantic partner; testosterone levels relate to a wide range of sexual behaviors and cortisol is a crucial component in the response to stress. To investigate this, we conducted a speed-dating study among heterosexual singles. We measured salivary testosterone and cortisol changes in men and women (n = 79) when they participated in a romantic condition (meeting opposite-sex others, i.e., potential romantic partners), as well as a control condition (meeting same-sex others, i.e., potential friends). Over the course of the romantic speed-dating event, results showed that women's but not men's testosterone levels increased and cortisol levels decreased for both men and women. These findings indicate that men's testosterone and cortisol levels were elevated in anticipation of the event, whereas for women, this appears to only be the case for cortisol. Concerning the relationship between attraction and hormonal change, four important findings can be distinguished. First, men were more popular when they arrived at the romantic speed-dating event with elevated cortisol levels. Second, in both men and women, a larger change in cortisol levels during romantic speed-dating was related to more selectivity. Third, testosterone alone was unrelated to any romantic speed-dating outcome (selectivity or popularity). However, fourth, women who arrived at the romantic speed-dating event with higher testosterone levels were more selective when their anticipatory cortisol response was low. Overall, our findings suggest that changes in the hormone cortisol may be stronger associated with the attraction of a romantic partner than testosterone.","Attraction; Cortisol; Human mating; Popularity; Selectivity; Social relation model; Speed-dating; Testosterone","en","journal article","","","","","","","","2020-11-06","","","Multimedia Computing","","",""
"uuid:cb2fe969-0544-4efd-9130-6353a83aee6a","http://resolver.tudelft.nl/uuid:cb2fe969-0544-4efd-9130-6353a83aee6a","Effect of Signals on the Encapsulation Performance of Parylene Coated Platinum Tracks for Active Medical Implants","Nanbakhsh, K. (TU Delft Bio-Electronics); Kluba, M.M. (TU Delft Electronic Components, Technology and Materials); Pahl, Barbara (Fraunhofer Institute for Reliability and Microintegration IZM); Bourgeois, Florian (Comelec, SA R&D, Switzerland); Dekker, R. (TU Delft Electronic Components, Technology and Materials); Serdijn, W.A. (TU Delft Bio-Electronics); Giagka, Vasiliki (TU Delft Bio-Electronics; Fraunhofer Institute for Reliability and Microintegration IZM)","","2019","Platinum is widely used as the electrode material for implantable devices. Owing to its high biostability and corrosion resistivity, platinum could also be used as the main metallization for tracks in active implants. Towards this goal, in this work we investigate the stability of parylene-coated Pt tracks using passive and active tests. The test samples in this study are Pt-on-SiO 2 interdigitated comb structures. During testing all samples were immersed in saline for 150 days; for passive testing, the samples were left unbiased, whilst for active testing, samples were exposed to two different stress signals: a 5 V DC and a 5 Vp 500 pulses per second biphasic signal. All samples were monitored over time using impedance spectroscopy combined with optical inspection. After the first two weeks of immersion, delamination spots were observed on the Pt tracks for both passive and actively tested samples. Despite the delamination spots, the unbiased samples maintained high impedances until the end of the study. For the actively stressed samples, two different failure mechanisms were observed which were signal related. DC stressed samples showed severe parylene cracking mainly due to the electrolysis of the condensed water. Biphasically stressed samples showed gradual Pt dissolution and migration. These results contribute to a better understanding of the failure mechanisms of Pt tracks in active implants and suggest that new testing paradigms may be necessary to fully assess the long-term reliability of these devices.","","en","conference paper","IEEE","","","","","","","","","","Bio-Electronics","","",""
"uuid:20aab331-c432-444d-af38-c7771029a502","http://resolver.tudelft.nl/uuid:20aab331-c432-444d-af38-c7771029a502","Managing knowledge for future-proof tunnels in The Netherlands","de Haas, K. (Centrum Ondergronds Bouwen (COB)); Broere, W. (TU Delft Geo-engineering); Dekker, H. (Rijkswaterstaat); van Gelder, L. (Soltegro)","Peila, Daniele (editor); Viggiani, Giulia (editor); Celestino, Tarcisio (editor)","2019","The COB is The Netherlands Knowledge Centre for Underground Construction and Underground Space. Over sixty organisations, from government, industry and knowledge institutes, work together to learn and develop smart solutions regarding tunnels. This network has developed a long-term vision on tunnels in The Netherlands. As a result, nineteen tunnels and all stakeholders collaborate on eight research topics of our tunnel programme. We found common ground and the key issues are already being addressed in both practice and science. Topics include risks, construction failure, modular renovation, digital tunnel twin, virtual testing, virtual education and system safety. The way clients, science and industry work together within the COB network has been a major precondition to achieve these great results in such a short period of time.","","en","conference paper","CRC Press / Balkema - Taylor & Francis Group","","","","","Green Open Access added to TU Delft Institutional Repository ‘You share, we take care!’ – Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.","","2019-11-09","","","Geo-engineering","","",""
"uuid:e695b8b3-6e7e-4257-8e22-388ea0459d50","http://resolver.tudelft.nl/uuid:e695b8b3-6e7e-4257-8e22-388ea0459d50","Bacteria-in-paper, a versatile platform to study bacterial ecology","Hol, F.J.H. (TU Delft BN/Cees Dekker Lab; Harvard University; Kavli institute of nanoscience Delft; Stanford University); Whitesides, George M. (Harvard University); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft)","","2019","Habitat spatial structure has a profound influence on bacterial life, yet there currently are no low-cost equipment-free laboratory techniques to reproduce the intricate structure of natural bacterial habitats. Here, we demonstrate the use of paper scaffolds to create landscapes spatially structured at the scales relevant to bacterial ecology. In paper scaffolds, planktonic bacteria migrate through liquid-filled pores, while the paper’s cellulose fibres serve as anchor points for sessile colonies (biofilms). Using this novel approach, we explore bacterial colonisation dynamics in different landscape topographies and characterise the community composition of Escherichia coli strains undergoing centimetre-scale range expansions in habitats structured at the micrometre scale. The bacteria-in-paper platform enables quantitative assessment of bacterial community dynamics in complex environments using everyday materials.","Bacteria; colonisation; dendritic networks; experimental tools; habitat structure; microfabrication; paper; population dynamics; range expansion; spatial structure","en","journal article","","","","","","","","","","","BN/Cees Dekker Lab","","",""
"uuid:1b18711b-c3e0-430d-9701-05008b184588","http://resolver.tudelft.nl/uuid:1b18711b-c3e0-430d-9701-05008b184588","Visualization of unstained DNA nanostructures with advanced in-focus phase contrast TEM techniques","Kabiri, Y. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Ravelli, Raimond B.G. (Maastricht Multimodal Molecular Imaging Institute); Lehnert, Tibor (University of Ulm); Qi, Haoyuan (University of Ulm); Katan, A.J. (TU Delft QN/Afdelingsbureau; Kavli institute of nanoscience Delft); Roest, Natascha (Maastricht Multimodal Molecular Imaging Institute); Kaiser, Ute (University of Ulm); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Peters, Peter J. (Maastricht Multimodal Molecular Imaging Institute); Zandbergen, H.W. (TU Delft QN/Zandbergen Lab; Kavli institute of nanoscience Delft)","","2019","Over the last few years, tremendous progress has been made in visualizing biologically important macromolecules using transmission electron microscopy (TEM) and understanding their structure-function relation. Yet, despite the importance of DNA in all forms of life, TEM visualization of individual DNA molecules in its native unlabeled form has remained extremely challenging. Here, we present high-contrast images of unstained single-layer DNA nanostructures that were obtained using advanced in-focus phase contrast TEM techniques. These include sub-Ångstrom low voltage electron microscopy (SALVE), the use of a volta-potential phase plate (VPP), and dark-field (DF) microscopy. We discuss the advantages and drawbacks of these techniques for broad applications in structural biology and materials science.","","en","journal article","","","","","","","","","","","BN/Cees Dekker Lab","","",""
"uuid:af885ac8-a4c7-4222-884e-a2ae68443510","http://resolver.tudelft.nl/uuid:af885ac8-a4c7-4222-884e-a2ae68443510","Single-Crystal Rutile TiO 2 Nanocylinders are Highly Effective Transducers of Optical Force and Torque","Ha, S. (TU Delft BN/Nynke Dekker Lab; Kavli institute of nanoscience Delft); Tang, Y. (TU Delft ImPhys/Optics); van Oene, M.M. (Kavli institute of nanoscience Delft; Student TU Delft); Janissen, R. (TU Delft BN/Nynke Dekker Lab; Kavli institute of nanoscience Delft); Dries, R.M. (TU Delft BN/Marileen Dogterom Lab; Kavli institute of nanoscience Delft); Solano Hermosilla, B.P. (TU Delft BN/Nynke Dekker Lab); Adam, A.J.L. (TU Delft ImPhys/Optics); Dekker, N.H. (TU Delft BN/Nynke Dekker Lab; Kavli institute of nanoscience Delft)","","2019","Optical trapping of (sub)micron-sized particles is broadly employed in nanoscience and engineering. The materials commonly employed for these particles, however, have physical properties that limit the transfer of linear or angular momentum (or both). This reduces the magnitude of forces and torques, and the spatiotemporal resolution, achievable in linear and angular traps. Here, we overcome these limitations through the use of single-crystal rutile TiO 2 , which has an exceptionally large optical birefringence, a high index of refraction, good chemical stability, and is amenable to geometric control at the nanoscale. We show that rutile TiO 2 nanocylinders form powerful joint force and torque transducers in aqueous environments by using only moderate laser powers to apply nN·nm torques at kHz rotational frequencies to tightly trapped particles. In doing so, we demonstrate how rutile TiO 2 nanocylinders outperform other materials and offer unprecedented opportunities to expand the control of optical force and torque at the nanoscale.","dielectric crystals; force spectroscopy; optical torque wrench; optical trapping; rutile titanium dioxide; torque spectroscopy","en","journal article","","","","","","","","","","","BN/Nynke Dekker Lab","","",""
"uuid:ff999fe2-8ec1-44d5-960b-b71031329fb2","http://resolver.tudelft.nl/uuid:ff999fe2-8ec1-44d5-960b-b71031329fb2","Anaerobic growth of Saccharomyces cerevisiae CEN.PK113-7D does not depend on synthesis or supplementation of unsaturated fatty acids","Dekker, W.J.C. (TU Delft BT/Industriele Microbiologie); Wiersma, S.J. (TU Delft BT/Industriele Microbiologie); Bouwknegt, J. (TU Delft BT/Industriele Microbiologie); Mooiman, C. (TU Delft BT/Industriele Microbiologie); Pronk, J.T. (TU Delft BT/Biotechnologie)","","2019","In Saccharomyces cerevisiae, acyl-coenzyme A desaturation by Ole1 requires molecular oxygen. Tween 80, a poly-ethoxylated sorbitan-oleate ester, is therefore routinely included in anaerobic growth media as a source of unsaturated fatty acids (UFAs). During optimization of protocols for anaerobic bioreactor cultivation of this yeast, we consistently observed growth of the laboratory strain S. cerevisiae CEN.PK113-7D in media that contained the anaerobic growth factor ergosterol, but lacked UFAs. To minimize oxygen contamination, additional experiments were performed in an anaerobic chamber. After anaerobic precultivation without ergosterol and Tween 80, strain CEN.PK113-7D and a congenic ole1Δ strain both grew during three consecutive batch-cultivation cycles on medium that contained ergosterol, but not Tween 80. During these three cycles, no UFAs were detected in biomass of cultures grown without Tween 80, while contents of C10 to C14 saturated fatty acids were higher than in biomass from Tween 80-supplemented cultures. In contrast to its UFA-independent anaerobic growth, aerobic growth of the ole1Δ strain strictly depended on Tween 80 supplementation. This study shows that the requirement of anaerobic cultures of S. cerevisiae for UFA supplementation is not absolute and provides a basis for further research on the effects of lipid composition on yeast viability and robustness.","S. cerevisiae; anaerobic; membrane composition; OLE1; oxygen requirement; unsaturated fatty acids","en","journal article","","","","","","","","","","BT/Biotechnologie","BT/Industriele Microbiologie","","",""
"uuid:00e4b451-2f23-4871-a281-6945b238192a","http://resolver.tudelft.nl/uuid:00e4b451-2f23-4871-a281-6945b238192a","Pressure measurement of geometrically curved ultrasound transducer array for spatially specific stimulation of the vagus nerve","Kawasaki, S. (TU Delft Electronic Components, Technology and Materials); Giagka, Vasiliki (TU Delft Bio-Electronics; Fraunhofer Institute for Reliability and Microintegration IZM); de Haas, M. (Philips Innovation Services); Louwerse, M. (Philips Research); Henneken, V. (Philips Research); van Heesch, C. (Philips Research); Dekker, R. (Philips Research)","","2019","Vagus nerve stimulators currently on the market can treat epilepsy and depression. Recent clinical trials show the potential for vagus nerve stimulation (VNS) to treat epilepsy, autoimmune disease, and traumatic brain injury. As we explore the benefits of VNS, it is expected that more possibilities for a new treatment will emerge in the future. However, existing VNS relies on electrical stimulation, whose limited selectivity (due to its poor spatial resolution) does not allow for any control over which therapeutic effect to induce. We hypothesize that by localizing the stimulation to fascicular level within the vagus nerve with focused ultrasound (US), it is possible to induce selective therapeutic effects with less side effects. A geometrically curve US transducer array that is small enough to wrap around the vagus nerve was fabricated. An experiment was conducted in water, with 48 US elements curved in a 1 mm radius and excited at 15 MHz to test the focusing capabilities of the device. The results show that the geometrical curvature focused the US to an area with a width and height of 110 μm and 550 μm. This will be equivalent to only 2.1% of the cross section of the vagus nerve, showing the potential of focused US to stimulate individual neuronal fibers within the vagus nerve selectively.","","en","conference paper","IEEE","","","","","","","","","","Electronic Components, Technology and Materials","","",""
"uuid:f207c691-66c4-47f5-8985-02919b8cafe3","http://resolver.tudelft.nl/uuid:f207c691-66c4-47f5-8985-02919b8cafe3","Towards a semi-flexible parylene-based platform technology for active implantable medical devices","Bakhshaee Babaroud, N. (TU Delft Bio-Electronics); Kluba, M.M. (TU Delft Electronic Components, Technology and Materials); Dekker, R. (TU Delft Electronic Components, Technology and Materials); Serdijn, W.A. (TU Delft Bio-Electronics); Giagka, Vasiliki (TU Delft Bio-Electronics; Fraunhofer Institute for Reliability and Microintegration IZM)","","2019","Active implantable medical devices have been developed for diagnosis, monitoring and treatment of large variety of neural disorders. Since the mechanical properties of these devices need to be matched to the tissue, soft materials, such as polymers are often preferred as a substrate [1]. Parylene is a good candidate, as it is highly biocompatible and it can be deposited/etched using standard Integrated Circuit (IC) fabrication methods/processes. Further, the implantable devices should be smart, a goal that can be accomplished by including ICs. These ICs, often come in the form of additional pre-packaged components that are assembled on the implant in a heterogenous process. Such a hybrid integration, however, does not allow for size minimization, which is so critical in these applications, as otherwise the implants can cause severe damage to the tissue. On the other hand, it is essential that all components are properly packaged to prevent early failure due to moisture penetration [2].
In this work we use a previously developed semi-flexible platform technology based on a Parylene substrate and Pt metallization, which allows integration of electronic components with a flexible substrate in a monolithic process. We use an IC fabrication-based platform that allows for the fabrication of several rigid regions including Application-Specific Integrated Circuits (ASICs) and other components connected to each other by means of flexible interconnects. We aim to add more functionality to this technology and thereby extend it to a platform for a variety of medical applications. An example of such functionality is integrating Light Emitting Diodes (LEDs) for optogenetic stimulation or integrating Capacitive Micromachined Ultrasound Transducers (CMUTs) for ultrasound stimulation or ultrasound wireless power transfer. Since the long-term reliability is critical for implantable devices, we intend to reinforce our implant with an extra Polydimethylsiloxane (PDMS) encapsulation layer that relies on the low viscosity of the uncured rubber to flow in every detail of the surface to prevent void formation [3]. Therefore, this work also focuses on enhancing the adhesion of PDMS to Parylene, as it must remain strong for the required lifetime of the device.","","en","abstract","","","","","","","","","","","Bio-Electronics","","",""
"uuid:19605bdf-173c-4ba8-a7b9-37ecf153be83","http://resolver.tudelft.nl/uuid:19605bdf-173c-4ba8-a7b9-37ecf153be83","Assessing the robustness of Dutch Inland Ports","Taneja, P. (TU Delft Rivers, Ports, Waterways and Dredging Engineering); Dekker, Milan (Student TU Delft); van Dorsser, Cornelis (TU Delft Rivers, Ports, Waterways and Dredging Engineering); Vellinga, T. (TU Delft Rivers, Ports, Waterways and Dredging Engineering)","","2019","In the present turbulent environment highlighted by energy transition, disruptive technology, and climate change impacts, adaptability and robustness are essential in long-term planning of infrastructures. This also applies to inland ports, which play an important role in the Dutch transport system. Inland ports have three major functions, i.e., transfer of goods, storage of goods, and eventually, facilitating (industrial) production of goods. A well-functioning inland port can contribute to efficient supply chains by offering multi-modal capabilities and value-added services, and importantly, contribute to a modal shift from road to environmentally friendly inland shipping.","Inland Waterway Transport; Transport trends; Modal Split; Sustainable transport; Infrastructure planning","en","conference paper","Pianc","","","","","","","","","","Rivers, Ports, Waterways and Dredging Engineering","","",""
"uuid:5b4a2a42-614c-4517-81d8-c7dd01830683","http://resolver.tudelft.nl/uuid:5b4a2a42-614c-4517-81d8-c7dd01830683","Intercalating Electron Dyes for TEM Visualization of DNA at the Single-Molecule Level","Kabiri, Y. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Angelin, Alessandro (Karlsruhe Institut für Technologie); Ahmed, Ishtiaq (Karlsruhe Institut für Technologie); Mutlu, Hatice (Karlsruhe Institut für Technologie); Bauer, Jens (Karlsruhe Institut für Technologie); Niemeyer, Christof M. (Karlsruhe Institut für Technologie); Zandbergen, H.W. (TU Delft QN/Zandbergen Lab; Kavli institute of nanoscience Delft); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft)","","2019","Staining compounds containing heavy elements (electron dyes) can facilitate the visualization of DNA and related biomolecules by using TEM. However, research into the synthesis and utilization of alternative electron dyes has been limited. Here, we report the synthesis of a novel DNA intercalator molecule, bis-acridine uranyl (BAU). NMR spectroscopy and MS confirmed the validity of the synthetic strategy and gel electrophoresis verified the binding of BAU to DNA. For TEM imaging of DNA, two-dimensional DNA origami nanostructures were used as a robust microscopy test object. By using scanning transmission electron microscopy (STEM) imaging, which is favored over conventional wide-field TEM for improved contrast, and therefore, quantitative image analysis, it is found that the synthesized BAU intercalator can render DNA visible, even at the single-molecule scale. For comparison, other staining compounds with a purported affinity towards DNA, such as dichloroplatinum, cisplatin, osmium tetroxide, and uranyl acetate, have been evaluated. The STEM contrast is discussed in terms of the DNA–dye association constants, number of dye molecules bound per base pair, and the electron-scattering capacity of the metal-containing ligands. These findings pave the way for the future development of electron dyes with specific DNA-binding motifs for high-resolution TEM imaging.","contrast agents; DNA; intercalation; scanning transmission electron microscopy; single-molecule studies","en","journal article","","","","","","","","","","","BN/Cees Dekker Lab","","",""
"uuid:7ba7f071-fd09-4ab8-b939-a923fcb6dc2f","http://resolver.tudelft.nl/uuid:7ba7f071-fd09-4ab8-b939-a923fcb6dc2f","Expertgroep City Distribution: De toekomst is dichterbij dan je denkt","Nelck, Anne-Marie; Sosef, Dirk; Zeeman, Dorine; Walvisch, Mick; Elsenaar, Erik Jan; Rodenburg, Paul; Lammers, Gerdwin; van Schaijk, Pieter; Quak, Hans (TNO); Havelaar, Rogier; van den Bosch, Jaap; Brinkhof, Rogier; Jongeneel, Joeri; van Duin, Ron (TU Delft Transport and Logistics; Rotterdam University of Applied Sciences); Dekker, Johan; Donkersloot, Vincent; Spoelstra, Jop; Boverhof, Willem; Sijtsma, Micha; van Hofwegen, Tom; Nieuwkerk, Michiel; van Gompel, Luc","","2019","1. Een Urban Consolidation Centre (UCC) maakt het mogelijk om de stad zero-emissie te beleveren en zorgt ervoor dat goederen gebundeld de stad in gaan. Met als doel het minder belasten van klimaat, gezondheid van mensen en leefbaarheid van de stad. 2. Het UCC is een multimodaal overslagpunt, geschikt voor een variëteit aan voertuigen. Consolidatie van stromen is belangrijk 3. Duidelijkheid over toekomstige zero-emissie-zones in steden is belangrijk om stappen te kunnen nemen. Een UCC bevindt zich niet ver buiten de rand van de zero-emissiezone, bij voorkeur op een bedrijventerrein.","","nl","book chapter","Thuiswinkel.org","","","","","","","","","","Transport and Logistics","","",""
"uuid:61574c04-194d-45cb-86c3-9efb185a5003","http://resolver.tudelft.nl/uuid:61574c04-194d-45cb-86c3-9efb185a5003","Electro-Mechanical Conductance Modulation of a Nanopore Using a Removable Gate","Zhao, Shidi (University of Illinois at Urbana-Champaign); Restrepo Perez, L. (TU Delft BN/Chirlmin Joo Lab; Kavli institute of nanoscience Delft); Soskine, Misha (Rijksuniversiteit Groningen); Maglia, Giovanni (Rijksuniversiteit Groningen); Joo, C. (TU Delft BN/Chirlmin Joo Lab; Kavli institute of nanoscience Delft); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Aksimentiev, A. (TU Delft BN/Cees Dekker Lab; University of Illinois at Urbana-Champaign)","","2019","Ion channels form the basis of information processing in living cells by facilitating the exchange of electrical signals across and along cellular membranes. Applying the same principles to man-made systems requires the development of synthetic ion channels that can alter their conductance in response to a variety of external manipulations. By combining single-molecule electrical recordings with all-atom molecular dynamics simulations, we here demonstrate a hybrid nanopore system that allows for both a stepwise change of its conductance and a nonlinear current-voltage dependence. The conductance modulation is realized by using a short flexible peptide gate that carries opposite electric charge at its ends. We show that a constant transmembrane bias can position (and, in a later stage, remove) the peptide gate right at the most-sensitive sensing region of a biological nanopore FraC, thus partially blocking its channel and producing a stepwise change in the conductance. Increasing or decreasing the bias while having the peptide gate trapped in the pore stretches or compresses the peptide within the nanopore, thus modulating its conductance in a nonlinear but reproducible manner. We envision a range of applications of this removable-gate nanopore system, e.g. from an element of biological computing circuits to a test bed for probing the elasticity of intrinsically disordered proteins.","biomimetic systems; gating; ion channel; molecular dynamics; protein sequencing","en","journal article","","","","","","Accepted Author Manuscript","","2020-02-04","","","BN/Chirlmin Joo Lab","","",""
"uuid:91c4ef06-c209-4c63-8b52-cc80cfd9f631","http://resolver.tudelft.nl/uuid:91c4ef06-c209-4c63-8b52-cc80cfd9f631","Membrane Tension–Mediated Growth of Liposomes","Deshpande, S.R. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Wunnava Venkata, S.S. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Hueting, D.A. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft)","","2019","Recent years have seen a tremendous interest in the bottom-up reconstitution of minimal biomolecular systems, with the ultimate aim of creating an autonomous synthetic cell. One of the universal features of living systems is cell growth, where the cell membrane expands through the incorporation of newly synthesized lipid molecules. Here, the gradual tension-mediated growth of cell-sized (≈10 µm) giant unilamellar vesicles (GUVs) is demonstrated, to which nanometer-sized (≈30 nm) small unilamellar vesicles (SUVs) are provided, that act as a lipid source. By putting tension on the GUV membranes through a transmembrane osmotic pressure, SUV–GUV fusion events are promoted and substantial growth of the GUV is caused, even up to doubling its volume. Thus, experimental evidence is provided that membrane tension alone is sufficient to bring about membrane fusion and growth is demonstrated for both pure phospholipid liposomes and for hybrid vesicles with a mixture of phospholipids and fatty acids. The results show that growth of liposomes can be realized in a protein-free minimal system, which may find useful applications in achieving autonomous synthetic cells that are capable of undergoing a continuous growth–division cycle.","growth; hybrid vesicles; liposomes; membrane fusion; membrane tension; microfluidics; synthetic cells","en","journal article","","","","","","Accepted Author Manuscript","","2020-07-18","","","BN/Cees Dekker Lab","","",""
"uuid:13af606f-b140-4120-ab80-3eb071bbb9fa","http://resolver.tudelft.nl/uuid:13af606f-b140-4120-ab80-3eb071bbb9fa","Spatiotemporal control of coacervate formation within liposomes","Deshpande, S.R. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Brandenburg, Frank (Kavli institute of nanoscience Delft; Student TU Delft); Lau, A.W.H.R. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Last, M.G.F. (Kavli institute of nanoscience Delft; Student TU Delft); Spoelstra, W.K. (Kavli institute of nanoscience Delft; Student TU Delft); Reese, L. (TU Delft BN/Marileen Dogterom Lab; Kavli institute of nanoscience Delft); Wunnava, Sreekar; Dogterom, A.M. (TU Delft BN/Bionanoscience; Kavli institute of nanoscience Delft); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft)","","2019","Liquid-liquid phase separation (LLPS), especially coacervation, plays a crucial role in cell biology, as it forms numerous membraneless organelles in cells. Coacervates play an indispensable role in regulating intracellular biochemistry, and their dysfunction is associated with several diseases. Understanding of the LLPS dynamics would greatly benefit from controlled in vitro assays that mimic cells. Here, we use a microfluidics-based methodology to form coacervates inside cell-sized (~10 µm) liposomes, allowing control over the dynamics. Protein-pore-mediated permeation of small molecules into liposomes triggers LLPS passively or via active mechanisms like enzymatic polymerization of nucleic acids. We demonstrate sequestration of proteins (FtsZ) and supramolecular assemblies (lipid vesicles), as well as the possibility to host metabolic reactions (β-galactosidase activity) inside coacervates. This coacervate-in-liposome platform provides a versatile tool to understand intracellular phase behavior, and these hybrid systems will allow engineering complex pathways to reconstitute cellular functions and facilitate bottom-up creation of synthetic cells.","","en","journal article","","","","","","","","","","BN/Bionanoscience","BN/Cees Dekker Lab","","",""
"uuid:0350813c-5d66-48b3-9e3d-1b63a1850a6f","http://resolver.tudelft.nl/uuid:0350813c-5d66-48b3-9e3d-1b63a1850a6f","Nano-Optical Tweezing of Single Proteins in Plasmonic Nanopores","Verschueren, D.V. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Shi, X. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft)","","2019","Single-molecule sensing technologies aim to detect and characterize single biomolecules, but generally need labeling while the measurement times and throughput are severely restricted by a lack of positional control over the molecule. Here, a plasmonic nanopore biosensor is reported where single molecules can be electrophoretically delivered into a nanopore sensor with a plasmonic nanoantenna that is used to optically trap single molecules for extended measurement times. Using the light transmission through the antenna as read-out, optical trapping of 20 nm diameter polystyrene nanoparticles and individual beta-amylase proteins, a 200 kDa enzyme, in the plasmonic nanoantenna are demonstrated. Application of an electrical bias voltage allows the increase of the event rate over an order of magnitude as well as shorten the residence time of the proteins in the plasmonic nanopore as they can controllably be drawn out of the trap by electrical forces. Trapping is found to be assisted by protein–surface interactions and trapped proteins can denature on the nanopore surface. The integration of two single-molecule sensors, a plasmonic nanoantenna and solid-state nanopore, creates independent control handles at the single-molecule level—the optical trapping force and electrophoretic force—which provides augmented control over single molecules.","nanoapertures; optical transmission; plasmonic nanopores; plasmonic nanotweezers; protein trapping","en","journal article","","","","","","","","2020-05-02","","","BN/Cees Dekker Lab","","",""
"uuid:6bed16e9-bf9d-4fab-aad0-3b52d90136e4","http://resolver.tudelft.nl/uuid:6bed16e9-bf9d-4fab-aad0-3b52d90136e4","Distinct Roles for Condensin's Two ATPase Sites in Chromosome Condensation","Elbatsh, Ahmed M.O. (Netherlands Cancer Institute); Kim, E. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Eeftens, J.M. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Raaijmakers, Jonne A. (Netherlands Cancer Institute); van der Weide, Robin H. (Netherlands Cancer Institute); García-Nieto, Alberto (Netherlands Cancer Institute); Bravo, Sol (European Molecular Biology Laboratory Heidelberg); Ganji, M. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft)","","2019","Condensin is a conserved SMC complex that uses its ATPase machinery to structure genomes, but how it does so is largely unknown. We show that condensin's ATPase has a dual role in chromosome condensation. Mutation of one ATPase site impairs condensation, while mutating the second site results in hyperactive condensin that compacts DNA faster than wild-type, both in vivo and in vitro. Whereas one site drives loop formation, the second site is involved in the formation of more stable higher-order Z loop structures. Using hyperactive condensin I, we reveal that condensin II is not intrinsically needed for the shortening of mitotic chromosomes. Condensin II rather is required for a straight chromosomal axis and enables faithful chromosome segregation by counteracting the formation of ultrafine DNA bridges. SMC complexes with distinct roles for each ATPase site likely reflect a universal principle that enables these molecular machines to intricately control chromosome architecture.","ABC ATPase; chromosome condensation; cohesin; condensin; DNA loop extrusion; SMC complexes","en","journal article","","","","","","","","","","","BN/Cees Dekker Lab","","",""
"uuid:ae357f3b-058d-4557-90e7-9d8dcc32cbdc","http://resolver.tudelft.nl/uuid:ae357f3b-058d-4557-90e7-9d8dcc32cbdc","Synthetic life on a chip","Deshpande, S.R. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft)","","2019","In this article, we argue that on-chip microfluidic systems provide an attractive technology when it comes to designing synthetic cells. We emphasize the importance of the surrounding environment for both living systems in nature and for developing artificial self-sustaining entities. On-chip microfluidic devices provide a high degree of control over the production of cell-like synthetic entities as well as over the local microenvironment that these soft-matter-based synthetic cells experience. Rapid progress in microfluidic fabrication technology has led to a variety of production and manipulation tools that establish on-chip environments as a versatile platform and arguably the best route forward for realizing synthetic life.","","en","journal article","","","","","","Accepted Author Manuscript","","2020-08-20","","","BN/Cees Dekker Lab","","",""
"uuid:413cfd2f-765f-4de1-9cfe-6023c5df5905","http://resolver.tudelft.nl/uuid:413cfd2f-765f-4de1-9cfe-6023c5df5905","Resolving Chemical Modifications to a Single Amino Acid within a Peptide Using a Biological Nanopore","Restrepo Perez, L. (TU Delft BN/Chirlmin Joo Lab; Kavli institute of nanoscience Delft); Huang, Gang (Rijksuniversiteit Groningen); Bohländer, Peggy R.; Worp, N.M. (TU Delft BN/Christophe Danelon Lab; Kavli institute of nanoscience Delft); Eelkema, R. (TU Delft ChemE/Advanced Soft Matter); Maglia, Giovanni (Rijksuniversiteit Groningen); Joo, C. (TU Delft BN/Chirlmin Joo Lab; Kavli institute of nanoscience Delft); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft)","","2019","While DNA sequencing is now amply available, fast, and inexpensive, protein sequencing remains a tremendous challenge. Nanopores may allow for developing a protein sequencer with single-molecule capabilities. As identification of 20 different amino acids currently presents an unsurmountable challenge, fingerprinting schemes are pursued, in which only a subset of amino acids is labeled and detected. This requires modification of amino acids with chemical structures that generate a distinct nanopore ionic current signal. Here, we use a model peptide and the fragaceatoxin C nanopore to characterize six potential tags for a fingerprinting approach using nanopores. We find that labeled and unlabeled proteins can be clearly distinguished and that sensitive detection is obtained for labels with a spectrum of different physicochemical properties such as mass (427-1275 Da), geometry, charge, and hydrophobicity. Additionally, information about the position of the label along the peptide chain can be obtained from individual current-blockade event features. The results represent an important advance toward the development of a single-molecule protein-fingerprinting device with nanopores.","amino acid labeling; biological nanopores; nanopore; protein analysis; protein fingerprinting; single-molecule protein sequencing","en","journal article","","","","","","","","","","","BN/Chirlmin Joo Lab","","",""
"uuid:29f98b57-998f-4f6f-ba8e-660f44b42e45","http://resolver.tudelft.nl/uuid:29f98b57-998f-4f6f-ba8e-660f44b42e45","Label-Free Detection of Post-translational Modifications with a Nanopore","Restrepo Perez, L. (TU Delft BN/Chirlmin Joo Lab; Kavli institute of nanoscience Delft); Wong, C.H. (TU Delft BUS/Quantum Delft; Kavli institute of nanoscience Delft); Maglia, Giovanni (Rijksuniversiteit Groningen); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Joo, C. (TU Delft BN/Chirlmin Joo Lab; Kavli institute of nanoscience Delft)","","2019","Post-translational modifications (PTMs) of proteins play key roles in cellular processes. Hence, PTM identification is crucial for elucidating the mechanism of complex cellular processes and disease. Here we present a method for PTM detection at the single-molecule level using FraC biological nanopores. We focus on two major PTMs, phosphorylation and glycosylation, that mutually compete for protein modification sites, an important regulatory process that has been implicated in the pathogenic pathways of many diseases. We show that phosphorylated and glycosylated peptides can be clearly differentiated from nonmodified peptides by differences in the relative current blockade and dwell time in nanopore translocations. Furthermore, we show that these PTM modifications can be mutually differentiated, demonstrating the identification of phosphorylation and glycosylation in a label-free manner. The results represent an important step for the single-molecule, label-free identification of proteoforms, which have tremendous potential for disease diagnosis and cell biology.","glycosylation; label-free detection; Nanopores; phosphorylation; post-translational modifications","en","journal article","","","","","","","","","","","BN/Chirlmin Joo Lab","","",""
"uuid:1db372da-197d-4b49-bb7d-3f0e702b73af","http://resolver.tudelft.nl/uuid:1db372da-197d-4b49-bb7d-3f0e702b73af","1/f noise in solid-state nanopores is governed by access and surface regions","Fragasso, A. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Pud, S. (TU Delft QN/Kavli Nanolab Delft; Kavli institute of nanoscience Delft); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft)","","2019","The performance of solid-state nanopores as promising biosensors is severely hampered by low-frequency 1/f noise in the through-pore ionic current recordings. Here, we develop a model for the 1/f noise in such nanopores, that, unlike previous reports, accounts for contributions from both the pore-cylinder, pore-surface, and access regions. To test our model, we present measurements of the open-pore current noise through solid-state nanopores of different diameters (1-50 nm). To describe the observed trends, it appears essential to include the access resistance in the modeling of the 1/f noise. We attribute a different Hooge constant for the charge carrier fluctuations occurring in the bulk electrolyte and at the pore surface. The model reported here can be used to accurately analyze different contributions to the nanopore low-frequency noise, rendering it a powerful tool for characterizing and comparing different membrane materials in terms of their 1/f noise properties.","1/f noise; access resistance; Hooges model; ion transport; nanopores","en","journal article","","","","","","Accepted Author Manuscript","","2020-07-16","","","BN/Cees Dekker Lab","","",""
"uuid:ec414630-ba14-4ec3-adf5-481b2db008e3","http://resolver.tudelft.nl/uuid:ec414630-ba14-4ec3-adf5-481b2db008e3","A cohesive XFEM model for simulating fatigue crack growth under mixed-mode loading and overloading","Dekker, R. (TU Delft Applied Mechanics); van der Meer, F.P. (TU Delft Materials and Environment); Maljaars, J. (Eindhoven University of Technology; TNO); Sluys, Lambertus J. (TU Delft Materials- Mechanics- Management & Design)","","2019","Structures are subjected to cyclic loads that can vary in direction and magnitude, causing constant amplitude mode I simulations to be too simplistic. This study presents a new approach for fatigue crack propagation in ductile materials that can capture mixed-mode loading and overloading. The extended finite element method is used to deal with arbitrary crack paths. Furthermore, adaptive meshing is applied to minimize computation time. A fracture process zone ahead of the physical crack tip is represented by means of cohesive tractions from which the energy release rate, and thus the stress intensity factor can be extracted for an elastic-plastic material. The approach is therefore compatible with the Paris equation, which is an empirical relation to compute the fatigue crack growth rate. Two different models to compute the cohesive tractions are compared. First, a cohesive zone model with a static cohesive law is used. The second model is based on the interfacial thick level set method in which tractions follow from a given damage profile. Both models show good agreement with a mode I analytical relation and a mixed-mode experiment. Furthermore, it is shown that the presented models can capture crack growth retardation as a result of an overload.","cohesive zone model; fatigue crack growth; interfacial thick level set; mixed-mode; overload; XFEM","en","journal article","","","","","","","","","","Materials- Mechanics- Management & Design","Applied Mechanics","","",""
"uuid:285a1cd4-c084-41b3-8ed1-1b1dc7449278","http://resolver.tudelft.nl/uuid:285a1cd4-c084-41b3-8ed1-1b1dc7449278","A microfluidic platform for the characterisation of membrane active antimicrobials","Al Nahas, K. (Cavendish Laboratory); Cama, J. (Cavendish Laboratory); Schaich, M. (Cavendish Laboratory); Hammond, K. (National Physical Laboratory); Deshpande, S.R. (TU Delft BN/Cees Dekker Lab; TU Delft QN/Quantum Nanoscience; Kavli institute of nanoscience Delft); Dekker, C. (TU Delft BN/Cees Dekker Lab; TU Delft QN/Quantum Nanoscience; Kavli institute of nanoscience Delft); Ryadnov, M. G. (National Physical Laboratory); Keyser, U. F. (Cavendish Laboratory)","","2019","The spread of bacterial resistance against conventional antibiotics generates a great need for the discovery of novel antimicrobials. Polypeptide antibiotics constitute a promising class of antimicrobial agents that favour attack on bacterial membranes. However, efficient measurement platforms for evaluating their mechanisms of action in a systematic manner are lacking. Here we report an integrated lab-on-a-chip multilayer microfluidic platform to quantify the membranolytic efficacy of such antibiotics. The platform is a biomimetic vesicle-based screening assay, which generates giant unilamellar vesicles (GUVs) in physiologically relevant buffers on demand. Hundreds of these GUVs are individually immobilised downstream in physical traps connected to separate perfusion inlets that facilitate controlled antibiotic delivery. Antibiotic efficacy is expressed as a function of the time needed for an encapsulated dye to leak out of the GUVs as a result of antibiotic treatment. This proof-of-principle study probes the dose response of an archetypal polypeptide antibiotic cecropin B on GUVs mimicking bacterial membranes. The results of the study provide a foundation for engineering quantitative, high-throughput microfluidics devices for screening antibiotics.","","en","journal article","","","","","","","","","","QN/Quantum Nanoscience","BN/Cees Dekker Lab","","",""
"uuid:7055c9cb-3f89-4477-a9c5-9ec2b24834d4","http://resolver.tudelft.nl/uuid:7055c9cb-3f89-4477-a9c5-9ec2b24834d4","Objective parameters to measure (in)stability of the knee joint during gait: A review of literature","Schrijvers, Jim (Vrije Universiteit Amsterdam); van den Noort, Josien C. (Vrije Universiteit Amsterdam; Universiteit van Amsterdam); van der Esch, Martin (Amsterdam Rehabilitation Research Center Reade; Hogeschool van Amsterdam); Dekker, Joost (Vrije Universiteit Amsterdam); Harlaar, J. (TU Delft Biomechatronics & Human-Machine Control; Vrije Universiteit Amsterdam)","","2019","Background: Instability of the knee joint during gait is frequently reported by patients with knee osteoarthritis or an anterior cruciate ligament rupture. The assessment of instability in clinical practice and clinical research studies mainly relies on self-reporting. Alternatively, parameters measured with gait analysis have been explored as suitable objective indicators of dynamic knee (in)stability. Research question: This literature review aimed to establish an inventory of objective parameters of knee stability during gait. Methods: Five electronic databases (Pubmed, Embase, Cochrane, Cinahl and SPORTDiscuss) were systematically searched, with keywords concerning knee, stability and gait. Eligible studies used an objective parameter(s) to assess knee (in)stability during gait, being stated in the introduction or methods section. Out of 10717 studies, 89 studies were considered eligible. Results: Fourteen different patient populations were investigated with kinematic, kinetic and/or electromyography measurements during (challenged) gait. Thirty-three possible objective parameters were identified for knee stability, of which the majority was based on kinematic (14 parameters) or electromyography (12 parameters) measurements. Thirty-nine studies used challenged gait (i.e. external perturbations, downhill walking) to provoke knee joint instability. Limited or conflicting results were reported on the validity of the 33 parameters. Significance: In conclusion, a large number of different candidates for an objective knee stability gait parameter were found in literature, all without compelling evidence. A clear conceptual definition for dynamic knee joint stability is lacking, for which we suggest : “The capacity to respond to a challenge during gait within the natural boundaries of the knee”. Furthermore biomechanical gait laboratory protocols should be harmonized, to enable future developments on clinically relevant measure(s) of knee stability during gait.","Biomechanics; Gait; Knee; Measurement; Stability","en","review","","","","","","Green Open Access added to TU Delft Institutional Repository 'You share, we take care!' - Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.","","2019-09-20","","","Biomechatronics & Human-Machine Control","","",""
"uuid:8679d6c3-13d0-4395-9903-9bd8804a8ca8","http://resolver.tudelft.nl/uuid:8679d6c3-13d0-4395-9903-9bd8804a8ca8","Movement dynamics of divisome proteins and PBP2x: FtsW in cells of Streptococcus pneumoniae","Perez, Amilcar J. (Indiana University - Purdue University); Cesbron, Yann (Newcastle University); Shaw, Sidney L. (Indiana University - Purdue University); Villicana, Jesus Bazan (Indiana University - Purdue University); Tsui, Ho Ching T. (Indiana University - Purdue University); Boersma, Michael J. (Indiana University - Purdue University); Ye, Ziyun A. (Indiana University - Purdue University); Tovpeko, Yanina (Indiana University - Purdue University); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft)","","2019","Bacterial cell division and peptidoglycan (PG) synthesis are orchestrated by the coordinated dynamic movement of essential protein complexes. Recent studies show that bidirectional treadmilling of FtsZ filaments/bundles is tightly coupled to and limiting for both septal PG synthesis and septum closure in some bacteria, but not in others. Here we report the dynamics of FtsZ movement leading to septal and equatorial ring formation in the ovoid-shaped pathogen, Streptococcus pneumoniae. Conventional and single-molecule total internal reflection fluorescence microscopy (TIRFm) showed that nascent rings of FtsZ and its anchoring and stabilizing proteins FtsA and EzrA move out from mature septal rings coincident with MapZ rings early in cell division. This mode of continuous nascent ring movement contrasts with a failsafe streaming mechanism of FtsZ/FtsA/EzrA observed in a ΔmapZ mutant and another Streptococcus species. This analysis also provides several parameters of FtsZ treadmilling in nascent and mature rings, including treadmilling velocity in wild-type cells and ftsZ(GTPase) mutants, lifetimes of FtsZ subunits in filaments and of entire FtsZ filaments/bundles, and the processivity length of treadmilling of FtsZ filament/bundles. In addition, we delineated the motion of the septal PBP2x transpeptidase and its FtsW glycosyl transferase-binding partner relative to FtsZ treadmilling in S. pneumoniae cells. Five lines of evidence support the conclusion that movement of the bPBP2x:FtsW complex in septa depends on PG synthesis and not on FtsZ treadmilling. Together, these results support a model in which FtsZ dynamics and associations organize and distribute septal PG synthesis, but do not control its rate in S. pneumoniae.","FtsZ treadmilling; Microhole vertical imaging; Nascent ring formation; PBP2x:FtsW shared dynamics; TIRF microscopy","en","journal article","","","","","","","","2019-08-04","","","BN/Cees Dekker Lab","","",""
"uuid:403c459e-0543-406c-8389-e11292874377","http://resolver.tudelft.nl/uuid:403c459e-0543-406c-8389-e11292874377","Direct imaging of the circular chromosome in a live bacterium","Wu, Fabai (Kavli institute of nanoscience Delft); Japaridze, A. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Zheng, X.Z. (TU Delft BN/Sander Tans Lab; Kavli institute of nanoscience Delft); Wiktor, J.M. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Kerssemakers, J.W.J. (TU Delft BN/Technici en Analisten; Kavli institute of nanoscience Delft); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft)","","2019","Although the physical properties of chromosomes, including their morphology, mechanics, and dynamics are crucial for their biological function, many basic questions remain unresolved. Here we directly image the circular chromosome in live E. coli with a broadened cell shape. We find that it exhibits a torus topology with, on average, a lower-density origin of replication and an ultrathin flexible string of DNA at the terminus of replication. At the single-cell level, the torus is strikingly heterogeneous, with blob-like Mbp-size domains that undergo major dynamic rearrangements, splitting and merging at a minute timescale. Our data show a domain organization underlying the chromosome structure of E. coli, where MatP proteins induce site-specific persistent domain boundaries at Ori/Ter, while transcription regulators HU and Fis induce weaker transient domain boundaries throughout the genome. These findings provide an architectural basis for the understanding of the dynamic spatial organization of bacterial genomes in live cells.","","en","journal article","","","","","","","","","","","BN/Cees Dekker Lab","","",""
"uuid:f1d33cea-2085-4f68-9b8c-ae6044a5caa5","http://resolver.tudelft.nl/uuid:f1d33cea-2085-4f68-9b8c-ae6044a5caa5","Shape and Size Control of Artificial Cells for Bottom-Up Biology","Fanalista, F. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Birnie, A.T.F. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Maan, R. (TU Delft BN/Marileen Dogterom Lab; Kavli institute of nanoscience Delft); Burla, Federica (AMOLF); Charles usagé Charles-Carty, K.V. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Pawlik, G. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Deshpande, S.R. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Koenderink, Gijsje H. (AMOLF); Dogterom, A.M. (TU Delft BN/Bionanoscience; Kavli institute of nanoscience Delft); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft)","","2019","Bottom-up biology is an expanding research field that aims to understand the mechanisms underlying biological processes via in vitro assembly of their essential components in synthetic cells. As encapsulation and controlled manipulation of these elements is a crucial step in the recreation of such cell-like objects, microfluidics is increasingly used for the production of minimal artificial containers such as single-emulsion droplets, double-emulsion droplets, and liposomes. Despite the importance of cell morphology on cellular dynamics, current synthetic-cell studies mainly use spherical containers, and methods to actively shape manipulate these have been lacking. In this paper, we describe a microfluidic platform to deform the shape of artificial cells into a variety of shapes (rods and discs) with adjustable cell-like dimensions below 5 μm, thereby mimicking realistic cell morphologies. To illustrate the potential of our method, we reconstitute three biologically relevant protein systems (FtsZ, microtubules, collagen) inside rod-shaped containers and study the arrangement of the protein networks inside these synthetic containers with physiologically relevant morphologies resembling those found in living cells.","bottom-up biology; droplets; lab-on-a-chip; liposomes; microfluidics; morphology control; synthetic cell","en","journal article","","","","","","","","","","BN/Bionanoscience","BN/Cees Dekker Lab","","",""
"uuid:05effcd5-fc75-43b8-9e11-f7995caee7cc","http://resolver.tudelft.nl/uuid:05effcd5-fc75-43b8-9e11-f7995caee7cc","An Integrated Microfluidic Platform for Quantifying Drug Permeation across Biomimetic Vesicle Membranes","Schaich, Michael (University of Cambridge); Cama, Jehangir (University of Exeter; University of Cambridge); Al Nahas, Kareem (University of Cambridge); Sobota, Diana (University of Cambridge); Sleath, Hannah (University of Cambridge); Jahnke, Kevin (Max Planck Institute for Medical Research; University of Cambridge; University of Heidelberg); Deshpande, S.R. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Keyser, Ulrich F. (University of Cambridge)","","2019","The low membrane permeability of candidate drug molecules is a major challenge in drug development, and insufficient permeability is one reason for the failure of antibiotic treatment against bacteria. Quantifying drug transport across specific pathways in living systems is challenging because one typically lacks knowledge of the exact lipidome and proteome of the individual cells under investigation. Here, we quantify drug permeability across biomimetic liposome membranes, with comprehensive control over membrane composition. We integrate the microfluidic octanol-assisted liposome assembly platform with an optofluidic transport assay to create a complete microfluidic total analysis system for quantifying drug permeability. Our system enables us to form liposomes with charged lipids mimicking the negative charge of bacterial membranes at physiological pH and salt concentrations, which proved difficult with previous liposome formation techniques. Furthermore, the microfluidic technique yields an order of magnitude more liposomes per experiment than previous assays. We demonstrate the feasibility of the assay by determining the permeability coefficient of norfloxacin and ciprofloxacin across biomimetic liposomes.","antibiotics; drug transport; GUV; lab on chip; liposomes; microfluidics; permeability","en","journal article","","","","","","Accepted Author Manuscript","","2020-04-17","","","BN/Cees Dekker Lab","","",""
"uuid:6006465e-6d5e-45ec-a0d0-9ee11b6d789d","http://resolver.tudelft.nl/uuid:6006465e-6d5e-45ec-a0d0-9ee11b6d789d","The value of travel time, noise pollution, recreation and biodiversity: A social choice valuation perspective","Mouter, N. (TU Delft Transport and Logistics); Cabral, Manuel Ojeda (University of Leeds); Dekker, T. (TU Delft Transport and Logistics); van Cranenburgh, S. (University of Leeds)","","2019","Environmental effects of transport projects have a weak position in Cost-Benefit Analysis (CBA) which might be rooted in the valuation approach adopted in the dominant style of CBA. This conventional valuation approach has been criticized for not valuing positive and negative impacts of transport projects in relation to each other and for not valuing such impacts in a public context, but in the context of private decisions. These critiques might be circumvented through valuing transport projects in a social choice context in which overall burdens and benefits of proposed transport projects are considered together in a public context. We investigate the extent to which a social choice valuation approach produces different outcomes than a conventional valuation approach. We conducted four social choice valuation experiments in which respondents were asked to choose between alternatives for a new road, trading off travel time and three environmental impacts (noise, recreation and biodiversity). Our findings suggest that, under social choice valuation, individuals assign substantially more value to environmental impacts than travel time as compared to conventional valuation studies. Moreover, in a social choice setting, respondents assigned monetary values to impacts that are not (or only qualitatively) considered in conventional CBAs of transport projects.","Biodiversity; Cost-benefit analysis; Environmental valuation; Noise; Recreation; Social choice valuation; Transport appraisal; Transport policy; Travel time","en","journal article","","","","","","Green Open Access added to TU Delft Institutional Repository ‘You share, we take care!’ – Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.","","2019-12-11","","","Transport and Logistics","","",""
"uuid:facbd3b6-eb86-4bb8-86f5-a57767f76826","http://resolver.tudelft.nl/uuid:facbd3b6-eb86-4bb8-86f5-a57767f76826","Cell Boundary Confinement Sets the Size and Position of the E. coli Chromosome","Wu, Fabai (Kavli institute of nanoscience Delft; California Institute of Technology; Student TU Delft); Swain, Pinaki (Indian Institute of Technology Hyderabad); Kuijpers, L.C. (TU Delft BN/Nynke Dekker Lab; Kavli institute of nanoscience Delft); Zheng, X.Z. (TU Delft BN/Sander Tans Lab; Kavli institute of nanoscience Delft); Felter, K.M. (TU Delft ChemE/Opto-electronic Materials; Kavli institute of nanoscience Delft); Guurink, M. (Kavli institute of nanoscience Delft; Student TU Delft); Solari, Jacopo (AMOLF); Jun, Suckjoon (University of California); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft)","","2019","Although the spatiotemporal structure of the genome is crucial to its biological function, many basic questions remain unanswered on the morphology and segregation of chromosomes. Here, we experimentally show in Escherichia coli that spatial confinement plays a dominant role in determining both the chromosome size and position. In non-dividing cells with lengths increased to 10 times normal, single chromosomes are observed to expand > 4-fold in size. Chromosomes show pronounced internal dynamics but exhibit a robust positioning where single nucleoids reside robustly at mid-cell, whereas two nucleoids self-organize at 1/4 and 3/4 positions. The cell-size-dependent expansion of the nucleoid is only modestly influenced by deletions of nucleoid-associated proteins, whereas osmotic manipulation experiments reveal a prominent role of molecular crowding. Molecular dynamics simulations with model chromosomes and crowders recapitulate the observed phenomena and highlight the role of entropic effects caused by confinement and molecular crowding in the spatial organization of the chromosome. Imaging chromosomes in E. coli within a broad length range, Wu et al. observe that chromosome size and position strongly depend on cell size. They provide evidence that this arises from a confinement-modulated entropic repulsion between chromosome and cytosolic crowders, highlighting the importance of confinement effects in cellular organization.","bacterial nucleoid; cell boundary confinement; chromosome segregation; chromosome size; crowders","en","journal article","","","","","","","","2020-07-08","","","BN/Nynke Dekker Lab","","",""
"uuid:8656fff5-2b28-4ec1-836b-cbe46dca5fc3","http://resolver.tudelft.nl/uuid:8656fff5-2b28-4ec1-836b-cbe46dca5fc3","Decreased pain and improved dynamic knee instability mediate the beneficial effect of wearing a soft knee brace on activity limitations in patients with knee osteoarthritis","Cudejko, Tomasz (Amsterdam UMC); van der Esch, Martin (Amsterdam Rehabilitation Research Center Reade); van den Noort, Josien C. (Amsterdam UMC); Rijnhart, Judith J.M. (Amsterdam UMC); van der Leeden, Marike (Amsterdam UMC); Roorda, Leo D. (Amsterdam Rehabilitation Research Center Reade); Lems, Willem (Reade and Amsterdam Rheumatology and Immunology Centre); Waddington, Gordon (University of Canberra); Harlaar, J. (TU Delft Biomechatronics & Human-Machine Control; Amsterdam UMC); Dekker, Joost (Amsterdam UMC)","","2019","Objective: To evaluate whether improvement of proprioception, pain, or dynamic knee instability mediates the effect of wearing a soft knee brace on activity limitations in patients with knee osteoarthritis (OA). Methods: We conducted an analysis of data for 44 patients with knee OA who were enrolled in a laboratory-based trial evaluating the effect of wearing a commercially available soft knee brace. Activity limitations were assessed with the 10-meter walk test and the Get Up and Go test. Knee joint proprioception was assessed by an active joint position sense test; pain was assessed on a numeric rating scale (NRS) (range 0–10); pressure pain threshold (PPT) was assessed with a hand-held pressure algometer; dynamic knee instability was expressed by the perturbation response, i.e., a measure reflecting a deviation in mean knee varus–valgus angle after a controlled mechanical perturbation on a treadmill, with respect to level walking. Mediation analysis was conducted using the product of coefficients approach. Confidence intervals were calculated with a bootstrap procedure. Results: A decrease in pain (scored on an NRS) and a decrease in dynamic knee instability mediated the effect of wearing a soft knee brace on the reduction of activity limitations (P < 0.05), while changes in proprioception and PPT did not mediate this effect (P > 0.05). Conclusion: This study shows that decreased pain and reduced dynamic knee instability are pathways by which wearing a soft knee brace decreases activity limitations in patients with knee OA.","","en","journal article","","","","","","","","","","","Biomechatronics & Human-Machine Control","","",""
"uuid:76cebc23-1790-4811-bccb-f9d3bde42056","http://resolver.tudelft.nl/uuid:76cebc23-1790-4811-bccb-f9d3bde42056","Novel method of alignment to buried cavities in cavity-SOI wafers for advanced MEMS devices","Mountain, Christopher (University of Sheffield); Kluba, M.M. (TU Delft Electronic Components, Technology and Materials); Bergers, L.I.J.C. (Eindhoven University of Technology; Philips Research); Snijder, Jaap (Philips Innovation Services); Dekker, R. (TU Delft Electronic Components, Technology and Materials; Philips Research)","","2019","Accurate alignment between the cavities in cavity-SOI (c-SOI) wafers and lithography on the wafer surface is essential to advanced MEMS production. Existing alignment methods are well defined, but often require specialized equipment or costly software packages available only in professional manufacturing environments. It would be beneficial for the microfabrication world to be able to utilize standard alignment techniques and tools that are easily available also in smaller MEMS fabrication units and especially the majority of research facilities. Therefore, we demonstrate a feasible method for c-SOI wafer alignment using an ASML PAS5500/100 wafer stepper with standard software configuration by relocating ASML alignment markers towards wafer's edges and utilizing a terracing process to reveal them for alignment. Moreover, we characterize the magnitude and behavior of image offset errors that are introduced using this method. The offset error is found to be inversely proportional to the value of the coordinate in each axis, resulting in images being shifted towards the center of the wafer. The measured offset errors are <160 nm, and are suitable for most applications. To further minimize these errors we propose a simple model or database of the offsets. We conclude that this alternative alignment method is feasible for a number of MEMS applications, and could promote increased integration of c-SOI technology into advanced MEMS production.","Alignment; Alignment marker; C-SOI; Cavity-SOI; Lithography; MEMS; Wafer stepper","en","journal article","","","","","","","","","","","Electronic Components, Technology and Materials","","",""
"uuid:152adf72-c56e-4af7-b46c-da08a8b41e7d","http://resolver.tudelft.nl/uuid:152adf72-c56e-4af7-b46c-da08a8b41e7d","DNA Sequence Is a Major Determinant of Tetrasome Dynamics","Ordu, O. (TU Delft BN/Nynke Dekker Lab; Kavli institute of nanoscience Delft); Lusser, Alexandra (Medical University of Innsbruck); Dekker, N.H. (TU Delft BN/Nynke Dekker Lab; Kavli institute of nanoscience Delft)","","2019","Eukaryotic genomes are hierarchically organized into protein-DNA assemblies for compaction into the nucleus. Nucleosomes, with the (H3-H4)2 tetrasome as a likely intermediate, are highly dynamic in nature by way of several different mechanisms. We have recently shown that tetrasomes spontaneously change the direction of their DNA wrapping between left- and right-handed conformations, which may prevent torque buildup in chromatin during active transcription or replication. DNA sequence has been shown to strongly affect nucleosome positioning throughout chromatin. It is not known, however, whether DNA sequence also impacts the dynamic properties of tetrasomes. To address this question, we examined tetrasomes assembled on a high-affinity DNA sequence using freely orbiting magnetic tweezers. In this context, we also studied the effects of mono- and divalent salts on the flipping dynamics. We found that neither DNA sequence nor altered buffer conditions affect overall tetrasome structure. In contrast, tetrasomes bound to high-affinity DNA sequences showed significantly altered flipping kinetics, predominantly via a reduction in the lifetime of the canonical state of left-handed wrapping. Increased mono- and divalent salt concentrations counteracted this behavior. Thus, our study indicates that high-affinity DNA sequences impact not only the positioning of the nucleosome but that they also endow the subnucleosomal tetrasome with enhanced conformational plasticity. This may provide a means to prevent histone loss upon exposure to torsional stress, thereby contributing to the integrity of chromatin at high-affinity sites.","","en","journal article","","","","","","Accepted Author Manuscript","","2020-08-21","","","BN/Nynke Dekker Lab","","",""
"uuid:503123b4-da08-4e07-a724-800e790f1db0","http://resolver.tudelft.nl/uuid:503123b4-da08-4e07-a724-800e790f1db0","Metal and Polymeric Strain Gauges for Si-based, Monolithically Fabricated Organs-on-Chips","Quiros Solano, W.F. (TU Delft Electronic Components, Technology and Materials; Instituto Tecnologico de Costa Rica; BIOND Solutions B.V.); Gaio, N. (TU Delft Electronic Components, Technology and Materials; BIOND Solutions B.V.); Silvestri, C. (BIOND Solutions B.V.); Pandraud, G. (TU Delft EKL Processing); Dekker, R. (TU Delft Electronic Components, Technology and Materials; Philips Research); Sarro, Pasqualina M (TU Delft Electronic Components, Technology and Materials)","","2019","Organ-on-chip (OOC) is becoming the alternative tool to conventional in vitro screening. Heart-on-chip devices including microstructures for mechanical and electrical stimulation have been demonstrated to be advantageous to study structural organization and maturation of heart cells. This paper presents the development of metal and polymeric strain gauges for in situ monitoring of mechanical strain in the Cytostretch platform for heart-on-chip application. Specifically, the optimization of the fabrication process of metal titanium (Ti) strain gauges and the investigation on an alternative material to improve the robustness and performance of the devices are presented. The transduction behavior and functionality of the devices are successfully proven using a custom-made set-up. The devices showed resistance changes for the pressure range (0-3 kPa) used to stretch the membranes on which heart cells can be cultured. Relative resistance changes of approximately 0.008% and 1.2% for titanium and polymeric strain gauges are respectively reported for membrane deformations up to 5%. The results demonstrate that both conventional IC metals and polymeric materials can be implemented for sensing mechanical strain using robust microfabricated organ-on-chip devices.","Cell; Membranes; MEMS; Organ-on-chip; PDMS; Silicon; Strain; Stress","en","journal article","","","","","","","","","","","Electronic Components, Technology and Materials","","",""
"uuid:dc256bad-ecb8-46c9-b379-e4c208c95fb3","http://resolver.tudelft.nl/uuid:dc256bad-ecb8-46c9-b379-e4c208c95fb3","Discovery of Enterovirus A71-like nonstructural genomes in recent circulating viruses of the Enterovirus A species","Lee, Kuo Ming (Chang Gung University); Gong, Yu Nong (Chang Gung University); Hsieh, Tzu Hsuan (Chang Gung University); Woodman, Andrew (The Pennsylvania State University); Dekker, N.H. (TU Delft BN/Nynke Dekker Lab); Cameron, Craig E. (The Pennsylvania State University); Shih, Shin Ru (Chang Gung University; Linkou Chang Gung Memorial Hospital; Chang Gung University of Science and Technology)","","2018","Enterovirus A71 (EV-A71) is an important nonpolio enterovirus that causes severe neurological complications. In 1998, Taiwan experienced an EV-A71 outbreak that caused 78 deaths. Since then, periodic epidemics of EV-A71 associated with newly emerging strains have occurred. Several of these strains are known to be recombinant; however, how these strains arose within such a short period of time remains unknown. Here, we sequenced 64 full-length genomes from clinical isolates collected from 2005 to 2016 and incorporated all 91 Taiwanese genomes downloaded from the Virus Pathogen Resource to extensively analyze EV-A71 recombination in Taiwan. We found that the B3 subgenotype was a potential recombinant parent of the EV-A71 C2-like and C4 strains by intratypic recombination. Such B3-similar regions were also found in many cocirculating coxsackieviruses belonging to Enterovirus A species (EV-A) through a series of intertypic recombinations. Therefore, locally enriched outbreaks of cocirculating viruses from different genotypes/serotypes may facilitate recombination. Most recombination breakpoints we found had nonrandom distributions and were located within the region spanning from the boundary of P1 (structural gene) and P2 (nonstructural) to the cis-Acting replication element at P2, indicating that specific genome reassembly of structural and nonstructural genes may be subject to natural selection. Through intensive recombination, 11 EV-A71-like signatures (including one in 3A, two in 3C, and eight in 3D) were found to be present in a variety of recently cocirculating EV-A viruses worldwide, suggesting that these viruses may be targets for wide-spectrum antiviral development.","","en","journal article","","","","","","","","","","","BN/Nynke Dekker Lab","","",""
"uuid:ba08c10c-44d8-49b7-a617-0e609cc877e5","http://resolver.tudelft.nl/uuid:ba08c10c-44d8-49b7-a617-0e609cc877e5","Reversible Immobilization of Proteins in Sensors and Solid-State Nanopores","Ananth, A.N. (TU Delft BN/Cees Dekker Lab); Genua, María (CIC biomaGUNE); Aissaoui, Nesrine (CIC biomaGUNE); Díaz, Leire (CIC biomaGUNE); Eisele, Nico B. (CIC biomaGUNE); Frey, Steffen (Max Planck Institute for Biophysical Chemistry (Karl Friedrich Bonhoeffer Institute); NanoTag Biotechnologies GmbH); Dekker, C. (TU Delft BN/Cees Dekker Lab); Richter, Ralf P. (CIC biomaGUNE; University of Leeds); Görlich, Dirk (Max Planck Institute for Biophysical Chemistry (Karl Friedrich Bonhoeffer Institute))","","2018","The controlled functionalization of surfaces with proteins is crucial for many analytical methods in life science research and biomedical applications. Here, a coating for silica-based surfaces is established which enables stable and selective immobilization of proteins with controlled orientation and tunable surface density. The coating is reusable, retains functionality upon long-term storage in air, and is applicable to surfaces of complex geometry. The protein anchoring method is validated on planar surfaces, and then a method is developed to measure the anchoring process in real time using silicon nitride solid-state nanopores. For surface attachment, polyhistidine tags that are site specifically introduced into recombinant proteins are exploited, and the yeast nucleoporin Nsp1 is used as model protein. Contrary to the commonly used covalent thiol chemistry, the anchoring of proteins via polyhistidine tag is reversible, permitting to take proteins off and replace them by other ones. Such switching in real time in experiments on individual nanopores is monitored using ion conductivity. Finally, it is demonstrated that silica and gold surfaces can be orthogonally functionalized to accommodate polyhistidine-tagged proteins on silica but prevent protein binding to gold, which extends the applicability of this surface functionalization method to even more complex sensor devices.","biosensing; histidine tag; nanopores; selective immobilization; sensors; surface functionalization","en","journal article","","","","","","Accepted Author Manuscript","","2019-04-03","","","BN/Cees Dekker Lab","","",""
"uuid:c1ee4c48-65f0-4848-bfbb-0a811c69057a","http://resolver.tudelft.nl/uuid:c1ee4c48-65f0-4848-bfbb-0a811c69057a","Quantifying the Precision of Single-Molecule Torque and Twist Measurements Using Allan Variance","van Oene, M.M. (TU Delft BN/Nynke Dekker Lab; Kavli institute of nanoscience Delft); Ha, S. (TU Delft BN/Nynke Dekker Lab; Kavli institute of nanoscience Delft); Jager, T. (Student TU Delft; Kavli institute of nanoscience Delft); Lee, M. (TU Delft BN/Nynke Dekker Lab; Kavli institute of nanoscience Delft); Pedaci, F. (TU Delft BN/Nynke Dekker Lab; Kavli institute of nanoscience Delft); Lipfert, J. (TU Delft BN/Nynke Dekker Lab; Ludwig Maximilians University; Kavli institute of nanoscience Delft); Dekker, N.H. (TU Delft BN/Nynke Dekker Lab; Kavli institute of nanoscience Delft)","","2018","Single-molecule manipulation techniques have provided unprecedented insights into the structure, function, interactions, and mechanical properties of biological macromolecules. Recently, the single-molecule toolbox has been expanded by techniques that enable measurements of rotation and torque, such as the optical torque wrench (OTW) and several different implementations of magnetic (torque) tweezers. Although systematic analyses of the position and force precision of single-molecule techniques have attracted considerable attention, their angle and torque precision have been treated in much less detail. Here, we propose Allan deviation as a tool to systematically quantitate angle and torque precision in single-molecule measurements. We apply the Allan variance method to experimental data from our implementations of (electro)magnetic torque tweezers and an OTW and find that both approaches can achieve a torque precision better than 1 pN · nm. The OTW, capable of measuring torque on (sub)millisecond timescales, provides the best torque precision for measurement times ≲10 s, after which drift becomes a limiting factor. For longer measurement times, magnetic torque tweezers with their superior stability provide the best torque precision. Use of the Allan deviation enables critical assessments of the torque precision as a function of measurement time across different measurement modalities and provides a tool to optimize measurement protocols for a given instrument and application.","","en","journal article","","","","","","Accepted Author Manuscript","","2019-04-25","","","BN/Nynke Dekker Lab","","",""
"uuid:88d76fda-0cbb-402e-a834-aa76b88a4e3d","http://resolver.tudelft.nl/uuid:88d76fda-0cbb-402e-a834-aa76b88a4e3d","Reliability modelling for fatigue life prediction: with application to components in dynamic systems of rotorcraft","Dekker, S.H. (TU Delft Structural Integrity & Composites)","Benedictus, R. (promotor); Alderliesten, R.C. (copromotor); Delft University of Technology (degree granting institution)","2018","A mechanical component can break due to repeated load cycling, even if these loads remain well below the component’s regular static strength. In a simplified fashion, a component’s fatigue life depends on the loads that it has to endure during its service life, as well as its fatigue strength to resist the formation of cracks. Since both of these factors can be considered as random variables, the time until a fatigue-induced rupture occurs can be considered as a random variable as well. Airworthiness regulations require that aircraft manufacturers show by numerical analysis that the probability that a fatigue failure occurs during a critical part’s maximum allowable service life does not exceed a specified probability.","","en","doctoral thesis","","978-94-6295-865-4","","","","","","","","","Structural Integrity & Composites","","",""
"uuid:ca1f7c4b-974f-4147-a7d7-a21644a494ec","http://resolver.tudelft.nl/uuid:ca1f7c4b-974f-4147-a7d7-a21644a494ec","DNA origami scaffold for studying intrinsically disordered proteins of the nuclear pore complex","Ketterer, Philip (Technische Universität München); Ananth, A.N. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Laman Trip, J.D.S. (TU Delft OLD BN/Hyun Youk Lab; Kavli institute of nanoscience Delft); Mishra, Ankur (University Medical Center Groningen); Bertosin, Eva (Technische Universität München); Ganji, M. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); van der Torre, J. (TU Delft BN/Technici en Analisten; Kavli institute of nanoscience Delft); Onck, Patrick (University Medical Center Groningen); Dietz, Hendrik (Technische Universität München); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft)","","2018","The nuclear pore complex (NPC) is the gatekeeper for nuclear transport in eukaryotic cells. A key component of the NPC is the central shaft lined with intrinsically disordered proteins (IDPs) known as FG-Nups, which control the selective molecular traffic. Here, we present an approach to realize artificial NPC mimics that allows controlling the type and copy number of FG-Nups. We constructed 34 nm-wide 3D DNA origami rings and attached different numbers of NSP1, a model yeast FG-Nup, or NSP1-S, a hydrophilic mutant. Using (cryo) electron microscopy, we find that NSP1 forms denser cohesive networks inside the ring compared to NSP1-S. Consistent with this, the measured ionic conductance is lower for NSP1 than for NSP1-S. Molecular dynamics simulations reveal spatially varying protein densities and conductances in good agreement with the experiments. Our technique provides an experimental platform for deciphering the collective behavior of IDPs with full control of their type and position.","","en","journal article","","","","","","","","","","","BN/Cees Dekker Lab","","",""
"uuid:a93d3d4f-209a-4b65-9ec7-4794e7b96236","http://resolver.tudelft.nl/uuid:a93d3d4f-209a-4b65-9ec7-4794e7b96236","Consumer surplus for random regret minimisation models","Chorus, C.G. (TU Delft Transport and Logistics); Dekker, Thijs (University of Leeds)","","2018","This paper is the first to develop a measure of consumer surplus for the Random Regret Minimisation (RRM) model. Following a not so well-known approach proposed two decades ago, we measure (changes in) consumer surplus by studying (changes in) observed behaviour, i.e. the choice probability, in response to price (changes). We interpret the choice probability as a well-behaved approximation of the probabilistic demand curve and accordingly measure the consumer surplus as the area underneath this demand curve. The developed welfare measure enables researchers to assign a measure of consumer surplus to specific alternatives in the context of a given choice set. Moreover, we are able to value changes in the non-price attributes of a specific alternative. We illustrate how differences in consumer surplus between random regret and random utility models follow directly from the differences in their behavioural premises.","Random regret minimisation; consumer surplus; welfare; probabilistic demand function; context dependency","en","journal article","","","","","","","","2019-01-01","","","Transport and Logistics","","",""
"uuid:c6b1e274-fa58-4b27-a562-fec1bf1b4c3b","http://resolver.tudelft.nl/uuid:c6b1e274-fa58-4b27-a562-fec1bf1b4c3b","Probing DNA Translocations with Inplane Current Signals in a Graphene Nanoribbon with a Nanopore","Heerema, S.J. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Vicarelli, L. (TU Delft QN/Zandbergen Lab; Kavli institute of nanoscience Delft); Pud, S. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Schouten, R.N. (TU Delft ALG/General; Kavli institute of nanoscience Delft); Zandbergen, H.W. (TU Delft QN/Zandbergen Lab; Kavli institute of nanoscience Delft); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft)","","2018","Many theoretical studies predict that DNA sequencing should be feasible by monitoring the transverse current through a graphene nanoribbon while a DNA molecule translocates through a nanopore in that ribbon. Such a readout would benefit from the special transport properties of graphene, provide ultimate spatial resolution because of the single-atom layer thickness of graphene, and facilitate high-bandwidth measurements. Previous experimental attempts to measure such transverse inplane signals were however dominated by a trivial capacitive response. Here, we explore the feasibility of the approach using a custom-made differential current amplifier that discriminates between the capacitive current signal and the resistive response in the graphene. We fabricate well-defined short and narrow (30 nm × 30 nm) nanoribbons with a 5 nm nanopore in graphene with a high-temperature scanning transmission electron microscope to retain the crystallinity and sensitivity of the graphene. We show that, indeed, resistive modulations can be observed in the graphene current due to DNA translocation through the nanopore, thus demonstrating that DNA sensing with inplane currents in graphene nanostructures is possible. The approach is however exceedingly challenging due to low yields in device fabrication connected to the complex multistep device layout.","graphene nanoribbon; nanopore; DNA sequencing; biosensing; STEM","en","journal article","","","","","","","","","","","BN/Cees Dekker Lab","","",""
"uuid:c2f08c2e-bdcc-4a24-b158-0b051efa465d","http://resolver.tudelft.nl/uuid:c2f08c2e-bdcc-4a24-b158-0b051efa465d","The Vibe of Skating: Design and Testing of a Vibro-Tactile Feedback System","Jansen, A.J. (TU Delft Product Architecture Design); Dekker, M.C. (TU Delft Applied Ergonomics and Design); van der Steen, Diederik","Espinosa, Hugo G. (editor); Rowlands, David R. (editor); Shepherd, Jonathan (editor); Thiel, David V. (editor)","2018","Providing athletes with real-time feedback on their performance is becoming common in many sports, also in speed skating. This research-by-design project aims at finding a tool that allows the speed skater to get real-time feedback on his performance. Speed skaters often mention a so-called “good feeling” when skating behind a better skater. It is the feeling nearly every speed skater is after when skating alone; skate with less power while maintaining the same speed and feeling of ease. A longer push-off phase at a constant cadence has proven to contribute to this ideal situation but is hard for the coach alone to influence this. Therefore, a system was designed that measures the skating cadence and challenges the skater to change his skating stroke by means of vibro-tactile feedback. Four subjects have tested the feedback system. From this test, we concluded that the system provides meaningful feedback towards changing the skating cycle.","skating; real-time feedback; vibro-tactile feedback; research-by-design","en","conference paper","MDPI","","","","","","","","","","Product Architecture Design","","",""
"uuid:1b75e581-cfb7-4cd9-938d-a316617bb49b","http://resolver.tudelft.nl/uuid:1b75e581-cfb7-4cd9-938d-a316617bb49b","A Platform for Mechano(-Electrical) Characterization of Free-Standing Micron-Sized Structures and Interconnects","Savov, A.M. (TU Delft Electronic Components, Technology and Materials); Joshi, S. (TU Delft Electronic Components, Technology and Materials); Shafqat, Salman (Eindhoven University of Technology); Hoefnagels, Johan (Eindhoven University of Technology); Louwerse, M.C. (Philips Research); Stoute, R. (TU Delft Electronic Components, Technology and Materials); Dekker, R. (TU Delft Electronic Components, Technology and Materials; Philips Research)","","2018","A device for studying the mechanical and electrical behavior of free-standing micro-fabricated metal structures, subjected to a very large deformation, is presented in this paper. The free-standing structures are intended to serve as interconnects in high-density, highly stretchable electronic circuits. For an easy, damage-free handling and mounting of these free-standing structures, the device is designed to be fabricated as a single chip/unit that is separated into two independently movable parts after it is fixed in the tensile test stage. Furthermore, the fabrication method allows for test structures of different geometries to be easily fabricated on the same substrate. The utility of the device has been demonstrated by stretching the free-standing interconnect structures in excess of 1000% while simultaneously measuring their electrical resistance. Important design considerations and encountered processing challenges and their solutions are discussed in this paper.","stretchable electronics; stretchable interconnects; MEMS; mechanical characterization; electrical characterization; free standing interconnects; OA-Fund TU Delft","en","journal article","","","","","","","","","","","Electronic Components, Technology and Materials","","",""
"uuid:49c7611d-0e4a-45a4-9981-9dde35700704","http://resolver.tudelft.nl/uuid:49c7611d-0e4a-45a4-9981-9dde35700704","Effect of tactile stimulation on termination and prevention of apnea of prematurity: A systematic review","Cramer, Sophie J.E. (Leiden University Medical Center); Dekker, Janneke (Leiden University Medical Center); Dankelman, J. (TU Delft Medical Instruments & Bio-Inspired Technology); Pauws, Steffen C. (Tilburg University); Hooper, Stuart B. (MIMR-PHI Institute of Medical Research); te Pas, Arjan B. (Leiden University Medical Center)","","2018","Apnea of prematurity (AOP) is one of the most common diagnoses in preterm infants. Severe and recurrent apneas are associated with cerebral injury and adverse neurodevelopmental outcome. Despite pharmacotherapy and respiratory support to prevent apneas, a proportion of infants continue to have apneas and often need tactile stimulation, mask, and bag ventilation and/or extra oxygen. The duration of the apnea and the concomitant hypoxia and bradycardia depends on the response time of the nurse. We systematically reviewed the literature with the aim of providing an overview of what is known about the effect of manual and mechanical tactile stimulation on AOP. Tactile stimulation, manual or mechanical, has been shown to shorten the duration of apnea, hypoxia, and or bradycardia or even prevent an apnea. Automated stimulation, using closed-loop pulsating or vibrating systems, has been shown to be effective in terminating apneas, but data are scarce. Several studies used continuous mechanical stimulation, with pulsating, vibrating, or oscillating stimuli, to prevent apneas, but the reported effect varied. More studies are needed to confirm whether automated stimulation using a closed loop is more effective than manual stimulation, how and where the automated stimulation should be performed and the potential side effects.","Apnea; Apnea of prematurity; Breathing; Preterm infants; Tactile stimulation","en","review","","","","","","","","","","","Medical Instruments & Bio-Inspired Technology","","",""
"uuid:9238348f-58fc-4ec5-affc-a04fc57ef98c","http://resolver.tudelft.nl/uuid:9238348f-58fc-4ec5-affc-a04fc57ef98c","Real-time imaging of DNA loop extrusion by condensin","Ganji, M. (TU Delft BN/Cees Dekker Lab); Shaltiel, Indra A. (European Molecular Biology Laboratory Heidelberg); Bisht, Shveta (European Molecular Biology Laboratory Heidelberg); Kim, E. (TU Delft BN/Cees Dekker Lab); Kalichava, A. (TU Delft BN/Cees Dekker Lab); Haering, Christian H. (European Molecular Biology Laboratory Heidelberg); Dekker, C. (TU Delft BN/Cees Dekker Lab)","","2018","It has been hypothesized that SMC protein complexes such as condensin and cohesin spatially organize chromosomes by extruding DNA into large loops. We directly visualized the formation and processive extension of DNA loops by yeast condensin in real time. Our findings constitute unambiguous evidence for loop extrusion. We observed that a single condensin complex is able to extrude tens of kilobase pairs of DNA at a force-dependent speed of up to 1500 base pairs per second, using the energy of adenosine triphosphate hydrolysis. Condensin-induced loop extrusion was strictly asymmetric, which demonstrates that condensin anchors onto DNA and reels it in from only one side. Active DNA loop extrusion by SMC complexes may provide the universal unifying principle for genome organization.","","en","journal article","","","","","","Accepted Author Manuscript","","","","","BN/Cees Dekker Lab","","",""
"uuid:f9f4385e-b873-4c16-9419-f7bd466d3e02","http://resolver.tudelft.nl/uuid:f9f4385e-b873-4c16-9419-f7bd466d3e02","Microfabricated tuneable and transferable porous PDMS membranes for Organs-on-Chips","Quiros Solano, W.F. (TU Delft Electronic Components, Technology and Materials); Gaio, N. (TU Delft Electronic Components, Technology and Materials; BIOND Solutions B.V.); Stassen, O.M.J.A. (Eindhoven University of Technology); Arik, Y.B. (University of Twente); Silvestri, C. (BIOND Solutions B.V.); Van Engeland, N.C.A. (Eindhoven University of Technology; Åbo Akademi University); Van der Meer, A. (University of Twente); Passier, R. (University of Twente); Sahlgren, C.M. (Eindhoven University of Technology; Åbo Akademi University); Bouten, C.V.C. (Eindhoven University of Technology); van den Berg, A. (University of Twente); Dekker, R. (TU Delft Electronic Components, Technology and Materials; Philips Research); Sarro, Pasqualina M (TU Delft Electronic Components, Technology and Materials)","","2018","We present a novel and highly reproducible process to fabricate transferable porous PDMS membranes for PDMS-based Organs-on-Chips (OOCs) using microelectromechanical systems (MEMS) fabrication technologies. Porous PDMS membranes with pore sizes down to 2.0 μm in diameter and a wide porosity range (2–65%) can be fabricated. To overcome issues normally faced when using replica moulding and extend the applicability to most OOCs and improve their scalability and reproducibility, the process includes a sacrificial layer to easily transfer the membranes from a silicon carrier to any PDMS-based OOC. The highly reliable fabrication and transfer method does not need of manual handling to define the pore features (size, distribution), allowing very thin (<10 μm) functional membranes to be transferred at chip level with a high success rate (85%). The viability of cell culturing on the porous membranes was assessed by culturing two different cell types on transferred membranes in two different OOCs. Human umbilical endothelial cells (HUVEC) and MDA-MB-231 (MDA) cells were successfully cultured confirming the viability of cell culturing and the biocompatibility of the membranes. The results demonstrate the potential of controlling the porous membrane features to study cell mechanisms such as transmigrations, monolayer formation, and barrier function. The high control over the membrane characteristics might consequently allow to intentionally trigger or prevent certain cellular responses or mechanisms when studying human physiology and pathology using OOCs.","OA-Fund TU Delft","en","journal article","","","","","","","","","","","Electronic Components, Technology and Materials","","",""
"uuid:55d28660-a0ea-44e2-8fde-dbccbefbb03c","http://resolver.tudelft.nl/uuid:55d28660-a0ea-44e2-8fde-dbccbefbb03c","Tailoring the appearance: what will synthetic cells look like?","Spoelstra, W.K. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Deshpande, S.R. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft)","","2018","Recently, the bottom-up assembly of a synthetic cell has emerged as a daring novel approach that can be expected to have major impact in generating fundamental insight in the organization and function of actual biological cells, as well as in stimulating a broad range of applications from drug delivery systems to chemical nanofactories. A crucial feature of any such synthetic cell is the architectural scaffold that defines its identity, compartmentalizes its inner content, and serves as a protective and selective barrier against its environment. Here we review a variety of potential scaffolds for building a synthetic cell. We categorize them as membranous structures (liposomes, fatty acid vesicles, polymersomes), emulsions (droplets and colloidosomes), and membrane-less coacervates. We discuss recent advances for each of them, and explore their salient features as candidates for designing synthetic cells.","","en","review","","","","","","Accepted Author Manuscript","","2018-11-26","","","BN/Cees Dekker Lab","","",""
"uuid:eede4816-b88f-4c01-896f-84cf654df9ed","http://resolver.tudelft.nl/uuid:eede4816-b88f-4c01-896f-84cf654df9ed","Investigation of ""fur-like"" residues post dry etching of polyimide using aluminum hard etch mask","Joshi, S. (TU Delft Electronic Components, Technology and Materials); Savov, A.M. (TU Delft Electronic Components, Technology and Materials); Shafqat, Salman (Eindhoven University of Technology); Dekker, R. (TU Delft Electronic Components, Technology and Materials; Philips Research)","","2018","The authors found that oxygen plasma etching of polyimide (PI) with aluminum (Al) as a hard-etch mask results in lightly textured arbitrary shaped “fur-like” residues. Upon investigation, the presence of Al was detected in these residues. Ruling out several causes of metal contamination that were already reported in literature, a new theory for the presence of the metal containing residues is described. Furthermore, different methods for the residue free etching of PI using an Al hard-etch by using different metal deposition and patterning methods are explored. A fur-free procedure for the etching of PI using a one step-reactive ion etch of the metal hard-etch mask is presented.","Polymers; Reactive ion etching; Sputtering; Residues; PI residues","en","journal article","","","","","","Accepted author manuscript","","2019-12-13","","","Electronic Components, Technology and Materials","","",""
"uuid:b0b672ea-1771-40c4-bd71-4b6e7932bf01","http://resolver.tudelft.nl/uuid:b0b672ea-1771-40c4-bd71-4b6e7932bf01","Dividing the Archaeal Way: The Ancient Cdv Cell-Division Machinery","Caspi, Y. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft)","","2018","Cell division in most prokaryotes is mediated by the well-studied fts genes, with FtsZ as the principal player. In many archaeal species, however, division is orchestrated differently. The Crenarchaeota phylum of archaea features the action of the three proteins, CdvABC. This Cdv system is a unique and less-well-studied division mechanism that merits closer inspection. In vivo, the three Cdv proteins form a composite band that contracts concomitantly with the septum formation. Of the three Cdv proteins, CdvA is the first to be recruited to the division site, while CdvB and CdvC are thought to participate in the active part of the Cdv division machinery. Interestingly, CdvB shares homology with a family of proteins from the eukaryotic ESCRT-III complex, and CdvC is a homolog of the eukaryotic Vps4 complex. These two eukaryotic complexes are key factors in the endosomal sorting complex required for transport (ESCRT) pathway, which is responsible for various budding processes in eukaryotic cells and which participates in the final stages of division in Metazoa. There, ESCRT-III forms a contractile machinery that actively cuts the membrane, whereas Vps4, which is an ATPase, is necessary for the turnover of the ESCRT membrane-abscission polymers. In contrast to CdvB and CdvC, CdvA is unique to the archaeal Crenarchaeota and Thaumarchaeota phyla. The Crenarchaeota division mechanism has often been suggested to represent a simplified version of the ESCRT division machinery thus providing a model system to study the evolution and mechanism of cell division in higher organisms. However, there are still many open questions regarding this parallelism and the division mechanism of Crenarchaeota. Here, we review the existing data on the role of the Cdv proteins in the division process of Crenarchaeota as well as concisely review the ESCRT system in eukaryotes. We survey the similarities and differences between the division and abscission mechanisms in the two cases. We suggest that the Cdv system functions differently in archaea than ESCRT does in eukaryotes, and that, unlike the eukaryotic case, the Cdv system's main function may be related to surplus membrane invagination and cell-wall synthesis.","the Cdv system; Crenarchaeota; archaeal division; the ESCRT system; membrane remodeling; OA-Fund TU Delft","en","journal article","","","","","","","","","","","BN/Cees Dekker Lab","","",""
"uuid:b04fc945-12b9-4e14-983f-553127176662","http://resolver.tudelft.nl/uuid:b04fc945-12b9-4e14-983f-553127176662","Reassessment of requirements for anaerobic xylose fermentation by engineered, non-evolved Saccharomyces cerevisiae strains","Bracher, J.M. (TU Delft BT/Industriele Microbiologie); Martinez-Rodriguez, Oscar A. (Genomatica, San Diego); Dekker, W.J.C. (TU Delft BT/Industriele Microbiologie); Verhoeven, M.D. (DSM); van Maris, A.J.A. (AlbaNova University Center); Pronk, J.T. (TU Delft BT/Industriele Microbiologie)","","2018","Expression of a heterologous xylose isomerase, deletion of the GRE3 aldose-reductase gene and overexpression of genes encoding xylulokinase (XKS1) and non-oxidative pentose-phosphate-pathway enzymes (RKI1, RPE1, TAL1, TKL1) enables aerobic growth of Saccharomyces cerevisiae on d-xylose. However, literature reports differ on whether anaerobic growth on d-xylose requires additional mutations. Here, CRISPR-Cas9-assisted reconstruction and physiological analysis confirmed an early report that this basic set of genetic modifications suffices to enable anaerobic growth on d-xylose in the CEN.PK genetic background. Strains that additionally carried overexpression cassettes for the transaldolase and transketolase paralogs NQM1 and TKL2 only exhibited anaerobic growth on d-xylose after a 7-10 day lag phase. This extended lag phase was eliminated by increasing inoculum concentrations from 0.02 to 0.2 g biomass L-1. Alternatively, a long lag phase could be prevented by sparging low-inoculum-density bioreactor cultures with a CO2/N2-mixture, thus mimicking initial CO2 concentrations in high-inoculum-density, nitrogen-sparged cultures, or by using l-aspartate instead of ammonium as nitrogen source. This study resolves apparent contradictions in the literature on the genetic interventions required for anaerobic growth of CEN.PK-derived strains on d-xylose. Additionally, it indicates the potential relevance of CO2 availability and anaplerotic carboxylation reactions for anaerobic growth of engineered S. cerevisiae strains on d-xylose.","","en","journal article","","","","","","","","","","","BT/Industriele Microbiologie","","",""
"uuid:2f05a799-bf94-4fba-a2c4-41f880d2711c","http://resolver.tudelft.nl/uuid:2f05a799-bf94-4fba-a2c4-41f880d2711c","Editorial: Special issue of the 5th Symposium of the European Association of Research in Transportation","van Cranenburgh, S. (TU Delft Transport and Logistics); Dekker, Thijs (University of Leeds)","","2018","This special issue presents seven selected papers from the 5th Symposium of the European Association of Research in Transportation (hEART) which was held in September 2016 in Delft, The Netherlands, and was organised by Delft University of Technology. The contributions cover a wide range of topics in transportation, reflecting the broad scope of the hEART symposium series, including but not limited to travel behaviour, travel survey methods, railway freight as well as (terminal) logistics. As editors of this special issue we are very grateful for the efforts made by the authors, in particular their enduring efforts to push the quality of their contributions to a higher level during the review process. Also, we like to take the opportunity to thank all the reviewers for their constructive feedback and suggestions for improvement. This editorial provides a brief overview of the hEART2016 symposium. After that, an overview is given of the seven contributions that form this special issue.","","en","contribution to periodical","","","","","","","","","","","Transport and Logistics","","",""
"uuid:d4f2d609-5c59-4b0d-8a4f-da0297d8fad5","http://resolver.tudelft.nl/uuid:d4f2d609-5c59-4b0d-8a4f-da0297d8fad5","FtsZ-Induced Shape Transformation of Coacervates","Fanalista, F. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Deshpande, S.R. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Lau, A.W.H.R. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Pawlik, G. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft)","","2018","Recently, both the cellular and synthetic biology communities have expressed a strong interest in coacervates, membrane‐less liquid droplets composed of densely packed multivalent molecules that form as a result of spontaneous phase separation. Here, it is studied how FtsZ, a protein that plays a key role in the bacterial division process, remodels coacervates made of polylysine (pLL) and guanosine triphosphate (GTP). It is shown that FtsZ strongly partitions at the surface of the coacervates and induces their disassembly due to the hydrolysis of GTP by FtsZ. Surprisingly, the coacervates are found to promote lateral interactions between FtsZ filaments, inducing the formation of an emanating network of FtsZ bundles that interconnect neighboring coacervates. Under mechanical stress, coacervates are shown to fracture, resulting in profound invaginations along their circumference. The results bring out the potential of coacervates for their use as membrane‐free scaffolds for building synthetic cells as well as are possibly relevant for coacervation in prokaryotic cells.","biointerface; coacervates; FtsZ; protein bundling; synthetic cell","en","journal article","","","","","","","","2019-11-18","","","BN/Cees Dekker Lab","","",""
"uuid:18d519e6-c894-4124-9710-4dc6887ac324","http://resolver.tudelft.nl/uuid:18d519e6-c894-4124-9710-4dc6887ac324","A Next Step in Disruption Management: Combining Operations Research and Complexity Science","Dekker, Mark M. (Universiteit Utrecht); van Lieshout, Rolf N. (Erasmus Universiteit Rotterdam); Ball, Robin C. (University of Warwick); Bouman, Paul C. (Erasmus Universiteit Rotterdam); Dekker, Stefan C. (Universiteit Utrecht); Dijkstra, Henk A. (Universiteit Utrecht); Goverde, R.M.P. (TU Delft Transport and Planning); Huisman, Dennis (N.V. Nederlandse Spoorwegen; Erasmus Universiteit Rotterdam); Panja, Deb (Universiteit Utrecht); Schaafsma, Alfons A.M. (ProRail); van den Akker, Marjan (Universiteit Utrecht)","","2018","Railway systems occasionally get into a state of out-of-control, meaning that there is barely any train is running, even though the required resources (infrastructure, rolling stock and crew) are available. These situations can either be caused by large disruptions or unexpected propagation and accumulation of delays. Because of the large number of affected resources and the absence of detailed, timely and accurate information, currently existing methods cannot be applied in out-of-control situations. Most of the contemporary approaches assume that there is only one single disruption with a known duration, that all information about the resources is available, and that all stakeholders in the operations act as expected. Another limitation is the lack of knowledge about why and how disruptions accumulate and whether this process can be predicted. To tackle these problems, we develop a multidisciplinary framework aiming at reducing the impact of these situations and - if possible - avoiding them. The key elements of this framework are (i) the generation of early warning signals for out-of-control situations using tools from complexity science and (ii) a set of rescheduling measures robust against the features of out-of-control situations, using tools from operations research.
1, interferometers2 and interference-based spin filters3. Consistent with the principles of subwavelength optics, the wave nature of electrons can give rise to various types of interference effects4, such as Fabry–Pérot resonances5, Fano resonances6 and the Aharonov–Bohm effect7. Quantum interference conductance oscillations8 have, indeed, been predicted for multiwall carbon nanotube shuttles and telescopes, and arise from atomic-scale displacements between the inner and outer tubes9,10. Previous theoretical work on graphene bilayers indicates that these systems may display similar interference features as a function of the relative position of the two sheets11,12. Experimental verification is, however, still lacking. Graphene nanoconstrictions represent an ideal model system to study quantum transport phenomena13–15 due to the electronic coherence16 and the transverse confinement of the carriers17. Here, we demonstrate the fabrication of bowtie-shaped nanoconstrictions with mechanically controlled break junctions made from a single layer of graphene. Their electrical conductance displays pronounced oscillations at room temperature, with amplitudes that modulate over an order of magnitude as a function of subnanometre displacements. Surprisingly, the oscillations exhibit a period larger than the graphene lattice constant. Charge-transport calculations show that the periodicity originates from a combination of the quantum interference and lattice commensuration effects of two graphene layers that slide across each other. Our results provide direct experimental observation of a Fabry–Pérot-like interference of electron waves that are partially reflected and/or transmitted at the edges of the graphene bilayer overlap region.","","en","journal article","","","","","","Accepted Author Manuscript","","2018-03-17","","","QN/van der Zant Lab","","",""
"uuid:d0d99406-5b8f-4292-89c0-cf02de707903","http://resolver.tudelft.nl/uuid:d0d99406-5b8f-4292-89c0-cf02de707903","Detection of CRISPR-dCas9 on DNA with Solid-State Nanopores","Yang, W.W.W. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Restrepo Perez, L. (TU Delft BN/Chirlmin Joo Lab; Kavli institute of nanoscience Delft); Bengtson, M.L. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Heerema, S.J. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Birnie, A.T.F. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); van der Torre, J. (TU Delft BN/Technici en Analisten; Kavli institute of nanoscience Delft); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft)","","2018","Solid-state nanopores have emerged as promising platforms for biosensing including diagnostics for disease detection. Here we show nanopore experiments that detect CRISPR-dCas9, a sequence-specific RNA-guided protein system that specifically binds to a target DNA sequence. While CRISPR-Cas9 is acclaimed for its gene editing potential, the CRISPR-dCas9 variant employed here does not cut DNA but instead remains tightly bound at a user-defined binding site, thus providing an excellent target for biosensing. In our nanopore experiments, we observe the CRISPR-dCas9 proteins as local spikes that appear on top of the ionic current blockade signal of DNA molecules that translocate through the nanopore. The proteins exhibit a pronounced blockade signal that allows for facile identification of the targeted sequence. Even at the high salt conditions (1 M LiCl) required for nanopore experiments, dCas9 proteins are found to remain stably bound. The binding position of the target sequence can be read from the spike position along the DNA signal. We anticipate applications of this nanopore-based CRISPR-dCas9 biosensing approach in DNA-typing based diagnostics such as quick disease-strain identification, antibiotic-resistance detection, and genome typing.","biosensing; CRISPR-Cas9; diagnostics; Nanopores","en","journal article","","","","","","","","","","","BN/Cees Dekker Lab","","",""
"uuid:ce1c4eed-5b27-42ad-a07c-79bafc9d1e2e","http://resolver.tudelft.nl/uuid:ce1c4eed-5b27-42ad-a07c-79bafc9d1e2e","Spatial structure of disordered proteins dictates conductance and selectivity in nuclear pore complex mimics","Ananth, A.N. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Mishra, Ankur (University Medical Center Groningen); Frey, Steffen (Max Planck Institute for Biophysical Chemistry (Karl Friedrich Bonhoeffer Institute)); Dwarkasing, A. (TU Delft ImPhys/Practicum support; Kavli institute of nanoscience Delft); Versloot, Roderick (Student TU Delft; Kavli institute of nanoscience Delft); van der Giessen, Erik (University Medical Center Groningen); Görlich, Dirk (Max Planck Institute for Biophysical Chemistry (Karl Friedrich Bonhoeffer Institute)); Onck, Patrick (University Medical Center Groningen); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft)","","2018","Nuclear pore complexes (NPCs) lined with intrinsically disordered FG-domains act as selective gatekeepers for molecular transport between the nucleus and the cytoplasm in eukaryotic cells. The underlying physical mechanism of the intriguing selectivity is still under debate. Here, we probe the transport of ions and transport receptors through biomimetic NPCs consisting of Nsp1 domains attached to the inner surface of solid-state nanopores. We examine both wildtype FG- domains and hydrophilic SG-mutants. FG-nanopores showed a clear selectivity as transport receptors can translocate across the pore whereas other proteins cannot. SG mutant pores lack such selectivity. To unravel this striking difference, we present coarse-grained molecular dynamics simulations that reveal that FG-pores exhibit a high-density, nonuniform protein distribution, in contrast to a uniform and significantly less-dense protein distribution in the SG-mutant. We conclude that the sequence-dependent density distribution of disordered proteins inside the NPC plays a key role for its conductivity and selective permeability.","","en","journal article","","","","","","","","","","","BN/Cees Dekker Lab","","",""
"uuid:e4320016-8106-440a-a2e5-89304672a19c","http://resolver.tudelft.nl/uuid:e4320016-8106-440a-a2e5-89304672a19c","Direct observation of end resection by RecBCD during double-stranded DNA break repair in vivo","Wiktor, J.M. (TU Delft BN/Cees Dekker Lab); van der Does, M. (TU Delft Applied Sciences); Büller, L.A. (TU Delft Applied Sciences); Sherratt, David J. (University of Oxford); Dekker, C. (TU Delft BN/Cees Dekker Lab)","","2018","The formation of 3 single-stranded DNA overhangs is a first and essential step during homology-directed repair of double-stranded breaks (DSB) of DNA, a task that in Escherichia coli is performed by RecBCD. While this protein complex has been well characterized through in vitro single-molecule studies, it has remained elusive how end resection proceeds in the crowded and complex environment in live cells. Here, we develop a two-color fluorescent reporter to directly observe the resection of individual inducible DSB sites within live E. coli cells. Realtime imaging shows that RecBCD during end resection degrades DNA with remarkably high speed (i""1.6 kb/s) and high processivity (>7sim;100 kb). The results show a pronounced asymmetry in the processing of the two DNA ends of a DSB, where much longer stretches of DNA are degraded in the direction of terminus. The microscopy observations are confirmed using quantitative polymerase chain reaction measurements of the DNA degradation. Deletion of the recD gene drastically decreased the length of resection, allowing for recombination with short ectopic plasmid homologies and significantly increasing the efficiency of horizontal gene transfer between strains.We thus visualized and quantified DNA end resection by the RecBCD complex in live cells, recorded DNA-degradation linked to end resection and uncovered a general relationship between the length of end resection and the choice of the homologous recombination template.","","en","journal article","","","","","","","","","Applied Sciences","","BN/Cees Dekker Lab","","",""
"uuid:0636166a-62d1-4f38-a10d-8f1a3a21f62c","http://resolver.tudelft.nl/uuid:0636166a-62d1-4f38-a10d-8f1a3a21f62c","Lithography-based fabrication of nanopore arrays in freestanding SiN and graphene membranes","Verschueren, D.V. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Yang, W.W.W. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft)","","2018","We report a simple and scalable technique for the fabrication of nanopore arrays on freestanding SiN and graphene membranes based on electron-beam lithography and reactive ion etching. By controlling the dose of the single-shot electron-beam exposure, circular nanopores of any size down to 16 nm in diameter can be fabricated in both materials at high accuracy and precision. We demonstrate the sensing capabilities of these nanopores by translocating dsDNA through pores fabricated using this method, and find signal-to-noise characteristics on par with transmission-electron-microscope-drilled nanopores. This versatile lithography-based approach allows for the high-throughput manufacturing of nanopores and can in principle be used on any substrate, in particular membranes made out of transferable two-dimensional materials.","","en","journal article","","","","","","","","2019-02-20","","","BN/Cees Dekker Lab","","",""
"uuid:3cd4a3bc-d9ea-4c04-95e3-176fff92e3a1","http://resolver.tudelft.nl/uuid:3cd4a3bc-d9ea-4c04-95e3-176fff92e3a1","Mechanical Division of Cell-Sized Liposomes","Deshpande, S.R. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Spoelstra, W.K. (TU Delft BN/Marileen Dogterom Lab; Kavli institute of nanoscience Delft); van Doorn, M.C. (Student TU Delft; Kavli institute of nanoscience Delft); Kerssemakers, J.W.J. (TU Delft BN/Technici en Analisten; Kavli institute of nanoscience Delft); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft)","","2018","Liposomes, self-assembled vesicles with a lipid-bilayer boundary similar to cell membranes, are extensively used in both fundamental and applied sciences. Manipulation of their physical properties, such as growth and division, may significantly expand their use as model systems in cellular and synthetic biology. Several approaches have been explored to controllably divide liposomes, such as shape transformation through temperature cycling, incorporation of additional lipids, and the encapsulation of protein division machinery. However, so far, these methods lacked control, exhibited low efficiency, and yielded asymmetric division in terms of volume or lipid composition. Here, we present a microfluidics-based strategy to realize mechanical division of cell-sized (∼6 μm) liposomes. We use octanol-assisted liposome assembly (OLA) to produce liposomes on chip, which are subsequently flowed against the sharp edge of a wedge-shaped splitter. Upon encountering such a Y-shaped bifurcation, the liposomes are deformed and, remarkably, are able to divide into two stable daughter liposomes in just a few milliseconds. The probability of successful division is found to critically depend on the surface area-to-volume ratio of the mother liposome, which can be tuned through osmotic pressure, and to strongly correlate to the mother liposome size for given microchannel dimensions. The division process is highly symmetric (∼3% size variation between the daughter liposomes) and is accompanied by a low leakage. This mechanical division of liposomes may constitute a valuable step to establish a growth-division cycle of synthetic cells.","liposomes; membrane biophysics; microfluidics; octanol-assisted liposome assembly; synthetic biology; Synthetic cell division","en","journal article","","","","","","","","","","","BN/Cees Dekker Lab","","",""
"uuid:60b3d2b4-a74d-4683-8f77-deee5e92543e","http://resolver.tudelft.nl/uuid:60b3d2b4-a74d-4683-8f77-deee5e92543e","Modification of the histone tetramer at the H3-H3 interface impacts tetrasome conformations and dynamics","Ordu, O. (TU Delft BN/Nynke Dekker Lab; Kavli institute of nanoscience Delft); Kremser, Leopold (Medical University of Innsbruck); Lusser, Alexandra (Medical University of Innsbruck); Dekker, N.H. (TU Delft BN/Nynke Dekker Lab; Kavli institute of nanoscience Delft)","","2018","Nucleosomes consisting of a short piece of deoxyribonucleic acid (DNA) wrapped around an octamer of histone proteins form the fundamental unit of chromatin in eukaryotes. Their role in DNA compaction comes with regulatory functions that impact essential genomic processes such as replication, transcription, and repair. The assembly of nucleosomes obeys a precise pathway in which tetramers of histones H3 and H4 bind to the DNA first to form tetrasomes, and two dimers of histones H2A and H2B are subsequently incorporated to complete the complex. As viable intermediates, we previously showed that tetrasomes can spontaneously flip between a left-handed and right-handed conformation of DNA-wrapping. To pinpoint the underlying mechanism, here we investigated the role of the H3-H3 interface for tetramer flexibility in the flipping process at the single-molecule level. Using freely orbiting magnetic tweezers, we studied the assembly and structural dynamics of individual tetrasomes modified at the cysteines close to this interaction interface by iodoacetamide (IA) in real time. While such modification did not affect the structural properties of the tetrasomes, it caused a 3-fold change in their flipping kinetics. The results indicate that the IA-modification enhances the conformational plasticity of tetrasomes. Our findings suggest that subnucleosomal dynamics may be employed by chromatin as an intrinsic and adjustable mechanism to regulate DNA supercoiling.","","en","journal article","","","","","","Accepted Author Manuscript","","","","","BN/Nynke Dekker Lab","","",""
"uuid:2a2ae475-c406-4c04-81ae-b7bfa502d30f","http://resolver.tudelft.nl/uuid:2a2ae475-c406-4c04-81ae-b7bfa502d30f","Label-Free Optical Detection of DNA Translocations through Plasmonic Nanopores","Verschueren, D.V. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Pud, S. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Shi, X. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft; East China University of Science and Technology); de Angelis, L. (TU Delft QN/Kuipers Lab); Kuipers, L. (TU Delft QN/Quantum Nanoscience); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft)","","2018","Solid-state nanopores are single-molecule sensors that hold great potential for rapid protein and nucleic-acid analysis. Despite their many opportunities, the conventional ionic current detection scheme that is at the heart of the sensor suffers inherent limitations. This scheme intrinsically couples signal strength to the driving voltage, requires the use of high-concentration electrolytes, suffers from capacitive noise, and impairs high-density sensor integration. Here, we propose a fundamentally different detection scheme based on the enhanced light transmission through a plasmonic nanopore. We demonstrate that translocations of single DNA molecules can be optically detected, without the need of any labeling, in the transmitted light intensity through an inverted-bowtie plasmonic nanopore. Characterization and the cross-correlation of the optical signals with their electrical counterparts verify the plasmonic basis of the optical signal. We demonstrate DNA translocation event detection in a regime of driving voltages and buffer conditions where traditional ionic current sensing fails. This label-free optical detection scheme offers opportunities to probe native DNA-protein interactions at physiological conditions.","DNA translocation; optical transmission; plasmon resonance sensing; plasmonic nanopores; solid-state nanopores","en","journal article","","","","","","","","","","QN/Quantum Nanoscience","BN/Cees Dekker Lab","","",""
"uuid:7bec86e7-54c1-48c8-8086-53ee473f39a0","http://resolver.tudelft.nl/uuid:7bec86e7-54c1-48c8-8086-53ee473f39a0","The immediate effect of a soft knee brace on dynamic knee instability in persons with knee osteoarthritis","Cudejko, Tomasz (Amsterdam UMC); Van Der Esch, Martin (Amsterdam UMC); Schrijvers, Jim (Amsterdam UMC); Richards, Rosie (Amsterdam UMC); Van Den Noort, Josien C. (Amsterdam UMC); Wrigley, Tim (University of Melbourne); Van Der Leeden, Marike (Amsterdam UMC); Roorda, Leo D. (Amsterdam UMC); Lems, Willem (Amsterdam UMC); Harlaar, J. (TU Delft Biomechatronics & Human-Machine Control; Amsterdam UMC); Dekker, Joost (Amsterdam UMC)","","2018","Objectives Wearing a soft knee brace has been shown to reduce self-reported knee instability in persons with knee OA. There is a need to assess whether a soft knee brace has a beneficial effect on objectively assessed dynamic knee instability as well. The aims of the study were to evaluate the effect of a soft knee brace on objectively assessed dynamic knee instability and to assess the difference in effect between a non-tight and a tight soft knee brace in persons with knee OA. Methods Thirty-eight persons with knee OA and self-reported knee instability participated in a laboratory study. A within-subject design was used comparing no brace vs brace and comparing a non-tight vs a tight brace. The primary outcome measure was dynamic knee instability, expressed by the perturbation response (PR). The PR reflects deviation in the mean knee varus-valgus angle during level walking after a controlled mechanical perturbation. Linear mixed-effect model analysis was used to evaluate the effect of a brace on dynamic knee instability. Results Wearing a brace significantly reduced the PR compared with not wearing a brace (B = -0.16, P = 0.01). There was no difference between a non-tight and a tight brace (B = -0.03, P = 0.60). Conclusion This study is the first to report that wearing a soft knee brace reduces objectively assessed dynamic knee instability in persons with knee OA. Wearing a soft brace results in an objective improvement of knee instability beyond subjectively reported improvement. Trial registration Nederlands Trial register (trialregister.nl) NTR6363","brace; knee; knee instability; orthotics; osteoarthritis","en","journal article","","","","","","Green Open Access added to TU Delft Institutional Repository 'You share, we take care!' - Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.","","2018-12-20","","","Biomechatronics & Human-Machine Control","","",""
"uuid:c6d11c61-0a13-42a3-8655-e9dba97f287a","http://resolver.tudelft.nl/uuid:c6d11c61-0a13-42a3-8655-e9dba97f287a","A multiwell plate Organ-on-Chip (OOC) device for in-vitro cell culture stimulation and monitoring","Gaio, N. (TU Delft Electronic Components, Technology and Materials); Waafi, A. (Student TU Delft); Vlaming, M.L.H. (Ncardia); Boschman, E. (Boschman Technologies); Dijkstra, P. (Philips Innovation Services); Nacken, O. (Ncardia); Braam, S.R. (Ncardia); Boucsein, C. (Multi Channel Systems GmbH); Sarro, Pasqualina M (TU Delft Electronic Components, Technology and Materials); Dekker, R. (TU Delft Electronic Components, Technology and Materials)","","2018","This work presents the first multi-well plate that allows for simultaneous mechanical stimulation and electrical monitoring of multiple in-vitro cell cultures in parallel. Each well of the plate is equipped with an Organ-on-Chip (OOC) device consisting of a stretchable micro-electrode array (MEA). For the first time, a film assisted molding (FAM) process was employed to embed an OOC into a multi well plate format packaging. The functionality of the MEA in the device was assessed with electrochemical impedance spectroscopy. Moreover, the biocompatibility of the plate was demonstrated with cardiomyocytes derived from human induced pluripotent stem cells (iPSC) cultured in the wells.","Electrodes; Monitoring; Silicon; Packaging; Biomedical monitoring; Biomembranes; Impedance","en","conference paper","IEEE","","","","","Green Open Access added to TU Delft Institutional Repository ‘You share, we take care!’ – Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.","","2021-08-02","","","Electronic Components, Technology and Materials","","",""
"uuid:df392e75-5fd0-4e1e-af54-8565dba7efb1","http://resolver.tudelft.nl/uuid:df392e75-5fd0-4e1e-af54-8565dba7efb1","A novel method to transfer porous PDMS membranes for high throughput Organ-on-Chip and Lab-on-Chip assembly","Quiros Solano, W.F. (TU Delft Electronic Components, Technology and Materials); Gaio, N. (TU Delft Electronic Components, Technology and Materials); Silvestri, C. (TU Delft Tera-Hertz Sensing); Arik, Y.B. (University of Twente); Stassen, O.M.J.A. (Eindhoven University of Technology); van der Meer, A.D. (University of Twente); Bouten, C.V.C. (Eindhoven University of Technology); van den Berg, A. (University of Twente); Dekker, R. (TU Delft Electronic Components, Technology and Materials); Sarro, Pasqualina M (TU Delft Electronic Components, Technology and Materials)","","2018","We present a novel method to easily and reliably transfer highly porous, large area, thin microfabricated Polydimethylsiloxane (PDMS) porous membranes on Lab-on-Chip (LOC) and Organ-on-Chip (OOC) devices. The use of silicon as carrier substrate and a water-soluble sacrificial layer allows a simple and reproducible transfer of the membranes to any PDMS-based OOC and LOC device. The use of IC and MEMS compatible techniques reduces significantly the fabrication time and the need of manual handling. Our method is suitable for automatic assembling systems, such as pick-and-place, crucial to significantly increase the throughput of OOC and LOC devices assembling. Membranes with 8 μm pore size and as thin as 4 μm are successfully transferred. The viability and biocompatibility of the transfer was assessed by culturing two different cell lines on an OOC with transferred porous PDMS membranes.","Biomembranes; Fabrication; Silicon; Throughput; Microchannels; Micromechanical devices; Manuals","en","conference paper","IEEE","","","","","","","","","","Electronic Components, Technology and Materials","","",""
"uuid:650501ce-5b65-4e84-a87f-c9b538f9145f","http://resolver.tudelft.nl/uuid:650501ce-5b65-4e84-a87f-c9b538f9145f","Investigating the effect of artists’ paint formulation on degradation rates of TiO2‑based oil paints","van Driel, B.A. (TU Delft (OLD) MSE-4; Rijksmuseum; Cultural Heritage Agency of the Netherlands); van den Berg, K. J. (Cultural Heritage Agency of the Netherlands); Smout, M. (AkzoNobel); Dekker, N. (AkzoNobel); Kooyman, P.J. (University of Cape Town); Dik, J. (TU Delft (OLD) MSE-4)","","2018","This study reports on the effect of artists’ paint formulation on degradation rates of TiO2-based oil paints. Titanium white oil paint exists in a multitude of different recipes, and the effect of the formulation on photocatalytic binder
degradation kinetics is unknown. These formulations contain, among others, one or both titanium dioxide polymorphs, zinc oxide, the extenders barium sulfate or calcium carbonate and various additives. Most research performed
on the photocatalytic degradation process focusses on pure titanium white-binder mixtures and thus does not take into account the complete paint system. Since photocatalytic oil degradation is a process initiated by the absorption of UV light, any ingredient or combination of ingredients influencing the light scattering and absorption properties of the paint films may affect the degradation rate. In this study three sets of experiments are conducted,
designed using the design of experiments (DoE) approach, to screen for the most important formulation factors influencing the degradation rate. The benefits of using DoE, compared to a more traditional ‘one factor at a time approach’ are robustness, sample efficiency, the ability of evaluate mixtures of multiple components as well as the ability to evaluate factor interactions. The three sets of experiments investigate (1) the influence of the TiO2 type, (2) the impact of different mixtures of two types of TiO2, ZnO and the additive aluminum stearate and (3) the influence of common extenders in combination with photocatalytic TiO2, on the photocatalytic degradation of the oil binder. The impact of the formulation on the degradation rate became apparent, indicating the shortcoming of oversimplified studies. The protective effect of photostable TiO2 pigments, even in a mixture with photocatalytic TiO2 pigments, as well as the negative effect of extenders was demonstrated. Furthermore, the ambiguous role of ZnO (photocatalytic or not) and aluminum stearate is highlighted. Neither can be ignored in a study of degradation behavior of modern oil paints and require further investigation.","Titanium white; Oil paint formulation; Gloss; Degradation rate; Design of Experiments (DoE); OA-Fund TU Delft","en","journal article","","","","","","","","","","","(OLD) MSE-4","","",""
"uuid:8a1740bc-20cc-4d50-bcf4-05b8d5443ef4","http://resolver.tudelft.nl/uuid:8a1740bc-20cc-4d50-bcf4-05b8d5443ef4","Catching DNA with hoops-biophysical approaches to clarify the mechanism of SMC proteins","Eeftens, J.M. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft)","","2017","Structural maintenance of chromosome (SMC) complexes are central regulators of chromosome architecture that are essential in all domains of life. For decades, the structural biology field has been debating how these conserved protein complexes use their intricate ring-like structures to structurally organize DNA. Here, we review the contributions of single-molecule biophysical approaches to resolving the molecular mechanism of SMC protein function.","","en","review","","","","","","","","2018-06-07","","","BN/Cees Dekker Lab","","",""
"uuid:5940a265-aeb4-46d3-a90b-3e05a25d1279","http://resolver.tudelft.nl/uuid:5940a265-aeb4-46d3-a90b-3e05a25d1279","What is all this fuss about Tus?: Comparison of recent findings from biophysical and biochemical experiments","Berghuis, B.A. (TU Delft BN/Nynke Dekker Lab); Raducanu, Vlad-Stefan (King Abdullah University of Science and Technology); Elshenawy, Mohamed M. (King Abdullah University of Science and Technology); Jergic, Slobodan (University of Wollongong); Depken, S.M. (TU Delft BN/Martin Depken Lab); Dixon, NE (University of Wollongong); Hamdan, Samir M. (King Abdullah University of Science and Technology); Dekker, N.H. (TU Delft BN/Nynke Dekker Lab)","","2017","Synchronizing the convergence of the two-oppositely moving DNA replication machineries at specific termination sites is a tightly coordinated process in bacteria. In Escherichia coli, a “replication fork trap” – found within a chromosomal region where forks are allowed to enter but not leave – is set by the protein–DNA roadblock Tus–Ter. The exact sequence of events by which Tus–Ter blocks replisomes approaching from one direction but not the other has been the subject of controversy for many decades. Specific protein–protein interactions between the nonpermissive face of Tus and the approaching helicase were challenged by biochemical and structural studies. These studies show that it is the helicase-induced strand separation that triggers the formation of new Tus–Ter interactions at the nonpermissive face – interactions that result in a highly stable “locked” complex. This controversy recently gained renewed attention as three single-molecule-based studies scrutinized this elusive Tus–Ter mechanism – leading to new findings and refinement of existing models, but also generating new questions. Here, we discuss and compare the findings of each of the single-molecule studies to find their common ground, pinpoint the crucial differences that remain, and push the understanding of this bipartite DNA–protein system further.","DNA–protein interactions; DNA replication; prokaryotic replication; replication termination; replisome; Tus–Ter; single-molecule techniques; magnetic tweezers","en","journal article","","","","","","","","","","","BN/Nynke Dekker Lab","","",""
"uuid:153c569a-1bff-4ec0-8f6d-2a62981fcf35","http://resolver.tudelft.nl/uuid:153c569a-1bff-4ec0-8f6d-2a62981fcf35","The condensin complex is a mechanochemical motor that translocates along DNA","Terakawa, Tsuyoshi (Columbia University); Bisht, Shveta (European Molecular Biology Laboratory Heidelberg); Eeftens, J.M. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Haering, Christian H. (European Molecular Biology Laboratory Heidelberg); Greene, Eric C. (Columbia University)","","2017","Condensin plays crucial roles in chromosome organization and compaction, but the mechanistic basis for its functions remains obscure. We used single-molecule imaging to demonstrate that Saccharomyces cerevisiae condensin is a molecular motor capable of adenosine triphosphate hydrolysis–dependent translocation along double-stranded DNA. Condensin’s translocation activity is rapid and highly processive, with individual complexes traveling an average distance of ≥10 kilobases at a velocity of ~60 base pairs per second. Our results suggest that condensin may take steps comparable in length to its ~50-nanometer coiled-coil subunits, indicative of a translocation mechanism that is distinct from any reported for a DNA motor protein. The finding that condensin is a mechanochemical motor has important implications for understanding the mechanisms of chromosome organization and condensation.","","en","journal article","","","","","","","","","","","BN/Cees Dekker Lab","","",""
"uuid:ea585f41-5a6a-4284-bf8a-cf6a5f9ec6dc","http://resolver.tudelft.nl/uuid:ea585f41-5a6a-4284-bf8a-cf6a5f9ec6dc","SDS-assisted protein transport through solid-state nanopores","Restrepo Perez, L. (TU Delft BN/Chirlmin Joo Lab; Kavli institute of nanoscience Delft); John, Shalini (University of Illinois); Aksimentiev, Aleksei (University of Illinois); Joo, C. (TU Delft BN/Chirlmin Joo Lab; Kavli institute of nanoscience Delft); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft)","","2017","Using nanopores for single-molecule sequencing of proteins – similar to nanopore-based sequencing of DNA – faces multiple challenges, including unfolding of the complex tertiary structure of the proteins and enforcing their unidirectional translocation through nanopores. Here, we combine molecular dynamics (MD) simulations with single-molecule experiments to investigate the utility of SDS (Sodium Dodecyl Sulfate) to unfold proteins for solid-state nanopore translocation, while simultaneously endowing them with a stronger electrical charge. Our simulations and experiments prove that SDS-treated proteins show a considerable loss of the protein structure during the nanopore translocation. Moreover, SDS-treated proteins translocate through the nanopore in the direction prescribed by the electrophoretic force due to the negative charge impaired by SDS. In summary, our results suggest that SDS causes protein unfolding while facilitating protein translocation in the direction of the electrophoretic force; both characteristics being advantageous for future protein sequencing applications using solid-state nanopores.","","en","journal article","","","","","","","","","","","BN/Chirlmin Joo Lab","","",""
"uuid:a95c0f70-e05f-4ff7-9587-444911b810cf","http://resolver.tudelft.nl/uuid:a95c0f70-e05f-4ff7-9587-444911b810cf","Distortion of DNA Origami on Graphene Imaged with Advanced TEM Techniques","Kabiri, Y. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Ananth, A.N. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); van der Torre, J. (TU Delft BN/Technici en Analisten; Kavli institute of nanoscience Delft); Katan, A.J. (TU Delft QN/Afdelingsbureau; Kavli institute of nanoscience Delft); Hong, Jin Yong (Massachusetts Institute of Technology); Malladi, S.R.K. (TU Delft QN/Zandbergen Lab; Kavli institute of nanoscience Delft); Kong, Jing (Massachusetts Institute of Technology); Zandbergen, H.W. (TU Delft QN/Zandbergen Lab; Kavli institute of nanoscience Delft); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft)","","2017","While graphene may appear to be the ultimate support membrane for transmission electron microscopy (TEM) imaging of DNA nanostructures, very little is known if it poses an advantage over conventional carbon supports in terms of resolution and contrast. Microscopic investigations are carried out on DNA origami nanoplates that are supported onto freestanding graphene, using advanced TEM techniques, including a new dark-field technique that is recently developed in our lab. TEM images of stained and unstained DNA origami are presented with high contrast on both graphene and amorphous carbon membranes. On graphene, the images of the origami plates show severe unwanted distortions, where the rectangular shape of the nanoplates is significantly distorted. From a number of comparative control experiments, it is demonstrated that neither staining agents, nor screening ions, nor the level of electron-beam irradiation cause this distortion. Instead, it is suggested that origami nanoplates are distorted due to hydrophobic interaction of the DNA bases with graphene upon adsorption of the DNA origami nanoplates.","DNA origami; graphene; nanostructures; transmission electron microscopy","en","journal article","","","","","","","","2018-06-16","","","BN/Cees Dekker Lab","","",""
"uuid:c4486afa-a5e5-48ba-976a-7ecc010d9dba","http://resolver.tudelft.nl/uuid:c4486afa-a5e5-48ba-976a-7ecc010d9dba","Through-membrane electron-beam lithography for ultrathin membrane applications","Neklyudova, M. (TU Delft QN/Zandbergen Lab; Kavli institute of nanoscience Delft); Erdamar, A.K. (TU Delft QN/Zandbergen Lab; Kavli institute of nanoscience Delft); Vicarelli, L. (TU Delft QN/Zandbergen Lab; Kavli institute of nanoscience Delft); Heerema, S.J. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Rehfeldt, T. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Pandraud, G. (TU Delft Else Kooi Laboratory); Koladouz Esfahani, Z. (TU Delft QN/Zandbergen Lab; Kavli institute of nanoscience Delft); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Zandbergen, H.W. (TU Delft QN/Zandbergen Lab; Kavli institute of nanoscience Delft)","","2017","We present a technique to fabricate ultrathin (down to 20 nm) uniform electron transparent windows at dedicated locations in a SiN membrane for in situ transmission electron microscopy experiments. An electron-beam (e-beam) resist is spray-coated on the backside of the membrane in a KOH-etched cavity in silicon which is patterned using through-membrane electron-beam lithography. This is a controlled way to make transparent windows in membranes, whilst the topside of the membrane remains undamaged and retains its flatness. Our approach was optimized for MEMS-based heating chips but can be applied to any chip design. We show two different applications of this technique for (1) fabrication of a nanogap electrode by means of electromigration in thin free-standing metal films and (2) making low-noise graphene nanopore devices.","","en","journal article","","","","","","","","2018-08-09","","Else Kooi Laboratory","QN/Zandbergen Lab","","",""
"uuid:383c4616-0fb6-4313-a49f-7182557a61e5","http://resolver.tudelft.nl/uuid:383c4616-0fb6-4313-a49f-7182557a61e5","On-chip density-based purification of liposomes","Deshpande, S.R. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Birnie, A.T.F. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft)","","2017","Due to their cell membrane-mimicking properties, liposomes have served as a versatile research tool in science, from membrane biophysics and drug delivery systems to bottom-up synthetic cells. We recently reported a novel microfluidic method, Octanol-assisted Liposome Assembly (OLA), to form cell-sized, monodisperse, unilamellar liposomes with excellent encapsulation efficiency. Although OLA provides crucial advantages over alternative methods, it suffers from the presence of 1-octanol droplets, an inevitable by-product of the production process. These droplets can adversely affect the system regarding liposome stability, channel clogging, and imaging quality. In this paper, we report a density-based technique to separate the liposomes from droplets, integrated on the same chip. We show that this method can yield highly pure (>95%) liposome samples. We also present data showing that a variety of other separation techniques (based on size or relative permittivity) were unsuccessful. Our density-based separation approach favourably decouples the production and separation module, thus allowing freshly prepared liposomes to be used for downstream on-chip experimentation. This simple separation technique will make OLA a more versatile and widely applicable tool.","","en","journal article","","","","","","","","2018-05-01","","","BN/Cees Dekker Lab","","",""
"uuid:19164e31-0f3e-49d6-b128-3af464f3cfd2","http://resolver.tudelft.nl/uuid:19164e31-0f3e-49d6-b128-3af464f3cfd2","Human centromeric CENP-A chromatin is a homotypic, octameric nucleosome at all cell cycle points","Nechemia-Arbely, Yael (University of California); Fachinetti, Daniele (University of California); Miga, Karen H. (University of California); Sekulic, Nikolina (University of Pennsylvania); Soni, G.V. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Kim, Dong Hyun (University of California); Wong, Adeline K. (University of California); Lee, Ah Young (University of California); Nguyen, Kristen (University of California); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Ren, Bing (University of California); Black, Ben E. (University of Pennsylvania); Cleveland, Don W. (University of California)","","2017","Chromatin assembled with centromere protein A (CENP-A) is the epigenetic mark of centromere identity. Using new reference models, we now identify sites of CENP-A and histone H3.1 binding within the megabase, α-satellite repeat-containing centromeres of 23 human chromosomes. The overwhelming majority (97%) of α-satellite DNA is found to be assembled with histone H3.1-containing nucleosomes with wrapped DNA termini. In both G1 and G2 cell cycle phases, the 2-4% of α-satellite assembled with CENP-A protects DNA lengths centered on 133 bp, consistent with octameric nucleosomes with DNA unwrapping at entry and exit. CENP-A chromatin is shown to contain equimolar amounts of CENP-A and histones H2A, H2B, and H4, with no H3. Solid-state nanopore analyses show it to be nucleosomal in size. Thus, in contrast to models for hemisomes that briefly transition to octameric nucleosomes at specific cell cycle points or heterotypic nucleosomes containing both CENP-A and histone H3, human CENP-A chromatin complexes are octameric nucleosomes with two molecules of CENP-A at all cell cycle phases.","","en","journal article","","","","","","","","2017-08-24","","","BN/Cees Dekker Lab","","",""
"uuid:c5ac63c9-b0be-4af6-b347-ac227e2158ca","http://resolver.tudelft.nl/uuid:c5ac63c9-b0be-4af6-b347-ac227e2158ca","Treadmilling by FtsZ filaments drives peptidoglycan synthesis and bacterial cell division","Bisson-Filho, Alexandre W. (Harvard University); Hsu, Yen Pang (Indiana University - Purdue University); Squyres, Georgia R. (Harvard University); Kuru, Erkin (Indiana University - Purdue University); Wu, F. (TU Delft BN/Cees Dekker Lab); Jukes, Calum (Newcastle University); Sun, Yingjie (Harvard University); Dekker, C. (TU Delft BN/Cees Dekker Lab); Holden, Seamus (Newcastle University); VanNieuwenhze, Michael S. (Indiana University - Purdue University); Brun, Yves V. (Indiana University - Purdue University); Garner, Ethan C. (Harvard University)","","2017","The mechanism by which bacteria divide is not well understood. Cell division is mediated by filaments of FtsZ and FtsA (FtsAZ) that recruit septal peptidoglycan-synthesizing enzymes to the division site. To understand how these components coordinate to divide cells, we visualized their movements relative to the dynamics of cell wall synthesis during cytokinesis. We found that the division septum was built at discrete sites that moved around the division plane. FtsAZ filaments treadmilled circumferentially around the division ring and drove the motions of the peptidoglycan-synthesizing enzymes. The FtsZ treadmilling rate controlled both the rate of peptidoglycan synthesis and cell division. Thus, FtsZ treadmilling guides the progressive insertion of new cell wall by building increasingly smaller concentric rings of peptidoglycan to divide the cell.","","en","journal article","","","","","","Accepted Author Manuscript","","","","","BN/Cees Dekker Lab","","",""
"uuid:01db7382-2b78-4e55-9989-80690b490d0a","http://resolver.tudelft.nl/uuid:01db7382-2b78-4e55-9989-80690b490d0a","The supercoiling state of DNA determines the handedness of both H3 and CENP-A nucleosomes","Vlijm, R. (TU Delft OLD Library Operations; German Cancer Research Center); Kim, S.H. (TU Delft BN/Cees Dekker Lab); De Zwart, P. L.; Dalal, Y. (National Cancer Institute); Dekker, C. (TU Delft BN/Cees Dekker Lab)","","2017","Nucleosomes form the unit structure of the genome in eukaryotes, thereby constituting a fundamental tenet of chromatin biology. In canonical nucleosomes, DNA wraps around the histone octamer in a left-handed toroidal ramp. Here, in single-molecule magnetic tweezers studies of chaperone-assisted nucleosome assembly, we show that the handedness of the DNA wrapping around the nucleosome core is intrinsically ambidextrous, and depends on the pre-assembly supercoiling state of the DNA, i.e., it is not uniquely determined by the octameric histone core. Nucleosomes assembled onto negatively supercoiled DNA are found to exhibit a left-handed conformation, whereas assembly onto positively supercoiled DNA results in right-handed nucleosomes. This intrinsic flexibility to adopt both chiralities is observed both for canonical H3 nucleosomes, and for centromere-specific variant CENP-A nucleosomes. These data support recent advances suggesting an intrinsic adaptability of the nucleosome, and provide insights into how nucleosomes might rapidly re-assemble after cellular processes that generate positive supercoiling in vivo.","","en","journal article","","","","","","","","2018-01-09","","","OLD Library Operations","","",""
"uuid:b4d8ef87-4459-4c1b-aa37-a892561924cb","http://resolver.tudelft.nl/uuid:b4d8ef87-4459-4c1b-aa37-a892561924cb","Applying torque to the Escherichia coli flagellar motor using magnetic tweezers","van Oene, M.M. (TU Delft BN/Nynke Dekker Lab; Kavli institute of nanoscience Delft); Dickinson, L.E. (TU Delft BN/Nynke Dekker Lab; Kavli institute of nanoscience Delft); Cross, B. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Pedaci, F. (TU Delft BN/Nynke Dekker Lab; Centre de Biochimie Structurale; Kavli institute of nanoscience Delft); Lipfert, J. (Ludwig Maximilians University); Dekker, N.H. (TU Delft BN/Nynke Dekker Lab; Kavli institute of nanoscience Delft)","","2017","The bacterial flagellar motor of Escherichia coli is a nanoscale rotary engine essential for bacterial propulsion. Studies on the power output of single motors rely on the measurement of motor torque and rotation under external load. Here, we investigate the use of magnetic tweezers, which in principle allow the application and active control of a calibrated load torque, to study single flagellar motors in Escherichia coli. We manipulate the external load on the motor by adjusting the magnetic field experienced by a magnetic bead linked to the motor, and we probe the motor's response. A simple model describes the average motor speed over the entire range of applied fields. We extract the motor torque at stall and find it to be similar to the motor torque at drag-limited speed. In addition, use of the magnetic tweezers allows us to force motor rotation in both forward and backward directions. We monitor the motor's performance before and after periods of forced rotation and observe no destructive effects on the motor. Our experiments show how magnetic tweezers can provide active and fast control of the external load while also exposing remaining challenges in calibration. Through their non-invasive character and straightforward parallelization, magnetic tweezers provide an attractive platform to study nanoscale rotary motors at the single-motor level.","","en","journal article","","","","","","For Corrigendum to this article (published on 18 May 2018) see 10.1038/srep46980: The Acknowledgements section in this Article is incomplete and should e read: “We thank Seungkyu Ha, Yera Ye. Ussembayev, Richard Janissen, and Hubertus J. E. Beaumont for discussions, Richard M. Berry and Ren Lim for providing the strains, and Theo van Laar for the remaining help with the bacteria. FP was supported by the European Research Council under the European Union’s Seventh Framework Program (FP/2007–2013)/ERC Grant 306475. This work is supported by NanoNextNL, a micro and nanotechnology consortium of the Government of the Netherlands and 130 partners, and by the Foundation for Fundamental Research on Matter (FOM).”","","","","","BN/Nynke Dekker Lab","","",""
"uuid:0b10aff7-7432-4f34-abfa-66c59654f672","http://resolver.tudelft.nl/uuid:0b10aff7-7432-4f34-abfa-66c59654f672","The Cargo Fare Class Mix problem for an intermodal corridor: revenue management in synchromodal container transportation","van Riessen, B. (TU Delft Transport Engineering and Logistics; Erasmus Universiteit Rotterdam); Negenborn, R.R. (TU Delft Transport Engineering and Logistics); Dekker, Rommert (Erasmus Universiteit Rotterdam)","","2017","The intermodal hinterland transportation of maritime containers is under pressure from port authorities and shippers to achieve a more integrated, efficient network operation. Current optimisation methods in literature yield limited results in practice, though, as the transportation product structure limits the flexibility to optimise network logistics. Synchromodality aims to overcome this by a new product structure based on differentiation in price and lead time. Each product is considered as a fare class with a related service level, allowing to target different customer segments and to use revenue management for maximising revenue. However, higher priced fare classes come with tighter planning restrictions and must be carefully balanced with lower priced fare classes to match available capacity and optimise network utilisation. Based on the developments of intermodal networks in North West European, such as the network of European Gateway Services, the Cargo Fare Class Mix problem is proposed. Its purpose is to set limits for each fare class at a tactical level, such that the expected revenue is maximised, considering the available capacity at the operational level. Setting limits at the tactical level is important, as it reflects the necessity of long-term agreements between the transportation provider and its customers. A solution method for an intermodal corridor is proposed, considering a single intermodal connection towards a region with multiple destinations. The main purpose of the article is to show that using a limit on each fare class increases revenue and reliability, thereby outperforming existing fare class mix policies, such as Littlewood.","Container transportation; Fare class sizes; Intermodal planning; Revenue management; Synchromodal planning","en","journal article","","","","","","","","","","","Transport Engineering and Logistics","","",""
"uuid:d5fba097-ca94-483f-a5cf-a5dc98edb3b3","http://resolver.tudelft.nl/uuid:d5fba097-ca94-483f-a5cf-a5dc98edb3b3","Retrospective biomonitoring of mercury and other elements in museum feathers of common kestrel Falco tinnunculus using instrumental neutron activation analysis (INAA)","Movalli, Paola (Naturalis Biodiversity Center); Bode, P. (TU Delft RST/Applied Radiation & Isotopes); Dekker, René (Naturalis Biodiversity Center); Fornasari, Lorenzo (Associazione FaunaViva); van der Mije, Steven (Naturalis Biodiversity Center); Yosef, Reuven (Ben-Gurion University of the Negev)","","2017","This study examines the potential to use instrumental neutron activation analysis (INAA) to explore temporal and geographical variation in exposure to heavy metals and other selected elements in common kestrel Falco tinnunculus using feathers from a natural history collection. The study gathered samples of two breast feathers from each of 16 adult male kestrel specimens from Naturalis Biodiversity Centre, collected in The Netherlands between 1901 and 2001. Feather samples were analysed for more than 50 elements, using INAA at the Reactor Institute Delft. Results (in mg/kg dw) were transformed into ratios of milligram of element per millimetre of feather length. The distribution of the mass fractions and ratios was plotted for each element against time and by geographical area. Observed mass fractions and/or ratios are discussed for selected elements (Hg, Cd, Zn, Pt, Pd, Se, Al, Rb, As, Sb, Cr, V, Cl, Br) known to have, at certain concentrations, adverse effects on raptors. Some samples show mass fractions of certain elements (Cr, Cd, Se, As) above levels known to have adverse effects. We conclude that the analysis of museum feathers using INAA provides reference values for concentrations of selected elements, including those of high societal concern such as Hg and Cd, against which to assess concentrations of these elements in feathers of present-day living raptor populations.","Common kestrel; Contaminant; Element; Exposure; Falco tinnunculus; Feather; INAA; Metal; Museum specimen; Raptor","en","journal article","","","","","","","","2018-09-23","","","RST/Applied Radiation & Isotopes","","",""
"uuid:182d1a75-3a30-49f3-a0b1-de68f707e6e6","http://resolver.tudelft.nl/uuid:182d1a75-3a30-49f3-a0b1-de68f707e6e6","Probing the salt dependence of the torsional stiffness of DNA by multiplexed magnetic torque tweezers","Kriegel, Franziska (Ludwig Maximilians University); Ermann, Niklas (Ludwig Maximilians University); Forbes, R.J.G. (TU Delft BN/Nynke Dekker Lab); Dulin, D. (TU Delft BN/Nynke Dekker Lab; Friedrich-Alexander-Universität Erlangen-Nürnberg); Dekker, N.H. (TU Delft BN/Nynke Dekker Lab); Lipfert, J. (Ludwig Maximilians University)","","2017","The mechanical properties of DNA fundamentally constrain and enable the storage and transmission of genetic information and its use in DNA nanotechnology. Many properties of DNA depend on the ionic environment due to its highly charged backbone. In particular, both theoretical analyses and direct singlemolecule experiments have shown its bending stiffness to depend on salt concentration. In contrast, the salt-dependence of the twist stiffness of DNA is much less explored. Here, we employ optimized multiplexed magnetic torque tweezers to study the torsional stiffness of DNA under varying salt conditions as a function of stretching force. At low forces (<3 pN), the effective torsional stiffness is ∼10% smaller for high salt conditions (500 mM NaCl or 10 mM MgCl2) compared to lower salt concentrations (20 mM NaCl and 100 mM NaCl). These differences, however, can be accounted for by taking into account the known salt dependence of the bending stiffness. In addition, the measured high-force (6.5 pN) torsional stiffness values of C = 103 ± 4 nm are identical, within experimental errors, for all tested salt concentration, suggesting that the intrinsic torsional stiffness of DNA does not depend on salt.","","en","journal article","","","","","","","","","","","BN/Nynke Dekker Lab","","",""
"uuid:8ae629c1-d4c5-4cda-b4c0-e753fce69756","http://resolver.tudelft.nl/uuid:8ae629c1-d4c5-4cda-b4c0-e753fce69756","Annealing helicase HARP closes RPA-stabilized DNA bubbles non-processively","Burnham, D.R. (TU Delft BN/Cees Dekker Lab); Nijholt, B. (TU Delft QN/Akhmerov Group); de Vlaminck, I. (TU Delft BN/Cees Dekker Lab); Quan, Jinhua (Harvard Medical School); Yusufzai, Timur (Harvard Medical School); Dekker, C. (TU Delft BN/Cees Dekker Lab)","","2017","We investigate the mechanistic nature of the Snf2 family protein HARP, mutations of which are responsible for Schimke immuno-osseous dysplasia. Using a single-molecule magnetic tweezers assay, we construct RPA-stabilized DNA bubbles within torsionally constrained DNA to investigate the annealing action of HARP on a physiologically relevant substrate. We find that HARP closes RPA-stabilized bubbles in a slow reaction, taking on the order of tens of minutes for ∼600 bp of DNA to be re-annealed. The data indicate that DNA re-anneals through the removal of RPA, which is observed as clear steps in the bubbleclosing traces. The dependence of the closing rate on both ionic strength and HARP concentration indicates that removal of RPA occurs via an association-dissociation mechanism where HARP does not remain associated with the DNA. The enzyme exhibits classical Michaelis-Menten kinetics and acts cooperatively with a Hill coefficient of 3 ± 1. Our work also allows the determination of some important features of RPA-bubble structures at low supercoiling, including the existence of multiple bubbles and that RPA molecules are mis-registered on the two strands.","","en","journal article","","","","","","","","","","","BN/Cees Dekker Lab","","",""
"uuid:d6f830b1-d10a-44e7-904a-8c72519d1226","http://resolver.tudelft.nl/uuid:d6f830b1-d10a-44e7-904a-8c72519d1226","Single-Step CMOS Compatible Fabrication of High Aspect Ratio Microchannels Embedded in Silicon","Kluba, M.M. (TU Delft Electronic Components, Technology and Materials); Arslan, A. (Philips Healthcare); Stoute, R. (TNO); Muganda, James (Eindhoven University of Technology); Dekker, R. (TU Delft Electronic Components, Technology and Materials)","","2017","This paper presents a new method for the CMOS compatible fabrication of microchannels integrated into a silicon substrate. In a single-step DRIE process (Deep Reactive Ion Etching) a network of microchannels with High Aspect Ratio (HAR) up to 10, can be etched in a silicon substrate through a mesh mask. In the same single etching step, multidimensional microchannels with various dimensions (width, length, and depth) can be obtained by tuning the process and design parameters. These fully embedded structures enable further wafer processing and integration of electronic components like sensors and actuators in wafers with microchannels.","embedded microchannel; HAR; mesh mask; single-step DRIE (Bosch process)","en","conference paper","","","","","","","","","","","Electronic Components, Technology and Materials","","",""
"uuid:4e28ba32-6f2e-45f9-a4b5-261f91c9cc80","http://resolver.tudelft.nl/uuid:4e28ba32-6f2e-45f9-a4b5-261f91c9cc80","Novel Method for Adhesion between PI-PDMS Using Butyl Rubber for Large Area Flexible Body Patches","Joshi, S. (TU Delft Electronic Components, Technology and Materials; Philips Research); Bagani, R. (External organisation); Beckers, Lucas (Philips Research); Dekker, R. (TU Delft Electronic Components, Technology and Materials; Philips Research)","","2017","This paper reports the use of rubber—Polybutadiene as an intermediate adhesive layer for improving the adhesion between polyimide (PI) and silicone polydimethylsiloxane (PDMS) which is required for a reliable fabrication of flexible/stretchable body patches for various applications. The adhesive bond initiated by the butyl rubber (BR), apart from being extremely strong, is also chemically resistant and mechanically stable as compared to the state of the art processes of improving adhesion between PI and Silicone.","PI-PDMS adhesion; rubber; flexible; stretchable; cross-linking; diffusive adhesion","en","conference paper","","","","","","","","","","","Electronic Components, Technology and Materials","","",""
"uuid:841b8ef1-dfcb-4265-b427-a9c2a1522f6f","http://resolver.tudelft.nl/uuid:841b8ef1-dfcb-4265-b427-a9c2a1522f6f","Real-time detection of condensin-driven DNA compaction reveals a multistep binding mechanism","Eeftens, J.M. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Bisht, Shveta (European Molecular Biology Laboratory Heidelberg); Kerssemakers, J.W.J. (TU Delft BN/Technici en Analisten; Kavli institute of nanoscience Delft); Kschonsak, Marc (European Molecular Biology Laboratory Heidelberg); Haering, Christian H. (European Molecular Biology Laboratory Heidelberg); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft)","","2017","Condensin, a conserved member of the SMC protein family of ring-shaped multi-subunit protein complexes, is essential for structuring and compacting chromosomes. Despite its key role, its molecular mechanism has remained largely unknown. Here, we employ single-molecule magnetic tweezers to measure, in real time, the compaction of individual DNA molecules by the budding yeast condensin complex. We show that compaction can proceed in large steps, driving DNA molecules into a fully condensed state against forces of up to 2 pN. Compaction can be reversed by applying high forces or adding buffer of high ionic strength. While condensin can stably bind DNA in the absence of ATP, ATP hydrolysis by the SMC subunits is required for rendering the association salt insensitive and for the subsequent compaction process. Our results indicate that the condensin reaction cycle involves two distinct steps, where condensin first binds DNA through electrostatic interactions before using ATP hydrolysis to encircle the DNA topologically within its ring structure, which initiates DNA compaction. The finding that both binding modes are essential for its DNA compaction activity has important implications for understanding the mechanism of chromosome compaction.","Condensin; DNA compaction; Magnetic tweezers; SMC proteins","en","journal article","","","","","","","","","","","BN/Cees Dekker Lab","","",""
"uuid:3767b56d-2610-4e6c-b157-d2bdb2d811a5","http://resolver.tudelft.nl/uuid:3767b56d-2610-4e6c-b157-d2bdb2d811a5","Ultra-Stretchable Interconnects for High-Density Stretchable Electronics","Shafqat, Salman (Eindhoven University of Technology); Hoefnagels, Johan P.M. (Eindhoven University of Technology); Savov, A.M. (TU Delft Electronic Components, Technology and Materials); Joshi, S. (TU Delft Electronic Components, Technology and Materials); Dekker, R. (TU Delft Electronic Components, Technology and Materials; Philips Research); Geers, Marc G.D. (Eindhoven University of Technology)","","2017","The exciting field of stretchable electronics (SE) promises numerous novel applications, particularly in-body and medical diagnostics devices. However, future advanced SE miniature devices will require high-density, extremely stretchable interconnects with micron-scale footprints, which calls for proven standardized (complementary metal-oxide semiconductor (CMOS)-type) process recipes using bulk integrated circuit (IC) microfabrication tools and fine-pitch photolithography patterning. Here, we address this combined challenge of microfabrication with extreme stretchability for high-density SE devices by introducing CMOS-enabled, free-standing, miniaturized interconnect structures that fully exploit their 3D kinematic freedom through an interplay of buckling, torsion, and bending to maximize stretchability. Integration with standard CMOS-type batch processing is assured by utilizing the Flex-to-Rigid (F2R) post-processing technology to make the back-end-of-line interconnect structures free-standing, thus enabling the routine microfabrication of highly-stretchable interconnects. The performance and reproducibility of these free-standing structures is promising: an elastic stretch beyond 2000% and ultimate (plastic) stretch beyond 3000%, with <0.3% resistance change, and >10 million cycles at 1000% stretch with <1% resistance change. This generic technology provides a new route to exciting highly-stretchable miniature devices.","Complementary metal-oxide semiconductor (CMOS) processing; Mechanical size-effects; Miniaturized interconnects; Stretchable electronics; Ultra-stretchability","en","journal article","","","","","","","","","","","Electronic Components, Technology and Materials","","",""
"uuid:a57098b3-8e44-400f-b53f-172b282f6da3","http://resolver.tudelft.nl/uuid:a57098b3-8e44-400f-b53f-172b282f6da3","Signatures of Nucleotide Analog Incorporation by an RNA-Dependent RNA Polymerase Revealed Using High-Throughput Magnetic Tweezers","Dulin, D. (TU Delft BN/Nynke Dekker Lab; Friedrich-Alexander-Universität Erlangen-Nürnberg; Kavli institute of nanoscience Delft); Arnold, Jamie J. (The Pennsylvania State University); van Laar, T. (TU Delft BN/Nynke Dekker Lab; Kavli institute of nanoscience Delft); Oh, Hyung Suk (The Pennsylvania State University); Lee, Cheri (The Pennsylvania State University); Perkins, Angela L. (University of Minnesota Twin Cities); Harki, Daniel A. (University of Minnesota Twin Cities); Depken, S.M. (TU Delft BN/Martin Depken Lab; Kavli institute of nanoscience Delft); Cameron, Craig E. (The Pennsylvania State University); Dekker, N.H. (TU Delft BN/Nynke Dekker Lab; Kavli institute of nanoscience Delft)","","2017","RNA viruses pose a threat to public health that is exacerbated by the dearth of antiviral therapeutics. The RNA-dependent RNA polymerase (RdRp) holds promise as a broad-spectrum, therapeutic target because of the conserved nature of the nucleotide-substrate-binding and catalytic sites. Conventional, quantitative, kinetic analysis of antiviral ribonucleotides monitors one or a few incorporation events. Here, we use a high-throughput magnetic tweezers platform to monitor the elongation dynamics of a prototypical RdRp over thousands of nucleotide-addition cycles in the absence and presence of a suite of nucleotide analog inhibitors. We observe multiple RdRp-RNA elongation complexes; only a subset of which are competent for analog utilization. Incorporation of a pyrazine-carboxamide nucleotide analog, T-1106, leads to RdRp backtracking. This analysis reveals a mechanism of action for this antiviral ribonucleotide that is corroborated by cellular studies. We propose that induced backtracking represents a distinct mechanistic class of antiviral ribonucleotides. Dulin et al. find that a prototypical RNA-dependent RNA polymerase (RdRp) visits several states during nucleotide synthesis, of which only one incorporates nucleotide analogs with therapeutic potential. Different analogs exhibit distinct kinetic signatures, with an analog thought to induce chain termination actually promoting RdRp backtracking.","backtracking; inhibitor; magnetic tweezers; nucleoside analog; pyrazine carboxamide; RNA polymerase; RNA virus; T-1106; T-705","en","journal article","","","","","","","","","","","BN/Nynke Dekker Lab","","",""
"uuid:ba3b2070-4e81-4a63-ba03-a98a0751b2ff","http://resolver.tudelft.nl/uuid:ba3b2070-4e81-4a63-ba03-a98a0751b2ff","Mapping out min protein patterns in fully confined fluidic chambers","Caspi, Y. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft)","","2016","The bacterial Min protein system provides a major model system for studying reaction-diffusion processes in biology. Here we present the first in vitro study of the Min system in fully confined three-dimensional chambers that are lithography-defined, lipid-bilayer coated and isolated through pressure valves. We identify three typical dynamical behaviors that occur dependent on the geometrical chamber parameters: pole-to-pole oscillations, spiral rotations, and traveling waves. We establish the geometrical selection rules and show that, surprisingly, Min-protein spiral rotations govern the larger part of the geometrical phase diagram. Confinement as well as an elevated temperature reduce the characteristic wavelength of the Min patterns, although even for confined chambers with a bacterial-level viscosity, the patterns retain a ~5 times larger wavelength than in vivo. Our results provide an essential experimental base for modeling of intracellular Min gradients in bacterial cell division as well as, more generally, for understanding pattern formation in reaction-diffusion systems.","","en","journal article","","","","","","","","","","","BN/Cees Dekker Lab","","",""
"uuid:b0535b8c-d564-4063-8de5-2f126de59dd2","http://resolver.tudelft.nl/uuid:b0535b8c-d564-4063-8de5-2f126de59dd2","Direct observation of DNA knots using a solid-state nanopore","Plesa, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Verschueren, D.V. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Pud, S. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); van der Torre, J. (TU Delft BN/Technici en Analisten; Kavli institute of nanoscience Delft); Ruitenberg, J.W. (TU Delft Education and Student Affairs; Kavli institute of nanoscience Delft); Witteveen, M.J. (TU Delft Education and Student Affairs; Kavli institute of nanoscience Delft); Jonsson, P.M. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Grosberg, Alexander Y. (New York University); Rabin, Yitzhak (Bar-Ilan University); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft)","","2016","Long DNA molecules can self-entangle into knots. Experimental techniques for observing such DNA knots (primarily gel electrophoresis) are limited to bulk methods and circular molecules below 10 kilobase pairs in length. Here, we show that solid-state nanopores can be used to directly observe individual knots in both linear and circular single DNA molecules of arbitrary length. The DNA knots are observed as short spikes in the nanopore current traces of the traversing DNA molecules and their detection is dependent on a sufficiently high measurement resolution, which can be achieved using high-concentration LiCl buffers. We study the percentage of molecules with knots for DNA molecules of up to 166 kilobase pairs in length and find that the knotting occurrence rises with the length of the DNA molecule, consistent with a constant knotting probability per unit length. Our experimental data compare favourably with previous simulation-based predictions for long polymers. From the translocation time of the knot through the nanopore, we estimate that the majority of the DNA knots are tight, with remarkably small sizes below 100 nm. In the case of linear molecules, we also observe that knots are able to slide out on application of high driving forces (voltage).","Nanopores","en","journal article","","","","","","Accepted Author Manuscript","","","","","BN/Cees Dekker Lab","","",""
"uuid:ebfe1d22-88f0-4445-bd55-5e23d2af9d7a","http://resolver.tudelft.nl/uuid:ebfe1d22-88f0-4445-bd55-5e23d2af9d7a","High-throughput, high-force probing of DNA-protein interactions with magnetic tweezers","Berghuis, B.A. (TU Delft BN/Nynke Dekker Lab; Kavli institute of nanoscience Delft); Köber, M. (TU Delft BN/Nynke Dekker Lab; Kavli institute of nanoscience Delft); van Laar, T. (TU Delft BN/Nynke Dekker Lab; Kavli institute of nanoscience Delft); Dekker, N.H. (TU Delft BN/Nynke Dekker Lab; Kavli institute of nanoscience Delft)","","2016","Recent advances in high-throughput single-molecule magnetic tweezers have paved the way for obtaining information on individual molecules as well as ensemble-averaged behavior in a single assay. Here we describe how to design robust high-throughput magnetic tweezers assays that specifically require application of high forces (>20. pN) for prolonged periods of time (>1000. s). We elaborate on the strengths and limitations of the typical construct types that can be used and provide a step-by-step guide towards a high tether yield assay based on two examples. Firstly, we discuss a DNA hairpin assay where force-induced strand separation triggers a tight interaction between DNA-binding protein Tus and its binding site Ter, where forces up to 90. pN for hundreds of seconds were required to dissociate Tus from Ter. Secondly, we show how the LTag helicase of Simian virus 40 unwinds dsDNA, where a load of 36. pN optimizes the assay readout. The approaches detailed here provide guidelines for the high-throughput, quantitative study of a wide range of DNA-protein interactions.","DNA construct design; High-throughput; Magnetic tweezers; SV40 large T antigen helicase; Tus-Ter","en","journal article","","","","","","","","","","","BN/Nynke Dekker Lab","","",""
"uuid:7cc2e9e2-0ef0-4d82-b33d-0c4ae99ebd4e","http://resolver.tudelft.nl/uuid:7cc2e9e2-0ef0-4d82-b33d-0c4ae99ebd4e","Cytostretch, an Organ-on-Chip Platform","Gaio, N. (TU Delft Electronic Components, Technology and Materials); van Meer, B. (Leiden University Medical Center); Quiros Solano, W.F. (TU Delft Electronic Components, Technology and Materials); Bergers, L. (Amsterdam UMC; Philips Research); van de Stolpe, A. (Philips Research); Mummery, CL (Leiden University Medical Center); Sarro, Pasqualina M (TU Delft Electronic Components, Technology and Materials); Dekker, R. (TU Delft Electronic Components, Technology and Materials; Philips Research)","","2016","Organ-on-Chips (OOCs) are micro-fabricated devices which are used to culture cells in order to mimic functional units of human organs. The devices are designed to simulate the physiological environment of tissues in vivo. Cells in some types of OOCs can be stimulated in situ by electrical and/or mechanical actuators. These actuations can mimic physiological conditions in real tissue and may include fluid or air flow, or cyclic stretch and strain as they occur in the lung and heart. These conditions similarly affect cultured cells and may influence their ability to respond appropriately to physiological or pathological stimuli. To date, most focus has been on devices specifically designed to culture just one functional unit of a specific organ: lung alveoli, kidney nephrons or blood vessels, for example. In contrast, the modular Cytostretch membrane platform described here allows OOCs to be customized to different OOC applications. The platform utilizes silicon-based micro-fabrication techniques that allow low-cost, high-volume manufacturing. We describe the platform concept and its modules developed to date. Membrane variants include membranes with (i) through-membrane pores that allow biological signaling molecules to pass between two different tissue compartments; (ii) a stretchable micro-electrode array for electrical monitoring and stimulation; (iii) micro-patterning to promote cell alignment; and (iv) strain gauges to measure changes in substrate stress. This paper presents the fabrication and the proof of functionality for each module of the Cytostretch membrane. The assessment of each additional module demonstrate that a wide range of OOCs can be achieved.
process flow overcomes the manually intensive procedures used in the previous works. The microfabricated upside-down CNT MEA consists of microelectrodes with an area of 110 μm2 covered with cobalt-grown CNTs. The surface area enhancement and the foamlike morphology of the CNTs allow an increase of the charge injection per unit area at the electrode–electrolyte interface, resulting in a significantly lower electrochemical impedance of the electrodes. In particular, at 1 kHz, the fabricated CNT-MEA electrodes show a reduction of the overall impedance up to 96% in comparison with benchmark TiN electrodes. The
obtained results confirm the effectiveness of the proposed surface texturing through CNT integration. Moreover, the quality and the morphology as well as the biocompatibility of the fabricated CNT-based electrodes were assessed. The obtained results demonstrate that significant improvement can be achieved by integrating structured nanoporous material on MEAs.","Microelectrode array; carbon nanotube; membrane; in vitro; electrochemical impedance spectroscopy; cardiomyocytes; Raman spectroscopy","en","journal article","","","","","","Accepted author manuscript","","","","","Electronic Components, Technology and Materials","","",""
"uuid:17eb6a8e-1f71-495f-b32a-e5ebed25e948","http://resolver.tudelft.nl/uuid:17eb6a8e-1f71-495f-b32a-e5ebed25e948","Substrate Transfer Technology for Stretchable Electronics","Joshi, S. (TU Delft Electronic Components, Technology and Materials; Philips Research); Savov, A.M. (TU Delft Electronic Components, Technology and Materials); Dekker, R. (TU Delft Electronic Components, Technology and Materials; Philips Research)","","2016","This paper focuses on the implementation of a new technique for the fabrication of stretchable electronic patches that can be used for medical applications. The technique is based on the Electronics on Plastics by Laser Release (EPlaR) technology which enables a one-step release of a stack of flexible/stretchable layers incorporating the active layers like interconnects and embedded devices. As a proof of concept meander shaped polyimide (PI) structures are fabricated on top of a glass substrate and then transferred to a PDMS substrate with the use of this technology. The stretchability in the device is enhanced by fabricating these meander shaped structures free from the PDMS substrate hence giving them the freedom to move out of plane.","substrate transfer; flexible; stretchable; body patches; ultrasound","en","journal article","","","","","","","","","","","Electronic Components, Technology and Materials","","",""
"uuid:de1e357d-5b4c-44c6-8143-b154177365a9","http://resolver.tudelft.nl/uuid:de1e357d-5b4c-44c6-8143-b154177365a9","Reliability modelling for rotorcraft component fatigue life prediction with assumed usage","Dekker, S.H. (TU Delft Structural Integrity & Composites; Airbus; Marenco); Wurzel, G. (Airbus); Alderliesten, R.C. (TU Delft Structural Integrity & Composites)","","2016","Fatigue life is a random variable. The reliability of a conservative fatigue life prediction for a component in the helicopter dynamic system thus needs to be substantiated. A standard analytical substantiation method uses averaged manoeuvre loads instead of seeing manoeuvre loads as a random variable whose distribution is estimated with limited precision. This simplification may lead to inaccuracies. A new simulation-based method is developed to conservatively predict fatigue life while also accounting for the full random distribution and uncertainty of manoeuvre loads. Both methods fully account for uncertain fatigue strength but assume that the mission profile is known or can at least be conservatively estimated. Simulations under synthetic but realistic engineering conditions demonstrate that both methods may be used for accurate substantiation of conservative fatigue life predictions. The simulations also demonstrate that, under the tested conditions, uncertainties from manoeuvre loads may be neglected in fatigue life substantiations as the resulting error is not significant with respect to uncertainties in component fatigue strength.","Fatigue life prediction; Service Life Limit; Reliability substantiation; Helicopter","en","journal article","","","","","","","","2017-05-31","","","Structural Integrity & Composites","","",""
"uuid:396dab4b-a568-4a86-8da7-3cf12b0b9f68","http://resolver.tudelft.nl/uuid:396dab4b-a568-4a86-8da7-3cf12b0b9f68","Nanofabricated structures and microfluidic devices for bacteria: From techniques to biology","Wu, F. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft)","","2016","Nanofabricated structures and microfluidic technologies are increasingly being used to study bacteria because of their precise spatial and temporal control. They have facilitated studying many long-standing questions regarding growth, chemotaxis and cell-fate switching, and opened up new areas such as probing the effect of boundary geometries on the subcellular structure and social behavior of bacteria. We review the use of nano/microfabricated structures that spatially separate bacteria for quantitative analyses and that provide topological constraints on their growth and chemical communications. These approaches are becoming modular and broadly applicable, and show a strong potential for dissecting the complex life of bacteria at various scales and engineering synthetic microbial societies.","","en","review","","","","","","Accepted Author Manuscript","","2017-01-21","","","BN/Cees Dekker Lab","","",""
"uuid:64c5ef9c-de66-4098-a5f8-39c3aed08a5b","http://resolver.tudelft.nl/uuid:64c5ef9c-de66-4098-a5f8-39c3aed08a5b","The progression of replication forks at natural replication barriers in live bacteria","Moolman, M.C. (TU Delft BN/Nynke Dekker Lab); Tiruvadi Krishnan, S. (TU Delft BN/Nynke Dekker Lab); Kerssemakers, J.W.J. (TU Delft BN/Technici en Analisten); de Leeuw, R. (TU Delft BN/Nynke Dekker Lab); Lorent, V.J.F. (Université Paris 13); Sherratt, David J. (University of Oxford); Dekker, N.H. (TU Delft BN/Nynke Dekker Lab)","","2016","Protein-DNA complexes are one of the principal barriers the replisome encounters during replication. One such barrier is the Tus-ter complex, which is a direction dependent barrier for replication fork progression. The details concerning the dynamics of the replisome when encountering these Tus-ter barriers in the cell are poorly understood. By performing quantitative fluorescence microscopy with microfuidics, we investigate the effect on the replisome when encountering these barriers in live Escherichia coli cells. We make use of an E. coli variant that includes only an ectopic origin of replication that is positioned such that one of the two replisomes encounters a Tus-ter barrier before the other replisome. This enables us to single out the effect of encountering a Tus-ter roadblock on an individual replisome. We demonstrate that the replisome remains stably bound after encountering a Tus-ter complex from the non-permissive direction. Furthermore, the replisome is only transiently blocked, and continues replication beyond the barrier. Additionally, we demonstrate that these barriers affect sister chromosome segregation by visualizing specific chromosomal loci in the presence and absence of the Tus protein. These observations demonstrate the resilience of the replication fork to natural barriers and the sensitivity of chromosome alignment to fork progression.","Genome integrity; repair and replication","en","journal article","","","","","","","","","","","BN/Nynke Dekker Lab","","",""
"uuid:f46b1afe-6060-458c-88cd-553422b1a441","http://resolver.tudelft.nl/uuid:f46b1afe-6060-458c-88cd-553422b1a441","Counterintuitive DNA Sequence Dependence in Supercoiling-Induced DNA Melting","Vlijm, R.; Torre, J.; Dekker, C.","","2015","The metabolism of DNA in cells relies on the balance between hybridized double-stranded DNA (dsDNA) and local de-hybridized regions of ssDNA that provide access to binding proteins. Traditional melting experiments, in which short pieces of dsDNA are heated up until the point of melting into ssDNA, have determined that AT-rich sequences have a lower binding energy than GC-rich sequences. In cells, however, the double-stranded backbone of DNA is destabilized by negative supercoiling, and not by temperature. To investigate what the effect of GC content is on DNA melting induced by negative supercoiling, we studied DNA molecules with a GC content ranging from 38% to 77%, using single-molecule magnetic tweezer measurements in which the length of a single DNA molecule is measured as a function of applied stretching force and supercoiling density. At low force (<0.5pN), supercoiling results into twisting of the dsDNA backbone and loop formation (plectonemes), without inducing any DNA melting. This process was not influenced by the DNA sequence. When negative supercoiling is introduced at increasing force, local melting of DNA is introduced. We measured for the different DNA molecules a characteristic force Fchar, at which negative supercoiling induces local melting of the dsDNA. Surprisingly, GC-rich sequences melt at lower forces than AT-rich sequences: Fchar = 0.56pN for 77% GC but 0.73pN for 38% GC. An explanation for this counterintuitive effect is provided by the realization that supercoiling densities of a few percent only induce melting of a few percent of the base pairs. As a consequence, denaturation bubbles occur in local AT-rich regions and the sequence-dependent effect arises from an increased DNA bending/torsional energy associated with the plectonemes. This new insight indicates that an increased GC-content adjacent to AT-rich DNA regions will enhance local opening of the double-stranded DNA helix.","OA-Fund TU Delft","en","journal article","Public Library of Science","","","","","","","","Applied Sciences","BN/Bionanoscience","","","",""
"uuid:056cd27c-3232-4428-b9ad-e51b7cc052f4","http://resolver.tudelft.nl/uuid:056cd27c-3232-4428-b9ad-e51b7cc052f4","Comparing the Assembly and Handedness Dynamics of (H3.3-H4)2 Tetrasomes to Canonical Tetrasomes","Vlijm, R.; Lee, M.; Ordu, O.; Boltengagen, A.; Lusser, A.; Dekker, N.H.; Dekker, C.","","2015","Eukaryotic nucleosomes consists of an (H3-H4)2 tetramer and two H2A-H2B dimers, around which 147 bp of DNA are wrapped in 1.7 left-handed helical turns. During chromatin assembly, the (H3-H4)2 tetramer binds first, forming a tetrasome that likely constitutes an important intermediate during ongoing transcription. We recently showed that (H3-H4)2 tetrasomes spontaneously switch between a left- and right-handed wrapped state of the DNA, a phenomenon that may serve to buffer changes in DNA torque induced by RNA polymerase in transcription. Within nucleosomes of actively transcribed genes, however, canonical H3 is progressively replaced by its variant H3.3. Consequently, one may ask if and how the DNA chirality dynamics of tetrasomes is altered by H3.3. Recent findings that H3.3-containing nucleosomes result in less stable and less condensed chromatin further underline the need to study the microscopic underpinnings of H3.3-containing tetrasomes and nucleosomes. Here we report real-time single-molecule studies of (H3.3-H4)2 tetrasome dynamics using Freely Orbiting Magnetic Tweezers and Electromagnetic Torque Tweezers. We find that the assembly of H3.3-containing tetrasomes and nucleosomes by the histone chaperone Nucleosome Assembly Protein 1 (NAP1) occurs in an identical manner to that of H3-containing tetrasomes and nucleosomes. Likewise, the flipping behavior of DNA handedness in tetrasomes is not impacted by the presence of H3.3. We also examine the effect of free NAP1, H3.3, and H4 in solution on flipping behavior and conclude that the probability for a tetrasome to occupy the left-handed state is only slightly enhanced by the presence of free protein. These data demonstrate that the incorporation of H3.3 does not alter the structural dynamics of tetrasomes, and hence that the preferred incorporation of this histone variant in transcriptionally active regions does not result from its enhanced ability to accommodate torsional stress, but rather may be linked to specific chaperone or remodeler requirements or communication with the nuclear environment.","OA-Fund TU Delft","en","journal article","Public Library of Science","","","","","","","","Applied Sciences","BN/Bionanoscience","","","",""
"uuid:8df13435-8c9c-4161-b7d7-c7550350d425","http://resolver.tudelft.nl/uuid:8df13435-8c9c-4161-b7d7-c7550350d425","Using GeoRM to Communicate Geotechnical Risks Between Engineers and Managers","Vervoorn, R.R.E.; Dekker, H.R.E.","","2015","Rijkswaterstaat has recently stated that the use of GeoRM is obligatory for projects with major geotechnical risks. Underground construction of freeway's in high-profile areas, such as the business district Zuidas in Amsterdam or railway links in densely populated areas, always introduce major geotechnical risks. It is not uncommon for these locations to have all the facets that require strong geotechnical risk management: underground construction occurs adjacent to high-rise structures, locations have a very busy surface area, there are financially dependent stake-holders and concerns prevail after issues on earlier projects. Rijkswaterstaat and their consultant firms are tackling this by forming a strong bridge between engineering and management using geotechnical risk management (GeoRM). In this article its main focus is translating the language of technical risks into managerial terms of cost, delay and reputation. Then actions are translated back again into countermeasures, which are often technical in nature. With a unique approach of subdividing and quantifying risks into sub-risks all the way down to a construction activity level, engineers have the ability to talk directly to the decision makers. To this end a visualization tool has been developed to assess and evaluate risk and counterfeit measures with management staff. The teams involved believe risk reduction is about real-life measures that require a level of detail and knowledge of the actual construction activities to be performed. This approach has led to real risk-reduction activities, for example: additional investigations into underground obstacles (e.g. existing steel anchors) and actions for removing them beforehand, preventing stagnation later. But also: site investigation activities associated with specific construction methods like soil injection which may turn out to be unfeasible if soil parameters don't come out as expected.","geotechnical risk management; GeoRM; communication; project management; cost, delay; reputation; Zuidasdok","en","conference paper","","","","","","","","","","","","","",""
"uuid:575286f9-9844-4f69-bf5b-521134ce138e","http://resolver.tudelft.nl/uuid:575286f9-9844-4f69-bf5b-521134ce138e","Ultrasound transducer assembly and method for manufacturing an ultrasound transducer assembly","Dekker, R.; Henneken, V.A.; Louwerse, M.C.; Raganato, M.F.","","2015","The present invention relates to an ultrasound transducer assembly (10), in particular for intravascular ultrasound systems. The ultrasound transducer assembly comprises at least one silicon substrate element (30) including an ultrasound transducer element (14) for emitting and receiving ultrasound waves and including electrical connectors for electrically connecting the transducer element. The substrate element has a top surface (44), a bottom surface (46) and a side surface connecting the top surface and the bottom surface. An isolation layer (32, 50) forms the side surface for electrically isolating the substrate element.","","en","patent","European Patent Office","","","","","","","","Electrical Engineering, Mathematics and Computer Science","Microelectronics","","","",""
"uuid:83a50284-3ab2-4cb5-b0d1-620daf35f682","http://resolver.tudelft.nl/uuid:83a50284-3ab2-4cb5-b0d1-620daf35f682","DNA nanopore translocation in glutamate solutions","Plesa, C.; Van Loo, N.; Dekker, C.","","2015","Nanopore experiments have traditionally been carried out with chloride-based solutions. Here we introduce silver/silver-glutamate-based electrochemistry as an alternative, and study the viscosity, conductivity, and nanopore translocation characteristics of potassium-, sodium-, and lithium-glutamate solutions. We show that it has a linear response at typical voltages and can be used to detect DNA translocations through a nanopore. The glutamate anion also acts as a redox-capable thickening agent, with high-viscosity solutions capable of slowing down the DNA translocation process by up to 11 times, with a corresponding 7 time reduction in signal. These results demonstrate that glutamate can replace chloride as the primary anion in nanopore resistive pulse sensing.","Gold for Gold; Open Access","en","journal article","RSC Publishing","","","","","","","","Applied Sciences","Bionanoscience","","","",""
"uuid:af1dcff9-1617-4835-a3a0-0469e1581337","http://resolver.tudelft.nl/uuid:af1dcff9-1617-4835-a3a0-0469e1581337","Essential validation methods for E. coli strains created by chromosome engineering","Krishnan, S.T.; Moolman, M.C.; Van Laar, T.; Meyer, A.S.; Dekker, N.H.","","2015","Background Chromosome engineering encompasses a collection of homologous recombination-based techniques that are employed to modify the genome of a model organism in a controlled fashion. Such techniques are widely used in both fundamental and industrial research to introduce multiple insertions in the same Escherichia coli strain. To date, ?-Red recombination (also known as recombineering) and P1 phage transduction are the most successfully implemented chromosome engineering techniques in E. coli. However, due to errors that can occur during the strain creation process, reliable validation methods are essential upon alteration of a strain’s chromosome. Results and discussion Polymerase chain reaction (PCR)-based methods and DNA sequence analysis are rapid and powerful methods to verify successful integration of DNA sequences into a chromosome. Even though these verification methods are necessary, they may not be sufficient in detecting all errors, imposing the requirement of additional validation methods. For example, as extraneous insertions may occur during recombineering, we highlight the use of Southern blotting to detect their presence. These unwanted mutations can be removed via transducing the region of interest into the wild type chromosome using P1 phages. However, in doing so one must verify that both the P1 lysate and the strains utilized are free from contamination with temperate phages, as these can lysogenize inside a cell as a large plasmid. Thus, we illustrate various methods to probe for temperate phage contamination, including cross-streak agar and Evans Blue-Uranine (EBU) plate assays, whereby the latter is a newly reported technique for this purpose in E. coli. Lastly, we discuss methodologies for detecting defects in cell growth and shape characteristics, which should be employed as an additional check. Conclusion The simple, yet crucial validation techniques discussed here can be used to reliably verify any chromosomally engineered E. coli strains for errors such as non-specific insertions in the chromosome, temperate phage contamination, and defects in growth and cell shape. While techniques such as PCR and DNA sequence verification should standardly be performed, we illustrate the necessity of performing these additional assays. The discussed techniques are highly generic and can be easily applied to any type of chromosome engineering.","chromosome engineering; Escherichia coli; recombineering; P1 phage transduction; strain validation; EBU plate assay; growth curve analysis; cell shape analysis; OA-Fund TU Delft","en","journal article","BioMed Central","","","","","","","","Applied Sciences","BN/Bionanoscience","","","",""
"uuid:87a91d50-26e3-4184-a903-124447f54a54","http://resolver.tudelft.nl/uuid:87a91d50-26e3-4184-a903-124447f54a54","The idiosyncrasy of spatial structure in bacterial competition","Hol, F.J.H.; Galajda, P.; Woolthuis, R.G.; Dekker, C.; Keymer, J.E.","","2015","Background The spatial structure of a habitat can have a strong impact on community dynamics. Different experimental approaches exist to explore the effect of spatial structure on bacterial communities. To investigate the effect of ‘space’, a single implementation of spatial structure is often contrasted to bacterial community dynamics in well-mixed cultures. While such comparisons are useful, it is likely that the observed dynamics will be particular to the specific experimental implementation of spatial structure. In order to address this question, we track the community dynamics of a two-strain Escherichia coli community in various spatial habitats and relate the observed dynamics to the structure of a habitat. Results By tracking the community dynamics of rpoS wild-type and mutant E. coli in radially expanding colonies on solid and semi-solid agar plates, we find that the mutant strain outcompetes the wild-type on semi-solid agar plates, whereas the two strains coexist on solid agar. We compare these results to previous studies in which the same two strains were shown to coexist in habitats spatially structured by microfabrication, while the mutant outcompeted the wild-type in well-mixed batch cultures. Together, these observations show that different implementations of space may result in qualitatively different community dynamics. Furthermore, we argue that the same competitive outcome (e.g. coexistence) may arise from distinct underlying dynamics in different experimental implementations of spatial structure. Conclusions Our observations demonstrate that different experimental implementations of spatial structure may not only lead to quantitatively different communities (changes in the relative abundance of types) but can also lead to qualitatively different outcomes of long-term community dynamics (coexistence versus extinction and loss of biodiversity).","spatial structure; bacterial competition; cooperation; OA-Fund TU Delft","en","journal article","BioMed Central","","","","","","","","Applied Sciences","BN/Bionanoscience","","","",""
"uuid:7c5f7686-c8b0-4b18-b2b4-c9f1247eb5e4","http://resolver.tudelft.nl/uuid:7c5f7686-c8b0-4b18-b2b4-c9f1247eb5e4","Biological Magnetometry: Torque on Superparamagnetic Beads in Magnetic Fields","Van Oene, M.M.; Dickinson, L.E.; Pedaci, F.; Köber, M.; Dulin, D.; Lipfert, J.; Dekker, N.H.","","2015","Superparamagnetic beads are widely used in biochemistry and single-molecule biophysics, but the nature of the anisotropy that enables the application of torques remains controversial. To quantitatively investigate the torques experienced by superparamagnetic particles, we use a biological motor to rotate beads in a magnetic field and demonstrate that the underlying potential is ? periodic. In addition, we tether a bead to a single DNA molecule and show that the angular trap stiffness increases nonlinearly with magnetic field strength. Our results indicate that the superparamagnetic beads’ anisotropy derives from a nonuniform intrabead distribution of superparamagnetic nanoparticles.","","en","journal article","American Physical Society","","","","","","","","Applied Sciences","BN/Bionanoscience","","","",""
"uuid:84aa1d11-793d-496c-8884-4f1e71fb5f83","http://resolver.tudelft.nl/uuid:84aa1d11-793d-496c-8884-4f1e71fb5f83","XNAT imaging platform for BioMedBridges and CTMM TraIT (meeting abstract)","Klein, S.; Vast, E.; Van Soest, J.; Dekker, A.; Koek, M.; Niessen, W.J.","","2015","1st Clinical Research Informatics (CRI) Solutions Day Duesseldorf, Germany, 26-27 May 2014","","en","journal article","BioMed Central","","","","","","","","Applied Sciences","ImPhys/Imaging Physics","","","",""
"uuid:ac9cc946-79dd-48c4-940f-466c9f620941","http://resolver.tudelft.nl/uuid:ac9cc946-79dd-48c4-940f-466c9f620941","Miniaturized Optical Data Link Assembly for 360 um Guidewires","Stoute, R.; Louwerse, M.C.; Van Rens, J.; Henneken, V.A.; Dekker, R.","","2015","We propose a novel concept for a high-speed optical data link in Ø 360 µm cardiovascular interventional imaging guidewires. The concept is based on the recently introduced Flex-to-Rigid (F2R) technology platform. This technology allows for smaller intravascular imaging devices with a more compact form-factor. We extended the existing F2R technology with a new optical data link assembly method to enable high speed data communication from the distal tip of the catheter to the proximal side. In this method, the fiber is aligned by inserting it into a through-wafer hole directly underneath the flip-chipped Vertical-Cavity-Surface Emitting Laser (VCSEL).Therefore, the total diameter of the optical data link is primarily limited by the size of the VCSEL. A wafer-scale demonstration setup was fabricated with a commercially available 350x250 µm VCSEL and a Ø 80 µm multimode optical fiber. Test results of our demonstrator show a correct optic coupling of the VCSEL into the fiber.","optical coupling; data link; Flex-to-Rigid; guidewire; CMUT; micro assembly; minimally invasive instrument","en","conference paper","NWO, STW and IPN","","","","","","","","Electrical Engineering, Mathematics and Computer Science","Microelectronics","","","",""
"uuid:26d716b9-5546-4cba-b78f-62a146c4c1b1","http://resolver.tudelft.nl/uuid:26d716b9-5546-4cba-b78f-62a146c4c1b1","New Product Ideas to Support Macro Breaks in Computer Work","Dekker, M.C.; Van Lochem, A.J.; Molenbroek, J.F.M.","","2015","A healthy work-to-rest ratio during computer work can be an important part of successful preventive workrelated upper limb disorders (WRULD) intervention. Existing break software applications designed to realise such a work-to-rest ratio often possess product features that limit their functionality. Most applications focus on physical relaxation by implementing (micro) breaks into computer work time. Through the emphasis on break time, these applications give the impression that there is no productivity, possibly strengthened by the applications themselves that often visualise the remainder of the break as a slowly decreasing time bar. Moreover, application features such as blocking input devices may counteract cognitive relaxation of computer workers. As imposed physical breaks can be cognitively stressful, especially when deadlines loom, combining physical and cognitive relaxation is a challenge. Actually, research shows that, instead of micro breaks, macro breaks need more attention. It is worthwhile to think of new products for both forms of relaxation within this time span. An idea for a possible product innovation is tested with a small sample and is presented here: a new software application that shows customisable video content during macro breaks.","cognitive relaxation; computer work; macro breaks; product innovation; repetitive strain injuries (RSI); workrelated upper extremity musculoskeletal disorders (WRUEMD); work-related upper limb disorders (WRULD); work-to-rest ratio; OA-Fund TU Delft","en","journal article","Bentham Open","","","","","","","","Industrial Design Engineering","Industrial Design","","","",""
"uuid:0561ab21-088b-4855-a22a-88e3c74265f3","http://resolver.tudelft.nl/uuid:0561ab21-088b-4855-a22a-88e3c74265f3","Elongation-Competent Pauses Govern the Fidelity of a Viral RNA-Dependent RNA Polymerase","Dulin, D.; Vilfan, I.D.; Berghuis, B.A.; Hage, S.; Bamford, D.H.; Poranen, M.M.; Depken, S.M.; Dekker, N.H.","","2015","RNA viruses have specific mutation rates that balance the conflicting needs of an evolutionary response to host antiviral defenses and avoidance of the error catastrophe. While most mutations are known to originate in replication errors, difficulties of capturing the underlying dynamics have left the mechanochemical basis of viral mutagenesis unresolved. Here, we use multiplexed magnetic tweezers to investigate error incorporation by the bacteriophage ?6 RNA-dependent RNA polymerase. We extract large datasets fingerprinting real-time polymerase dynamics over four magnitudes in time, in the presence of nucleotide analogs, and under varying NTP and divalent cation concentrations and fork stability. Quantitative analysis reveals a new pause state that modulates polymerase fidelity and so ties viral polymerase pausing to the biological function of optimizing virulence. Adjusting the frequency of such pauses offers a target for therapeutics and may also reflect an evolutionary strategy for virus populations to track the gradual evolution of their hosts.","","en","journal article","Elsevier (Cell Press)","","","","","","","","Applied Sciences","BN/Bionanoscience","","","",""
"uuid:75c89b91-d3a2-44e6-a444-5cf8db25cb7f","http://resolver.tudelft.nl/uuid:75c89b91-d3a2-44e6-a444-5cf8db25cb7f","Onderzoeksrapportage kaderstelling Fysieke Werkomgeving Rijk: Kwaliteit en kosten","De Been, I.; Thoolen, F.; Cox, H.; Dekker, K.; Van Erpers Roijaards, F.; Mollerus, R.; Schols, I.","","2015","","","nl","report","Center for People and Buildings","","","","","","","","Architecture and The Built Environment","Real Estate and Housing","","","",""
"uuid:26a5d4ba-b57e-4e04-9ad4-fb09bdbf4d8d","http://resolver.tudelft.nl/uuid:26a5d4ba-b57e-4e04-9ad4-fb09bdbf4d8d","Nucleosome Assembly Dynamics Involve Spontaneous Fluctuations in the Handedness of Tetrasomes","Vlijm, R.; Lee, M.; Lipfert, J.; Lusser, A.; Dekker, C.; Dekker, N.H.","","2015","DNA wrapping around histone octamers generates nucleosomes, the basic compaction unit of eukaryotic chromatin. Nucleosome stability is carefully tuned to maintain DNA accessibility in transcription, replication, and repair. Using freely orbiting magnetic tweezers, which measure the twist and length of single DNA molecules, we monitor the real-time loading of tetramers or complete histone octamers onto DNA by Nucleosome Assembly Protein-1 (NAP1). Remarkably, we find that tetrasomes exhibit spontaneous flipping between a preferentially occupied left-handed state (?Lk = ?0.73) and a right-handed state (?Lk = +1.0), separated by a free energy difference of 2.3 kBT (1.5 kcal/mol). This flipping occurs without concomitant changes in DNA end-to-end length. The application of weak positive torque converts left-handed tetrasomes into right-handed tetrasomes, whereas nucleosomes display more gradual conformational changes. Our findings reveal unexpected dynamical rearrangements of the nucleosomal structure, suggesting that chromatin can serve as a “twist reservoir,” offering a mechanistic explanation for the regulation of DNA supercoiling in chromatin.","","en","journal article","Elsevier","","","","","","","","Applied Sciences","BN/Bionanoscience","","","",""
"uuid:160cd365-73d2-4f7b-a27a-9878f78bec08","http://resolver.tudelft.nl/uuid:160cd365-73d2-4f7b-a27a-9878f78bec08","Torque spectroscopy for the study of rotary motion in biological systems","Lipfert, J. (TU Delft BN/Nynke Dekker Lab; Ludwig Maximilians University); van Oene, M.M. (TU Delft BN/Nynke Dekker Lab); Lee, M. (TU Delft BN/Nynke Dekker Lab); Pedaci, F. (CNRS); Dekker, N.H. (TU Delft BN/Nynke Dekker Lab)","","2015","","","en","journal article","","","","","","Accepted Author Manuscript","","","","","BN/Nynke Dekker Lab","","",""
"uuid:376b7dc9-92d7-4ee7-9abf-daa1c33613f4","http://resolver.tudelft.nl/uuid:376b7dc9-92d7-4ee7-9abf-daa1c33613f4","Strand separation establishes a sustained lock at the Tus-Ter replication fork barrier","Berghuis, B.A. (TU Delft BN/Nynke Dekker Lab; Kavli institute of nanoscience Delft); Dulin, D. (TU Delft BN/Nynke Dekker Lab; Kavli institute of nanoscience Delft); Xu, Zhi Qiang (University of Wollongong); van Laar, T. (TU Delft BN/Nynke Dekker Lab; Kavli institute of nanoscience Delft); Cross, B. (TU Delft BN/Cees Dekker Lab; Karlstad University; Kavli institute of nanoscience Delft); Janissen, R. (TU Delft BN/Nynke Dekker Lab; Kavli institute of nanoscience Delft); Jergic, Slobodan (University of Wollongong); Dixon, Nicholas E. (University of Wollongong); Depken, S.M. (TU Delft BN/Martin Depken Lab; Kavli institute of nanoscience Delft); Dekker, N.H. (TU Delft BN/Nynke Dekker Lab; Kavli institute of nanoscience Delft)","","2015","The bidirectional replication of a circular chromosome by many bacteria necessitates proper termination to avoid the head-on collision of the opposing replisomes. In Escherichia coli, replisome progression beyond the termination site is prevented by Tus proteins bound to asymmetric Ter sites. Structural evidence indicates that strand separation on the blocking (nonpermissive) side of Tus-Ter triggers roadblock formation, but biochemical evidence also suggests roles for protein-protein interactions. Here DNA unzipping experiments demonstrate that nonpermissively oriented Tus-Ter forms a tight lock in the absence of replicative proteins, whereas permissively oriented Tus-Ter allows nearly unhindered strand separation. Quantifying the lock strength reveals the existence of several intermediate lock states that are impacted by mutations in the lock domain but not by mutations in the DNA-binding domain. Lock formation is highly specific and exceeds reported in vivo efficiencies. We postulate that protein-protein interactions may actually hinder, rather than promote, proper lock formation.","DNA-binding proteins; nucleic acids; single-molecule biophysics","en","journal article","","","","","","Accepted Author Manuscript","","","","","BN/Nynke Dekker Lab","","",""
"uuid:f8f90c4b-f48b-407a-ac5a-9caa1e849512","http://resolver.tudelft.nl/uuid:f8f90c4b-f48b-407a-ac5a-9caa1e849512","A miniaturized, high frequency mechanical scanner for high speed atomic force microscope using suspension on dynamically determined points","Herfst, R. (TNO); Dekker, B. (TNO); Witvoet, G. (TNO); Crowcombe, W.E. (TNO); de Lange, D. (TNO); Sadeghian Marnani, H. (TU Delft Computational Design and Mechanics; TNO)","","2015","One of the major limitations in the speed of the atomic force microscope (AFM) is the bandwidth of the mechanical scanning stage, especially in the vertical (z) direction. According to the design principles of “light and stiff” and “static determinacy,” the bandwidth of the mechanical scanner is limited by the first eigenfrequency of the AFM head in case of tip scanning and by the sample stage
in terms of sample scanning. Due to stringent requirements of the system, simply pushing the first eigenfrequency to an ever higher value has reached its limitation. We have developed a miniaturized, high speed AFM scanner in which the dynamics of the z-scanning stage are made insensitive to its surrounding dynamics via suspension of it on specific dynamically determined points. This
resulted in a mechanical bandwidth as high as that of the z-actuator (50 kHz) while remaining insensitive to the dynamics of its base and surroundings. The scanner allows a practical z scan range of 2.1 µm. We have demonstrated the applicability of the scanner to the high speed scanning of nanostructures.","atomic force microscopy; image scanners; position sensitive detectors; atomic force microscopes; aluminium","en","journal article","","","","","","","","","","","Computational Design and Mechanics","","",""
"uuid:c9aff527-a262-46e3-a9f3-da1086503c90","http://resolver.tudelft.nl/uuid:c9aff527-a262-46e3-a9f3-da1086503c90","Essential validation methods for E. coli strains created by chromosome engineering","Tiruvadi Krishnan, S. (TU Delft BN/Nynke Dekker Lab; Kavli institute of nanoscience Delft); Moolman, M.C. (TU Delft BN/Nynke Dekker Lab; Kavli institute of nanoscience Delft); van Laar, T. (TU Delft BN/Nynke Dekker Lab; Kavli institute of nanoscience Delft); Meyer, A.S. (TU Delft BN/Anne Meyer Lab; Kavli institute of nanoscience Delft); Dekker, N.H. (TU Delft BN/Nynke Dekker Lab; Kavli institute of nanoscience Delft)","","2015","Background: Chromosome engineering encompasses a collection of homologous recombination-based techniques that are employed to modify the genome of a model organism in a controlled fashion. Such techniques are widely used in both fundamental and industrial research to introduce multiple insertions in the same Escherichia coli strain. To date, λ-Red recombination (also known as recombineering) and P1 phage transduction are the most successfully implemented chromosome engineering techniques in E. coli. However, due to errors that can occur during the strain creation process, reliable validation methods are essential upon alteration of a strain's chromosome. Results and discussion: Polymerase chain reaction (PCR)-based methods and DNA sequence analysis are rapid and powerful methods to verify successful integration of DNA sequences into a chromosome. Even though these verification methods are necessary, they may not be sufficient in detecting all errors, imposing the requirement of additional validation methods. For example, as extraneous insertions may occur during recombineering, we highlight the use of Southern blotting to detect their presence. These unwanted mutations can be removed via transducing the region of interest into the wild type chromosome using P1 phages. However, in doing so one must verify that both the P1 lysate and the strains utilized are free from contamination with temperate phages, as these can lysogenize inside a cell as a large plasmid. Thus, we illustrate various methods to probe for temperate phage contamination, including cross-streak agar and Evans Blue-Uranine (EBU) plate assays, whereby the latter is a newly reported technique for this purpose in E. coli. Lastly, we discuss methodologies for detecting defects in cell growth and shape characteristics, which should be employed as an additional check. Conclusion: The simple, yet crucial validation techniques discussed here can be used to reliably verify any chromosomally engineered E. coli strains for errors such as non-specific insertions in the chromosome, temperate phage contamination, and defects in growth and cell shape. While techniques such as PCR and DNA sequence verification should standardly be performed, we illustrate the necessity of performing these additional assays. The discussed techniques are highly generic and can be easily applied to any type of chromosome engineering.","Cell shape analysis; Chromosome engineering; EBU plate assay; Escherichia coli; Growth curve analysis; P1 phage transduction; Recombineering; Strain validation","en","journal article","","","","","","","","","","","BN/Nynke Dekker Lab","","",""
"uuid:aecce8f2-e3a9-493e-b295-467bae75633d","http://resolver.tudelft.nl/uuid:aecce8f2-e3a9-493e-b295-467bae75633d","Untangling reaction pathways through modern approaches to high-throughput single-molecule force-spectroscopy experiments","Dulin, D. (University of Oxford); Berghuis, B.A. (TU Delft BN/Nynke Dekker Lab); Depken, S.M. (TU Delft BN/Martin Depken Lab); Dekker, N.H. (TU Delft BN/Nynke Dekker Lab)","","2015","Single-molecule experiments provide a unique means for real-time observation of the activity of individual biomolecular machines. Through such techniques, insights into the mechanics of for example, polymerases, helicases, and packaging motors have been gleaned. Here we describe the recent advances in single-molecule force spectroscopy instrumentation that have facilitated high-throughput acquisition at high spatiotemporal resolution. The large datasets attained by such methods can capture rare but important events, and contain information regarding stochastic behaviors covering many orders of magnitude in time. We further discuss analysis of such data sets, and with a special focus on the pause states described in the general literature on RNA polymerase pausing we compare and contrast the signatures of different reaction pathways.","","en","journal article","","","","","","","","","","","BN/Nynke Dekker Lab","","",""
"uuid:9471a88b-c13e-42f6-bae0-29b6f3e6e551","http://resolver.tudelft.nl/uuid:9471a88b-c13e-42f6-bae0-29b6f3e6e551","Gebruikersinvloed energieverbruik kantoorgebouwen: Hoe energie te besparen op kantoor?","Thoolen, F.; De Been, I.; Beijer, M.; Dekker, K.","","2014","","","nl","report","Center for People and Buildings","","","","","","","","Architecture and The Built Environment","Stichting Kenniscentrum Center for People and Buildings","","","",""
"uuid:8e45480a-a59b-4ac9-88f7-8a09118e875b","http://resolver.tudelft.nl/uuid:8e45480a-a59b-4ac9-88f7-8a09118e875b","Slow unloading leads to DNA-bound ?2-sliding clamp accumulation in live Escherichia coli cells","Moolman, M.C.; Tiruvadi Krishnan, S.; Kerssemakers, J.W.J.; Van den Berg, A.; Tulinski, P.; Depken, M.; Reyes-Lamothe, R.; Sherratt, D.J.; Dekker, N.H.","","2014","The ubiquitous sliding clamp facilitates processivity of the replicative polymerase and acts as a platform to recruit proteins involved in replication, recombination and repair. While the dynamics of the E. coli ?2-sliding clamp have been characterized in vitro, its in vivo stoichiometry and dynamics remain unclear. To probe both ?2-clamp dynamics and stoichiometry in live E. coli cells, we use custom-built microfluidics in combination with single-molecule fluorescence microscopy and photoactivated fluorescence microscopy. We quantify the recruitment, binding and turnover of ?2-sliding clamps on DNA during replication. These quantitative in vivo results demonstrate that numerous ?2-clamps in E. coli remain on the DNA behind the replication fork for a protracted period of time, allowing them to form a docking platform for other enzymes involved in DNA metabolism.","biological sciences; biophysics; molecular biology","en","journal article","Nature Publishing Group","","","","","","","","Applied Sciences","BN/Bionanoscience","","","",""
"uuid:2996bccb-7b2d-4c35-9f54-054c4b6623c3","http://resolver.tudelft.nl/uuid:2996bccb-7b2d-4c35-9f54-054c4b6623c3","Coating of graphene","Schneider, G.F.; Dekker, C.","","2014","The present invention is in the field of highly crystalline graphene and coating said graphene with a layer. Said graphene may have further structures, such as nanopores, nanogaps, and nanoribbons. The coated graphene can be used for biomolecular analysis and modification, such as DNA-sequencing, as a sensor, etc. The invention therefor also relates to use of coated graphene.","","en","patent","European Patent Office","","","","","","","","Delft University of Technology","","","","",""
"uuid:b438dbeb-6322-410d-b64d-26372811e5bb","http://resolver.tudelft.nl/uuid:b438dbeb-6322-410d-b64d-26372811e5bb","Skewed brownian fluctuations in single-molecule magnetic tweezers.","Burnham, D.R.; De Vlaminck, I.; Henighan, T.; Dekker, C.","","2014","Measurements in magnetic tweezers rely upon precise determination of the position of a magnetic microsphere. Fluctuations in the position due to Brownian motion allows calculation of the applied force, enabling deduction of the force-extension response function for a single DNA molecule that is attached to the microsphere. The standard approach relies upon using the mean of position fluctuations, which is valid when the microsphere axial position fluctuations obey a normal distribution. However, here we demonstrate that nearby surfaces and the non-linear elasticity of DNA can skew the distribution. Through experiment and simulations, we show that such a skewing leads to inaccurate position measurements which significantly affect the extracted DNA extension and mechanical properties, leading to up to two-fold errors in measured DNA persistence length. We develop a simple, robust and easily implemented method to correct for such mismeasurements.","","en","journal article","Public Library of Science","","","","","","","","Applied Sciences","BN/Bionanoscience","","","",""
"uuid:743720e3-3263-4a02-a4e4-430c2478ea5c","http://resolver.tudelft.nl/uuid:743720e3-3263-4a02-a4e4-430c2478ea5c","Science and technology roadmap for graphene, related two-dimensional crystals, and hybrid systems","Ferrari, A.C.; Dekker, C.; Vandersypen, L.M.K.; Van Der Zant, H.S.J.","","2014","We present the science and technology roadmap for graphene, related two-dimensional crystals, and hybrid systems, targeting an evolution in technology, that might lead to impacts and benefits reaching into most areas of society. This roadmap was developed within the framework of the European Graphene Flagship and outlines the main targets and research areas as best understood at the start of this ambitious project. We provide an overview of the key aspects of graphene and related materials (GRMs), ranging from fundamental research challenges to a variety of applications in a large number of sectors, highlighting the steps necessary to take GRMs from a state of raw potential to a point where they might revolutionize multiple industries. We also define an extensive list of acronyms in an effort to standardize the nomenclature in this emerging field.","Hybrid systems; Fundamental research; Roadmap; Science and Technology; Two-dimensional crystals; Graphene","en","journal article","RSC publishers","","","","","","","","Applied Sciences","Bionanoscience","","","",""
"uuid:0554691b-6250-41d1-b0cb-e19e02229fc7","http://resolver.tudelft.nl/uuid:0554691b-6250-41d1-b0cb-e19e02229fc7","Nutrient-responsive regulation determines biodiversity in a colicin-mediated bacterial community","Hol, F.J.H.; Voges, M.J.; Dekker, C.; Keymer, J.E.","","2014","Background: Antagonistic interactions mediated by antibiotics are strong drivers of bacterial community dynamics which shape biodiversity. Colicin production by Escherichia coli is such an interaction that governs intraspecific competition and is involved in promoting biodiversity. It is unknown how environmental cues affect regulation of the colicin operon and thus influence antibiotic-mediated community dynamics. Results: Here, we investigate the community dynamics of colicin-producing, -sensitive, and -resistant/non-producer E. coli strains that colonize a microfabricated spatially-structured habitat. Nutrients are found to strongly influence community dynamics: when growing on amino acids and peptides, colicin-mediated competition is intense and the three strains do not coexist unless spatially separated at large scales (millimeters). Surprisingly, when growing on sugars, colicin-mediated competition is minimal and the three strains coexist at the micrometer scale. Carbon storage regulator A (CsrA) is found to play a key role in translating the type of nutrients into the observed community dynamics by controlling colicin release. We demonstrate that by mitigating lysis, CsrA shapes the community dynamics and determines whether the three strains coexist. Indeed, a mutant producer that is unable to suppress colicin release, causes the collapse of biodiversity in media that would otherwise support co-localized growth of the three strains. Conclusions: Our results show how the environmental regulation of an antagonistic trait shapes community dynamics. We demonstrate that nutrient-responsive regulation of colicin release by CsrA, determines whether colicin producer, resistant non-producer, and sensitive strains coexist at small spatial scales, or whether the sensitive strain is eradicated. This study highlights how molecular-level regulatory mechanisms that govern interference competition give rise to community-level biodiversity patterns.","interference competition; community dynamics; colicin; biodiversity; OA-Fund TU Delft","en","journal article","BioMed Central","","","","","","","","Applied Sciences","BN/Bionanoscience","","","",""
"uuid:ee24162e-211f-40e5-b997-aac5c08e0b38","http://resolver.tudelft.nl/uuid:ee24162e-211f-40e5-b997-aac5c08e0b38","Invincible DNA tethers: Covalent DNA anchoring for enhanced temporal and force stability in magnetic tweezers experiments","Janissen, R.; Berghuis, B.A.; Dulin, D.; Wink, M.; Van Laar, T.; Dekker, N.H.","","2014","Magnetic tweezers are a powerful single-molecule technique that allows real-time quantitative investigation of biomolecular processes under applied force. High pulling forces exceeding tens of picoNewtons may be required, e.g. to probe the force range of proteins that actively transcribe or package the genome. Frequently, however, the application of such forces decreases the sample lifetime, hindering data acquisition. To provide experimentally viable sample lifetimes in the face of high pulling forces, we have designed a novel anchoring strategy for DNA in magnetic tweezers. Our approach, which exploits covalent functionalization based on heterobifunctional poly(ethylene glycol) crosslinkers, allows us to strongly tether DNA while simultaneously suppressing undesirable non-specific adhesion. A complete force and lifetime characterization of these covalently anchored DNA-tethers demonstrates that, compared to more commonly employed anchoring strategies, they withstand 3-fold higher pulling forces (up to 150 pN) and exhibit up to 200-fold higher lifetimes (exceeding 24 h at a constant force of 150 pN). This advance makes it possible to apply the full range of biologically relevant force scales to biomolecular processes, and its straightforward implementation should extend its reach to a multitude of applications in the field of single-molecule force spectroscopy.","","en","journal article","Oxford University Press","","","","","","","","Applied Sciences","BN/Bionanoscience","","","",""
"uuid:45277a14-40de-4827-bb21-7534743b7f91","http://resolver.tudelft.nl/uuid:45277a14-40de-4827-bb21-7534743b7f91","H2O2 Production in Species of the Lactobacillus acidophilus Group: A Central Role for a Novel NADH-Dependent Flavin Reductase","Hertzberger, R.; Arents, J.; Dekker, H.L.; Pridmore, D.; Gysler, C.; Kleerebezem, M.; Teixeira de Mattosa, M.J.","","2014","Hydrogen peroxide production is a well-known trait of many bacterial species associated with the human body. In the presence of oxygen, the probiotic lactic acid bacterium Lactobacillus johnsonii NCC 533 excretes up to 1 mM H2O2, inducing growth stagnation and cell death. Disruption of genes commonly assumed to be involved in H2O2 production (e.g., pyruvate oxidase, NADH oxidase, and lactate oxidase) did not affect this. Here we describe the purification of a novel NADH-dependent flavin reductase encoded by two highly similar genes (LJ_0548 and LJ_0549) that are conserved in lactobacilli belonging to the Lactobacillus acidophilus group. The genes are predicted to encode two 20-kDa proteins containing flavin mononucleotide (FMN) reductase conserved domains. Reductase activity requires FMN, flavin adenine dinucleotide (FAD), or riboflavin and is specific for NADH and not NADPH. The Km for FMN is 30 ± 8 ?M, in accordance with its proposed in vivo role in H2O2 production. Deletion of the encoding genes in L. johnsonii led to a 40-fold reduction of hydrogen peroxide formation. H2O2 production in this mutant could only be restored by in trans complementation of both genes. Our work identifies a novel, conserved NADH-dependent flavin reductase that is prominently involved in H2O2 production in L. johnsonii.","","en","journal article","American Society for Microbiology","","","","","","","","Applied Sciences","Biotechnology","","","",""
"uuid:4baba775-5ae5-40dc-a9fd-5a6cd9aa4be9","http://resolver.tudelft.nl/uuid:4baba775-5ae5-40dc-a9fd-5a6cd9aa4be9","Single molecule protein sequencing","Joo, C.; Dekker, C.; Van Ginkel, H.G.T.M.; Meyer, A.S.","","2014","The invention provides a device for determining the type of protein in a liquid, the device comprising (a) an immobilized ATP dependent protease based molecular transporter machine configured to guide a protein that is functionalized with labels through a detection area of a detector, (b) said detector, configured to detect a signal as function of the labels of the labelled amino acids, (c) a processor unit, configured to identify from the detector signal a sequence of amino acids of the functionalized protein, wherein the processor unit is further configured to compare the identified sequence of amino acids with the occurrence of such sequence in a database of proteins and to identify the type of protein.","","en","patent","European Patent Office","","","","","","","","Applied Sciences","BN/Bionanoscience","","","",""
"uuid:b3785637-7f11-47bc-abd1-3f4016e865d1","http://resolver.tudelft.nl/uuid:b3785637-7f11-47bc-abd1-3f4016e865d1","The modelling of suction caisson foundations for multi-focused structures","Dekker, M.","Moan, T. (mentor)","2014","","","","master thesis","","","","","","","","indefinite","Mechanical, Maritime and Materials Engineering","Marine and Transport Technology","Offshore and Dredging Engineering","","",""
"uuid:6cf5c7c3-e2d3-4b77-99b4-c7e4ed6986b3","http://resolver.tudelft.nl/uuid:6cf5c7c3-e2d3-4b77-99b4-c7e4ed6986b3","Energiezuinig financieren: ESCo's als financiële propositie","Van Hal, J.D.M.; Van Sprundel, M.; Dekker, T.J.; Van der Heijden, H.M.H.","","2014","","","nl","book chapter","Stichting Fundatie Bachiene","","","","","","","","Architecture and The Built Environment","Real Estate and Housing","","","",""
"uuid:36ee4a81-d112-4634-8ac1-44ac23f82609","http://resolver.tudelft.nl/uuid:36ee4a81-d112-4634-8ac1-44ac23f82609","Spatial structure facilitates cooperation in a social dilemma: Empirical evidence from a bacterial community","Hol, F.J.H.; Galajda, P.; Nagy, K.; Woolthuis, R.G.; Dekker, C.; Keymer, J.E.","","2013","Cooperative organisms are ubiquitous in nature, despite their vulnerability to exploitation by cheaters. Although numerous theoretical studies suggest that spatial structure is critical for cooperation to persist, the spatial ecology of microbial cooperation remains largely unexplored experimentally. By tracking the community dynamics of cooperating (rpoS wild-type) and cheating (rpoS mutant) Escherichia coli in well-mixed flasks and microfabricated habitats, we demonstrate that spatial structure stabilizes coexistence between wild-type and mutant and thus facilitates cooperator maintenance. We develop a method to interpret our experimental results in the context of game theory, and show that the game wild-type and mutant bacteria play in an unstructured environment changes markedly over time, and eventually obeys a prisoner’s dilemma leading to cheater dominance. In contrast, when wild-type and mutant E. coli co-inhabit a spatially-structured habitat, cooperators and cheaters coexist at intermediate frequencies. Our findings show that even in microhabitats lacking patchiness or spatial heterogeneities in resource availability, surface growth allows cells to form multi-cellular aggregates, yielding a self-structured community in which cooperators persist.","","en","journal article","Public Library of Science PLOS","","","","","","","","Applied Sciences","Bionanoscience","","","",""
"uuid:2e81c1c5-e9c2-4487-b6ac-e6c9e6ca247e","http://resolver.tudelft.nl/uuid:2e81c1c5-e9c2-4487-b6ac-e6c9e6ca247e","Impact and relevance of transit disturbances on planning in intermodal container networks using disturbance cost analysis","Van Riessen, B.; Negenborn, R.R.; Dekker, R.; Lodewijks, G.","","2013","An intermodal container transportation network is being developed between Rotterdam and several inland terminals in North West Europe: the EUROPEAN GATEWAY SERVICES network. This network is developed and operated by the sea terminals of EUROPE CONTAINER TERMINALS (ECT). To use this network cost-efficiently, centralised planning by the sea terminal of the container transportation is required. For adequate planning it is important to adapt to occurring disturbances. In this paper, a new mathematical model is proposed: the Linear Container Allocation model with Time-restrictions (LCAT). This model is used for determining the influence of three main types of transit disturbances on the network performance: early departure, late departure, and cancellation of inland services. The influence of a disturbance is measured in two ways. The impact measures the additional cost incurred by an updated planning in case of a disturbance. The relevance measures the cost difference between a fully updated and a locally updated plan. With the results of the analysis, key service properties of disturbed services that result in a high impact or high relevance can be determined. Based on this, the network operator can select focus areas to prevent disturbances with high impact and to improve the planning updates in case of disturbances with high relevance. In a case study of the EGS network, the impact and relevance of transit disturbances on all network services are assessed.","intermodal planning; synchromodal planning; container transportation; disturbances","en","journal article","Erasmus School of Economics (ESE)","","","","","","","","Mechanical, Maritime and Materials Engineering","Marine and Transport Technology","","","",""
"uuid:51612dc6-2400-43e7-a408-b7fcbf37b180","http://resolver.tudelft.nl/uuid:51612dc6-2400-43e7-a408-b7fcbf37b180","Towards more behaviourally robust travel demand forecasts: Catering to utility maximisers and regret minimisers","Dekker, T.; Van Cranenburgh, S.; Chorus, C.G.","","2013","Choice probabilities and related outputs of discrete choice models form a critical input to many travel demand forecasting and transport project evaluation studies. The decision rule underlying a discrete choice model describes how individuals make their decisions and thereby co-determines the choice probabilities. Uncertainty from the side of the analyst regarding the underlying decision rule(s) may therefore translate into alternative predictions regarding the behavioural response to changing travel conditions. In this paper, we contrast the well-known Random Utility Maximization framework, on which most travel demand forecasts are based, with its Random Regret Minimization counterpart. Based on a review of the existing empirical comparisons between the two frameworks we discuss the connections and dissimilarities between both model types and the associated implications for travel demand forecasting. The empirical comparisons reveal that both models perform about equally well in terms of model fit and external validation, which makes it hard to identify one model as a superior specification for forecasting. Despite these small differences in overall model fit, choice probabilities and elasticities can differ substantially (and predictably) in specific choice-contexts. One such example is the compromise effect where the Random Regret Minimization framework predicts a market share bonus for ‘in-between’ alternatives. The paper discusses model averaging techniques to generate predictions when a clear winning model cannot be identified. Finally, the paper puts these considerations in the context of a regret-based Dutch National Model, which is currently under construction.","","en","conference paper","","","","","","","","","Technology, Policy and Management","Infrastructures, Systems and Services","","","",""
"uuid:7919534c-e1e7-4fdb-8f2e-9e3c9397b517","http://resolver.tudelft.nl/uuid:7919534c-e1e7-4fdb-8f2e-9e3c9397b517","Random Regret Minimization for consumer choice modelling: Assessment of empirical evidence","Chorus, C.G.; Dekker, T.","","2013","This paper introduces to the field of marketing a regret-based discrete choice model for the analysis of multi-attribute consumer choices from multinomial choice sets. This random regret minimization model (RRM), which has two years ago been introduced in the field of transport, forms a regret-based counterpart of the canonical random utility maximization paradigm (RUM). Since its very recent introduction, a relatively small but growing body of literature has emerged focusing on RRM’s theoretical properties and on empirical comparisons with RUM. This paper assesses theoretical and empirical results that have been obtained so far, with the aim of finding out to what extent, when, and how RRM can form a viable addition to the consumer choice modeller’s toolkit. The paper shows that RRM or hybrid RRM-RUM models outperform RUM counterparts (which are equally parsimonious) in a majority of studies in terms of model fit and predictive ability. Although these differences in performance are quite small, the two paradigms often result in markedly different managerial implications due to often considerable differences in elasticities and market share forecasts. We elaborate on how RRM and RUM can be used jointly to arrive at ‘behaviourally robust’ marketing strategies.","","en","conference paper","","","","","","","","","Technology, Policy and Management","Engineering, Systems and Services","","","",""
"uuid:c8f21905-e951-4c54-8421-32dade46edb9","http://resolver.tudelft.nl/uuid:c8f21905-e951-4c54-8421-32dade46edb9","Scanning a DNA molecule for bound proteins using hybrid magnetic and optical tweezers","Van Loenhout, M.T.; De Vlaminck, I.; Flebus, B.; Den Blanken, J.F.; Zweifel, L.P.; Hooning, K.M.; Kerssemakers, J.W.; Dekker, C.","","2013","The functional state of the genome is determined by its interactions with proteins that bind, modify, and move along the DNA. To determine the positions and binding strength of proteins localized on DNA we have developed a combined magnetic and optical tweezers apparatus that allows for both sensitive and label-free detection. A DNA loop, that acts as a scanning probe, is created by looping an optically trapped DNA tether around a DNA molecule that is held with magnetic tweezers. Upon scanning the loop along the ?-DNA molecule, EcoRI proteins were detected with ?17 nm spatial resolution. An offset of 33±5 nm for the detected protein positions was found between back and forwards scans, corresponding to the size of the DNA loop and in agreement with theoretical estimates. At higher applied stretching forces, the scanning loop was able to remove bound proteins from the DNA, showing that the method is in principle also capable of measuring the binding strength of proteins to DNA with a force resolution of 0.1 pN/[Formula: see text]. The use of magnetic tweezers in this assay allows the facile preparation of many single-molecule tethers, which can be scanned one after the other, while it also allows for direct control of the supercoiling state of the DNA molecule, making it uniquely suitable to address the effects of torque on protein-DNA interactions.","","en","journal article","Public Library of Science","","","","","","","","Applied Sciences","BN/Bionanoscience","","","",""
"uuid:913d9ce8-4a22-471d-8adf-311937698992","http://resolver.tudelft.nl/uuid:913d9ce8-4a22-471d-8adf-311937698992","Design of an ergonomic electric guitar","Genani, G.; Dekker, M.C.; Molenbroek, J.F.M.","","2013","An investigation of existing literature reveals that guitar players are most prone to musculoskeletal injuries amongst all musicians. In the light of recent injuries to prominent guitar players such as Eddie Van Halen, this article explores ergonomics of electric guitars. By means of surveys, user observations, biomechanical analysis and laboratory measurement, the root of the problem has been determined. Bad posture while playing and high wrist flexion seem to be the two prominent issues that are omnipresent. The article culminates with the design of an electric guitar that presents a solution to the ergonomic issues associated with the existing design.","","en","journal article","Nederlandse Vereniging voor Ergonomie","","","","","","","","Industrial Design Engineering","Industrial Design","","","",""
"uuid:2001e7dc-cb99-4806-8137-782b2902a8bd","http://resolver.tudelft.nl/uuid:2001e7dc-cb99-4806-8137-782b2902a8bd","Structural and torsional properties of the RAD51-dsDNA nucleoprotein filament","Lee, M.; Lipfert, J.; Sanchez, H.; Wyman, C.; Dekker, N.H.","","2013","Human RAD51 is a key protein in the repair of DNA by homologous recombination. Its assembly onto DNA, which induces changes in DNA structure, results in the formation of a nucleoprotein filament that forms the basis of strand exchange. Here, we determine the structural and mechanical properties of RAD51-dsDNA filaments. Our measurements use two recently developed magnetic tweezers assays, freely orbiting magnetic tweezers and magnetic torque tweezers, designed to measure the twist and torque of individual molecules. By directly monitoring changes in DNA twist on RAD51 binding, we determine the unwinding angle per RAD51 monomer to be 45°, in quantitative agreement with that of its bacterial homolog, RecA. Measurements of the torque that is built up when RAD51-dsDNA filaments are twisted show that under conditions that suppress ATP hydrolysis the torsional persistence length of the RAD51-dsDNA filament exceeds that of its RecA counterpart by a factor of three. Examination of the filament's torsional stiffness for different combinations of divalent ions and nucleotide cofactors reveals that the Ca2+ ion, apart from suppressing ATPase activity, plays a key role in increasing the torsional stiffness of the filament. These quantitative measurements of RAD51-imposed DNA distortions and accumulated mechanical stress suggest a finely tuned interplay between chemical and mechanical interactions within the RAD51 nucleoprotein filament.","","en","journal article","Oxford University Press","","","","","","","","Applied Sciences","BN/Bionanoscience","","","",""
"uuid:cce55f3d-9e9f-475d-801b-b695d38c5f58","http://resolver.tudelft.nl/uuid:cce55f3d-9e9f-475d-801b-b695d38c5f58","Social Media and Interethnic Contact: An analysis of social media use by second generation migrant youth","Dekker, Rianne (Erasmus Universiteit Rotterdam); Belabas, Warda; Scholten, Peter","","2013","It is often asserted that ethnic minorities have a marginalized position in the city. Interethnic contact theory argues that due to spatial segregation, minorities’ access to interethnic contact is limited and they have less access to social resources. Social media have the potential to overcome spatial boundaries and provide new opportunities for bonding and bridging social capital.We studied what implications social media have for interethnic contact and the integration and empowerment of minority groups. Some scholars argue that social media provide new social network infrastructures with access to bridging interethnic social capital. Others contend that social media will only strengthen intra-ethnic and transnational relations and facilitate virtual parallel lives in the host country, solidifying minorities’ marginalized position. We studied the role of social media in inter-ethnic contact, intra-ethnic contact and transnational contact and the consequences of this for the position of minority groups in the city. We conducted semi-structured interviews with 59 second generation migrant adolescents in Rotterdam from a variety of ethnic groups. They have proven to be avid social media users while at the same time being subject of the integration debate. We found no evidence that social media are facilitating interethnic contact that was previously unattainable due to spatial or social boundaries. In cases where new interethnic contact was established, they were rarely continued offline. We did find that social media support interethnic solidarity by providing insight in other people’s opinions and ways of life. Furthermore, intra-ethnic and transnational uses of social media are not hindering social media use that is oriented on the country of residence. We therefore conclude that there is a need to put earlier research on ethnic social media venues in perspective. Even though social media facilitate intra-ethnic and transnational contact, there is no evidence of virtual segregation based on ethnicity.","","en","conference paper","","","","","","","","","","","","","",""
"uuid:70661db4-eb62-4b44-b5da-bc208d3f6ee7","http://resolver.tudelft.nl/uuid:70661db4-eb62-4b44-b5da-bc208d3f6ee7","Organ-on-a-Chip: Interfacing with living tissue","Dekker, R.","","2013","“A what on a chip?” is what most people ask with disbelief when they hear for the first time of the new and very exciting research area “Organ on a Chip.” The topic has nothing to do with Science Fiction, but everything with a very surprising encounter between two completely different research fields: Microfabrication and Stem-Cell Biology! The final goal is to build simplified, but very well controlled models of human organs and diseases.","","en","journal article","Delft University of Technology","","","","","","","","Electrical Engineering, Mathematics and Computer Science","Microelectronics","","","",""
"uuid:a57410a4-3e59-4dca-80a8-d895e3405d40","http://resolver.tudelft.nl/uuid:a57410a4-3e59-4dca-80a8-d895e3405d40","Electron beam fabrication of a microfluidic device for studying submicron-scale bacteria","Moolman, M.C.; Huang, Z.; Krishnan, S.T.; Kerssemakers, J.W.J.; Dekker, N.H.","","2013","Background: Controlled restriction of cellular movement using microfluidics allows one to study individual cells to gain insight into aspects of their physiology and behaviour. For example, the use of micron-sized growth channels that confine individual Escherichia coli has yielded novel insights into cell growth and death. To extend this approach to other species of bacteria, many of whom have dimensions in the sub-micron range, or to a larger range of growth conditions, a readily-fabricated device containing sub-micron features is required. Results: Here we detail the fabrication of a versatile device with growth channels whose widths range from 0.3 ?m to 0.8 ?m. The device is fabricated using electron beam lithography, which provides excellent control over the shape and size of different growth channels and facilitates the rapid-prototyping of new designs. Features are successfully transferred first into silicon, and subsequently into the polydimethylsiloxane that forms the basis of the working microfluidic device. We demonstrate that the growth of sub-micron scale bacteria such as Lactococcus lactis or Escherichia coli cultured in minimal medium can be followed in such a device over several generations. Conclusions: We have presented a detailed protocol based on electron beam fabrication together with specific dry etching procedures for the fabrication of a microfluidic device suited to study submicron-sized bacteria. We have demonstrated that both Gram-positive and Gram-negative bacteria can be successfully loaded and imaged over a number of generations in this device. Similar devices could potentially be used to study other submicron-sized organisms under conditions in which the height and shape of the growth channels are crucial to the experimental design.","microfluidics; poly(dimethylsiloxane); electron beam lithography; micro-nanofabrication; bacterial growth; lactococcus lactis; escherichia coli","en","journal article","BioMed Central","","","","","","","","Applied Sciences","BN/Bionanoscience","","","",""
"uuid:d2f1ada0-a5ff-4705-9fc0-7f1930ecb0a1","http://resolver.tudelft.nl/uuid:d2f1ada0-a5ff-4705-9fc0-7f1930ecb0a1","A nanopore sensor and method for selective detection of analytes in a sample","De Vlaminck, I.; Plesa, C.; Dekker, C.","","2013","","","en","patent","European Patent Office","","","","","","","","Applied Sciences","BN/Bionanoscience","","","",""
"uuid:70b4a840-5695-4a2c-9720-01ac5635ac06","http://resolver.tudelft.nl/uuid:70b4a840-5695-4a2c-9720-01ac5635ac06","Residue-free plasma etching of polyimide coatings for small pitch vias with improved step coverage","Mimoun, B.A.Z.; Pham, H.T.M.; Henneken, V.; Dekker, R.","","2013","The authors have found that patterning polyimide coatings containing organosilane adhesion promoter using pure oxygen plasma resulted in a thin silicon-rich residue layer. They show in this paper that adding small amounts of fluorine-containing gas to the etching gas mixture is necessary in order to achieve residue-free polyimide plasma etching. They report residue-free plasma etching of polyimide coatings with both isotropic and anisotropic profiles, using either metal or oxide hard masks. These etching methods are however not sufficient for the fabrication of high density metal filled vias in 10??m thick polyimide coatings. In order to improve the metal step coverage over the vias while keeping the pitch as small as possible, the authors have developed a two-step etching recipe combining both isotropic and anisotropic profiles, resulting in wine-glass shaped vias.","adhesion; coatings; gas mixtures; polymer films; sputter etching","en","journal article","American Vacuum Society","","","","","","","","Electrical Engineering, Mathematics and Computer Science","Microelectronics","","","",""
"uuid:8c6de115-9c4e-4e96-8f80-197db0a3f545","http://resolver.tudelft.nl/uuid:8c6de115-9c4e-4e96-8f80-197db0a3f545","Studying genomic processes at the single-molecule level: introducing the tools and applications","Dulin, D. (TU Delft BN/Nynke Dekker Lab); Lipfert, J. (TU Delft BN/Nynke Dekker Lab); Moolman, M.C. (TU Delft BN/Nynke Dekker Lab); Dekker, N.H. (TU Delft BN/Nynke Dekker Lab)","","2013","To understand genomic processes such as transcription, translation or splicing, we need to be able to study their spatial and temporal organization at the molecular level. Single-molecule approaches provide this opportunity, allowing researchers to monitor molecular conformations, interactions or diffusion quantitatively and in real time in purified systems and in the context of the living cell. This Review introduces the types of application of single-molecule approaches that can enhance our understanding of genome function.","Gene expression; Genomics; Microbial genetics; Technology","en","journal article","","","","","","Accepted Author Manuscript","","","","","BN/Nynke Dekker Lab","","",""
"uuid:6ea55a4a-ee36-4fb1-919a-86ffc0a544f6","http://resolver.tudelft.nl/uuid:6ea55a4a-ee36-4fb1-919a-86ffc0a544f6","NAP1-Assisted Nucleosome Assembly on DNA Measured in Real Time by Single-Molecule Magnetic Tweezers","Vlijm, R.; Smitshuijzen, J.S.J.; Lusser, A.; Dekker, C.","","2012","While many proteins are involved in the assembly and (re)positioning of nucleosomes, the dynamics of protein-assisted nucleosome formation are not well understood. We study NAP1 (nucleosome assembly protein 1) assisted nucleosome formation at the single-molecule level using magnetic tweezers. This method allows to apply a well-defined stretching force and supercoiling density to a single DNA molecule, and to study in real time the change in linking number, stiffness and length of the DNA during nucleosome formation. We observe a decrease in end-to-end length when NAP1 and core histones (CH) are added to the dsDNA. We characterize the formation of complete nucleosomes by measuring the change in linking number of DNA, which is induced by the NAP1-assisted nucleosome assembly, and which does not occur for non-nucleosomal bound histones H3 and H4. By rotating the magnets, the supercoils formed upon nucleosome assembly are removed and the number of assembled nucleosomes can be counted. We find that the compaction of DNA at low force is about 56 nm per assembled nucleosome. The number of compaction steps and associated change in linking number indicate that NAP1-assisted nucleosome assembly is a two-step process.","","en","journal article","Public Library of Science","","","","","","","","Applied Sciences","BN/Bionanoscience","","","",""
"uuid:512439d9-8b9a-442a-beb3-07c636aedb88","http://resolver.tudelft.nl/uuid:512439d9-8b9a-442a-beb3-07c636aedb88","A Platform for Manufacturable Stretchable Micro-electrode Arrays","Khoshfetrat Pakazad, S.; Savov, A.; Braam, S.R.; Dekker, R.","","2012","A platform for the batch fabrication of pneumatically actuated Stretchable Micro-Electrode Arrays (SMEAs) by using state-of-the-art micro-fabrication techniques and materials is demonstrated. The proposed fabrication process avoids the problems normally associated with processing of thin film structures on polydimethylsiloxane (PDMS), by first fabricating the electrodes and electrical interconnects on the silicon wafer using fine-pitched stepper lithography, and afterwards transferring the structures to the elastomer. Stretchability is achieved by a novel spiral design for the interconnects. Experiments demonstrate the biocompatibility of the fabricated devices for in vitro cell culturing.","retchable electronics; MEA; multi electrode arrays; micro electrode arrays; mechano-biology; mechanotransduction","en","journal article","Elsevier","","","","","","","","Electrical Engineering, Mathematics and Computer Science","Microelectronics","","","",""
"uuid:d668be08-30ea-47fd-a09f-b1954cfdc53d","http://resolver.tudelft.nl/uuid:d668be08-30ea-47fd-a09f-b1954cfdc53d","Formation and control of wrinkles in graphene by the wedging transfer method","Calado, V.E.; Schneider, G.F.; Theulings, A.M.M.G.; Dekker, C.; Vandersypen, L.M.K.","","2012","We study the formation of wrinkles in graphene upon wet transfer onto a hydrophilic target substrate, whereby draining of water appears to play an important role. We are able to control the orientation of the wrinkles by tuning the surface morphology. Wrinkles are absent in flakes transferred to strongly hydrophobic substrates, a further indication of the role of the interaction of water with the substrate in wrinkle formation. The electrical and structural integrity of the graphene is not affected by the wrinkles, as inferred from Raman measurements and electrical conductivity measurements.","electrical conductivity; graphene; Raman spectra; surface morphology","en","journal article","American Institute of Physics","","","","","","","","Applied Sciences","Quantum Nanoscience","","","",""
"uuid:71578df8-2b52-4e79-8256-3e42af4c253b","http://resolver.tudelft.nl/uuid:71578df8-2b52-4e79-8256-3e42af4c253b","Magnetic Forces and DNA Mechanics in Multiplexed Magnetic Tweezers","De Vlaminck, I.; Henighan, T.; Van Loenhout, M.T.J.; Burnham, D.R.; Dekker, C.","","2012","Magnetic tweezers (MT) are a powerful tool for the study of DNA-enzyme interactions. Both the magnet-based manipulation and the camera-based detection used in MT are well suited for multiplexed measurements. Here, we systematically address challenges related to scaling of multiplexed magnetic tweezers (MMT) towards high levels of parallelization where large numbers of molecules (say 103) are addressed in the same amount of time required by a single-molecule measurement. We apply offline analysis of recorded images and show that this approach provides a scalable solution for parallel tracking of the xyz-positions of many beads simultaneously. We employ a large field-of-view imaging system to address many DNA-bead tethers in parallel. We model the 3D magnetic field generated by the magnets and derive the magnetic force experienced by DNA-bead tethers across the large field of view from first principles. We furthermore experimentally demonstrate that a DNA-bead tether subject to a rotating magnetic field describes a bicircular, Limaçon rotation pattern and that an analysis of this pattern simultaneously yields information about the force angle and the position of attachment of the DNA on the bead. Finally, we apply MMT in the high-throughput investigation of the distribution of the induced magnetic moment, the position of attachment of DNA on the beads, and DNA flexibility. The methods described herein pave the way to kilo-molecule level magnetic tweezers experiments.","","en","journal article","Public Library of Science","","","","","","","","Applied Sciences","BN/Bionanoscience","","","",""
"uuid:3bd22c2b-2c6c-4135-b478-3cd8f98ef87f","http://resolver.tudelft.nl/uuid:3bd22c2b-2c6c-4135-b478-3cd8f98ef87f","A comprehensive sediment budget for the Mississippi Barrier Islands","Walstra, D.J.R.; De Vroeg, J.H.; Van Thiel de Vries, J.S.M.; Swinkels, C.; Luijendijk, A.P.; De Boer, W.P.; Hoekstra, R.; Hoonhout, B.; Henrotte, J.; Smolders, T.; Dekker, F.; Godsey, E.","","2012","In order to conceive any realistic plan for post-Katrina island restoration, it is necessary to understand the physical processes that move sand along the littoral drift zone off the coast of Mississippi. This littoral zone influences the character of the Mississippi barrier islands as they exist in an ever changing cycle. To help in this understanding, a sediment transport model was conducted to establish a current sediment budget for the islands. This study evaluated the existing regional sediment transport magnitudes and directions for the Mississippi and Alabama barrier islands fronting Mississippi Sound including daily conditions and hurricanes. A method was developed to incorporate all relevant hurricanes from 1917 to 2010 in the analysis. For the long term average net longshore transport along the southern shorelines of the barriers (i.e. exposed to the Gulf of Mexico), the contribution of year averaged conditions and hurricanes are of similar order of magnitude, although the mean annual percentage occurrence of hurricanes is no more than about 3%. Along the northern shores (Mississippi Sound side) the transport is considerably smaller and the contributions of cold fronts and hurricanes to the sediment transports are more or less equal. For the year-averaged conditions (excluding hurricanes) a westward directed net transport is found. The net effect of the historic hurricanes is also westward in direction. However, for individual hurricanes (e.g. Camille and Katrina) the net transport along Ship Island can be directed eastward due to the dominance of ebb flows after the eye of the hurricane had passed.","sediment budget; Mississippi; barrier islands; transport modeling; Delft3D; MsCIP","en","conference paper","Coastal Engineering Research Council","","","","","","","","Civil Engineering and Geosciences","Hydraulic Engineering","","","",""
"uuid:6f315dba-97f0-4238-b91a-3ef7019109a5","http://resolver.tudelft.nl/uuid:6f315dba-97f0-4238-b91a-3ef7019109a5","Mechanism of Homology Recognition in DNA Recombination from Dual-Molecule Experiments","De Vlaminck, I.; Van Loenhout, M.T.J.; Zweifel, L.; Den Blanken, J.; Hooning, K.; Hage, S.; Kerssemakers, J.; Dekker, C.","","2012","In E. coli homologous recombination, a filament of RecA protein formed on DNA searches and pairs a homologous sequence within a second DNA molecule with remarkable speed and fidelity. Here, we directly probe the strength of the two-molecule interactions involved in homology search and recognition using dual-molecule manipulation, combining magnetic and optical tweezers. We find that the filament's secondary DNA-binding site interacts with a single strand of the incoming double-stranded DNA during homology sampling. Recognition requires opening of the helix and is strongly promoted by unwinding torsional stress. Recognition is achieved upon binding of both strands of the incoming dsDNA to each of two ssDNA-binding sites in the filament. The data indicate a physical picture for homology recognition in which the fidelity of the search process is governed by the distance between the DNA-binding sites.","","en","journal article","Elsevier","","","","","","","","Applied Sciences","BN/Bionanoscience","","","",""
"uuid:c7ca86df-92c1-4e2a-aa0a-7363b8c1b7ec","http://resolver.tudelft.nl/uuid:c7ca86df-92c1-4e2a-aa0a-7363b8c1b7ec","Non-Bias-Limited Tracking of Spherical Particles, Enabling Nanometer Resolution at Low Magnification","Van Loenhout, M.T.J.; Kerssemakers, J.W.J.; De Vlaminck, I.; Dekker, C.","","2012","We present a three-dimensional tracking routine for nondiffraction-limited particles, which significantly reduces pixel bias. Our technique allows for increased resolution compared to that of previous methods, especially at low magnification or at high signal/noise ratio. This enables tracking with nanometer accuracy in a wide field of view and tracking of many particles. To reduce bias induced by pixelation, the tracking algorithm uses interpolation of the image on a circular grid to determine the x-, y-, and z-positions. We evaluate the proposed algorithm by tracking simulated images and compare it to well-known center-of-mass and cross-correlation methods. The final resolution of the described method improves up to an order of magnitude in three dimensions compared to conventional tracking methods. We show that errors in x,y-tracking can seriously affect z-tracking if interpolation is not used. We validate our results with experimental data obtained for conditions matching those used in the simulations. Finally, we show that the increased performance of the proposed algorithm uniquely enables it to extract accurate data for the persistence length and end-to-end distance of 107 DNA tethers in a single experiment","","en","journal article","Elsevier","","","","","","","","Applied Sciences","BN/Bionanoscience","","","",""
"uuid:81fa5235-1c6a-48f1-936e-4cbcf63f49c7","http://resolver.tudelft.nl/uuid:81fa5235-1c6a-48f1-936e-4cbcf63f49c7","Robustness and accuracy of cell division in Escherichia coli in diverse cell shapes","Männik, J.; Wu, F.; Hol, F.J.H.; Bisicchia, P.; Sherratt, D.J.; Keymer, J.E.; Dekker, C.","","2012","Cell division in typical rod-shaped bacteria such as Escherichia coli shows a remarkable plasticity in being able to adapt to a variety of irregular cell shapes. Here, we investigate the roles of the Min system and the nucleoid-occlusion factor SlmA in supporting this adaptation. We study “squeezed” E. coli in narrow nanofabricated channels where these bacteria exhibit highly irregular shapes and large volumes. Despite the severely anomalous morphologies we find that most of these bacteria maintain their ability to divide into two equally sized daughters with an accuracy comparable to that of normal rod-shaped cells (about 4%). Deletion of either slmA or minC shows that the molecular systems associated with these genes are largely dispensable for accurate cell division in these irregular cell shapes. Using fluorescence time-lapse microscopy, we determine that the functionality of the Min system is affected by the cell shape, whereas the localization of a nucleoid relative to the cell division proteins (the divisome) remains unperturbed in a broad spectrum of morphologies, consistent with nucleoid occlusion. The observed positioning of the nucleoid relative to the divisome appears not to be affected by the nucleoid-occlusion factor SlmA. The current study underscores the importance of nucleoid occlusion in positioning the divisome and shows that it is robust against shape irregularities.","cytokinesis; FtsZ; lab-on-a-chip; microfluidics","en","journal article","National Academy of Sciences","","","","","","","","Applied Sciences","BN/Bionanoscience","","","",""
"uuid:8b5ccb75-5892-471f-bf90-3371f86a53a9","http://resolver.tudelft.nl/uuid:8b5ccb75-5892-471f-bf90-3371f86a53a9","Calibration of the optical torque wrench","Pedaci, F.; Huang, Z.; Van Oene, M.; Dekker, N.H.","","2012","The optical torque wrench is a laser trapping technique that expands the capability of standard optical tweezers to torque manipulation and measurement, using the laser linear polarization to orient tailored microscopic birefringent particles. The ability to measure torque of the order of kBT (?4 pN nm) is especially important in the study of biophysical systems at the molecular and cellular level. Quantitative torque measurements rely on an accurate calibration of the instrument. Here we describe and implement a set of calibration approaches for the optical torque wrench, including methods that have direct analogs in linear optical tweezers as well as introducing others that are specifically developed for the angular variables. We compare the different methods, analyze their differences, and make recommendations regarding their implementations.","optomechanics; optical tweezers or optical manipulation","en","journal article","Optical Society of America","","","","","","","","Applied Sciences","BN/Bionanoscience","","","",""
"uuid:de5d18fc-b381-4136-9844-a4d4b1ffc4b3","http://resolver.tudelft.nl/uuid:de5d18fc-b381-4136-9844-a4d4b1ffc4b3","Method for sensing an analyte in a fluid and sensor unit for such method","Dekker, N.H.; Pedaci, F.; Barland, S.","","2012","The invention provides a method for sensing with a sensor system an analyte in an analyte fluid. The sensor system comprises a micron scale birefringent entity, a laser unit configured to generate polarized laser light, a polarization rotation device, wherein the laser unit and polarization rotation device are configured to rotate at a polarization rotation frequency the polarization of the laser light, and a detection unit. The method comprises feeding the analyte fluid along the micron scale birefringent entity while keeping with the laser light and the polarization rotation device the micron scale birefringent entity in an optical torque trap at a polarization rotation frequency; keeping the polarization rotation frequency at a sub-critical polarization rotation frequency; and measuring with the detection unit downstream of the micron scale birefringent entity the polarization of the laser light, and sensing a perturbation on the polarization of the laser light due to the analyte.","","en","patent","European Patent Office","","","","","","","","Applied Sciences","BN/Bionanoscience","","","",""
"uuid:294b8972-b283-40f0-acbd-cf5be0bb14a3","http://resolver.tudelft.nl/uuid:294b8972-b283-40f0-acbd-cf5be0bb14a3","Method for determining one or more characterizing features of a macromolecule and an apparatus for carrying out said method","Dekker, N.H.; Kerssemakers, J.; Lipfert, J.","","2011","The invention concerns a method and apparatus for determining one or more characterizing features of a macromolecule, in particular torque and/or twist of nucleic acids like DNA, using magnetic fields.","","en","patent","European Patent Office","","","","","","","","Applied Sciences","BN/Bionanoscience","","","",""
"uuid:9e322f56-f4a4-4baf-b2c3-7b7bf6287f17","http://resolver.tudelft.nl/uuid:9e322f56-f4a4-4baf-b2c3-7b7bf6287f17","Landscape Architecture at TU Delft 1973-2011: Ter gelegenheid afscheid Prof. Dr. Clemens Steenbergen","Homan, A.; Van der Weide, A.; Bordes, B.; Kwast, B.; Van den Heuvel, D.; Stegewerns, C.; Jongsma, C.; Van Ees, C.; Wouters, C.; Jauslin, D.; Wijnen, D.; Piccinini, D.; Dekker, E.; Van der Kooij, E.; Luiten, E.; De Jong, E.; Toni, F.; Aerts, F.; Verschuure-Stuip, G.; Stotijn, H.; Bakker, I.; Bobbink, I.; Meulenberg, I.; Woltjer, J.; Wilbers, J.; Niemeijer, J.; Lonsdale, J.; Wiers, J.; Pouderoijen, M.; Roos, A.; Hellendoorn, D.; Visser, K.; Storm-Prins, M.; Van der Helm, M.; De Vos, L.; Veldman, M.; Hartveld, M.; Den Ruijter, M.; Verbruggen, N.; Rickert, N.; De Graaf, P.; Van der Ree, P.; Aben, R.; Buijs, R.; Rooij, R.; Van der Velde, R.; De Wit, S.; Nijhuis, S.; Holtappels, S.; Meeks, S.; Van Assen, S.; Van Oosten, S.; Van den Busken, S.; Hermans, W.","","2011","Het is haast onmogelijk om de werkzame jaren van Prof. Dr. Clemens Steenbergen hier op de TU Delft in het kort samen te vatten. Dit is een persoonlijk boek van collega's, medewerkers en studenten ter gelegenheid van zijn afscheid op 15. December 2011.","","nl","book","TU Delft Landscape Architecture","","","","","","","2012-02-09","Architecture","Urbanism","","","",""
"uuid:d403c8d7-3be8-4506-8464-2baead6a1141","http://resolver.tudelft.nl/uuid:d403c8d7-3be8-4506-8464-2baead6a1141","High-Speed AFM Reveals the Dynamics of Single Biomolecules at the Nanometer Scale","Katan, A.J.; Dekker, C.","","2011","Atomic force microscopy allows visualization of biomolecules with nanometer resolution under physiological conditions. Recent advances have improved the time resolution of the technique from minutes to tens of milliseconds, meaning that it is now possible to watch single biomolecules in action in real time. Here, we review this development.","","en","journal article","Elsevier","","","","","","","","Applied Sciences","BN/Bionanoscience","","","",""
"uuid:d1c49091-8643-4968-9c5c-3c28a170af74","http://resolver.tudelft.nl/uuid:d1c49091-8643-4968-9c5c-3c28a170af74","Atomic-scale electron-beam sculpting of defect-free graphene nanostructures","Song, B.; Schneider, G.F.; Xu, Q.; Pandraud, G.; Dekker, C.; Zandbergen, H.","","2011","Extended abstract of a paper presented at Microscopy and Microanalysis 2011 in Nashville, Tennessee, USA, August 7–August 11, 2011.","","en","journal article","Cambridge University Press","","","","","","","2012-10-31","Applied Sciences","Bionanoscience","","","",""
"uuid:b9082b81-adae-436a-9ca3-167154e88cd6","http://resolver.tudelft.nl/uuid:b9082b81-adae-436a-9ca3-167154e88cd6","A method to track rotational motion for use in single-molecule biophysics","Lipfert, J.; Kerssemakers, J.J.W.; Rojer, M.; Dekker, N.H.","","2011","The double helical nature of DNA links many cellular processes such as DNA replication, transcription, and repair to rotational motion and the accumulation of torsional strain. Magnetic tweezers (MTs) are a single-molecule technique that enables the application of precisely calibrated stretching forces to nucleic acid tethers and to control their rotational motion. However, conventional magnetic tweezers do not directly monitor rotation or measure torque. Here, we describe a method to directly measure rotational motion of particles in MT. The method relies on attaching small, non-magnetic beads to the magnetic beads to act as fiducial markers for rotational tracking. CCD images of the beads are analyzed with a tracking algorithm specifically designed to minimize crosstalk between translational and rotational motion: first, the in-plane center position of the magnetic bead is determined with a kernel-based tracker, while subsequently the height and rotation angle of the bead are determined via correlation-based algorithms. Evaluation of the tracking algorithm using both simulated images and recorded images of surface-immobilized beads demonstrates a rotational resolution of 0.1°, while maintaining a translational resolution of 1–2 nm. Example traces of the rotational fluctuations exhibited by DNA-tethered beads confined in magnetic potentials of varying stiffness demonstrate the robustness of the method and the potential for simultaneous tracking of multiple beads. Our rotation tracking algorithm enables the extension of MTs to magnetic torque tweezers (MTT) to directly measure the torque in single molecules. In addition, we envision uses of the algorithm in a range of biophysical measurements, including further extensions of MT, tethered particle motion, and optical trapping measurements.","biological techniques; DNA; image resolution; molecular biophysics; motion measurement; radiation pressure; torque measurement","en","journal article","American Institute of Physics","","","","","","","","Applied Sciences","BN/Bionanoscience","","","",""
"uuid:2159f443-aaef-4450-9428-3821c3ce9d83","http://resolver.tudelft.nl/uuid:2159f443-aaef-4450-9428-3821c3ce9d83","Flexibel huisvesten en kostenempirie: Casus rijkshuisvesting","Dekker, K.; De Bruyne, E.; Gosselink, A.M.; Pullen, W.R.; Le Roux, P.","","2011","","","nl","report","Center for People and Buildings","","","","","","","","Architecture and The Built Environment","Real Estate and Housing","","","",""
"uuid:836de9f6-3e5f-4370-9bfa-71d060c3595d","http://resolver.tudelft.nl/uuid:836de9f6-3e5f-4370-9bfa-71d060c3595d","Effect of the BRCA2 CTRD domain on RAD51 filaments analyzed by an ensemble of single molecule techniques","Holthausen, J.T.; Van Loenhout, M.T.J.; Sanchez, H.; Ristic, D.; Van Rossum-Fikkert, S.E.; Modesti, M.; Dekker, C.; Kanaar, R.; Wyman, C.","","2011","Homologous recombination is essential for the preservation of genome stability, thereby preventing cancer. The recombination protein RAD51 drives DNA strand exchange, which requires the assembly, rearrangement and disassembly of a RAD51 filament on DNA, coupled to ATP binding and hydrolysis. This process is facilitated and controlled by recombination mediators and accessory factors. Here, we have employed a range of single molecule techniques to determine the influence of the C-terminal RAD51 interaction domain (CTRD) of the breast cancer tumor suppressor BRCA2 on intrinsic aspects of RAD51-DNA interactions. We show that at high concentration the CTRD entangles RAD51 filaments and reduces RAD51 filament formation in a concentration dependent manner. It does not affect the rate of filament disassembly measured as the loss of fluorescent signal due to intrinsic RAD51 protein dissociation from double-stranded DNA (dsDNA). We conclude that, outside the context of the full-length protein, the CTRD does not reduce RAD51 dissociation kinetics, but instead hinders filament formation on dsDNA. The CTRDs mode of action is most likely sequestration of multiple RAD51 molecules thereby rendering them inactive for filament formation on dsDNA.","","en","journal article","Oxford University Press","","","","","","","","Applied Sciences","BN/Bionanoscience","","","",""
"uuid:d404d31c-2025-455c-8f75-2583098495ce","http://resolver.tudelft.nl/uuid:d404d31c-2025-455c-8f75-2583098495ce","Forced relocation: Reason for dissatisfaction with the dwelling and the neighbourhood? (draft version)","Dekker, K.; Kleinhans, R.","","2010","This paper focuses on the relationship between voluntary and involuntary reasons for relocation, and the satisfaction with the dwelling and the neighbourhood. We distinguish between voluntary reasons to move and forced reasons to move (demolition or renovation versus divorce). While these separate reasons have been extensively studied in the field of urban regeneration and gentrification, life-course studies, or social psychology, forced reasons are hardly studied in direct comparison. We hypothesize that a forced reason to move, net of other factors, initially has a negative effect on the satisfaction with the new dwelling and the new neighbourhood. However, there may be a positive effect of time: the longer ago the forced move, the more positive the evaluation of the dwelling and the neighbourhood. Furthermore, we investigate the extent to which different forced moving reasons (demolition or renovation, divorce) have different effects on satisfaction with the dwelling and the neighbourhood. The analyses are based on the Dutch Housing Survey (2006). The results show that a forced move due to a divorce initially results in lower satisfaction with the dwelling, but this negative effect disappears after a year. A forced move due to renovation or demolition leads is not of influence on the level of satisfaction with the dwelling. Forced and voluntary movers are equally satisfied with the neighbourhood, depending on the evaluation of the characteristics of that neighbourhood.","","en","conference paper","","","","","","","","","","","","","",""
"uuid:1e09fcf1-2147-4a23-a469-741d5a244bf5","http://resolver.tudelft.nl/uuid:1e09fcf1-2147-4a23-a469-741d5a244bf5","Torsional sensing of small-molecule binding using magnetic tweezers","Lipfert, J.; Klijnhout, S.; Dekker, N.H.","","2010","DNA-binding small molecules are widespread in the cell and heavily used in biological applications. Here, we use magnetic tweezers, which control the force and torque applied to single DNAs, to study three small molecules: ethidium bromide (EtBr), a well-known intercalator; netropsin, a minor-groove binding anti-microbial drug; and topotecan, a clinically used anti-tumor drug. In the low-force limit in which biologically relevant torques can be accessed (<10 pN), we show that ethidium intercalation lengthens DNA ~1.5-fold and decreases the persistence length, from which we extract binding constants. Using our control of supercoiling, we measure the decrease in DNA twist per intercalation to be 27.3 ± 1º and demonstrate that ethidium binding delays the accumulation of torsional stress in DNA, likely via direct reduction of the torsional modulus and torque-dependent binding. Furthermore, we observe that EtBr stabilizes the DNA duplex in regimes where bare DNA undergoes structural transitions. In contrast, minor groove binding by netropsin affects neither the contour nor persistence length significantly, yet increases the twist per base of DNA. Finally, we show that topotecan binding has consequences similar to those of EtBr, providing evidence for an intercalative binding mode. These insights into the torsional consequences of ligand binding can help elucidate the effects of small-molecule drugs in the cellular environment.","","en","journal article","Oxford University Press","","","","","","","","Applied Sciences","BN/Bionanoscience","","","",""
"uuid:1a32d601-717c-465a-b81d-c9ac72b4c47b","http://resolver.tudelft.nl/uuid:1a32d601-717c-465a-b81d-c9ac72b4c47b","A commercial spaceflight evangelist; an interview with space tourist Anousheh Ansari","Van Gent, I.; Dekker, S.","","2010","","","en","journal article","Society for Aerospace Engineering Students VSV Leonardo da Vinci","","","","","","","","Aerospace Engineering","","","","",""
"uuid:57a2f9c9-c91f-4150-a0ce-2ada4205ba19","http://resolver.tudelft.nl/uuid:57a2f9c9-c91f-4150-a0ce-2ada4205ba19","Flight forward, the future of air transportation; VSV ""Leonardo da Vinci"" symposium; Delft, March 26th, 2010","Dekker, S.; De Graaf, M.; Van Houten, D.; Van Ettinger, A.","","2010","","","en","journal article","Society for Aerospace Engineering Students VSV Leonardo da Vinci","","","","","","","","Aerospace Engineering","","","","",""
"uuid:ba180658-da35-4470-a3ee-c03c48657e40","http://resolver.tudelft.nl/uuid:ba180658-da35-4470-a3ee-c03c48657e40","Flexible labor and innovation performance: Evidence from longitudinal firm-level data","Dekker, R (Ronald.Dekker@tudelft.nl; TU Delft, Technology, Policy and Management, Innovation Systems); Kleinknecht, A.H. (A.H.Kleinknecht@tudelft.nl; TU Delft, Technology, Policy and Management, Innovation Systems); Zhou, H (Erasmus University Rotterdam, Erasmus School of Economics, CASBEC)","","2010","Firms with high shares of workers on fixed-term contracts have significantly higher sales of imitative new products but perform significantly worse on sales of innovative new products (“first on the market”). High functional flexibility in “insider-outsider” labor markets enhances a firm’s new product sales, as do training efforts and highly educated personnel. We find weak evidence that larger and older firms have higher new product sales than do younger and smaller firms. Our findings should be food for thought to economists making unqualified pleas for the deregulation of labor markets.","Innovation performance; new product sales; numerical flexibility; functional flexibility; SMEs; OSA longitudinal data; RePEc","","working paper","","","","","","","","","","","","","",""
"uuid:69a92955-68cc-4140-b487-d79ee10c6ece","http://resolver.tudelft.nl/uuid:69a92955-68cc-4140-b487-d79ee10c6ece","Building satellites; an interview with Joost Elstak","Van Ettinger, A.; Dekker, S.","","2010","","","en","journal article","Society for Aerospace Engineering Students VSV Leonardo da Vinci","","","","","","","","Aerospace Engineering","","","","",""
"uuid:d6b9ee77-e8c9-4382-9463-ac9b78f28b5a","http://resolver.tudelft.nl/uuid:d6b9ee77-e8c9-4382-9463-ac9b78f28b5a","Torsional regulation of hRPA-induced unwinding of double-stranded DNA","De Vlaminck, I.; Vidic, I.; Van Loenhout, M.T.J.; Kanaar, R.; Lebbink, J.H.G.; Dekker, C.","","2010","All cellular single-stranded (ss) DNA is rapidly bound and stabilized by single stranded DNA-binding proteins (SSBs). Replication protein A, the main eukaryotic SSB, is able to unwind double-stranded (ds) DNA by binding and stabilizing transiently forming bubbles of ssDNA. Here, we study the dynamics of human RPA (hRPA) activity on topologically constrained dsDNA with single-molecule magnetic tweezers. We find that the hRPA unwinding rate is exponentially dependent on torsion present in the DNA. The unwinding reaction is selflimiting, ultimately removing the driving torsional stress. The process can easily be reverted: release of tension or the application of a rewinding torque leads to protein dissociation and helix rewinding. Based on the force and salt dependence of the in vitro kinetics we anticipate that the unwinding reaction occurs frequently in vivo. We propose that the hRPA unwinding reaction serves to protect and stabilize the dsDNA when it is structurally destabilized by mechanical stresses.","","en","journal article","Oxford University Press","","","","","","","","Applied Sciences","BN/Bionanoscience","","","",""
"uuid:0225d5cd-55a9-4c6a-9b61-bbc0dd9b7036","http://resolver.tudelft.nl/uuid:0225d5cd-55a9-4c6a-9b61-bbc0dd9b7036","Controlling nanopore size, shape and stability","Van den Hout, M.; Hall, A.R.; Wu, M.Y.; Zandbergen, H.W.; Dekker, C.; Dekker, N.H.","","2010","Solid-state nanopores are considered a promising tool for the study of biological polymers such as DNA and RNA, due largely to their flexibility in size, potential in device integration and robustness. Here, we show that the precise shape of small nanopores (?5 nm diameter in 20 nm SiN membranes) can be controlled by using transmission electron microscope (TEM) beams of different sizes. However, when some of these small nanopores are immersed in an aqueous solution, their resistance is observed to decrease over time. By comparing nanopores of different shapes using (scanning) TEM both before and after immersion in aqueous solution, we demonstrate that the stability of small nanopores is related to their three-dimensional geometry, which depends on the TEM beam size employed during pore fabrication. Optimal stability is obtained using a TEM beam size of approximately the same size as the intended nanopore diameter. In addition, we show that thermal oxidation can serve as a means to independently control nanopore size following TEM fabrication. These observations provide key guidelines for the fabrication of stable solid-state nanopores on the scale of nucleic acids and small proteins","","en","journal article","Institute of Physics","","","","","","","","Applied Sciences","","","","",""
"uuid:2b09a20e-4ef5-4453-a6f4-af5eb42b650e","http://resolver.tudelft.nl/uuid:2b09a20e-4ef5-4453-a6f4-af5eb42b650e","Note: Interference technique for minimally invasive, subnanometer, microsecond measurements of displacements","Dujovne, I.; Kerssemakers, J.; Capello, G.; Dekker, C.","","2010","We present a novel high-resolution technique for single-molecule experiments, viz., differential traveling wave tracking. This is an interference-based scattering technique where we use gold nanoparticles for high scattering intensities and incorporate differential measurements along one in-plane direction to subtract mechanical noise and drift of the system. In addition, out-of-plane distances are measured via scattered light intensity in a total internal reflectance illumination field. In plane, we demonstrate a rms noise level of only 0.10 nm at 10 kHz and less than 0.5 nm at 600 kHz.","","en","journal article","American Institute of Physics","","","","","","","","Applied Sciences","BN/Bionanoscience","","","",""
"uuid:e21671c4-e29e-4e07-8360-59318b5acd4d","http://resolver.tudelft.nl/uuid:e21671c4-e29e-4e07-8360-59318b5acd4d","Low-frequency noise in solid-state nanopores","Smeets, R.M.M.; Dekker, N.H.; Dekker, C.","","2009","Low-frequency ionic current noise in solid-state nanopores imposes a limitation on the time resolution achieved in translocation experiments. Recently, this 1/ f noise was described as obeying Hooge’s phenomenological relation, where the noise scales inversely with the number of charge carriers present. Here, we consider an alternative model in which the low-frequency noise originates from surface charge fluctuations. We compare the models and show that Hooge’s relation gives the best description for the low-frequency noise in solid-state nanopores over the entire salt regime from 10?3 to 1.6 M KCl.","","en","journal article","Institute of Physics","","","","","","","","Applied Sciences","Kavli Institute of Nanoscience","","","",""
"uuid:a72fa5c1-64d6-43a8-9fe3-389963c254c9","http://resolver.tudelft.nl/uuid:a72fa5c1-64d6-43a8-9fe3-389963c254c9","Three-dimensional Modeling of Anode-supported Planar SOFC with Direct Internal Reforming","Qu, Z.; Aravind, P.V.; Ye, H.; Dekker, N.J.J.; Woudstra, N.; Verkooijen, A.H.M.","","2009","This paper presents a three-dimensional model of an anode-supported planar SOFC with corrugated bipolar plates serving as gas channels and current collector above the active area of the cell, based on the direct internal reforming reaction of methane and the electrochemical reaction of hydrogen. A co-flow system with gas mixture of methane, water vapor and a small amount of hydrogen as anode gas and air as cathode gas fed at an inlet temperature of 973K was modeled at a single cell unit level. A simple equation for the cell resistance with measured values for the quasi ohmic resistance is used for the calculation of the current density. The modeling results show the current density distribution and temperature profiles in the cell and gas concentrations profiles along the length of the cell channel. Furthermore, the temperature gradient inside the cell was investigated.","","en","journal article","The Electrochemical Society","","","","","","","","Mechanical, Maritime and Materials Engineering","Process and Energy","","","",""
"uuid:d27e06f6-dbea-4956-9d1f-83f1a18585cf","http://resolver.tudelft.nl/uuid:d27e06f6-dbea-4956-9d1f-83f1a18585cf","Three-dimensional Modeling of Anode-supported Planar SOFC with Direct Internal Reforming","Qu, Z.; Aravind, P.V.; Ye, H.; Dekker, N.J.J.; Woudstra, N.; Verkooijen, A.H.M.","","2009","","","en","journal article","The Electrochemical Society","","","","","","","","Mechanical, Maritime and Materials Engineering","Process and Energy","","","",""
"uuid:a62960ed-4f24-44a1-b528-3cd148c90a47","http://resolver.tudelft.nl/uuid:a62960ed-4f24-44a1-b528-3cd148c90a47","Bacterial growth and motility in sub-micron constrictions","Männik, J.; Driessen, R.; Galajda, P.; Keymer, J.E.; Dekker, C.","","2009","In many naturally occurring habitats, bacteria live in micrometer-size confined spaces. Although bacterial growth and motility in such constrictions is of great interest to fields as varied as soil microbiology, water purification, and biomedical research, quantitative studies of the effects of confinement on bacteria have been limited. Here, we establish how Gram-negative Escherichia coli and Gram-positive Bacillus subtilis bacteria can grow, move, and penetrate very narrow constrictions with a size comparable to or even smaller than their diameter. We show that peritrichously flagellated E. coli and B. subtilis are still motile in microfabricated channels where the width of the channel exceeds their diameters only marginally (?30%). For smaller widths, the motility vanishes but bacteria can still pass through these channels by growth and division. We observe E. coli, but not B. subtilis, to penetrate channels with a width that is smaller than their diameter by a factor of approximately 2. Within these channels, bacteria are considerably squeezed but they still grow and divide. After exiting the channels, E. coli bacteria obtain a variety of anomalous cell shapes. Our results reveal that sub-micron size pores and cavities are unexpectedly prolific bacterial habitats where bacteria exhibit morphological adaptations.","OA-Fund TU Delft","en","journal article","PNAS","","","","","","","","Applied Sciences","Kavli Institute of Nanoscience Delft","","","",""
"uuid:a921960f-0f16-4ae8-8ba1-91e1a5b4a134","http://resolver.tudelft.nl/uuid:a921960f-0f16-4ae8-8ba1-91e1a5b4a134","Dynamics of RecA filaments on single-stranded DNA","Van Loenhout, M.T.J.; Van der Heijden, T.; Kanaar, R.; Wyman, C.; Dekker, C.","","2009","RecA, the key protein in homologous recombination, performs its actions as a helical filament on single-stranded DNA (ssDNA). ATP hydrolysis makes the RecA–ssDNA filament dynamic and is essential for successful recombination. RecA has been studied extensively by single-molecule techniques on double-stranded DNA (dsDNA). Here we directly probe the structure and kinetics of RecA interaction with its biologically most relevant substrate, long ssDNA molecules. We find that RecA ATPase activity is required for the formation of long continuous filaments on ssDNA. These filaments both nucleate and extend with a multimeric unit as indicated by the Hill coefficient of 5.4 for filament nucleation. Disassembly rates of RecA from ssDNA decrease with applied stretching force, corresponding to a mechanism where protein-induced stretching of the ssDNA aids in the disassembly. Finally, we show that RecA–ssDNA filaments can reversibly interconvert between an extended, ATPbound, and a compressed, ADP-bound state. Taken together, our results demonstrate that ATP hydrolysis has a major influence on the structure and state of RecA filaments on ssDNA.","RecA","en","journal article","","","","","","","","","Applied Sciences","Kavli Institute of Nanoscience","","","",""
"uuid:8a23ad65-9905-49d7-87b8-fd7dca2eff27","http://resolver.tudelft.nl/uuid:8a23ad65-9905-49d7-87b8-fd7dca2eff27","Flexible labor and innovation performance: Evidence from longitudinal firm-level data","Kleinknecht, A.; Dekker, R.; Zhou, H.","","2009","Firms with high shares of workers on fixed-term contracts have significantly higher sales of imitative new products but perform significantly worse on sales of innovative new products (“first on the market”). High functional flexibility in “insider-outsider” labor markets enhances a firm’s new product sales, as do training efforts and highly educated personnel. We find weak evidence that larger and older firms have higher new product sales than do younger and smaller firms. Our findings should be food for thought to economists making unqualified pleas for the deregulation of labor markets.","Innovation performance; new product sales; numerical flexibility","en","journal article","Delft University of Technology","","","","","","","","Technology, Policy and Management","","","","",""
"uuid:5e555f02-8fc1-4c8b-a24c-d774dfb8301e","http://resolver.tudelft.nl/uuid:5e555f02-8fc1-4c8b-a24c-d774dfb8301e","De revolutie van een enkel molecuul","Dekker, N.","","2009","","Intreerede","nl","public lecture","Delft University of Technology","","","","","","","","Applied Sciences","","","","",""
"uuid:ded08214-25e7-47ee-ab86-ea60bcf26e4e","http://resolver.tudelft.nl/uuid:ded08214-25e7-47ee-ab86-ea60bcf26e4e","Acquisitions, Divestitures and Innovation Performance in the Netherlands.","Van Beers, C.; Dekker, R.","","2009","This aim of this paper is twofold. First it examines the determinants of acquisitions and divestitures of Dutch firms in the period 1996-2004. Second, it investigates the impact of acquisitions and divestitures on the firm’s innovative output performance. An econometric model is specified and estimated with Community Innovation Survey data for the Netherlands in the period 1996-2004. The main findings of this study are as follows. First, innovating firms are significantly more involved in acquisition activities than non-innovating firms, which suggests that acquisitions are a strategy to gain access to new technologies or knowledge. Second, lack of knowledge as a barrier to innovate increases the chance of acquiring assets of other firms although not significantly. Lack of finance as a barrier to innovate increases significantly the chance of divesting assets. Third, acquisitions motivated by knowledge barriers in the innovation process affect the probability of positive innovative sales positively while acquisitions motivated by other reasons than innovation barriers affect this probability negatively. No effect of knowledge barriers induced acquisitions on the level of the innovative sales could be found","","en","journal article","Delft University of Technology","","","","","","","","Technology, Policy and Management","","","","",""
"uuid:5018c9e7-28ac-49cb-bb7d-b86ebe41d2a5","http://resolver.tudelft.nl/uuid:5018c9e7-28ac-49cb-bb7d-b86ebe41d2a5","Reinitiated viral RNA-dependent RNA polymerase resumes replication at a reduced rate","Vilfan, I.D.; Candelli, A.; Hage, S.; Aalto, A.P.; Poranen, M.M.; Bamford, D.H.; Dekker, N.H.","","2008","RNA-dependent RNA polymerases (RdRP) form an important class of enzymes that is responsible for genome replication and transcription in RNA viruses and involved in the regulation of RNA interference in plants and fungi. The RdRP kinetics have been extensively studied, but pausing, an important regulatory mechanism for RNA polymerases that has also been implicated in RNA recombination, has not been considered. Here, we report that RdRP experience a dramatic, long-lived decrease in its elongation rate when it is reinitiated following stalling. The rate decrease has an intriguingly weak temperature dependence, is independent of both the nucleotide concentration during stalling and the length of the RNA transcribed prior to stalling; however it is sensitive to RNA structure. This allows us to delineate the potential factors underlying this irreversible conversion of the elongation complex to a less active mode.","","en","journal article","Oxford University Press","","","","","","","","Applied Sciences","Kavli Institute of Nanoscience","","","",""
"uuid:861bee3e-a2c4-41e0-ae79-884ecba82e48","http://resolver.tudelft.nl/uuid:861bee3e-a2c4-41e0-ae79-884ecba82e48","Controlling the surface properties of nanostructures for studies of polymerases","Crut, A.; Koster, D.A.; Huang, Z.; Hage, S.; Dekker, N.H.","","2008","","","en","journal article","IOP","","","","","","","","Applied Sciences","","","","",""
"uuid:18accdb4-9cb9-4d6f-b863-db9958f647c9","http://resolver.tudelft.nl/uuid:18accdb4-9cb9-4d6f-b863-db9958f647c9","Single-Molecule Observation of Anomalous Electrohydrodynamic Orientation of Microtubules","Van den Heuvel, M.G.L.; Bondesan, R.; Lagomarsino, M.C.; Dekker, C.","","2008","We use fluorescence microscopy to measure the orientation and shape of microtubules—which serve as a model system for semiflexible rods—that are electrophoretically driven. Surprisingly, a bimodal orientation distribution is observed, with microtubules in either parallel or perpendicular orientations to the electric field. The occupancy of these states varies nonmonotonically with the microtubule length L and the electric field E. We also observe a surprising bending deformation of microtubules. Interestingly, all data collapse onto a universal scaling curve when the average alignment is plotted as a function of B - EL3, which reflects the ratio between the driving force and a restoring elastic force. Our results have important implications for the interpretation of electrical birefringence experiments and, more generally, for a better understanding of the electrokinetics of rods.","","en","journal article","American Physical Society","","","","","","","","Applied Sciences","Kavli Institute of Nanoscience Delft","","","",""
"uuid:4be0798b-b9b8-41a4-8314-3f406290951f","http://resolver.tudelft.nl/uuid:4be0798b-b9b8-41a4-8314-3f406290951f","Conformation and Dynamics of DNA Confined in Slitlike Nanofluidic Channels","Bonthuis, D.J.; Meyer, C.; Stein, D.; Dekker, C.","","2008","Using laser fluorescence microscopy, we study the shape and dynamics of individual DNA molecules in slitlike nanochannels confined to a fraction of their bulk radius of gyration. With a confinement size spanning 2 orders of magnitude, we observe a transition from the de Gennes regime to the Odijk regime in the scaling of both the radius of gyration and the relaxation time. The radius of gyration and the relaxation time follow the predicted scaling in the de Gennes regime, while, unexpectedly, the relaxation time shows a sharp decrease in the Odijk regime. The radius of gyration remains constant in the Odijk regime. Additionally, we report the first measurements of the effect of confinement on the shape anisotropy.","","en","journal article","American Physical Society","","","","","","","","Applied Sciences","Kavli Institute of Nanoscience Delft","","","",""
"uuid:ad9976fb-37f8-4249-ac0c-27842df2ebd8","http://resolver.tudelft.nl/uuid:ad9976fb-37f8-4249-ac0c-27842df2ebd8","Dataset Preservation for the Long Term: Results of the DareLux Project","Van der Meer, K.; Luxemburg, W.; Dekker, R.; Dürr, E.","","2008","The purpose of the DareLux (Data Archiving River Environment Luxembourg) Project was the preservation of unique and irreplaceable datasets, for which we chose hydrology data that will be required to be used in future climatic models. The results are: an operational archive built with XML containers, the OAI-PMH protocol and an architecture based upon web services. Major conclusions are: quality control on ingest is important; digital rights management demands attention; and cost aspects of ingest and retrieval cannot be underestimated. We propose a new paradigm for information retrieval of this type of dataset. We recommend research into visualisation tools for the search and retrieval of this type of dataset.","","en","journal article","UKOLN University of Bath","","","","","","","","Delft University of Technology","","","","",""
"uuid:9a4cc8f2-ae8d-4349-8627-7dea96bdce13","http://resolver.tudelft.nl/uuid:9a4cc8f2-ae8d-4349-8627-7dea96bdce13","Circuit: The ?SCOPE: A poor man's oscilloscope","Dekker, R.","","2008","The oscilloscope is still one of the most important measurement tools of the electronic engineer. With the advent of the often very reasonably priced USB scopes, such an instrument is now within reach of everybody. Twentyfive years ago that was quite a different story. A (good) oscilloscope was then a very expensive instrument available only to a happy few. As a result many electronics hobbyist made their own scope. The popular electronics magazines in the sixties and seventies were full of scope designs almost always based on vacuum tubes. This period was closed in 1975 when the Dutch electronics magazine Elektuur (in the rest of the world known as Elektor) published their fully transistorised “Elektorscoop”. Despite all this, the purchase of a cathode ray tube and Special high voltage transformer remained too expensive for many people.","","en","journal article","Delft University of Technology","","","","","","","","Electrical Engineering, Mathematics and Computer Science","","","","",""
"uuid:43f36586-aad3-40fe-91cc-91f05285e5f2","http://resolver.tudelft.nl/uuid:43f36586-aad3-40fe-91cc-91f05285e5f2","PARAP-levensduurkostenmodel: Besluitvormingsondersteunend instrument voor huisvesting van kantoororganisaties. Handleiding en verantwoording","Bijleveld, S.W.; Dekker, K.; Gerritse, K.; van Houten, W.; Melis, R.; Meijer, W.; Vonk, M.","","2008","","","nl","report","Center for People and Buildings","","","","","","","","Architecture and The Built Environment","Real Estate and Housing","","","",""
"uuid:2004af16-a103-4fff-bb59-57888a96d2dc","http://resolver.tudelft.nl/uuid:2004af16-a103-4fff-bb59-57888a96d2dc","Motor step size and ATP coupling efficiency of the dsDNA translocase EcoR124I","Seidel, R.; Bloom, J.G.P.; Dekker, C.; Szczelkun, M.D.","","2008","The Type I restriction-modification enzyme EcoR124I is an archetypical helicase-based dsDNA translocase that moves unidirectionally along the 3'–5' strand of intact duplex DNA. Using a combination of ensemble and single-molecule measurements, we provide estimates of two physicochemical constants that are fundamental to a full description of motor protein activity—the ATP coupling efficiency (the number of ATP consumed per base pair) and the step size (the number of base pairs transported per motor step). Our data indicate that EcoR124I makes small steps along the DNA of 1 bp in length with 1 ATP consumed per step, but with some uncoupling of the ATPase and translocase cycles occurring so that the average number of ATP consumed per base pair slightly exceeds unity. Our observations form a framework for understanding energy coupling in a great many other motors that translocate along dsDNA rather than ssDNA.","ATPase; helicase; molecular motor; single molecule; stopped flow","en","journal article","Nature Publishing Group","","","","","","","","Applied Sciences","Kavli Institute of Nanoscience Delft","","","",""
"uuid:6d59c99f-0828-42c3-b60f-ab9e803da03e","http://resolver.tudelft.nl/uuid:6d59c99f-0828-42c3-b60f-ab9e803da03e","Moore with less silicon: How the silicon substrate slowly comes alive","Dekker, R.","","2008","There has been much attention for the tremendous developments integrated circuit technology has went through. The focus is always on the size and speed of the devices. In past years, however, the substrate itself also underwent remarkable developments. This has resulted in silicon-on-glass technology and flexible circuits. The future holds even more, with stretchable circuits and even LivingChips on the horizon. The following article presents an overview.","","en","journal article","Delft University of Technology","","","","","","","","Electrical Engineering, Mathematics and Computer Science","","","","",""
"uuid:1275d50c-bdc3-4270-90a3-f2f0e6c51dac","http://resolver.tudelft.nl/uuid:1275d50c-bdc3-4270-90a3-f2f0e6c51dac","Single-molecule observations of topotecan-mediated TopIB activity at a unique DNA sequence","Koster, D.A.; Czerwinski, F.; Halby, L.; Crut, A.; Vekhoff, P.; Palle, K.; Arimondo, P.B.; Dekker, N.H.","","2008","The rate of DNA supercoil removal by human topoisomerase IB (TopIB) is slowed down by the presence of the camptothecin class of antitumor drugs. By preventing religation, these drugs also prolong the lifetime of the covalent TopIB–DNA complex. Here, we use magnetic tweezers to measure the rate of supercoil removal by drugbound TopIB at a single DNA sequence in real time. This is accomplished by covalently linking camptothecins to a triple helix-forming oligonucleotide that binds at one location on the DNA molecule monitored. Surprisingly, we find that the DNA dynamics with the TopIB–drug interaction restricted to a single DNA sequence are indistinguishable from the dynamics observed when the TopIB–drug interaction takes place at multiple sites. Specifically, the DNA sequence does not affect the instantaneous supercoil removal rate or the degree to which camptothecins increase the lifetime of the covalent complex. Our data suggest that sequencedependent dynamics need not to be taken into account in efforts to develop novel camptothecins.","","en","journal article","Oxford University Press","","","","","","","","Applied Sciences","Kavli Institute of Nanotechnology Delft","","","",""
"uuid:ae3592dd-2315-4e0c-8f31-fe9bdf8fcea5","http://resolver.tudelft.nl/uuid:ae3592dd-2315-4e0c-8f31-fe9bdf8fcea5","End-joining long nucleic acid polymers","Van den Hout, M.; Hage, S.; Dekker, C.; Dekker, N.H.","","2008","Many experiments involving nucleic acids require the hybridization and ligation of multiple DNA or RNA molecules to form a compound molecule. When one of the constituents is single stranded, however, the efficiency of ligation can be very low and requires significant individually tailored optimization. Also, when the molecules involved are very long (>10 kb), the reaction efficiency typically reduces dramatically. Here, we present a simple procedure to efficiently and specifically end-join two different nucleic acids using the well-known biotin–streptavidin linkage. We introduce a twostep approach, in which we initially bind only one molecule to streptavidin (STV). The second molecule is added only after complete removal of the unbound STV. This primarily forms heterodimers and nearly completely suppresses formation of unwanted homodimers. We demonstrate that the joining efficiency is 50 plus/minus25% and is insensitive to molecule length (up to at least 20 kb). Furthermore, our method eliminates the requirement for specific complementary overhangs and can therefore be applied to both DNA and RNA. Demonstrated examples of the method include the efficient end-joining of DNA to single-stranded and double-stranded RNA, and the joining of two double-stranded RNA molecules. End-joining of long nucleic acids using this procedure may find applications in bionanotechnology and in single-molecule experiments.","","en","journal article","Oxford University Press","","","","","","","","Applied Sciences","Kavli Institute of Nanoscience Delft","","","",""
"uuid:433a0dd7-c2fd-4b14-a2eb-f02e5862bf13","http://resolver.tudelft.nl/uuid:433a0dd7-c2fd-4b14-a2eb-f02e5862bf13","The ERTMS railway signaling system: Deals on wheels? An inquiry into the safety architecture of high speed train safety","Stoop, J.A.A.M.; Dekker, S.","","2008","","","en","conference paper","Mines Pris, Les presses, Collection Science Economiques","","","","","","","","Aerospace Engineering","","","","",""
"uuid:5938392b-07cc-4913-9ccd-62d458b247b3","http://resolver.tudelft.nl/uuid:5938392b-07cc-4913-9ccd-62d458b247b3","Reinitiated viral RNA-dependent RNA polymerase resumes replication at a reduced rate","Vilfan, I.D.; Candelli, A.; Hage, S.; Aalto, A.P.; Poranen, M.M.; Bamford, D.H.; Dekker, N.H.","","2008","RNA-dependent RNA polymerases (RdRP) form an important class of enzymes that is responsible for genome replication and transcription in RNA viruses and involved in the regulation of RNA interference in plants and fungi. The RdRP kinetics have been extensively studied, but pausing, an important regulatory mechanism for RNA polymerases that has also been implicated in RNA recombination, has not been considered. Here, we report that RdRP experience a dramatic, long-lived decrease in its elongation rate when it is reinitiated following stalling. The rate decrease has an intriguingly weak temperature dependence, is independent of both the nucleotide concentration during stalling and the length of the RNA transcribed prior to stalling; however it is sensitive to RNA structure. This allows us to delineate the potential factors underlying this irreversible conversion of the elongation complex to a less active mode.","","en","journal article","","","","","","","","","Applied Sciences","Kavli Intsitute of Nanoscience Delft","","","",""
"uuid:57b238fb-1295-4f80-a53a-83e07466ec06","http://resolver.tudelft.nl/uuid:57b238fb-1295-4f80-a53a-83e07466ec06","An RNA toolbox for single-molecule force spectroscopy studies","Vilfan, I.D.; Kamping, W.; Van den Hout, M.; Candelli, A.; Hage, S.; Dekker, N.H.","","2007","Precise, controllable single-molecule force spectroscopy studies of RNA and RNA-dependent processes have recently shed new light on the dynamics and pathways of RNA folding and RNAenzyme interactions. A crucial component of this research is the design and assembly of an appropriate RNA construct. Such a construct is typically subject to several criteria. First, single-molecule force spectroscopy techniques often require an RNA construct that is longer than the RNA molecules used for bulk biochemical studies. Next, the incorporation of modified nucleotides into the RNA construct is required for its surface immobilization. In addition, RNA constructs for singlemolecule studies are commonly assembled from different single-stranded RNA molecules, demanding good control of hybridization or ligation. Finally, precautions to prevent RNase- and divalent cationdependent RNA digestion must be taken. The rather limited selection of molecular biology tools adapted to the manipulation of RNA molecules, as well as the sensitivity of RNA to degradation, make RNA construct preparation a challenging task. We briefly illustrate the types of single-molecule force spectroscopy experiments that can be performed on RNA, and then present an overview of the toolkit of molecular biology techniques at one’s disposal for the assembly of such RNA constructs. Within this context, we evaluate the molecular biology protocols in terms of their effectiveness in producing long and stable RNA constructs.","","en","journal article","Oxford University Press","","","","","","","","Applied Sciences","Kavli Institute of Nanoscience Delft","","","",""
"uuid:df035d76-0295-4769-9ba5-a01505b9b6f8","http://resolver.tudelft.nl/uuid:df035d76-0295-4769-9ba5-a01505b9b6f8","Carbon nanotube biosensors: The critical role of the reference electrode","Minot, E.D.; Janssens, A.M.; Heller, I.; Heering, H.A.; Dekker, C.; Lemay, S.G.","","2007","Carbon nanotube transistors show tremendous potential for electronic detection of biomolecules in solution. However, the nature and magnitude of the sensing signal upon molecular adsorption have so far remained controversial. Here, the authors show that the choice of the reference electrode is critical and resolves much of the previous controversy. The authors eliminate artifacts related to the reference electrode by using a well-defined reference electrode to accurately control the solution potential. Upon addition of bovine serum albumin proteins, the authors measure a transistor threshold shift of ?15?mV which can be unambiguously attributed to the adsorption of biomolecules in the vicinity of the nanotube.","biomedical electrodes; biosensors; carbon nanotubes; nanobiotechnology","en","journal article","American Institute of Physics","","","","","","","","Applied Sciences","Kavli Institute of Nanoscience","","","",""
"uuid:0b43597d-ea93-4ce3-ac45-8f5461ce1d02","http://resolver.tudelft.nl/uuid:0b43597d-ea93-4ce3-ac45-8f5461ce1d02","Real-time assembly and disassembly of human RAD51 filaments on individual DNA molecules","Van der Heijden, T.; Seidel, R.; Modesti, M.; Kanaar, R.; Wyman, C.; Dekker, C.","","2007","The human DNA repair protein RAD51 is the crucial component of helical nucleoprotein filaments that drive homologous recombination. The molecular mechanistic details of how this structure facilitates the requisite DNA strand rearrangements are not known but must involve dynamic interactions between RAD51 and DNA. Here, we report the real-time kinetics of human RAD51 filament assembly and disassembly on individual molecules of both single- and double-stranded DNA, as measured using magnetic tweezers. The relative rates of nucleation and filament extension are such that the observed filament formation consists of multiple nucleation events that are in competition with each other. For varying concentration of RAD51, a Hill coefficient of 4.3±0.5 is obtained for both nucleation and filament extension, indicating binding to dsDNA with a binding unit consisting of multiple (?4) RAD51 monomers. We report Monte Carlo simulations that fit the (dis)assembly data very well. The results show that, surprisingly, human RAD51 does not form long continuous filaments on DNA. Instead each nucleoprotein filament consists of a string of many small filament patches that are only a few tens of monomers long. The high flexibility and dynamic nature of this arrangement is likely to facilitate strand exchange.","","en","journal article","Oxford University Press","","","","","","","","Applied Sciences","Kavli Institute of Nanoscience Delft","","","",""
"uuid:5b4c57ea-e719-40e9-82a6-1eedbeb36151","http://resolver.tudelft.nl/uuid:5b4c57ea-e719-40e9-82a6-1eedbeb36151","Mobility in a labour market with non-standard jobs: A panel data analysis for the Netherlands","Dekker, R.","","2007","In the last 25 years the number of flexible jobs has been expanding in most European countries. For example, in the Netherlands in 1995, about 11 per cent of workers was working in a fixed-term temporary job and about 37 per cent of workers was working in a part-time job. Seven years later, in 2002 these percentages had increased to 14 per cent and 44 per cent. It should be noted however, that the increase in temporary jobs already reached 13 per cent in 1998 and is fairly stable since, whereas the percentage of part-time jobs is still increasing in 2002. For the purpose of this paper, the focus will be on several forms of contractual flexibilisation: temporary contracts , small part-time contracts , on-call and replacement contracts, casual and seasonal work and work with temporary work agencies. These jobs are all defined as non-standard employment.","Labor and Demographic Economics > J6 - Mobility; Unemployment; Vacancies; Job; Occupational; Intergenerational Mobility","en","report","","","","","","","","","Technology, Policy and Management","","","","",""
"uuid:ef161bfe-883c-4596-b0a6-f723bc1b87b3","http://resolver.tudelft.nl/uuid:ef161bfe-883c-4596-b0a6-f723bc1b87b3","Role of tension and twist in single-molecule DNA condensation","Besteman, K.; Hage, S.; Dekker, N.H.; Lemay, G.","","2007","","","en","journal article","American Physical Society","","","","","","","","Applied Sciences","","","","",""
"uuid:d0edea80-40a8-49ee-a11c-7aecd7260eb7","http://resolver.tudelft.nl/uuid:d0edea80-40a8-49ee-a11c-7aecd7260eb7","The importance of having data-sets.","Dekker, R.","","2006","Much scientific research is based on the gathering and analysis of measurement data. Scientific data-sets are, at least, intermediate results in many scientific research projects. For some time data-sets weren’t even published and even if they were published it was mostly as a (not re-usable) by-product of the publication. But an interesting phenomenon might be observed here: data-sets (often in combination with models and parameters) are becoming more important themselves and can sometimes be seen as the primary intellectual output of the research. Publishing and preserving data-sets should therefore seriously be considered. This will especially be the case if the data cannot be reproduced (as they result from unique events) and will be necessary in the future for longitudinal research or to test or check future insights.","","en","conference paper","IATUL","","","","","","","","Delft University of Technology","","","","",""
"uuid:cd80acb6-5724-40e6-ad0a-b736f9bb3e6c","http://resolver.tudelft.nl/uuid:cd80acb6-5724-40e6-ad0a-b736f9bb3e6c","Arbeidsproductiviteit en gebouw: Een exploratieve studie in de verpleegzorg","Achterberg, J.; Dekker, K.; Pullen, W.R.","","2006","Dit rapport bevat de resultaten van een exploratieve studie over de relatie tussen de ontwikkeling van arbeidsproductiviteit in de verpleegzorg als gevolg van interventies in de de gebouwde omgeving.","","nl","report","Center for People and Buildings","","","","","","","","Architecture and The Built Environment","Real Estate and Housing","","","",""
"uuid:3b18e40f-8740-490c-9ff7-f325e0b4e789","http://resolver.tudelft.nl/uuid:3b18e40f-8740-490c-9ff7-f325e0b4e789","Charge inversion at high ionic strength studied by streaming currents","van der Heyden, F.H.J.; Stein, D.; Besteman, K.; Lemay, S.G.; Dekker, C.","","2006","","","en","journal article","American Physical Society","","","","","","","","Applied Sciences","Kavli Institute of Nanoscience Delft","","","",""
"uuid:980b6834-d436-48f4-a9e0-4b6e82cebb2e","http://resolver.tudelft.nl/uuid:980b6834-d436-48f4-a9e0-4b6e82cebb2e","Tunneling in suspended carbon nanotubes assisted by longitudinal phonons","Sapmaz, S.; Jarillo-Herrero, P.; Blanter, Ya.M.; Dekker, C.; van der Zant, H.S.J.","","2006","","","en","journal article","American Physical Society","","","","","","","","Applied Sciences","","","","",""
"uuid:7b70c53a-b7ba-4633-88c5-dabc784d2f69","http://resolver.tudelft.nl/uuid:7b70c53a-b7ba-4633-88c5-dabc784d2f69","Nanobubbles in solid-state nanopores","Smeets, R.M.M.; Keyser, U.F.; Wu, M.Y.; Dekker, N.H.; Dekker, C.","","2006","","","en","journal article","American Physical Society","","","","","","","","Applied Sciences","","","","",""
"uuid:3cd566af-b632-41f5-ae52-1f23b363d320","http://resolver.tudelft.nl/uuid:3cd566af-b632-41f5-ae52-1f23b363d320","Multiple events on single molecules: Unbiased estimation in single-molecule biophysics","Koster, D.A.; Wiggins, C.H.; Dekker, N.H.","","2006","","","en","journal article","The National Academy of Sciences of the USA","","","","","","","","Applied Sciences","","","","",""
"uuid:d40f8cc3-2b29-4849-8662-7e009add6d2a","http://resolver.tudelft.nl/uuid:d40f8cc3-2b29-4849-8662-7e009add6d2a","Structural analysis of hyperperiodic DNA from Caenorhabditis elegans.","Moreno-Herrero, F.; Seidel, R.; Johnson, S.M.; Fire, A.; Dekker, N.H.","","2006","","","en","journal article","PubMed","","","","","","","","Applied Sciences","","","","",""
"uuid:f16ef251-80da-4c1c-8351-44886c3b8fe9","http://resolver.tudelft.nl/uuid:f16ef251-80da-4c1c-8351-44886c3b8fe9","Process for creating a double-stranded polyribonucleotide sequence with terminal overhang, as well as a process for creating a double-stranded polynucleotide construct and an application","Dekker, N.H.; Veenhuizen, P.","","2005","The invention relates to a process for creating double-stranded RNA (16) having a terminal overhang. In accordance with the invention a DNA amplification is used for this purpose, followed by a transcription of the amplified DNA. When amplifying the DNA, primer pairs are used and care is taken that additional sequences (18, 19) are present that will ultimately provide the terminal overhangs.","","en","patent","European Patent Office","","","","","","","","Applied Sciences","","","","",""
"uuid:2ef7274a-e99f-444a-8827-2eb37345975f","http://resolver.tudelft.nl/uuid:2ef7274a-e99f-444a-8827-2eb37345975f","Productieberekeningen hydraulische randvoorwaarden 2006 IJburg en de Eem (RI-4393A): Hoofdrapport + bijlage bij hoofdrapport","Schijndel, S.A.H. van.; Smale, A.; Vuren, S. van.; Dekker, J.; Zijlstra, R.","","2005","","hydraulisch onderzoek; hydraulic research; waterkeringen; flood protection works; risico-analyse; risk analysis; IJburg","nl","report","Deltares (WL)","","","","","","","","","","","","",""
"uuid:b54ea021-e1a6-43cf-bbb4-643a53123336","http://resolver.tudelft.nl/uuid:b54ea021-e1a6-43cf-bbb4-643a53123336","Beyond the photocopy machine revisited: Document delivery in a digital library environment","Delhez, A.N.; De Leeuwe, J.; Dekker, R.","","2005","Purpose – To discuss the recent strategic developments of Library at TU Delft. Design/methodology/approach – Developments at TU Delft are contrasted with the five key requirements for document delivery identified in an earlier article in 2001. Findings – That the strategy in most libraries is to evolve rapidly to a digital library as far as possible. That there is still an important role for libraries as document suppliers. That much discussion between libraries and suppliers will be necessary in order to give document delivery a stable position within the digital library. Originality/value – Gives an insight into the working and thinking of a major European document supplier operating from the Technical University in Delft.","electronic document delivery; digital libraries; interlending; university libraries","en","journal article","Emerald","","","","","","","","","","","","",""
"uuid:d2a4a5ac-63c4-4818-8d6c-91018fee2cb5","http://resolver.tudelft.nl/uuid:d2a4a5ac-63c4-4818-8d6c-91018fee2cb5","Hand supports to assist toilet use among the elderly","Dekker, D.; Buzink, S.N.; Molenbroek, J.F.M.; De Bruin, R.","","2005","Improving the toilet environment holds promises for increasing the quality of life for elderly and disabled persons. This is one of the goals of the Friendly Rest Room (FRR) project. The study described in this article explored the preference and use of supports in the toilet environment during the entire toilet ritual. An adjustable test frame was built with a toilet and three types of supports. Fourteen subjects were asked which positions they favoured for each support. After using all three supports they were asked which support they found most comfortable. In general, the preferred positions depended on personal preferences more than on dimensions of the body. It was concluded that there is a preference for vertical supports for sitting down and standing up. During toilet use the side supports were equally appreciated.","support; toilet; elderly","en","journal article","Elsevier","","","","","","","","Industrial Design Engineering","Industrial Design","","","",""
"uuid:ff610e7b-cbc5-4a78-a53a-d241744e463c","http://resolver.tudelft.nl/uuid:ff610e7b-cbc5-4a78-a53a-d241744e463c","Electron-beam-induced deformations of SiO2 nanostructures","Storm, A.J.; Chen, J.H.; Ling, X.S.; Zandbergen, H.W.; Dekker, C.","","2005","The imaging beam of a transmission electron microscope can be used to fine tune critical dimensions in silicon oxide nanostructures. This technique is particularly useful for the fabrication of nanopores with single-nanometer precision, down to 2 nm. We report a detailed study on the effect of electron-beam irradiation on apertures with various geometries. We show that, on the same wafer, pores that are smaller than a certain critical size shrink and that larger ones expand. Our results are in agreement with the hypothesis that surface-tension effects drive the modifications. Additionally, we have determined the chemical composition in the pore region before and after modifications and found no significant changes. This result proves that contamination growth is not the underlying mechanism of pore closure.","silicon compounds; electron beam effects; deformation; transmission electron microscopy; surface tension; chemical analysis; nanoporous materials; nanotechnology","en","journal article","American Institute of Physics","","","","","","","","Applied Sciences","Kavli Institute of Nanoscience","","","",""
"uuid:7224341e-cd4d-4d4e-a5ba-f262ee089305","http://resolver.tudelft.nl/uuid:7224341e-cd4d-4d4e-a5ba-f262ee089305","Port investment: Towards an integrated planning of port capacity","Dekker, S.","Sanders, F.M. (promotor)","2005","This study supports strategic planning of a node in a transportation network. It contributes to this by the development of a methodology for planning of port capacity in which port-commercial and public interests are integrated. The focus is the reaction of a single port on a change in the transportation network. A scenario for such change, which has been worked out, is the entry of new routes via a competing port in addition to expected demand growth. The proposed methodology is based on analysis with a partial equilibrium model. This modeling approach building on partial approaches for network design, capacity expansion, transportation modeling and investment financing addresses the simultaneous solution of determining 1) the optimal port expansion size, and 2) the investment recovery period. An application has been carried out to a hypothetical expansion of Rotterdam port to demonstrate the methodology and to illustrate trade offs in a ports investment planning.","Port investment; capacity planning; infrastructure","en","doctoral thesis","","","","","","","","","Civil Engineering and Geosciences","","","","",""
"uuid:5ad1bb5f-2b85-453a-a2ab-074db3f456f7","http://resolver.tudelft.nl/uuid:5ad1bb5f-2b85-453a-a2ab-074db3f456f7","Integration of a gate electrode into carbon nanotube devices for scanning tunneling microscopy","Kong, J.; LeRoy, B.J.; Lemay, S.G.; Dekker, C.","","2005","We have developed a fabrication process for incorporating a gate electrode into suspended single-walled carbon nanotube structures for scanning tunneling spectroscopy studies. The nanotubes are synthesized by chemical vapor deposition directly on a metal surface. The high temperature (800?°C) involved in the growth process poses challenging issues such as surface roughness and integrity of the structure which are addressed in this work. We demonstrate the effectiveness of the gate on the freestanding part of the nanotubes by performing tunneling spectroscopy that reveals Coulomb blockade diamonds. Our approach enables combined scanning tunneling microscopy and gated electron transport investigations of carbon nanotubes.","platinum; carbon nanotubes; nanotube devices; metallic thin films; chemical vapour deposition; surface roughness; Coulomb blockade; scanning tunnelling spectroscopy","en","journal article","American Institute of Physics","","","","","","","","Applied Sciences","Kavli Institute of Nanoscience","","","",""
"uuid:9d097a23-9d5e-478d-bdd7-4b02118c303b","http://resolver.tudelft.nl/uuid:9d097a23-9d5e-478d-bdd7-4b02118c303b","Torque-limited RecA polymerization on dsDNA","van der Heijden, T.; van Noort, J.; van Leest, H.; Kanaar, R.; Wyman, C.; Dekker, N.H.; Dekker, N.; Dekker, C.","","2005","","","en","journal article","Oxford University Press","","","","","","","","","","","","",""
"uuid:f57fb569-5beb-4a0c-af4b-2a328b0f9fe5","http://resolver.tudelft.nl/uuid:f57fb569-5beb-4a0c-af4b-2a328b0f9fe5","Electronic excitation spectrum of metallic carbon nanotubes","Sapmaz, S.; Jarillo-Herrero, P.; Kong, J.; Dekker, C.; Kouwenhoven, L.P.; van der Zant, H.S.J.","","2005","","","en","journal article","American Physical Society","","","","","","","","","","","","",""
"uuid:7994ded7-a7f8-411e-9f06-680171a145fe","http://resolver.tudelft.nl/uuid:7994ded7-a7f8-411e-9f06-680171a145fe","Single-Molecule Measurements of the Persistence Length of Double-Stranded RNA","Abels, J.A.; Moreno-Herrero, F.; van der Heijden, T.; Dekker, C.; Dekker, N.H.","","2005","","","en","journal article","Biophysical Society","","","","","","","","","","","","",""
"uuid:fc78493e-d735-42bf-8ad9-97e3f7c4e677","http://resolver.tudelft.nl/uuid:fc78493e-d735-42bf-8ad9-97e3f7c4e677","Three-terminal scanning tunneling spectroscopy of suspended carbon nanotubes","LeRoy, B.J.; Kong, J.; Pahilwani, V.K.; Dekker, C.; Lemay, S.G.","","2005","","","en","journal article","American Physical Society","","","","","","","","","","","","",""
"uuid:c5f2cfda-e0c6-43db-9b16-71a591673606","http://resolver.tudelft.nl/uuid:c5f2cfda-e0c6-43db-9b16-71a591673606","Electronic transport spectroscopy of carbon nanotubes in a magnetic field","Jarillo-Herrero, P.; Kong, J.; van der Zant, H.S.J.; Dekker, C.; Kouwenhoven, L.P.; De Franceschi, S.","","2005","","","en","journal article","American Physical Society","","","","","","","","","","","","",""
"uuid:d92ad301-1f32-4141-8244-9a3623dbd797","http://resolver.tudelft.nl/uuid:d92ad301-1f32-4141-8244-9a3623dbd797","Streaming currents in a single nanofluidic channel","Van der Heyden, F.H.J.; Stein, D.; Dekker, C.","","2005","","","en","journal article","American Physical Society","","","","","","","","","","","","",""
"uuid:f1ff3d23-5324-4c10-9037-2c0caddc38eb","http://resolver.tudelft.nl/uuid:f1ff3d23-5324-4c10-9037-2c0caddc38eb","Translocation of double-strand DNA through a silicon oxide nanopore","Storm, A.J.; Chen, J.H.; Zandbergen, H.W.; Dekker, C.","","2005","","","en","journal article","American Physical Society","","","","","","","","","","","","",""
"uuid:2488ce6a-b121-4b85-af7f-f809725371c6","http://resolver.tudelft.nl/uuid:2488ce6a-b121-4b85-af7f-f809725371c6","Atomic force microscopy shows that vaccinia topoisomerase IB generates filaments on DNA in a cooperative fashion","Moreno-Herrero, F.; Holtzer, L.; Koster, D.A.; Shuman, S.; Dekker, C.; Dekker, N.H.","","2005","","","en","journal article","Oxford University Press","","","","","","","","","","","","",""
"uuid:362dcfc0-1d06-4593-b2bd-ef4c8b033991","http://resolver.tudelft.nl/uuid:362dcfc0-1d06-4593-b2bd-ef4c8b033991","Scanning tunneling spectroscopy of suspended single-wall carbon nanotubes","LeRoy, B.J.; Lemay, S.G.; Kong, J.; Dekker, C.","","2004","We have performed low-temperature scanning tunneling microscopy measurements on single-wall carbon nanotubes that are freely suspended over a trench. The nanotubes were grown by chemical vapor deposition on a Pt substrate with predefined trenches etched into it. Atomic resolution was obtained on the freestanding portions of the nanotubes. Spatially resolved spectroscopy on the suspended portion of both metallic and semiconducting nanotubes was also achieved, showing a Coulomb-staircase behavior superimposed on the local density of states. The spacing of the Coulomb blockade peaks changed with tip position reflecting a changing tip-tube capacitance.","carbon nanotubes; scanning tunnelling microscopy; Coulomb blockade; scanning tunnelling spectroscopy","en","journal article","American Institute of Physics","","","","","","","","Applied Sciences","Kavli Institute of Nanoscience","","","",""
"uuid:25c5a878-119c-416c-926d-adbb977cde69","http://resolver.tudelft.nl/uuid:25c5a878-119c-416c-926d-adbb977cde69","Dual architectural roles of HU: Formation of flexible hinges and rigid filaments","van Noort, J.; Verbrugge, S.; Goosen, N.; Dekker, C.; Dame, R.T.","","2004","","","en","journal article","The National Academy of Sciences","","","","","","","","Applied Sciences","","","","",""
"uuid:d7d59a8d-8123-46bc-ac41-09ccd5811e3a","http://resolver.tudelft.nl/uuid:d7d59a8d-8123-46bc-ac41-09ccd5811e3a","Surface-Charge-Governed Ion Transport in Nanofluidic Channels","Stein, D.; Kruithof, M.; Dekker, C.","","2004","","","en","journal article","American Physical Society","","","","","","","","Applied Sciences","","","","",""
"uuid:585e38f8-1e6f-41bc-a0d2-5c1cad697e05","http://resolver.tudelft.nl/uuid:585e38f8-1e6f-41bc-a0d2-5c1cad697e05","A back-wafer contacted silicon-on-glass integrated bipolar process. Part I. The conflict electrical versus thermal isolation","Nanver, L.K.; Nenadovic, N.; d'Alessandro, V.; Schellevis, H.; van Zeijl, H.W.; Dekker, R.; de Mooij, D.B.; Zieren, V.; Slotboom, J.W.","","2004","","","en","journal article","IEEE","","","","","","","","Electrical Engineering, Mathematics and Computer Science","","","","",""
"uuid:70abbb32-c491-4a7b-afc9-f5bfc3f0f37e","http://resolver.tudelft.nl/uuid:70abbb32-c491-4a7b-afc9-f5bfc3f0f37e","Initiation of translocation by Type I restriction-modification enzymes is associated with a short DNA extrusion","van Noort, J.; van der Heijden, T.; Dutta, C.F.; Firman, K.; Dekker, C.","","2004","","","en","journal article","Oxford University Press","","","","","","","","Applied Sciences","","","","",""
"uuid:a027ac38-b1a4-44a0-91f5-71c57b55e991","http://resolver.tudelft.nl/uuid:a027ac38-b1a4-44a0-91f5-71c57b55e991","Joining of long double-stranded RNA molecules through controlled overhangs","Dekker, N.H.; Abels, J.A.; Veenhuizen, P.T.; Bruinink, M.M.; Dekker, C.","","2004","","","en","journal article","Oxford University Press","","","","","","","","Applied Sciences","","","","",""
"uuid:2896620a-348d-4842-87ad-b95b9460ce8d","http://resolver.tudelft.nl/uuid:2896620a-348d-4842-87ad-b95b9460ce8d","Direct observation of confined states in metallic single-walled carbon nanotubes","Maltezopoulos, T.; Kubetzka, A.; Morgenstern, M.; Wiesendanger, R.; Lemay, S.G.; Dekker, C.","","2003","We investigated the local density of states (LDOS) of extended individual metallic single-walled carbon nanotubes using low-temperature scanning tunneling spectroscopy. We observed that the LDOS oscillates with energy close to the Fermi level. The oscillation period of about 50 meV varies with position on the nanotube. Maps of the LDOS reveal that the peaks in the oscillation are related to confined states. The widths of the peaks increase with increasing distance from the Fermi level.","carbon nanotubes; electronic density of states; scanning tunnelling spectroscopy","en","journal article","American Institute of Physics","","","","","","","","Applied Sciences","BN/Bionanoscience","","","",""
"uuid:7d03b091-2b9e-4631-8a23-1a41e4f18488","http://resolver.tudelft.nl/uuid:7d03b091-2b9e-4631-8a23-1a41e4f18488","Electronic device using carbon nanotubes","Bachtold, A.; Dekker, C.","","2003","Electronic device incorporating a tubular shaped carbon-molecule supported by a substrate, which molecule is provided with source and drain electrodes, and a gate electrode, wherein the gate electrode is a metallic electrode. The metallic electrode has a surface layer of oxide, preferably native oxide. The metallic electrode is selected from the group aluminium, zinc, copper","","en","patent","European Patent Office","","","","","","","","Applied Sciences","","","","",""
"uuid:d89a63e5-12a5-439c-854f-4e8fc8e58fb7","http://resolver.tudelft.nl/uuid:d89a63e5-12a5-439c-854f-4e8fc8e58fb7","Nanotechnologie, fascinatie voor het kleine","Dekker, C.","","2003","","Dies Natalis 161","nl","public lecture","","","","","","","","","","","","","",""
"uuid:af80837e-cb98-4424-86b8-2d93fdc03de1","http://resolver.tudelft.nl/uuid:af80837e-cb98-4424-86b8-2d93fdc03de1","The coiled-coil of the human Rad50 DNA repair protein contains specific segments of increased flexibility","van Noort, J.; van der Heijden, T.; de Jager, M.; Wyman, C.; Kanaar, R.; Dekker, C.","","2003","","","en","journal article","The National Academy of Sciences","","","","","","","","","","","","",""
"uuid:c641f83a-1ce8-42c3-985a-520755859330","http://resolver.tudelft.nl/uuid:c641f83a-1ce8-42c3-985a-520755859330","An Electronic Archive for Academic Communities","Dekker, R.; Dürr, E.; Slabbertje, M.; Van der Meer, K.","","2002","","","en","conference paper","ICEIS Press","","","","","","","","Electrical Engineering, Mathematics and Computer Science","","","","",""
"uuid:5b468ded-1211-4021-827e-e01247075963","http://resolver.tudelft.nl/uuid:5b468ded-1211-4021-827e-e01247075963","Scanning tunneling spectroscopy on crossed carbon nanotubes","Janssen, J.W.; Lemay, S.G.; Kouwenhoven, L.P.; Dekker, C.","","2002","","","en","journal article","American Physical Society","","","","","","","","","","","","",""
"uuid:7d0c523f-30a2-491f-afb7-760dc7dc8383","http://resolver.tudelft.nl/uuid:7d0c523f-30a2-491f-afb7-760dc7dc8383","Transport through the interface between a semiconducting carbon nanotube and a metal electrode","Nakanishi, T.; Bachtold, A.; Dekker, C.","","2002","","","en","journal article","American Physical Society","","","","","","","","","","","","",""
"uuid:5c7ea16b-8fc5-47fe-b8d7-21f29697bdcd","http://resolver.tudelft.nl/uuid:5c7ea16b-8fc5-47fe-b8d7-21f29697bdcd","Backbone-induced semiconducting behavior in short DNA wires","Cuniberti, G.; Craco, L.; Porath, D.; Dekker, C.","","2002","","","en","journal article","American Physical Society","","","","","","","","","","","","",""
"uuid:d6f008ec-9da8-4fd2-a181-135601bc19d7","http://resolver.tudelft.nl/uuid:d6f008ec-9da8-4fd2-a181-135601bc19d7","Beyond the photocopy machine: Document delivery in a hybrid library environment","Dekker, R.; Waaijers, L.","","2001","Document delivery bridges the gap between where the customer is and where the document is. Libraries have to offer user-friendly access to hybrid collections, and design and implement document delivery mechanisms from paper originals to provide a seamless integration between delivery from electronic and paper articles. Apart from improved service, a document delivery service provider could benefit internally from rationalising and automating the logistics of the delivery process. This article analyses the document delivery process, starting by defining five requirements for document delivery. By looking at document delivery from both the customer's and the organisation's perspective, the real needs of the customer are defined. From a basic distinction between the search and find function and the order and receive functions, the internal logistics of document delivery are analysed. The DocUTrans document delivery concept and system as used in Delft show how its implementation improves the whole system. The analysis itself can be highly beneficial.","document supply; libraries; electronic publishing","en","journal article","MCB University Press","","","","","","","","Delft University of Technology","","","","",""
"uuid:326f4aa7-3d3b-43ce-9867-d8ed0213facb","http://resolver.tudelft.nl/uuid:326f4aa7-3d3b-43ce-9867-d8ed0213facb","ANALYSE VAN STROMINGSMETINGEN BINNEN EN BUITEN EEN SNIJKOP","Dekker, M.A","","2001","","","","report","","","","","","","","indefinite","Mechanical, Maritime and Materials Engineering","Marine and Transport Technology","Transport Engineering and Logistics","","",""
"uuid:b8dcaa08-2bab-4e8f-bfe4-3593365e9ef3","http://resolver.tudelft.nl/uuid:b8dcaa08-2bab-4e8f-bfe4-3593365e9ef3","NUMERIEKE SIMULATIE VAN DE STROMING BINNEN EN BUITEN EEN SNIJKOP","Dekker, M.A","","2001","","","","report","","","","","","","","indefinite","Mechanical, Maritime and Materials Engineering","Marine and Transport Technology","Transport Engineering and Logistics","","",""
"uuid:3b41a953-40dc-42d3-aea3-53a8536a86ba","http://resolver.tudelft.nl/uuid:3b41a953-40dc-42d3-aea3-53a8536a86ba","Inzicht in extreme golfcondities: Stormmetingen en SWAN berekeningen","Dekker, J.","","2000","","golfvoortplanting; wave propagation; golfgegevens; wave data; stormen; storms","nl","report","Deltares (WL)","","","","","","","","","","","","",""
"uuid:ca026c0c-e366-472d-901d-032001576f2a","http://resolver.tudelft.nl/uuid:ca026c0c-e366-472d-901d-032001576f2a","Het kleine is groots","Dekker, C.","","2000","","","nl","lecture notes","","","","","","","","","","","","","",""
"uuid:0bc738e7-c602-4a35-8cbf-53548ec74291","http://resolver.tudelft.nl/uuid:0bc738e7-c602-4a35-8cbf-53548ec74291","Controle database Rand2001","Dekker, J.","","2000","","golfgegevens; wave data; computerprogramma's; software","nl","report","Deltares (WL)","","","","","","","","","","","","",""
"uuid:7517be9e-1c90-476e-940e-4ff9a5d86305","http://resolver.tudelft.nl/uuid:7517be9e-1c90-476e-940e-4ff9a5d86305","Spatially resolved scanning tunneling spectroscopy on single-walled carbon nanotubes","Venema, L.C.; Janssen, J.W.; Buitelaar, M.R.; Wildoer, J.W.G.; Lemay, S.G.; Kouwenhoven, L.P.; Dekker, C.","","2000","","","en","journal article","American Physical Society","","","","","","","","","","","","",""
"uuid:a7bec89c-304e-4c44-bdd7-ce853647bc17","http://resolver.tudelft.nl/uuid:a7bec89c-304e-4c44-bdd7-ce853647bc17","High-field electrical transport in single-wall carbon nanotubes","Yao, Z.; Kane, C.L.; Dekker, C.","","2000","","","en","journal article","American Physical Society","","","","","","","","","","","","",""
"uuid:4a685138-cb39-40f3-b7c2-802fac63e23f","http://resolver.tudelft.nl/uuid:4a685138-cb39-40f3-b7c2-802fac63e23f","Charge-density-wave current conversion in submicron NbSe3 wires","Mantel, O.C.; Chalin, F.; Dekker, C.; van der Zant, H.S.J.; Latyshev, Yu.I.; Pannetier, B.; Monceau, P.","","2000","","","en","journal article","American Physical Society","","","","","","","","","","","","",""
"uuid:1ceb3e11-9542-40bc-9d2c-2776dc1b4615","http://resolver.tudelft.nl/uuid:1ceb3e11-9542-40bc-9d2c-2776dc1b4615","Electrical transport through carbon nanotube junctions created by mechanical manipulation","Postma, H.W.Ch.; de Jonge, M.; Yao, Z.; Dekker, C.","","2000","","","en","journal article","American Physical Society","","","","","","","","","","","","",""
"uuid:a72c186c-c727-4148-961e-92fb42f330fe","http://resolver.tudelft.nl/uuid:a72c186c-c727-4148-961e-92fb42f330fe","Parallel GMRES and domain decomposition","Dekker, K.","","2000","","","en","report","Delft University of Technology, Faculty of Electrical Engineering, Mathematics and Computer Science, Delft Institute of Applied Mathematics","","","","","","","","Electrical Engineering, Mathematics and Computer Science","","","","",""
"uuid:af849938-fe23-4d8e-9d30-391b6145f655","http://resolver.tudelft.nl/uuid:af849938-fe23-4d8e-9d30-391b6145f655","Atomic structure of carbon nanotubes from scanning tunneling microscopy","Venema, L.C.; Meunier, V.; Lambin, Ph.; Dekker, C.","","2000","","","en","journal article","American Physical Society","","","","","","","","","","","","",""
"uuid:b74147af-1d1b-4a96-9795-c5171e85af3e","http://resolver.tudelft.nl/uuid:b74147af-1d1b-4a96-9795-c5171e85af3e","Comparing GMRES and P-GMRES in domain decomposition with approximate subdomain solution","Dekker, K.","","2000","","","en","report","Delft University of Technology, Faculty of Electrical Engineering, Mathematics and Computer Science, Delft Institute of Applied Mathematics","","","","","","","","Electrical Engineering, Mathematics and Computer Science","","","","",""
"uuid:d47f3162-0eff-4fea-83c2-c7131cf07333","http://resolver.tudelft.nl/uuid:d47f3162-0eff-4fea-83c2-c7131cf07333","Stroomsnelheden in en rond een in water vrij draaiende snijkop","Verhoeven, H.J.B.; Dekker, M.A.","","2000","","Experimental assignment","","report","","","","","","","","indefinite","Mechanical, Maritime and Materials Engineering","Marine and Transport Technology","Transport Engineering and Logistics","","",""
"uuid:284f9fea-f631-4e81-a795-e210e6b4301e","http://resolver.tudelft.nl/uuid:284f9fea-f631-4e81-a795-e210e6b4301e","Meetverslag van stroomsnelheden in en rond een snijkop vrijdraaiend in water","Verhoeven, H.J.B; Dekker, M.A.","","2000","","","","master thesis","","","","","","","","indefinite","Mechanical, Maritime and Materials Engineering","Marine and Transport Technology","Offshore and Dredging Engineering","","",""
"uuid:0f40ae8b-cf1a-426d-ae3b-ed120615be0c","http://resolver.tudelft.nl/uuid:0f40ae8b-cf1a-426d-ae3b-ed120615be0c","Data of Simona population for MDHMS application: Collecting and deriving data for human modelling sotware to use in Flight Simulator Design","Dekker, M.C.; Molenbroek, J.F.M.","","1999","For the interior design of a flight simulator, the ergonomic software MDHMS has been used to test different interior layout issues. The MDHMS program includes an accommodation analysis capability, which generates a digital sample of the specific target group. This report shows the data required for this analysis. Since there are just a few reference files available for only parts of the Dutch population, some methods to derive data from related files in order to make the chart complete are presented.","anthropometry; digital human model","en","report","Section Applied Ergonomics & Design","","","","","","","","Industrial Design Engineering","Industrial Design","","","",""
"uuid:50586fe0-be03-428f-a542-1bc3aa912a16","http://resolver.tudelft.nl/uuid:50586fe0-be03-428f-a542-1bc3aa912a16","Slijtage-onderzoek aan componenten van een baggerpomp","Dekker, M.A","","1999","","","","master thesis","","","","","","","","indefinite","Mechanical, Maritime and Materials Engineering","Marine and Transport Technology","Offshore and Dredging Engineering","","",""
"uuid:710e55f8-42b0-4b33-8768-b594994297d6","http://resolver.tudelft.nl/uuid:710e55f8-42b0-4b33-8768-b594994297d6","Meetverslag van stroomsnelheden in en rond een snijkop","Velthoen, A.A.G; Dekker, M.A.","","1999","","","","master thesis","","","","","","","","indefinite","Mechanical, Maritime and Materials Engineering","Marine and Transport Technology","Offshore and Dredging Engineering","","",""
"uuid:c825b06d-4bfe-402b-9535-f29968cbfb04","http://resolver.tudelft.nl/uuid:c825b06d-4bfe-402b-9535-f29968cbfb04","Sliding charge-density-wave transport in micron-sized wires of Rb0.30MoO3","Mantel, O.C.; Bal, C.A.W.; Langezaal, C.; Dekker, C.; Van der Zant, H.S.J.","","1999","","","en","journal article","American Physical Society","","","","","","","","","","","","",""
"uuid:253761a6-5b60-471f-bb77-1987df84715d","http://resolver.tudelft.nl/uuid:253761a6-5b60-471f-bb77-1987df84715d","Het visualiseren van het stroombeeld in de snijkop met behulp van Matlab en aan de hand van gegevens berekend met COMPASS","Vredevoort, M.; den Burger, M.; Dekker, M.A.","","1999","","Computer assignment","","report","","","","","","","","indefinite","Mechanical, Maritime and Materials Engineering","Marine and Transport Technology","Transport Engineering and Logistics","","",""
"uuid:ec6cd1ac-5ca2-46ba-9f92-8750bd1d6951","http://resolver.tudelft.nl/uuid:ec6cd1ac-5ca2-46ba-9f92-8750bd1d6951","Schatting van de slijtage aan centrifugaalpomphuizen","Dekker, M.A","","1999","","","","master thesis","","","","","","","","indefinite","Mechanical, Maritime and Materials Engineering","Marine and Transport Technology","Offshore and Dredging Engineering","","",""
"uuid:8ea0f12a-8c58-4457-bbf0-1e1b909aad92","http://resolver.tudelft.nl/uuid:8ea0f12a-8c58-4457-bbf0-1e1b909aad92","Slijtage-onderzoek aan componenten van een baggerpomp","Dekker, M.A.","","1999","","","","master thesis","","","","","","","","indefinite","Mechanical, Maritime and Materials Engineering","Marine and Transport Technology","Transport Engineering and Logistics","","",""
"uuid:a0729ec7-e37e-4e60-b08c-a83c3fe4b68d","http://resolver.tudelft.nl/uuid:a0729ec7-e37e-4e60-b08c-a83c3fe4b68d","Architecture scalability of parallel vector computers with a shared memory","Dekker, E.","","1998","","","en","journal article","IEEE","","","","","","","","","","","","",""
"uuid:b5ef80ba-8c83-4911-b4dd-2245434c4505","http://resolver.tudelft.nl/uuid:b5ef80ba-8c83-4911-b4dd-2245434c4505","Epitaxial film growth of the charge-density-wave conductor Rb0.30MoO3 on SrTiO3(001)","Steinfort, A.J.; van der Zant, H.S.J.; Smits, A.B.; Mantel, O.C.; Scholte, P.M.L.O.; Dekker, C.","","1998","","","en","journal article","American Physical Society","","","","","","","","","","","","",""
"uuid:9b0d1576-5270-4e78-b26e-b45241a8b21e","http://resolver.tudelft.nl/uuid:9b0d1576-5270-4e78-b26e-b45241a8b21e","Multiprobe transport experiments on individual single-wall carbon nanotubes","Bezryadin, A.; Verschueren, A.R.M.; Tans, S.J.; Dekker, C.","","1998","","","en","journal article","American Physical Society","","","","","","","","","","","","",""
"uuid:c7a76411-e32d-4dcc-8515-4ab57098f293","http://resolver.tudelft.nl/uuid:c7a76411-e32d-4dcc-8515-4ab57098f293","Length control of individual carbon nanotubes by nanostructuring with a scanning tunneling microscope","Venema, L.C.; Wildoer, J.W.G.; Tuinstra, H.L.J.T.; Dekker, C.; Rinzler, A.G.; Smalley, R.E.","","1997","","A6146 Structure of solid clusters, nanoparticles, and nanostructured materials; A6820 Solid surface structure; C; carbon; carbon nanotube; carbon nanotubes; Current voltage curves; electronic properties; imaging; individual C nanotubes; INSPEC; length control; nanostructured materials; nanostructuring; nanotubes; quantum size effect; quantum size effects; scanning tunneling microscope; scanning tunneling microscopy; scanning tunnelling microscopy; size effect; stepwise current increase; STM; STM spectroscopy; surface topography; topographic imaging","en","journal article","AIP","","","","","","","","","","","","",""
"uuid:6f6a783a-12ae-47af-86c4-2c5e5921fcca","http://resolver.tudelft.nl/uuid:6f6a783a-12ae-47af-86c4-2c5e5921fcca","Parallelisme, een nieuwe dimensie in de wetenschap?!: Wie experimenteren niet eert, is modelleren en simuleren niet weert","Dekker, L.","","1997","","Uittreerede","nl","public lecture","","","","","","","","","","","","","",""
"uuid:365b26b4-b02c-4db6-8e23-a0b220a52352","http://resolver.tudelft.nl/uuid:365b26b4-b02c-4db6-8e23-a0b220a52352","Nanofabrication of electrodes with sub-5 nm spacing for transport experiments on single molecules and metal clusters","Bezryadin, A.; Dekker, C.","","1997","","5 nm; A6146 Structure of solid clusters, nanoparticles, and nanostructured materials; A8115G Vacuum deposition; AuPd; C; carbon; carbon nanotube; carbon nanotubes; conducting nanoparticle; conjugated polymer; direct visual control; electrical transport; electrodes; electron beam deposition; electron microscope; electrostatic trapping; free standing carbon electrode; INSPEC; metal cluster; metal clusters; metal film coating; nanoelectrodes; nanofabrication; nanotechnology; nanotubes; nanowire; Pd; single molecule; single molecules; transport; transport properties; trapping","en","journal article","AIP for American Vacuum Soc","","","","","","","","","","","","",""
"uuid:dd15ceb0-4b02-4336-97bd-4de9968710a4","http://resolver.tudelft.nl/uuid:dd15ceb0-4b02-4336-97bd-4de9968710a4","Deposition and atomic force microscopy of individual phthalocyanine polymers between nanofabricated electrodes","Tans, S.J.; Geerligs, L.J.; Dekker, C.; Wu, J.; Wegner, G.","","1997","","1 nm; A6140K Structure of polymers, elastomers, and plastics; A6817 Monolayers and Langmuir Blodgett films; A8115L Deposition from liquid phases melts and solutions; atomic force microscopy; cellulose monolayer; conducting polymers; electrodes; immobilization; INSPEC; Langmuir Blodgett deposition; Langmuir Blodgett films; metal electrode; metal electrodes; monolayers; nanofabricated electrode; nanofabricated electrodes; nanotechnology; one dimensional conducting polymer; phthalocyanine polymer; phthalocyanine polymers; phthalocyaninepolysiloxane; polymer films; rigid rod polymer","en","journal article","AIP for American Vacuum Soc","","","","","","","","","","","","",""
"uuid:4e58e2bc-5f69-4dbe-9942-aabcc9eaad35","http://resolver.tudelft.nl/uuid:4e58e2bc-5f69-4dbe-9942-aabcc9eaad35","Individual single-wall carbon nanotubes as quantum wires","Tans, S.J.; Devoret, M.H.; Dai, H.; Thess, A.; Smalley, R.E.; Georliga, L.J.; Dekker, C.","","1997","","140 nm; A6146 Structure of solid clusters, nanoparticles, and nanostructured materials; A7170E Spin orbit coupling, Zeeman, Stark and strain splitting condensed matter; A7320D Electron states in low dimensional structures; A7335 Mesoscopic systems and quantum interference; A7340L Electrical properties of semiconductor to semiconductor contacts, p n junctions, and heterojunctions; A7820L Magneto optical effects condensed matter; A7865J Optical properties of nonmetallic thin films; B2530C Semiconductor superlattices, quantum wells and related structures; C; carbon; carbon nanotube; carbon nanotubes; disorder; electrical conduction; electrical properties; electrical transport; electrical transport measurements; highly symmetric structures; individual single wall C nanotubes; individual single wall carbon nanotubes; INSPEC; magnetic field; mesoscopic systems; molecular quantum wires; molecular wavefunctions; multi wall nanotubes; nanostructured materials; nanotubes; quantum wires; Zeeman effect","en","journal article","Macmillan Magazines","","","","","","","","","","","","",""
"uuid:4fb1277b-8789-4c18-a8a5-bf0c57d5e927","http://resolver.tudelft.nl/uuid:4fb1277b-8789-4c18-a8a5-bf0c57d5e927","Photolithographic patterning of the charge-density-wave conductor Rb 0.30 MoO 3","Van der Zant, H.S.J.; Mantel, O.C.; Heij, C.P.; Dekker, C.","","1997","","180 K; 2.5 mum; 20 to 300 K; 400 to 500 C; 600 nm; A6820 Solid surface structure; A6855 Thin film growth, structure, and epitaxy; A7145L Charge density wave systems; A7215N Collective modes: low dimensional conductors; A7335 Mesoscopic systems and quantum interference; A7360 Electrical properties of thin films and low dimensional structures; A8115I Pulsed laser deposition; A8160J Surface treatment and degradation of polymers and plastics; CDW; charge density wave; charge density wave conductor; charge density waves; current voltage characteristics; electrical resistivity; electrical transport; electrical transport measurements; grain size; INSPEC; mesoscopic phenomena; mesoscopic systems; nonlinear current voltage characteristics; patterned structures; Peierls instability; Peierls transition; phase coherent CDW transport; photolithographic patterning; photolithography; pulsed laser deposition; Rb sub 0.30 MoO sub 3; rubidium compounds; scanning electron microscopy; SEM; thin films; transport","en","journal article","Elsevier","","","","","","","","","","","","",""
"uuid:f27c246f-a135-40b9-9977-994d7b31109f","http://resolver.tudelft.nl/uuid:f27c246f-a135-40b9-9977-994d7b31109f","Orientation of the charge-density-wave chains in thin films of Rb 0.30 MoO 3","Mantel, O.C.; Van der Zant, H.S.J.; Steinfort, A.J.; Traeholt, C.; Dekker, C.","","1997","","A6820 Solid surface structure; A6855 Thin film growth, structure, and epitaxy; A7145L Charge density wave systems; CDW; chain orientation; charge density wave; charge density wave chains; charge density waves; crystal microstructure; grain size; INSPEC; Rb sub 0.3 MoO sub 3; Rb sub 0.3 MoO sub 3 SrTiO sub 3; rubidium compounds; scanning electron microscopy; SEM; SrTiO sub 3; substrate; substrate surface lattice; surface morphology; surface topography; TEM; thin film; thin films; transmission electron microscopy; X ray diffraction","en","journal article","Elsevier","","","","","","","","","","","","",""
"uuid:1f8b2797-50aa-4ec1-aa9c-ca052fd01f6f","http://resolver.tudelft.nl/uuid:1f8b2797-50aa-4ec1-aa9c-ca052fd01f6f","Thin films of the charge-density-wave oxide Rb(0.30) MoO(3) by pulsed-laser deposition","Mantel, O.C.; Van der Zant, H.S.J.; Steinfort, A.J.; Dekker, C.; Traeholt, C.; Zandbergen, H.W.","","1997","","182 K; A6855 Thin film growth, structure, and epitaxy; A7145L Charge density wave systems; A7215N Collective modes: low dimensional conductors; A7360 Electrical properties of thin films and low dimensional structures; A8115I Pulsed laser deposition; A8140E Cold working, work hardening: post deformation annealing, recovery and recrystallisation: textures; blue bronze; charge density wave; charge density wave chains; charge density wave oxide; charge density waves; epitaxial layers; heteroepitaxial growth; INSPEC; model; one dimensional conductivity; preferential orientation; pulsed laser deposition; Rb sub 0.30 MoO sub 3; resistance; rubidium compounds; single phase; SrTiO sub 3; SrTiO sub 3 100 substrates; substrate; texture; thin film; thin films; vapour phase epitaxial growth","en","journal article","APS through AIP","","","","","","","","","","","","",""
"uuid:6974e1e3-2719-4189-8760-c067af2f55d4","http://resolver.tudelft.nl/uuid:6974e1e3-2719-4189-8760-c067af2f55d4","Particle-precipitation-aided chemical vapor deposition of titanium nitride","Dekker, J.P.; Van der Put, P.J.; Veringa, H.J.; Schoonman, J.","","1997","","thermophoretic deposition rapid growth tio2 films","en","journal article","","","","","","","","","","","","","",""
"uuid:e8234cfd-37f1-420d-ae5a-e654277c366e","http://resolver.tudelft.nl/uuid:e8234cfd-37f1-420d-ae5a-e654277c366e","STM imaging and spectroscopy of single copperphthalocyanine molecules","Dekker, C.; Tans, S.J.; Oberndorff, B.; Meyer, R.; Venema, L.C.","","1997","","35 K; 77 K; A3120P Other semi empirical calculations atoms and molecules; A3520B General molecular conformation and symmetry: stereochemistry; A3620C Macromolecular conformation statistics and dynamics; A6820 Solid surface structure; A6845B Sorption equilibrium at solid fluid interfaces; A7320A Surface states, band structure, electron density of states; A7330 Surface double layers, Schottky barriers, and work functions; A7340G Tunnelling: general electronic transport; adsorbed layers; Current voltage curves; Fermi level; imaging; INSPEC; liquid nitrogen cooled graphite substrates; macromolecules; molecular electronic states; molecular level; organic compounds; resonant states; resonant tunneling; scanning tunneling microscope; scanning tunnelling microscopy; scanning tunnelling spectroscopy; single copperphthalocyanine molecules; STM; STM imaging; STM spectroscopy; substrate; synthetic metals; ultrahigh vacuum scanning tunneling microscope; work function","en","journal article","Elsevier","","","","","","","","","","","","",""
"uuid:cd096e8a-4f22-46b9-b20d-97ad2021ee81","http://resolver.tudelft.nl/uuid:cd096e8a-4f22-46b9-b20d-97ad2021ee81","Towards electrical transport on single molecules","Dekker, C.; Tans, S.J.; Geerligs, L.J.; Bezryadin, A.; Wu, J.; Wegner, G.","","1997","","contact spacings; electric transport properties; electrical transport; ELECTRICAL-TRANSPORT; electrodes; MICROSCOPY; model; mol wire elec transport; MOLECULES; monolayers; PHYSICS; SFS; SINGLE; single molecule; single molecules; single wire bridging; SINGLE-MOLECULE; space charge limited current model; transport; transport measurements; transport properties","en","journal article","","","","","","","","","","","","","",""
"uuid:04775569-4b43-4b82-b16c-7d6645c078cc","http://resolver.tudelft.nl/uuid:04775569-4b43-4b82-b16c-7d6645c078cc","Thin films of the charge-density-wave oxide Rb0.30MoO3 by pulsed-laser deposition","Mantel, O.C.; van der Zant, H.S.J.; Steinfort, A.J.; Dekker, C.; Træholt, C.; Zandbergen, H.W.","","1997","","","en","journal article","American Physical Society","","","","","","","","","","","","",""
"uuid:64482b59-1f34-4070-afad-4853f2cf3bef","http://resolver.tudelft.nl/uuid:64482b59-1f34-4070-afad-4853f2cf3bef","Electrical transport in monolayers of phthalocyanine molecular wires and AFM imaging of a single wire bridging two electrodes","Tans, S.J.; Miedema, R.; Geerligs, L.J.; Dekker, C.; Wu, J.; Wegner, G.","","1997","","0.05 to 10 V; 135 to 360 K; 25 nm; A6817 Monolayers and Langmuir Blodgett films; A6820 Solid surface structure; A7220F Low field transport and mobility: piezoresistance semiconductors/insulators; A7340C Contact resistance, contact potential, and work functions; A7360F Electronic properties of semiconductor thin films; AFM; AFM imaging; atomic force microscopy; current voltage measurements; electrical contacts; electrical transport; electrodes; high resolution atomic force microscopy images; imaging; INSPEC; Langmuir Blodgett films; Langmuir Blodgett monolayer; metal electrode; metal electrodes; model; molecular electronics; molecular wire bridging; molecular wires; monolayers; organic compounds; organic semiconductors; phthalocyanine molecular wires; phthalocyaninepolysiloxane; Pt; single wire bridging; space charge limited conduction; space charge limited current model; substrate; synthetic metals; transport","en","journal article","Elsevier","","","","","","","","","","","","",""
"uuid:c635075f-6302-4041-9ac6-b98e7ea25116","http://resolver.tudelft.nl/uuid:c635075f-6302-4041-9ac6-b98e7ea25116","Fullerene 'crop circles'","Liu, J.; Dai, H.J.; Hafner, J.H.; Colbert, D.T.; Smalley, R.E.; Tans, S.J.; Dekker, C.","","1997","","fullerene; nanotubes","en","journal article","","","","","","","","","","","","","",""
"uuid:be82a2e8-f591-4b4e-a7dd-3d667ae6dd8f","http://resolver.tudelft.nl/uuid:be82a2e8-f591-4b4e-a7dd-3d667ae6dd8f","Development procedures of the on-board attitude control software for the SAX satellite","Dekker, G.J.","","1996","The Italian/Dutch SAX satellite, launched at April 30, 1996, is a scientific spacecraft, built to explore celestial X-ray sources. The software for the Attitude and Orbit Control Subsystem onboard computer for SAX consists of special purpose Basic Software, which performs operating system functions, and of Application Software (ASW). The ASW has been developed by NLR, under contract with Fokker Space. Main goal of the application software is to ensure an accurate and stable pointing of the satellite's main axis during periods of up to 28 hours. Due to the mission critical nature of the ASW, which shall be able to operate during extended periods without ground contact, it has to be very reliable. This software has been developed in two phases. At first, an iterative full scale development process has been executed, supported by a separate independent integration and test team. This has led to a high quality end product, ready for AOCS subsystem integration. While the AOCS subsystem integration tests were executed (by Alenia Spazio), a number of new requirements were introduced. These were implemented during the second (maintenance) phase of ASW development, during which a smaller development team worked on the software, while the ASW integration tests were combined with AOCS subsystem integration tests. The differences in PA during the full scale development phase and the maintenance phase are compared. The operational experience with the attitude control software during the first months after launch is documented. The PA approach during the software development has proven its value by the shown high operational reliability and high flexibility of the software. The latter flexibility was needed to solve a number of operational problems in the AOCS sensors. The quality of the delivered software can be expressed as 0.05 detected errors per 1000 lines of (non-comment) code, which is an exceptionally low value. Paper presented at the 27th BIAS '96 Conference, Milan, Italy, 26-28 November, 1996.","","en","report","Nationaal Lucht- en Ruimtevaartlaboratorium","","","","","","Campus only","","","","","","",""
"uuid:be2df9d9-4848-44c4-a810-5ae0b9bd5eb9","http://resolver.tudelft.nl/uuid:be2df9d9-4848-44c4-a810-5ae0b9bd5eb9","Ecologisch profiel van de draadworm Heteromastus filiformis (Polychaeta)","Bijkerk, R.; Dekker, P.I.; Tydeman, P.","Rijkswaterstaat","1996","(See below for an extended English summary. Although the main content of the rapport is in Dutch) De borstelworm Heteromastus filiformis (""draadworm"") komt algemeen voor in de intergetijdezone en het sublitoraal van de Nederlandse kustwateren en estuaria. De soort prefereert fijnzandige, slikkige sedimenten. Het dier leeft permanent ingegraven op een diepte van 10 tot 40 cm en voedt zich met organisch materiaal in de anaërobe zone. Zijn voedsel bestaat voor een belangrijk deel uit bacteriën geassociëerd met organische stof (detritus). Opgeloste organische stof levert vermoedelijk een bijdrage. Ook wierfragmenten worden geconsumeerd, maar de mate van vertering is onbekend. Twee eigenschappen van het dier maken het hem mogelijk door te dringen in milieu's rijk aan organische stof: zijn tolerantie voor langdurig lage zuurstofgehalten (tot ca. 1,5 mg.dm-3) en zijn tolerantie voor langdurig lage zoutgehalten (tot 5,5%o Cl""). In intergetijdegebieden van de Waddenzee en de Westerschelde zijn de dichtheden van Heteromastus in de periode 1978 tot omstreeks 1987 toegenomen met circa een factor vijf. In het Grevelingenmeer en Veerse Meer zijn de dichtheden toegenomen direct na de afsluitingen (resp. in 1971 en 1961). Het Veerse Meer is sterk geëutrofiëerd. In het voorjaar van 1988 werden de hoogste aantallen Heteromastus gevonden in opeenhopingen van rottende zeesla. Op de twee locaties in de westelijke en de oostelijke Waddenzee laten de biomassagegevens van Heteromastus uit de penode 1988-1994 een duidelijk overeenkomstig verloop zien. Het bestand aan Heteromastus in de Dollard fluctueert in deze periode min of meer op dezelfde wijze. De gemeenschappelijke terugval in biomassa in 1993 en 1994 op deze drie locaties kan niet worden verklaard uit een teruggedrongen nutriëntenbelasting vanuit het IJsselmeer, en ook niet uit de predator-prooi relatie met de polychaet Nephtys hombergii. In de periode 1990-1994 neemt de biomassa van Heteromastus op de platen van de Wester- en Oosterschelde af. Ook in het sublitoraal van de Westerschelde is een dergelijke teruggang te zien. Verwacht mag worden dat de biomassaproductie van Heteromastus gerelateerd is aan het organisch-stofgehaite van het sediment. Meerjarige aantalsverlopen op een locatie op het Groninger wad bleken echter niet duidelijk gecorreleerd met het organisch-stofgehalte. Sommige aantalstoenames zijn bovendien zo groot dat het onwaarschijnlijk is dat ze veroorzaakt worden door een toename van organische stof op de foerageerdiepte van Heteromastus. Er zijn duidelijke aanwijzingen dat de populatie-ontwikkeling in het afgelopen decennium verband houdt met een verminderde predatiedruk uitgeoefend door de zandzager, Nephtys hombergii. Koude winters die gepaard gaan met ijsvorming op het wad leiden tot grote sterfte onder Nephtys. Een jaar later kunnen relatief hoge aantallen van Heteromastus worden aangetroffen. In langere tijdreeksen kan dit verschijnsel geconstateerd worden, bijvoorbeeld op Schiermonnikoog (1964 en 1973), het Groninger wad (1973) en het Balgzand (1980,1983,1985). In hoeverre de maximale dichtheden zijn toegenomen door eutrofiëring is niet met zekerheid te zeggen. Dichtheden in 1987/88 op plaatsen in de Westerschelde zijn 50-200% hoger dan het maximum op een voorkeursstandplaats in het Duitse Waddengebied in de dertiger jaren. Uit zijn voorkomen in vervuilde bodems kan enige tolerantie worden afgeleid voor zware metalen. Olieafzetting op sedimenten belemmert de vestiging en ontwikkeling van juveniele Heteromastus. Een aanzienlijke sterfte (50-90%) wordt veroorzaakt door de kokkelvisserij en plerenspitterij. Baggerspeciestortingen die leiden tot enige depositie van fijn matenaal, kunnen gevolgd worden door een toename van Heteromastus. -English- Biology/ecology Heteromastus filiformis is a common polychaete in Dutch intertidal and subtidal coastal and estuarine waters. The species has a preference for fine sandy and muddy sediments. It lives in the sediment at 10 - 40 cm depth and feeds on organic matter. Its food consists mainly of organic matter (detritus) associated bacteria. Dissolved organic matter and fragments of algae may also be taken up. The worm is adapted to living in organic enriched environments by its tolerance of long lasting low oxygen conditions (down to ca. 1.5 mg.dm""^) and its tolerance to long lasting low salinities (down to 5.5 %o CI-). Heteromastus filiformis reproduces at the end of its second year. Reproduction is in January-April. Larvae are planktonic for some time until during spring they settle in the sediment. Dispersal is mediated by primarily through the larval phase. Juveniles may be able to migrate. Population dynamics and eutrophication In the intertidal areas of Wadden Sea and Westerschelde numerical densities have increased by factor almost Five in the period 1978-1987. In the saline lakes Grevelingenmeer and Veerse Meer, densities increased immediately after closure of these water bodies from the sea in 1971 and 1961 respectively. Veerse Meer is highly eutrophicated. In spring 1988 highest numbers were found in accumulations of decaying Ulva. At two locations in the Wadden Sea biomass shows parallel fluctuation patterns over the 1988-1994 period, In the Dollard, similar patterns were found. At these locations biomass decreased in 1993-1994. This decrease, however, can not be explained by the reduced nutrient load from lake IJsselmeer, and neither by a change in predator-prey relationship involving the polychaete Nephtys hombergii. In the Westerschelde and Oosterschelde biomass at the intertidal flats decreased in the period 1990-1994. A similar decrease was observed in the sublittoral of the Westerschelde. It is supposed that biomass production by Heteromastus filiformis is related to the organic matter content of the sediment. Such a relationship, however, can not be demonstrated in the long-term data set from Groninger Wad. Sometimes increase in numbers of this worm is so large that it is unlikely to be caused by an increase of organic matter at its feeding depth. There are clear indications that the population development during the last 10 years is related to decreased predation pressure by Nephtys hombergii. Cold winters with formation of ice on the tidal flats cause mortality among this predatory worm. One year later, large numbers of Heteromastus filiformis can be found. This phenomenon can be observed in long time series, e.g. at Schiermonnikoog (in 1964 and 1973), Groninger Wad (in 1973) and Balgzand (in 1980, 1983 and 1985). No clearcut conclusion can be drawn with respect to eutrophication as the cause of the occurrence of maximal densities. In the Westerschelde, densities in 1987/88 are 50-200% higher than the maximal density at a preference location in the German Wadden Sea in the 1930s. Other effects The occurrence of Heteromastus filiformis in polluted sediments suggests some tolerance of heavy metal concentrations. Deposition of oil on sediments prevents settlement and development of juveniles. Fishery for cockles, and bait digging for lugworms causes a considerable (50-90%) mortality. Dumping of dredged material, leading to deposition of fine sediment, may cause an increase of the numbers of Heteromastus filiformis.","ecologie; milieu; draadworm; heteromastus filiformis; polychaeta; zoute wateren; ecologisch profiel; ecology","en","report","Rijkswaterstaat, RIKZ","","","","","","","","","","","","Watersysteemverkenningen (WSV) 1996",""
"uuid:f5469a9f-533b-476b-bb9f-4875f8d4979d","http://resolver.tudelft.nl/uuid:f5469a9f-533b-476b-bb9f-4875f8d4979d","Thin-film growth of the charge-density-wave oxide Rb0.30MoO3","Van der Zant, H.S.J.; Mantel, O.C.; Dekker, C.; Mooij, J.E.; Traeholt, C.","","1996","","182 K; A6855 Thin film growth, structure, and epitaxy; A7145L Charge density wave systems; A7215N Collective modes: low dimensional conductors; A7360 Electrical properties of thin films and low dimensional structures; A8115I Pulsed laser deposition; CDW; CDW state; charge density wave; charge density wave oxide; charge density waves; electrical resistance; electrical resistivity; epitaxial layers; INSPEC; model; one dimensional conductivity; phase coherent CDW transport; pulsed laser deposition; Rb sub 0.30 MoO sub 3; resistance; rubidium compounds; single phase; single phase epitaxial films; SrTiO sub 3; substrate; thin film; thin films; transport; vapour phase epitaxial growth","en","journal article","AIP","","","","","","","","","","","","",""
"uuid:65090329-ce2d-45fd-8c08-639f3bc3bb09","http://resolver.tudelft.nl/uuid:65090329-ce2d-45fd-8c08-639f3bc3bb09","Product assurance for the development of the SAX AOCS application software","Dekker, G.J.; Kesseler, E.","","1996","The Italian/Dutch SAX satellite, to be launched end of April 1996, is a scientific spacecraft, built to explore celestial X-ray sources. The software for the Attitude and Orbit Control Subsystem on-board computer for SAX consists of special purpose Basic Software, which perfonns operating system functions, and of Application Software (ASW). The ASW has been developed by NLR, under contact with Fokker Space. Main goal of the application software is to ensure an accurate and stable pointing of the satellite's main axis during periods of up to 28 hours. Due to the mission critical nature of the ASW, which shall be able to operate during extended periods widiout ground contact, it has to be very reliable.","","en","report","Nationaal Lucht- en Ruimtevaartlaboratorium","","","","","","Campus only","","","","","","",""
"uuid:f182a00c-9a9b-4edc-be70-0d8d8cc8d107","http://resolver.tudelft.nl/uuid:f182a00c-9a9b-4edc-be70-0d8d8cc8d107","The influence of surface kinetics in modelling chemical vapour deposition processes in porous preforms","Dekker, J.P.; Moene, R.; Schoonman, J.","","1996","","ceramic materials high-temperature gas-phase infiltration composites cvd diffusion silicon densification pressure","en","journal article","","","","","","","","","","","","","",""
"uuid:494f8be3-eae0-4cde-b642-251232444263","http://resolver.tudelft.nl/uuid:494f8be3-eae0-4cde-b642-251232444263","Simulatiemodel huisvesting hoger onderwijs","Dekker, H.; Van Langen, H.G.P.","","1995","","facility management; huisvesting; financieel beheerinstrument; onderwijs","en","book","Delft University Press","","","","","","","","Architecture","","","","",""
"uuid:2028bb62-2a5f-4a07-9033-92ba58fb34dc","http://resolver.tudelft.nl/uuid:2028bb62-2a5f-4a07-9033-92ba58fb34dc","Interaction between algorithms and architectures in parallel computation","Dekker, E.","Elzas, M.S. (promotor); van den Bos, A. (promotor)","1995","","inner product equations; high performance computing; parallel algorithms; parallel architectures","en","doctoral thesis","Delft University Press","","","","","","","","Applied Sciences","","","","",""
"uuid:279488a8-73ec-40f0-ac06-fb4a8a6a12ac","http://resolver.tudelft.nl/uuid:279488a8-73ec-40f0-ac06-fb4a8a6a12ac","Extreme wave conditions along the coast of the Netherlands: Wave propagation models for the coast between Cadzand and Hoek van Holland","Dekker, J.; Hartsuiker, G.","","1995","","golfvoortplanting; wave propagation; golfmodellen; wave models; North Sea; Zeeland; Zuid-Holland","en","report","Deltares (WL)","","","","","","","","","","","","",""
"uuid:c7262b2b-aec1-49df-ad9c-5ad9fa594c34","http://resolver.tudelft.nl/uuid:c7262b2b-aec1-49df-ad9c-5ad9fa594c34","Thin film fuel cells","Van Dieten, V.E.J.; Dekker, J.P.; Schoonman, J.","","1995","","","en","book chapter","MATERIALS RESEARCH SOC","","","","","","","","","","","","",""
"uuid:872667b1-e661-4506-88e1-347d55722541","http://resolver.tudelft.nl/uuid:872667b1-e661-4506-88e1-347d55722541","Parallel minimal norm method for tridiagonal linear systems","Dekker, E.; Dekker, L.","","1995","","","en","journal article","IEEE","","","","","","","","","","","","",""
"uuid:a9c9948b-3bdc-4528-a186-849da4ef2480","http://resolver.tudelft.nl/uuid:a9c9948b-3bdc-4528-a186-849da4ef2480","Finite-size effects on the vortex-glass transition in thin YBa2Cu3O7-d films","Woeltgens, P.J.M.; Dekker, C.; Koch, R.H.; Hussey, B.W.; Gupta, A.","","1995","","current density; current voltage characteristics; film thickness; FILMS; finite size effects; glass transition; high magnetic fields; magnetic field; magnetic flux; nonlinear current voltage characteristics; scaling; SFS; size effect; three dimensional; vortex excitations; vortex glass; vortex glass phase; vortex glass phase transition; vortex glass transition; yttrium barium cuprate vortex glass transition","en","journal article","","","","","","","","","","","","","",""
"uuid:79af09ad-bfe3-4fbe-9220-e6b4b8c0f71f","http://resolver.tudelft.nl/uuid:79af09ad-bfe3-4fbe-9220-e6b4b8c0f71f","Voltage noise of YBa2Cu3O7-d films in the vortex-liquid phase","Woeltgens, P.J.M.; Dekker, C.; Gielkens, S.W.A.; De Wijn, H.W.","","1995","","FILMS; frequency dependence; high magnetic fields; magnetic field; magnetic flux; model; noise; noise barium copper yttrium oxide superconductor; PHYSICS; SFS; voltage noise; vortex glass; vortex glass transition; vortex liquid phase","en","journal article","","","","","","","","","","","","","",""
"uuid:6172326f-27a9-4ded-ac38-c136ac9a6381","http://resolver.tudelft.nl/uuid:6172326f-27a9-4ded-ac38-c136ac9a6381","Extreme wave conditions along the coast of the Netherlands: Wave propagation models for the coast between Hoek van Holland and Rottumeroog","Dekker, J.","","1994","","golfvoortplanting; wave propagation; golfmodellen; wave models; North Sea","en","report","Deltares (WL)","","","","","","","","","","","","",""
"uuid:834c98c8-5b52-4325-97f8-a06f697213de","http://resolver.tudelft.nl/uuid:834c98c8-5b52-4325-97f8-a06f697213de","CVD Techniques for the Synthesis or Modification of Porous Ceramics","Dekker, J.P.","Schoonman, J. (promotor)","1994","","","en","doctoral thesis","","","","","","","","","Applied Sciences","","","","",""
"uuid:22869047-fde5-4a74-8905-79dcbb6e4db4","http://resolver.tudelft.nl/uuid:22869047-fde5-4a74-8905-79dcbb6e4db4","2D-3D crossover effects on the vortex-glass phase transition in thin YBa2Cu3 O7-delta films","Woeltgens, P.J.M.; Dekker, C.; Koch, R.H.; Hussey, B.W.; Gupta, A.","","1994","","16 to 400 AA; 2D 3D crossover effects; 3D vortex glass; A7460G Flux pinning, flux motion, fluxon defect interactions; A7470V Perovskite phase superconductors; A7475 Superconducting films; barium compounds; critical scaling behavior; current voltage characteristics; dimensionality effect; film thickness; flux line lattice; high magnetic fields; high temperature superconductor; high temperature superconductors; INSPEC; low currents; magnetic field; nonlinear current voltage characteristics; scaling; scaling analysis; superconducting thin films; thick films; three dimensional; vortex excitations; vortex glass; vortex glass phase; vortex glass phase transition; YBa sub 2 Cu sub 3 O sub 7 delta films; yttrium compounds","en","journal article","","","","","","","","","","","","","",""
"uuid:4f76b967-0cbd-42d5-9848-8df22b62de67","http://resolver.tudelft.nl/uuid:4f76b967-0cbd-42d5-9848-8df22b62de67","Vapour-phase synthesis of titanium nitride powder","Dekker, J.P.; Van der Put, P.J.; Veringa, H.J.; Schoonman, J.","","1994","","Powder Inorganic compound Titanium Nitrides Titanium Chlorides (ENT) Ammonia (ENT) Hydrogen (ENT) Particle size X ray diffraction Lattice parameters Surface area Electron microscopy Poudre Compose mineral Titane Nitrure Titane Chlorure (ENT) Ammoniac (ENT","en","journal article","","","","","","","","","","","","","",""
"uuid:61374d07-d660-44e3-8745-a87a8d6ca643","http://resolver.tudelft.nl/uuid:61374d07-d660-44e3-8745-a87a8d6ca643","Vapor phase manufacture of porous TiN deposits on/in porous supports. Vapor phase manufacture of materials","Dekker, J.P.; Schoonman, J.; Pratsinis, S.; Kodas, T.T.","","1994","","Experimental study Crystal growth methods Crystal growth from vapors CVD Precipitation Aerosol deposition Binary compounds Titanium nitrides Porous materials Temperature gradients Porosity Substrates Etude experimentale Methode croissance cristalline Croi","en","journal article","","","","","","","","","","","","","",""
"uuid:b834473c-331f-44dc-8b14-3668ebcf36a3","http://resolver.tudelft.nl/uuid:b834473c-331f-44dc-8b14-3668ebcf36a3","A kinetic study of titanium nitride chemical vapor deposition using nitrogen, hydrogen, and titanium tetrachloride","Dekker, J.P.; Van der Put, P.J.; Veringa, H.J.; Schoonman, J.","","1994","","titanium nitride chem vapor deposition kinetics chloride titanium reaction hydrogen nitrogen","en","journal article","","","","","","","","","","","","","",""
"uuid:d78dc13d-426d-465c-9135-0976dc218107","http://resolver.tudelft.nl/uuid:d78dc13d-426d-465c-9135-0976dc218107","Evaluation of Isothermal Chemical-Vapor Infiltration with Langmuir-Hinshelwood Type Kinetics","Moene, R.; Dekker, J.P.; Makkee, M.; Schoonman, J.; Moulijn, J.A.","","1994","","deposition diffusion","en","journal article","","","","","","","","","","","","","",""
"uuid:2ebdc6b5-ba7f-4a7a-9ebf-5cac9f744a17","http://resolver.tudelft.nl/uuid:2ebdc6b5-ba7f-4a7a-9ebf-5cac9f744a17","Chemical vapour infiltration of TiB2 and TiN in porous Al2O3","Dekker, J.P.; Van der Put, P.J.; Veringa, H.J.; Schoonman, J.","","1994","","Oxide ceramics Alumina Aluminium oxide Porous material Chemical vapor deposition Infiltration Titanium boride Titanium nitride Physical properties Permeability Mechanical properties Porous membrane Experimental study Ceramique oxyde Alumine Aluminium oxyd","en","journal article","","","","","","","","","","","","","",""
"uuid:aa78528a-1afb-4585-81af-e27119e1be8a","http://resolver.tudelft.nl/uuid:aa78528a-1afb-4585-81af-e27119e1be8a","Nonlinear Hall resistivity in YBa 2Cu 3O 7- delta films near the vortex-glass transition","Woeltgens, P.J.M.; Dekker, C.; De Wijn, H.W.","","1993","","A7460J Critical currents in type II superconductors; A7470V Perovskite phase superconductors; A7475 Superconducting films; barium compounds; critical current density superconductivity; current density; Hall effect; Hall electric field; high temperature superconductor; high temperature superconductors; INSPEC; longitudinal resistivity; magnetic field; nonlinear Hall resistivity; resistivity; superconducting thin films; vortex glass; vortex glass transition; YBa sub 2 Cu sub 3 O sub 7; YBa sub 2 Cu sub 3 O sub 7 delta films; yttrium compounds","en","journal article","","","","","","","","","","","","","",""
"uuid:c70abad0-0c4f-432e-8748-21b6bceee514","http://resolver.tudelft.nl/uuid:c70abad0-0c4f-432e-8748-21b6bceee514","Superconducting phase of YBa 2Cu 3O 7- delta films in high magnetic fields: Vortex glass or Bose glass","Woeltgens, P.J.M.; Dekker, C.; Swuste, J.; De Wijn, H.W.","","1993","","A7460G Flux pinning, flux motion, fluxon defect interactions; A7470V Perovskite phase superconductors; A7475 Superconducting films; barium compounds; Bose glass; C; critical glass exponents; critical scaling analysis; disorder; flux line lattice; glass transition; glass transition temperature; high magnetic fields; high temperature superconductors; I V curves; INSPEC; laser ablated; magnetic field; model; scaling; scaling analysis; SrTiO sub 3; superconducting thin films; vortex glass; YBa sub 2 Cu sub 3 O sub 7 delta films; yttrium compounds","en","journal article","","","","","","","","","","","","","",""
"uuid:18d29e67-cf31-43c0-a6ee-6bd98852387b","http://resolver.tudelft.nl/uuid:18d29e67-cf31-43c0-a6ee-6bd98852387b","Het gebruik van case tools bij de ontwikkeling van on-board ruimtevaartprogrammatuur","Dekker, G.J.; Hameetman, G.J.","","1993","Bij het ontwikkelen van de standregelprogrammatuur voor de Italiaanse satelliet SAX is gebruik gemaakt van een aantal CASE tools. Naast een beschrijving van de standregelprogrammatuur, met als hoofdeisen een hoge mate van bedrijfszekerheid en een hoge flexibiliteit, worden de ontwikkelsituatie en de ontwikkelomgeving beschreven. Geschetst wordt hoe het gebruik van CASE tools de bedrijfszekerheid van de programmatuur beïnvloedt. De resultaten van onafhankelijke integratie testen tonen aan dat de gebruikte ontwikkelstrategie inderdaad heeft geleid tot de vereiste bedrijfszekerheid","Applications programs (computers); Computer aided design; Program verification (computers); Programming environments; Requirements; Satellite attitude control; SAX satellite; Software development tools; Software reliability","nl","report","Nationaal Lucht- en Ruimtevaartlaboratorium","","","","","","Campus only","","","","","","",""
"uuid:26d0652b-11ad-4edd-aa67-d4add95d6bc9","http://resolver.tudelft.nl/uuid:26d0652b-11ad-4edd-aa67-d4add95d6bc9","Wave conditions along the Dutch coast","Booij, N.; Eldeberky, Y.; Dekker, J.","","1993","","Nederland; golfmodellen; wave models; golfmeting; wave measurement; kustwateren; coastal waters; validatie; validation","en","report","Deltares (WL)","","","","","","","","","","","","",""
"uuid:f989fbc9-d66b-461c-b8ed-660c5a1ed1ad","http://resolver.tudelft.nl/uuid:f989fbc9-d66b-461c-b8ed-660c5a1ed1ad","Voltage noise of YBa 2Cu 3O 7-delta films in the vortex-liquid phase","Woeltgens, P.J.M.; Dekker, C.; Gielkens, S.W.A.; De Wijn, H.W.","","1993","","1 f type; A7440 Fluctuations and critical effects in superconductors; A7460E Mixed state, H/sub c/sub 2, surface sheath; A7470V Perovskite phase superconductors; A7475 Superconducting films; barium compounds; critically divergent lifetimes; fluctuations; high magnetic fields; high temperature superconductors; INSPEC; magnetic field; mixed state; model; noise; random noise; spectral density; superconducting phase transition; superconducting thin films; voltage noise; vortex glass; vortex glass transition; vortex liquid phase; YBa sub 2 Cu sub 3 O sub 7 delta films; yttrium compounds","en","conference paper","","","","","","","","","","","","","",""
"uuid:c030dbf1-5923-4e1e-9392-1c23eaee09b2","http://resolver.tudelft.nl/uuid:c030dbf1-5923-4e1e-9392-1c23eaee09b2","Simulation of Systems","Dekker, L.","","1993","","mathematics","","book","","","","","","","","","Mechanical, Maritime and Materials Engineering","Marine and Transport Technology","Ship Hydromechanics and Structures","","",""
"uuid:403656a9-9b4c-4929-b2a2-094900515f05","http://resolver.tudelft.nl/uuid:403656a9-9b4c-4929-b2a2-094900515f05","Chemical vapor deposition techniques for thin films of solid electrolytes and electrodes","Van Dieten, V.E.J.; Dekker, J.P.; Van Zomeren, A.A.; Schoonman, J.","","1993","","electrochem vapor deposition yttria stabilized zirconia CVD electrochem titanium silicide lithium battery","en","book chapter","","","","","","","","","","","","","",""
"uuid:f1410e96-05eb-48d9-9f33-f115a64fd4ed","http://resolver.tudelft.nl/uuid:f1410e96-05eb-48d9-9f33-f115a64fd4ed","Chemical vapor deposition of titanium diboride using boron tribromide, titanium tetrachloride, and hydrogen","Dekker, J.P.; Van der Put, P.J.; Schoonman, J.; Veringa, H.J.","","1993","","titanium boride CVD reaction kinetics titanium tetrachloride CVD titanium boride boron bromide CVD titanium boride","en","journal article","","","","","","","","","","","","","",""
"uuid:41be0b93-9eb2-40ec-a3a0-737d1c399a78","http://resolver.tudelft.nl/uuid:41be0b93-9eb2-40ec-a3a0-737d1c399a78","Gas-to-particle conversion in the particle precipitation-aided chemical vapor deposition process. II: Synthesis of the perovskite oxide yttrium chromite. The role of aerosols in materials processing","Van Dieten, V.E.J.; Dekker, J.P.; Hurkmans, E.J.; Schoonman, J.","","1993","","Experimental study Aerosol deposition Particle precipitation Chemical vapor deposition Powder Ternary compound Yttrium Oxides (FIN) Chromium Oxides Perovskite type compound Gas mixture Steam (ENT) Oxygen Molecules (ENT) Binary compound Yttrium Chlorides (","en","journal article","","","","","","","","","","","","","",""
"uuid:7ed01cde-cde9-46f7-ac33-909d46797845","http://resolver.tudelft.nl/uuid:7ed01cde-cde9-46f7-ac33-909d46797845","Low-temperature current-voltage characteristics of YBa 2Cu 3O 7-delta films in a magnetic field: Direct evidence for a vortex-glass phase","Dekker, C.; Eidelloth, W.; Koch, R.H.","","1993","","A7460G Flux pinning, flux motion, fluxon defect interactions; A7470V Perovskite phase superconductors; A7475 Superconducting films; barium compounds; C; current density; current voltage characteristics; disordered superconductor; flux line lattice; high magnetic fields; high temperature superconductors; I V curves; INSPEC; magnetic field; superconducting thin films; superconducting transition; superconducting transition temperature; thin film; thin films; vortex glass; vortex glass phase; YBa sub 2 Cu sub 3 O sub 7 delta films; yttrium compounds","en","journal article","","","","","","","","","","","","","",""
"uuid:1655afd3-552c-495b-b3f6-43452c0a3418","http://resolver.tudelft.nl/uuid:1655afd3-552c-495b-b3f6-43452c0a3418","Gas-to-particle conversion in the particle precipitation-aided chemical vapor deposition process. I: Synthesis of the binary compound titanium nitride. The role of aerosols in materials processing","Dekker, J.P.; Van der Put, P.J.; Veringa, H.J.; Schoonman, J.; Pratsinis, S.E.","","1993","","Experimental study Aerosol deposition Particle precipitation Chemical vapor deposition Powder Binary compound Titanium Nitrides (FIN) Gas mixture Titanium Chlorides (ENT) Ammonia (ENT) Nitrogen Molecules (ENT) Hydrogen Molecules (ENT) Instrumentation Hete","en","journal article","","","","","","","","","","","","","",""
"uuid:cbcccac6-e143-4289-ba3c-f84463448b77","http://resolver.tudelft.nl/uuid:cbcccac6-e143-4289-ba3c-f84463448b77","Toetsing uitgangspunten rivierdijkversterkingen. Deelrapport 3: Constructief ontwerp","Dekker, J.; Janse, E.","Boertien, C. (contributor); Rijkswaterstaat","1993","In deel I 'Technische mogelijkheden voor de beoordeling van faal- en schademechanismen' wordt nagegaan in hoeverre op basis van de huidige inzichten en rekenmethoden mogelijkheden voorhanden zijn om, bij een gegeven normstelling voor de veiligheid, de ontwerpmethoden, zoals thans in de praktijk gehanteerd, zodanig te verbeteren dat dit ,leidt tot minder rigoureuze ingrepen in andere functies en waarden. Tevens wordt nagegaan in hoeverre die mogelijkheden daadwerkelijk worden benut en in hoeverre andere ontwerpaspecten dan strikt technische een rol spelen. In deel II 'Invloed van Maatgevende Hoogwaterstanden (MHW) op de noodzaak tot dijkversterking' is aan de hand van uitgevoerde case studies, beschikbare onderzoeksrapporten en interviews, nagegaan wat het. effect is van verlaging van MHW op de omvang van de d ij kversterkingen. In deel III 'Gebruik van uitgekiend ontwerpen' wordt nagegaan welke technische mogelijkheden voorhanden zijn om de dijkversterkingsmethoden zodanig te verbeteren dat dit tot minder schade aan landschaps-, natuur- en cultuurhistorische (LNC) waarden leidt. Tevens is een schatting gemaakt in hoeverre met een strategie, waarbij meer gebruik wordt gemaakt van uitgekiend ontwerpen, de schade in het onderzoeksgebied kan worden verminderd en welke extra kosten daarmee gemoeid zijn.","rivierdijken; Boertien; dijkversterking; Geotechnische stabiliteit","nl","report","Rijkswaterstaat","","","","","","","","","","","","Boertien",""
"uuid:105c83ec-6c79-4296-9ddb-2b49128dc0f1","http://resolver.tudelft.nl/uuid:105c83ec-6c79-4296-9ddb-2b49128dc0f1","Magnetic field effects on switching noise in a quantum point contact","Liefrink, F.; Scholten, A.J.; Dekker, C.; Dijkhuis, J.I.; Alphenaar, B.W.; Van Houten, H.; Foxon, C.T.","","1992","","A7220M Galvanomagnetic and other magnetotransport effects semiconductors/insulators; A7270 Noise processes and phenomena in electronic transport; A7320A Surface states, band structure, electron density of states; A7340L Electrical properties of semiconductor to semiconductor contacts, p n junctions, and heterojunctions; aluminium compounds; conduction band; conduction band bottom; conduction bands; fluctuations; g factor; GaAs Al sub x Ga sub 1 x As; gallium arsenide; III V semiconductors; INSPEC; interface electron states; Lande g factor; magnetic field; magnetic field effects; model; noise; point contacts; quantum Hall effect; quantum Hall regime; quantum point contact; quantum size effect; random noise; semiconductor; size effect; switching noise; temporal electrostatic fluctuations; transconductance; zero magnetic field","en","journal article","","","","","","","","","","","","","",""
"uuid:29d7a45b-f21d-4d03-9194-ca0ba6a5b5ed","http://resolver.tudelft.nl/uuid:29d7a45b-f21d-4d03-9194-ca0ba6a5b5ed","Regerative desulphurization in interconnected fluidized bed combustion of coal","Dekker, J.; Eijssen, J.H.","","1992","Docuement(en) uit de collectie Chemische Procestechnologie","","en","report","Delft University of Technology","","","","","","","","Applied Sciences","DelftChemTech","","","",""
"uuid:f634d908-cd37-4df8-a2a3-bcfb61a9147a","http://resolver.tudelft.nl/uuid:f634d908-cd37-4df8-a2a3-bcfb61a9147a","Absence of a finite-temperature vortex-glass phase transition in two-dimensional YBa 2Cu 3O 7-delta films","Dekker, C.; Woeltgens, P.J.M.; Koch, R.H.; Hussey, B.W.; Gupta, A.","","1992","","2D vortex glass; 3D vortex glass; A7460G Flux pinning, flux motion, fluxon defect interactions; A7460J Critical currents in type II superconductors; A7470V Perovskite phase superconductors; A7475 Superconducting films; barium compounds; critical current density superconductivity; critical scaling analysis; current density; current voltage characteristics; flux line lattice; high magnetic field state; high temperature superconductivity; high temperature superconductors; INSPEC; nonlinear current voltage characteristics; nonlinearity; power law temperature dependence; scaling; scaling analysis; superconducting thin films; temperature dependence; two dimensional; vortex glass; vortex glass phase; vortex glass phase transition; YBa sub 2 Cu sub 3 O sub 7 delta films; yttrium compounds","en","journal article","","","","","","","","","","","","","",""
"uuid:92a8867f-12f2-47fc-9fb2-3bbf871b5eda","http://resolver.tudelft.nl/uuid:92a8867f-12f2-47fc-9fb2-3bbf871b5eda","Measurement of the exponent mu in the low-temperature phase of YBa 2Cu 3O 7-delta films in a magnetic field: Direct evidence for a vortex-glass phase","Dekker, C.; Eidelloth, W.; Koch, R.H.","","1992","","A7460G Flux pinning, flux motion, fluxon defect interactions; A7460J Critical currents in type II superconductors; A7460M Material effects on T/sub c, K, critical currents in type II superconductors; A7470V Perovskite phase superconductors; A7475 Superconducting films; barium compounds; critical current density superconductivity; current density; disordered superconductor; flux line lattice; high magnetic fields; high temperature superconductor; high temperature superconductors; I V curves; INSPEC; low temperature phase; magnetic field; superconducting thin films; superconducting transition; superconducting transition temperature; thin film; thin films; vortex glass; vortex glass phase; YBa sub 2 Cu sub 3 O sub 7 delta films; yttrium compounds","en","journal article","","","","","","","","","","","","","",""
"uuid:b1870ffa-a95f-4799-867d-df4b1ed84e30","http://resolver.tudelft.nl/uuid:b1870ffa-a95f-4799-867d-df4b1ed84e30","Troebelheid Nederlandse zoute wateren: Inventarisatie en trendanalyse 1930-1990","Boon, J.G.; Dekker, E.A.; Postma, L.; Savornin Lohman, A.A.M. de","","1992","","Nederland; Noordzee; troebelheid; turbidity; zoutgehalte; salinity; slibgehalte; mud content; zwevende stoffen; suspended matter; zout water; salt water","nl","report","Deltares (WL)","","","","","","","","","","","","",""
"uuid:e33fe132-9229-433e-ac85-08cbee394535","http://resolver.tudelft.nl/uuid:e33fe132-9229-433e-ac85-08cbee394535","The growth of electrochemical vapor deposited YSZ films","Dekker, J.P.; Van Dieten, V.E.J.; Schoonman, J.","","1992","","yttria zirconia film electrochem vapor deposition","en","journal article","","","","","","","","","","","","","",""
"uuid:c243886f-8afd-4dae-bf08-d47dd9a38ee2","http://resolver.tudelft.nl/uuid:c243886f-8afd-4dae-bf08-d47dd9a38ee2","Expert judgment in maintenance optimization","van Noortwijk, J.M.; Dekker, A.; Cooke, R.M.; Mazzuchi, T.A.","","1992","","","en","journal article","IEEE","","","","","","","","","","","","",""
"uuid:e6cedfe5-c16c-476b-a377-7194db11054f","http://resolver.tudelft.nl/uuid:e6cedfe5-c16c-476b-a377-7194db11054f","Low-frequency noise in quantum point contacts","Liefrink, F.; Scholten, A.J.; Dekker, C.; Dijkhuis, J.I.; Eppenga, R.; Van Houten, H.; Foxon, C.T.","","1992","","A7270 Noise processes and phenomena in electronic transport; A7340L Electrical properties of semiconductor to semiconductor contacts, p n junctions, and heterojunctions; aluminium compounds; B2530B Semiconductor junctions; electron traps; electrostatic potential; fluctuations; GaAs Al sub x Ga sub 1 x As; gallium arsenide; III V semiconductors; INSPEC; low frequency noise; noise; point contacts; quantum point contact; quantum point contacts; resistance; resistance noise; single electron trap; trapped electron","en","conference paper","IOS Press","","","","","","","","","","","","",""
"uuid:71f24028-787c-415f-949e-7a64c142a574","http://resolver.tudelft.nl/uuid:71f24028-787c-415f-949e-7a64c142a574","Oxygen Diffusion in the Sofc Interconnection Material Lacr(1-X)Mgxo3","Van Dieten, V.E.J.; Dekker, J.P.; Schoonman, J.","","1992","","electrolyte","en","journal article","","","","","","","","","","","","","",""
"uuid:67408fa6-8c22-4586-95b4-9a73322605ee","http://resolver.tudelft.nl/uuid:67408fa6-8c22-4586-95b4-9a73322605ee","Low-frequency noise of quantum point contacts in the ballistic and quantum Hall regime","Liefrink, F.; Scholten, A.J.; Dekker, C.; Eppenga, R.; Van Houten, H.; Foxon, C.T.","","1991","","A7220M Galvanomagnetic and other magnetotransport effects semiconductors/insulators; A7270 Noise processes and phenomena in electronic transport; A7335 Mesoscopic systems and quantum interference; backscattering; ballistic regime; conductance; electrostatic potential; fluctuations; INSPEC; low frequency noise; magnetic field; noise; point contacts; quantum Hall effect; quantum Hall regime; quantum interference phenomena; quantum point contact; quantum point contacts; resistance; resistance noise; spin degeneracy; strong magnetic field","en","journal article","","","","","","","","","","","","","",""
"uuid:d133c0ed-854f-4c34-8642-0ec948552b86","http://resolver.tudelft.nl/uuid:d133c0ed-854f-4c34-8642-0ec948552b86","Dimensionality crossover of the superconducting-normal transition in YBa2Cu3O7-delta thin films both at high magnetic fields and at zero field","Dekker, C.; Koch, R.H.; Oh, B.; Gupta, A.","","1991","","","en","journal article","","","","","","","","","","","","","",""
"uuid:4fc059eb-42fd-4902-82ac-94913261d2ff","http://resolver.tudelft.nl/uuid:4fc059eb-42fd-4902-82ac-94913261d2ff","The development of flexible sotfware for the Italian/Dutch satellite SAX : Advantages and disadvantages of the use of CASE tools","Dekker, G.J.; Hameetman, G.J.","","1991","The Italian/Dutch satellite SAX is a scientific satellite which has the mission to study röntgen sources. One main requirement for the Attitude and Orbit Control Subsystem (AOCS) is to achieve and maintain a stable accuracy with a limit cycle of less than 90 arcsec during pointings of maximal 28 hours. The main SAX instrument, the Narrow Field Instrument, is highly sensitive to (indirect) radiation coming from the Sun. This sensitivity leads to another main requirement that under no circumstances the safe attitude domain may be left.","","en","report","Nationaal Lucht- en Ruimtevaartlaboratorium","","","","","","Campus only","","","","","","",""
"uuid:06a694bc-6bdc-4bf3-9014-8eeac94a7623","http://resolver.tudelft.nl/uuid:06a694bc-6bdc-4bf3-9014-8eeac94a7623","Spontaneous resistance switching and low-frequency noise in quantum point contacts","Dekker, C.; Scholten, A.J.; Liefrink, F.; Eppenga, R.; Van Houten, H.; Foxon, C.T.","","1991","","A7220J Charge carriers: generation, recombination, lifetime, and trapping semiconductors/insulators; A7270 Noise processes and phenomena in electronic transport; A7320D Electron states in low dimensional structures; A7340L Electrical properties of semiconductor to semiconductor contacts, p n junctions, and heterojunctions; carrier mobility; charge transport; conductance; electron device noise; electron traps; electrostatic potential; frequency dependence; INSPEC; local electrostatic potential; low frequency noise; low frequency noise spectroscopy; model; noise; point contacts; quantum point contact; quantum point contacts; quantum size effect; resistance; resistance switching; semiconductor quantum dots; semiconductors; size effect; spectral density; temperature dependence; transport; trapping; white noise","en","journal article","","","","","","","","","","","","","",""
"uuid:a6bf18a7-5390-4d44-8e47-f03866bff3f9","http://resolver.tudelft.nl/uuid:a6bf18a7-5390-4d44-8e47-f03866bff3f9","Chemical Vapor Precipitation of Submicron Titanium Nitride Powder","Dekker, J.P.; Van der Put, P.J.; Nieuwenhuis, R.R.; Veringa, H.J.; Schoonman, J.","","1991","","","en","journal article","","","","","","","","","","","","","",""
"uuid:85059b73-5645-47f5-a724-8780377edae1","http://resolver.tudelft.nl/uuid:85059b73-5645-47f5-a724-8780377edae1","Electrochemical vapor deposition of stabilized zirconia and interconnection materials for solid oxide fuel cells","Schoonman, J.; Dekker, J.P.; Broers, J.W.; Kiwiet, N.J.","","1991","","review electrochem vapor deposition stabilized zirconia electrolyte solid fuel cell review yttria stabilized zirconia electrolyte review interconnect lanthanum chromite fuel cell review","en","journal article","","","","","","","","","","","","","",""
"uuid:7e93d271-9dd1-46df-9b31-3542208515e6","http://resolver.tudelft.nl/uuid:7e93d271-9dd1-46df-9b31-3542208515e6","Solid state ionics in solid oxide fuel cells","Schoonman, J.; Dekker, J.P.; Broers, J.W.; Kiwiet, N.J.","","1991","","electrolyte; review fuel cell solid state ionics yttria zirconia fuel cell review lanthanum chromium oxide conductor review","en","book chapter","","","","","","","","","","","","","",""
"uuid:605330f2-bc06-4144-a8d3-f574412fccf6","http://resolver.tudelft.nl/uuid:605330f2-bc06-4144-a8d3-f574412fccf6","Electrical properties of gas sensor materials","Dekker, M.","Schoonman, J. (promotor)","1990","","","en","doctoral thesis","","","","","","","","","Applied Sciences","","","","",""
"uuid:1e4433ee-7ce7-44cf-b746-4f62b6da258f","http://resolver.tudelft.nl/uuid:1e4433ee-7ce7-44cf-b746-4f62b6da258f","Spin-glass dynamics in the two-dimensional Ising system rubidium copper cobalt fluoride (Rb2Cu1-xCoxF4)","Arts, A.F.M.; Dekker, C.; De Wijn, H.W.","","1990","","loss cobalt copper rubidium fluoride; magnetic susceptibility; model; relaxation cobalt copper rubidium fluoride; SFS; spin dynamics; spin glass; spin glass cobalt copper rubidium fluoride; spin glasses; susceptibility; susceptibility cobalt copper rubidium fluoride; two dimensional; PHYSICS","en","conference paper","","","","","","","","","","","","","",""
"uuid:fc8eb89d-3fa2-419b-a401-9da38c22adc4","http://resolver.tudelft.nl/uuid:fc8eb89d-3fa2-419b-a401-9da38c22adc4","Activated dynamics in a two-dimensional Ising spin glass: Rubidium copper cobalt fluoride (Rb2Cu1-xCoxF4)","Dekker, C.; Arts, A.F.M.; De Wijn, H.W.; Van Duyneveldt, A.J.; Mydosh, J.A.","","1989","","activated dynamic scaling; activated dynamics; Cole Cole formalism; magnetic susceptibility; out of phase susceptibility; relaxation magnetic rubidium copper cobalt fluoride; relaxation times; scaling; SFS; spin glass; spin glasses; spin spin correlation function; susceptibility; susceptibility rubidium copper cobalt fluoride; time decay; two dimensional; two dimensional Ising spin glass","en","journal article","","","","","","","","","","","","","",""
"uuid:87fd14d3-e71b-4543-9397-217046abf3ea","http://resolver.tudelft.nl/uuid:87fd14d3-e71b-4543-9397-217046abf3ea","Nh4y and Hy Zeolites as Electrolytes in Hydrogen Sensors","Dekker, M.; Tzand, I.; Schram, J.; Schoonman, J.","","1989","","electrolyte","en","journal article","","","","","","","","","","","","","",""
"uuid:ee984325-11b1-4323-93f4-521331aae3c3","http://resolver.tudelft.nl/uuid:ee984325-11b1-4323-93f4-521331aae3c3","Offshore lifting operations with synthetic fibre ropes","Dekker, A.K.","Hoogervorst, J. (mentor)","1989","","offshore","","master thesis","","","","","","","","indefinite","Mechanical, Maritime and Materials Engineering","Marine and Transport Technology","Offshore and Dredging Engineering","","",""
"uuid:c456afc0-8a72-4d5f-9a1c-02e89a5d109c","http://resolver.tudelft.nl/uuid:c456afc0-8a72-4d5f-9a1c-02e89a5d109c","Electrochemical vapor deposition of SOFC [solid oxide fuel cell] components","Dekker, J.P.; Kiwiet, N.J.; Schoonman, J.","","1989","","zirconia yttria electrochem vapor deposition kinetics oxidn zirconia electrolyte model fuel cell zirconia electrolyte deposition","en","conference paper","","","","","","","","","","","","","",""
"uuid:467994a4-4fcf-47d8-af50-2c9da8fbb548","http://resolver.tudelft.nl/uuid:467994a4-4fcf-47d8-af50-2c9da8fbb548","Dijkkruising Waardenburg","Dekker, H.R.E.","Rijkswaterstaat","1988","Gevraagd wordt op welke minimale hoogte een oprit voor een nieuwe brug tussen Waardenburg en Zaltbommel, direct ten westen van de huidige oeververbinding, de Waalbandijk mag kruisen. De huidige bandijk, die geheel zal worden opgenomen in het zandlichaam van de oprit, moet zijn waterkerende functie behouden. Op grond van de uitgevoerde probabilistische berekening wordt geadviseerd de dijkkruising ( = bovenzijde wegdek ) te realiseren op een hoogte van NAP + 11.45 m. Het verdient aanbeveling om tot een hoogte van NAP + 11.10 m een waterkerend element aan te brengen. Hierbij kan enerzijds worden gedacht aan het aanbrengen van een waterkerend element in het zandlichaam boven de huidige rivierdijk ( bijv. een folie ) en anderzijds aan een ( relatief ) ondoorlatende bekleding op het talud van het zandlichaam ( bijv. 1 m klei van voldoende kwaliteit ).","dijkkruising; Waardenburg; hoogtebepaling; brug","nl","report","Rijkswaterstaat, DWW","","","","","","","","","","","","W-88.04/03",""
"uuid:e2ef0ea1-4e9d-46ff-b090-6c121430f5a7","http://resolver.tudelft.nl/uuid:e2ef0ea1-4e9d-46ff-b090-6c121430f5a7","Magnetic order in the two-dimensional randomly mixed ferromagnet-antiferromagnet Rb2Cu1-xCoxF4","Dekker, C.; Arts, A.F.M.; De Wijn, H.W.","","1988","","A7530C Magnetic moments and susceptibility in magnetically ordered materials; A7530K Magnetic phase boundaries; A7540C Static properties of magnetic materials; A7550D Ferromagnetism of nonmetals; A7550E Antiferromagnetics; A7550L Spin glasses magnetic materials; AC susceptibility; antiferromagnetic properties of substances; cobalt compounds; copper compounds; DC susceptibility; domain wall dynamics; ferromagnetic antiferromagnetic transitions; ferromagnetic properties of substances; INSPEC; magnetic domain walls; magnetic order; magnetic susceptibility; magnetic transitions; mixed two dimensional ferromagnet antiferromagnet; Rb sub 2 Cu sub 1 x Co sub x F sub 4; rubidium compounds; specific heat; specific heat of solids; spin glass; spin glass transition; spin glasses; susceptibility; two dimensional; zero temperature; zero temperature spin glass transition","en","journal article","","","","","","","","","","","","","",""
"uuid:f48e1aa3-fa2e-4c40-b4d2-49e692f685de","http://resolver.tudelft.nl/uuid:f48e1aa3-fa2e-4c40-b4d2-49e692f685de","Static and dynamic properties of the two-dimensional Ising spin glass Rb2Cu1-xCo xF4","Dekker, C.; Arts, A.F.M.; De Wijn, H.W.","","1988","","A7530C Magnetic moments and susceptibility in magnetically ordered materials; A7540C Static properties of magnetic materials; A7540G Dynamic properties of magnetic materials; A7550L Spin glasses magnetic materials; A7560E Magnetization curves, hysteresis, Barkhausen and related effects; AC susceptibility; activated dynamic scaling; cobalt compounds; copper compounds; DC magnetization; Edwards Anderson model; INSPEC; Ising model; magnetic susceptibility; magnetisation; magnetization; model; Rb sub 2 Cu sub 1 x Co sub x F sub 4; rubidium compounds; scaling; spin glass; spin glasses; susceptibility; two dimensional; two dimensional Ising spin glass","en","journal article","","","","","","","","","","","","","",""
"uuid:d7c640f7-1758-4fff-8386-d9971a54bbce","http://resolver.tudelft.nl/uuid:d7c640f7-1758-4fff-8386-d9971a54bbce","Static critical behavior of the two-dimensional Ising spin glass Rb2Cu1-xCo xF4","Dekker, C.; Arts, A.F.M.; De Wijn, H.W.","","1988","","A7510N Spin glass models magnetism; A7530C Magnetic moments and susceptibility in magnetically ordered materials; A7530K Magnetic phase boundaries; A7540C Static properties of magnetic materials; A7550L Spin glasses magnetic materials; A7560E Magnetization curves, hysteresis, Barkhausen and related effects; cobalt compounds; copper compounds; critical exponents; Edwards Anderson Ising spin glass; INSPEC; Ising model; lower critical dimensionality; magnetic field dependence; magnetic susceptibility; magnetic transitions; magnetisation; magnetization; nonlinear susceptibility; random nearest neighbor bonds; Rb sub 2 Cu sub 1 x Co sub x F sub 4; rubidium compounds; scaling; spin glass; spin glass transition; spin glasses; static critical behaviour; static scaling; susceptibility; temperature dependence; two dimensional; two dimensional Ising spin glass; zero temperature","en","journal article","","","","","","","","","","","","","",""
"uuid:fcda7092-ba9d-41a5-af49-01fa401fcf3d","http://resolver.tudelft.nl/uuid:fcda7092-ba9d-41a5-af49-01fa401fcf3d","Activated dynamics in the two-dimensional Ising spin-glass Rb2Cu1-xCo xF4","Dekker, C.; Arts, A.F.M.; De Wijn, H.W.; Van Duyneveldt, A.J.; Mydosh, J.A.","","1988","","A7540G Dynamic properties of magnetic materials; A7550L Spin glasses magnetic materials; AC complex susceptibility; activated dynamic scaling; activated dynamics; C; cobalt compounds; copper compounds; critical exponents; INSPEC; Ising model; magnetic susceptibility; median relaxation time; model; out of phase susceptibility; random nearest neighbor bonds; Rb sub 2 Cu sub 1 x Co sub x F sub 4; relaxation times; rubidium compounds; scaling; spin glass; spin glasses; susceptibility; two dimensional; two dimensional Ising spin glass","en","journal article","","","","","","","","","","","","","",""
"uuid:89cc9571-add3-4c6c-90e2-14bdf43111c3","http://resolver.tudelft.nl/uuid:89cc9571-add3-4c6c-90e2-14bdf43111c3","Rb2Cu1-xCoxF4, a two-dimensional Ising spin glass","Dekker, C.; Arts, A.F.M.; De Wijn, H.W.","","1988","","A7510H Ising and other classical spin models magnetism; A7510N Spin glass models magnetism; A7530C Magnetic moments and susceptibility in magnetically ordered materials; A7550L Spin glasses magnetic materials; cobalt compounds; copper compounds; DC susceptibility; Edwards Anderson model; INSPEC; Ising model; longitudinal spin components; lower critical dimensionality; magnetic susceptibility; model; Rb sub 2 Cu sub 1 x Co sub x F sub 4; rubidium compounds; scaling; short range Edwards Anderson model; spin glass; spin glasses; susceptibility; two dimensional; two dimensional Ising spin glass","en","journal article","","","","","","","","","","","","","",""
"uuid:3cf4af50-a3c9-46d5-9c73-082672c3eea6","http://resolver.tudelft.nl/uuid:3cf4af50-a3c9-46d5-9c73-082672c3eea6","Dijkhoogte langs voorhaven Den Oever","Dekker, H.R.E.","Rijkswaterstaat","1988","De dijkhoogten langs de voorhaven van Den Oever variëren van NAP + 5.20 m tot 5.30 m aan de oostzijde en van NAP + 5.33 m tot 6.00 m aan de westzijde. Het ontwerppeil bij Den Oever bedraagt NAP + 5.25 m (met een overschrijdingsfrequentie van 7*10-4 per jaar). Rekening houdend met een zeespiegelrijzing van 0.1 m en (waarschijnlijk niet optredende ) bui-oscillaties met een amplitude van 0.25 m, kan de waterstand plaatselijk 0.4 m boven de aanwezige kruinhoogte liggen. In deze notitie zal worden nagegaan welke stroomsnelheden hierbij op het talud aan de IJsselmeerzijde te verwachten zijn. Aan de hand van de te berekenen snelheden moet vervolgens de ""overloopbestendigheid"" van de bedoelde dijkvakken worden beoordeeld. Geconcludeerd kan worden dat de ""overloopbestendigheid"" van het beschouwde profiel onvoldoende is indien de waterstand boven NAP + 5.32 m komt. Indien uitsluitend met het ontwerppeil ( van NAP + 5.25 m ) en een zeespiegelrijzing van 0.10 m zou worden gerekend, is een kruinhoogte van NAP + 5.35 m voldoende. Het optreden van bui-oscillaties zal in dat geval leiden tot te hoge stroomsnelheden op het talud aan de ijsselmeerzijde. Gelet op de vrij hoge en continu optredende stroomsnelheden bij overlopen ( H > 0.1 m ) wordt geadviseerd de dijken rond de voorhaven op traditionele wijze ( = met grond ) te verhogen tot de ""maatgevende waterstand"" + 0.5 m. Alhoewel het toepassen van keermuurtjes als een effectieve maatregel kan worden gezien om de hoeveelheid overslag te beperken, lijkt het niet logisch om deze rond de voorhaven te gebruiken. De dijken rond de voorhaven zijn immers al voor een groot deel voorzien van een harde bekleding. Voor de verbindingsdijken tussen de kunstwerken is de toepassing van keermuurtjes wèl goed te verdedigen. Door muurtjes toe te passen tot dezelfde hoogte als de betonwanden van de kunstwerken ( NAP + 7.00 m ) wordt in technische en visuele zin een aantrekkelijke oplossing verkregen omdat grote discontinuïteiten in ""kruin"" hoogte worden vermeden.","dijkhoogte; Den Oever; stroomsnelheden; overloopbestendigheid; dijkbeoordeling","nl","report","Rijkswaterstaat, DWW","","","","","","","","","","","","C.86.09/03",""
"uuid:dc9aa7e2-2e1e-4129-85c4-5d4461dcd9ce","http://resolver.tudelft.nl/uuid:dc9aa7e2-2e1e-4129-85c4-5d4461dcd9ce","Impedance Spectroscopy of Sulfate Solid Electrolytes","Dekker, M.; Kalwij, R.A.; Schram, J.; Schoonman, J.","","1988","","electrolyte","en","journal article","","","","","","","","","","","","","",""
"uuid:fc785a0a-becd-4d43-93dd-637cb92260ba","http://resolver.tudelft.nl/uuid:fc785a0a-becd-4d43-93dd-637cb92260ba","Dynamica van spinglazen","Dekker, C.; Arts, A.F.M.","","1988","","spin glass; spin glasses; two dimensional","nl","journal article","Nederlandse Natuurkundige Vereniging","","","","","","","","","","","","",""
"uuid:46bc6d33-18a6-4927-86d5-376ede9dfec2","http://resolver.tudelft.nl/uuid:46bc6d33-18a6-4927-86d5-376ede9dfec2","Breakup of long-range order in the diluted antiferromagnet K2MnxZn1-xF4 in zero magnetic field","Dekker, C.; Arts, A.F.M.; De Wijn, H.W.; Kjems, J.K.","","1987","","A7525 Spin arrangements in magnetically ordered materials; A7530E Exchange and superexchange interactions in magnetically ordered materials; A7550E Antiferromagnetics; antiferromagnetic properties of substances; C; correlation lengths; diluted antiferromagnet K sub 2 Mn sub x Zn sub 1 x F sub 4; exchange interactions; exchange interactions electron; INSPEC; long range order; magnetic field; magnetic properties of dilute systems; manganese compounds; neutron diffraction; neutron diffraction examination of materials; potassium compounds; site random fields; zero magnetic field; zinc compounds","en","journal article","","","","","","","","","","","","","",""
"uuid:8b90da5c-bb54-422d-b58a-17566aa8f1ba","http://resolver.tudelft.nl/uuid:8b90da5c-bb54-422d-b58a-17566aa8f1ba","Study on NAVSAT system evaluation, final report on phase 2. Part 1. Study results","Dekker, G.J.; de Jong, H.; Moek, G.","","1987","Under contract to ESA, NLR has developed a flexible simulation package, named PROMISE, and a set of simulation models of the ESA proposed NAVSAT satellite-based navigation system. These were completed in 1984. In a continuation contract, described in this report, a number of extensions have been developed and implemented, and a number of detailed simulations have been performed. The extensions to the PROMISE package mainly concern the enhancement of the user interaction with the package. In addition, the package has been installed on an IBM 4381 computer at ESTEC. The extensions to the simulation models concern the improvement of their realism. The most important extensions are the implementation of a realistic model for the ionosphere and the various models used within the NAVSAT system, which estimate the ionospheric effects, and the implementation of a more sophisticated user position estimation algorithm. The simulations performed indicate that the NAVSAT concept studied in this contract can provide a worldwide navigation facility with a position error of about 5 - 25 m. In most of cases studied the error was below 10 m. A number of conclusions is drawn from the simulation results that can be used to improve the design of the final NAVSAT system as it is currently being defined.","","en","report","Nationaal Lucht- en Ruimtevaartlaboratorium","","","","","","Campus only","","","","","","",""
"uuid:95d827e3-fe09-490f-b17f-ff6934c7588a","http://resolver.tudelft.nl/uuid:95d827e3-fe09-490f-b17f-ff6934c7588a","Study on NAVSAT system evaluation, final report on phase 2. Part 2. Detailed simulation results","Dekker, G.J.; de Jong, H.; Moek, G.","","1987","","","en","report","Nationaal Lucht- en Ruimtevaartlaboratorium","","","","","","Campus only","","","","","","",""
"uuid:fd48f501-651f-44ce-b0e2-97540000c520","http://resolver.tudelft.nl/uuid:fd48f501-651f-44ce-b0e2-97540000c520","Fatigue load measurements and evaluation of the 25 m hawt at Petten, the Netherlands","van der Linden, H.H.; Hartsuiker, L.; ten Have, A.A.; Dekker, J.W.M.; Rieffe, H.Ch.","","1986","Load measurements on the 25 m. Horizontal Axis Wind Turbine (HAWT) have been carried out to establish fatigue load spectra for 7 load channels in 9 modes of operation, i.e. 7 wind speed classes and the start and stop at the cutout wind speed. Special attention has been paid to the location of the zero levels for the different recordings. The fatigue load data have been reduced and counted by the ""Rainflow"" method, resulting in 32 x 32 Markov ""from-to"" matrices for each combination of wind speed /event class and load channel. Rainflow matrices for one year of operation have been derived. Results will be presented","","en","report","Nationaal Lucht- en Ruimtevaartlaboratorium","","","","","","Campus only","","","","","","",""
"uuid:d7567bd3-22e6-48de-ae20-fe282a37ff43","http://resolver.tudelft.nl/uuid:d7567bd3-22e6-48de-ae20-fe282a37ff43","A simulation tool for the study of satellite based navigation systems","de Pagter, P.J.; Dekker, G.J.; Joosten, L.J.M.","","1986","","","en","report","Nationaal lucht- en ruimtevaartlaboratorium","","","","","","Campus only","","","","","","",""
"uuid:f575c86b-3e6f-4dea-838b-a4ceefd641e0","http://resolver.tudelft.nl/uuid:f575c86b-3e6f-4dea-838b-a4ceefd641e0","Werkmethode voor een snijkopzuiger voorzien van deiningsgecompenseerde werkspudinstallatie en ladder","Dekker, C.","","1986","","","","master thesis","","","","","","","","indefinite","Mechanical, Maritime and Materials Engineering","Marine and Transport Technology","Offshore and Dredging Engineering","","",""
"uuid:fb97246e-ae09-41d5-935d-0f1c9bb7ff0e","http://resolver.tudelft.nl/uuid:fb97246e-ae09-41d5-935d-0f1c9bb7ff0e","Ontwerp van een deiningsgecompenseerde spudinstallatie","Dekker, C.","","1986","","","","master thesis","","","","","","","","indefinite","Mechanical, Maritime and Materials Engineering","Marine and Transport Technology","Offshore and Dredging Engineering","","",""
"uuid:ef1ba221-9bac-47c9-bb5f-c1f34f152f20","http://resolver.tudelft.nl/uuid:ef1ba221-9bac-47c9-bb5f-c1f34f152f20","NMR study of local magnetizations in diluted two-dimensional antiferromagnets","Dikken, B.J.; Dekker, C.; Arts, A.F.M.; De Wijn, H.W.","","1985","","A7530D Spin waves in magnetically ordered materials; A7550E Antiferromagnetics; A7560E Magnetization curves, hysteresis, Barkhausen and related effects; A7660 Nuclear magnetic resonance and relaxation condensed matter; antiferromagnetic properties of substances; average dilution; cobalt compounds; diluted two dimensional antiferromagnets; diluted weakly anisotropic 2D Heisenberg antiferromagnet; INSPEC; Ising antiferromagnet; Ising model; K sub 2 Co sub 0.83 Zn sub 0.17 F sub 4; K sub 2 Ni sub x Zn sub 1 x F sub 4; local magnetizations; magnetic excitations; magnetic neighbors; magnetisation; magnetization; nickel compounds; NMR study; nuclear magnetic resonance; Onsager's result; potassium compounds; spin wave like; spin waves; sublattice magnetization; sup 19 F; two dimensional; zinc compounds","en","journal article","","","","","","","","","","","","","",""
"uuid:d4f1e432-6a40-4d49-aa42-2a9eee8fd87f","http://resolver.tudelft.nl/uuid:d4f1e432-6a40-4d49-aa42-2a9eee8fd87f","Hydraulisch/morfologisch onderzoek naar de geulontwikkeling in het Schaar van Spijkerplaatgebied","Dekker, L.","Rijkswaterstaat","1985","In deze nota worden de resultaten van het hydraulisch/morfologisch onderzoek naar de geulontwikkeling in het Schaar van Spijkerplaatgebied gepresenteerd.","geulontwikkeling; Spijkerplaatgebied; hydraulisch; morfologisch; onderzoek","nl","report","Rijkswaterstaat, RIKZ","","","","","","","","","","","","",""
"uuid:19b465a5-271c-4002-8d8f-828fbbcf66e1","http://resolver.tudelft.nl/uuid:19b465a5-271c-4002-8d8f-828fbbcf66e1","Monte Carlo investigation of diluted antiferromagnets in high magnetic fields","Dekker, C.; Dikken, B.J.; Arts, A.F.M.","","1985","","A7510H Ising and other classical spin models magnetism; A7560C Magnetic domain walls and domain structure; antiferromagnetism; diluted antiferromagnets; domain walls; energy gain; high magnetic fields; INSPEC; Ising antiferromagnet; Ising antiferromagnets; Ising model; magnetic domain walls; magnetic field; Monte Carlo investigation; Monte Carlo methods; stable domain states; three dimensional; two dimensional","en","journal article","","","","","","","","","","","","","",""
"uuid:fcfde2b4-dedb-4f22-9d54-b59a1311f079","http://resolver.tudelft.nl/uuid:fcfde2b4-dedb-4f22-9d54-b59a1311f079","Analyse van een spudsysteem voor een dei-ningsgecompenseerde snijkopzuiger","Dekker, C.","","1985","","Computer assignment","","report","","","","","","","","indefinite","Mechanical, Maritime and Materials Engineering","Marine and Transport Technology","Offshore and Dredging Engineering","","",""
"uuid:e0640621-cb55-4a1e-92e2-daa88f8c9339","http://resolver.tudelft.nl/uuid:e0640621-cb55-4a1e-92e2-daa88f8c9339","Strategie voor de scheepsreparatiewerven","Dekker, W.A.; Dekker consultancy ","","1985","","","","other","","","","","","","","indefinite","Mechanical, Maritime and Materials Engineering","Marine and Transport Technology","Ship Design, Production and Operation","","",""
"uuid:6ddd06f0-d2e2-42d7-a6e1-6678c70908fd","http://resolver.tudelft.nl/uuid:6ddd06f0-d2e2-42d7-a6e1-6678c70908fd","Erosiebestendigheid van gras op klei taluds","Meerendonk, E. van; Dekker, J.","","1984","","dijkbekleding; dike lining; taludverdediging; slope protection; klei; clay; gras; grass","nl","report","Deltares (WL)","","","","","","","","","","","","",""
"uuid:45827470-80ab-47a5-b3b4-4469f426e0ba","http://resolver.tudelft.nl/uuid:45827470-80ab-47a5-b3b4-4469f426e0ba","De winning van riviergrind","Dekker, C.","","1984","","","","report","","","","","","","","indefinite","Mechanical, Maritime and Materials Engineering","Marine and Transport Technology","Offshore and Dredging Engineering","","",""
"uuid:ee9cc634-ad05-42af-ac4b-a19bda6ad023","http://resolver.tudelft.nl/uuid:ee9cc634-ad05-42af-ac4b-a19bda6ad023","Reliability aspects of software for digital avionics","Dekker, G.J.","","1982","Modern commercial transport aircraft contain digital avionics systems for more and more safety critical functions. The reliability and safety of those new systems depend on the hardware reliability and on the reliability of the embedded software. In this report, an overview is given of available methods and techniques to develop reliable software-based avionics systems, especially for safety critical functions. After a description of the differences between analog and digital systems, the policy of the FAA to certify software-based systems is presented. The subsequent chapters deal with methods to minimize the number of errors during software development, methods to remove as many errors as possible via testing and methods to minimize the effect of remaining errors during operational flights. A safety analysis regarding commonmode failures is given, followed by a short ov.erview of reliability related techniques which are used by avionics manufacturers.","avionics; reliability; quality control; certification; assurance; aircraft safety; error analysis; fault-tolerance; computer systems performance; program verification (computers); software (computers); computer programming; computer program integrity; configioration management; simulation; automatic test equipment; flight instruments; airborne/spaceborne; computers; digital systems; flight control","en","report","Nationaal Lucht- en Ruimtevaartlaboratorium","","","","","","Campus only","","","","","","",""
"uuid:61fd20f9-e5b3-48e1-b854-219dc9951bea","http://resolver.tudelft.nl/uuid:61fd20f9-e5b3-48e1-b854-219dc9951bea","A software-cost database for the development of aerospace software","Dekker, G.J.","","1982","Cost estimation of software development and control of the cost dioring the development are difficult due to the lack of an accurate cost estimation and management method. For the development of such a method cost figures from previous projects are needed and these are not readily available. In order to improve this situation, a user-friendly method for the collection, storage and retrieval of software-cost data has been developed, with emphasis on aerospace software projects. Data is and will be collected regarding k'J welldefined cost factors, divided in 8 classes. It is felt that the clear definition of these cost factors will be of main importajice for the applicability of the collected data. When suitable data is available from completed projects, the impact of these factors on the software development cost can be estimated, thus leading to a more reliable cost estimation and cost management method. The paper describes the cost estimation method that will be calibrated by means of the collected data, the implemented data collection and retrieval system, called a software-cost database, and the use of this system as management tool during rxinning projects. For some projects, the cost database is already in use.","","en","report","Nationaal Lucht- en Ruimtevaartlaboratorium","","","","","","Campus only","","","","","","",""
"uuid:f74313c8-3987-4252-b4f6-efef8b35a897","http://resolver.tudelft.nl/uuid:f74313c8-3987-4252-b4f6-efef8b35a897","A software-cost database for aerospace software development","Dekker, G.J.","","1982","Cost estimation of software development and control of the cost during the development are difficult due to the lack of applicable cost figures from previous projects, and consequently due to the lack of an accurate cost estimation and management method. In order to improve this situation, a user-friendly method for the collection, storage and retrieval of software-cost data has been developed, with emphasis on aerospace software projects. Data is and will be collected regarding 47 welldefined cost factors, divided in 8 classes. It is felt that the clear definition of these cost factors will be of main importance for the applicability of the collected data. When suitable data is available from completed projects, the impact of these factors on the software development cost can be estimated. This will lead to a more reliable cost estimation and cost management method. The paper describes the cost estimation method that will be calibrated by means of the collected data, the implemented data collection and retrieval system, called a software-cost database, and the use of this system as management tool during running projects. For some projects, the cost database is already in use. Paper presented at the 44th symposium of AGARD avionics panel on ""Software for Avionics"", the Hague, the Netherlands, September 6-10, 1982.","","en","report","","","","","","","Campus only","","","","","","",""
"uuid:223e1657-e6eb-496d-a77a-d037637e48f0","http://resolver.tudelft.nl/uuid:223e1657-e6eb-496d-a77a-d037637e48f0","Functional requirements for a software cost database","Dekker, G.J.; van der Wilt, M.; van den Bosch, F.J.","","1981","Cost estimation of software development and control of the cost during the development, are difficult due to the lack of useful cost figures from previous projects, and consequently due to the lack of an accurate cost estimation and management method. This report describes the results of the first phase of a study to develop a software cost database. This cost database will be used to develop such an accurate cost estimation method and to support cost management. The study is performed under contractnumber 18T0 of the Netherlands Agency for Aerospace prograjns (NIVE). During this first phase, a literature survey has'been performed on software cost estimation techniques and on already available cost data bases. This survey, together with the experience, available at NLR, has led to a proposal for a cost estimation method. To support this method, kj cost factors have been defined. It is felt that the clear definition of those cost factors will be of main importance for the usefullness of the method. The next phase of this study will be the implementation of a cost database, which will contain data about these kj cost factors. This data will be gathered from running projects. The cost database will ultimately be used to determine the constants of the proposed cost estimation method.","Value engineering; Costs; Cost estimates; Databases; Requirements; Lifecycle service life; Computer systems programs; Design; Computer programming; Product development; Project planning; Project management; Software (computers); Manpower","en","report","Nationaal Lucht- en Ruimtevaartlaboratorium","","","","","","Campus only","","","","","","",""
"uuid:ea2a0c26-ca13-4679-8a53-fa4c573a811c","http://resolver.tudelft.nl/uuid:ea2a0c26-ca13-4679-8a53-fa4c573a811c","Afmeren en olie-laden op volle zee - Modelonderzoek en toepassing van éénpunts-meersystemen","Blok, Jan J.; Dekker, J.N.","","1980","","hydrodynamics","","journal article","","","","","","","","","Mechanical, Maritime and Materials Engineering","Marine and Transport Technology","Ship Hydromechanics and Structures","","",""
"uuid:3ba9065d-7d2d-4aba-b7ca-58711c7d0880","http://resolver.tudelft.nl/uuid:3ba9065d-7d2d-4aba-b7ca-58711c7d0880","Buckling Strength of Plywood, Results of Tests and Design Recommendations","Dekker, J.; Kuipers, J.; Ploos van Amstel, H.","","1978","Tests were carried out on 100 specimens of Canadian Douglas fir plywood to verify that reasonably good agreement exists between the buckling theories and the actual behaviour of plywood. From load-deflection curves values for a critical buckling strength can be determined, which are in good agreement with theoretical values in the case of simply-supported edges. A clamped boundary condition could not be realised in such a way that the theoretical values were approximated. For' design purposes this condition should not be presumed. Attention has been paid to combinations of normal and shear stresses on the basis of theoretical considerations. This leads to proposals for the scope of design recommendations, which have not been worked out in detail here.","","en","journal article","Delft University of Technology","","","","","","","","Civil Engineering and Geosciences","","","","",""
"uuid:6b1b49c8-2674-4f93-b4cc-a766372c3087","http://resolver.tudelft.nl/uuid:6b1b49c8-2674-4f93-b4cc-a766372c3087","Proton magnetic resonance spectra and stereochemistry of amminenitrocobalt(III) complexes","Balt, S.; De Bolster, M.W.G.; Dekker, C.","","1976","","nuclear magnetic resonance; PMR cobalt nitro ammine; SFS; stereochemistry cobalt nitro ammine","en","journal article","","","","","","","","","","","","","",""
"uuid:eb124cc9-beea-4536-b971-34a466dc9c4b","http://resolver.tudelft.nl/uuid:eb124cc9-beea-4536-b971-34a466dc9c4b","Magnetization reversal processes in thin MnBi films","Dekker, P.","Middelhoek, S. (promotor)","1974","","","en","doctoral thesis","","","","","","","","","Electrical Engineering, Mathematics and Computer Science","","","","",""
"uuid:b79fe7b6-2481-4444-9295-251a16eefba4","http://resolver.tudelft.nl/uuid:b79fe7b6-2481-4444-9295-251a16eefba4","Human Rad51 filaments on double- and single-stranded DNA: Correlating regular and irregular forms with recombination function","Ristic, D.; Modesti, M.; Van der Heijden, T.; Van Noort, J.; Dekker, C.; Kanaar, R.; Wyman, C.","","","Recombinase proteins assembled into helical filaments on DNA are believed to be the catalytic core of homologous recombination. The assembly, disassembly and dynamic rearrangements of this structure must drive the DNA strand exchange reactions of homologous recombination. The sensitivity of eukaryotic recombinase activity to reaction conditions in vitro suggests that the status of bound nucleotide cofactors is important for function and possibly for filament structure. We analyzed nucleoprotein filaments formed by the human recombinase Rad51 in a variety of conditions on double-stranded and singlestrandedDNAby scanningforce microscopy. Regular filaments with extended double-stranded DNA correlated with active in vitro recombination, possibly due to stabilizing the DNA products of these assays. Though filaments formed readily on single-stranded DNA, they were very rarely regular structures. The irregular structure of filaments on single-stranded DNA suggests that Rad51 monomers are dynamic in filaments and that regular filaments are transient. Indeed, single molecule force spectroscopy of Rad51 filament assembly and disassembly in magnetic tweezers revealed protein association and disassociation from many points along the DNA, with kinetics different from those of RecA. The dynamic rearrangements of proteins and DNA within Rad51 nucleoprotein filaments could be key events driving strand exchange in homologous recombination.","","en","journal article","Oxford University Press","","","","","","","2005-06-08","Applied Sciences","Kavli Institute of Nanoscience Delft","","","",""
"uuid:d26dc6bf-91b2-48bd-a21a-e425b84f8f19","http://resolver.tudelft.nl/uuid:d26dc6bf-91b2-48bd-a21a-e425b84f8f19","The local pile oscillator as a device for measuring temperature dependence in epithermal-neutron absorption","Dekker, A.L.","Went, J.J. (promotor)","1969","","","en","doctoral thesis","Delftsche Uitgevers Maatschappij","","","","","","","","Applied Sciences","","","","",""
"uuid:4c29449d-e143-4009-8dd9-b6eeb373148a","http://resolver.tudelft.nl/uuid:4c29449d-e143-4009-8dd9-b6eeb373148a","Hybrid rekenen","Dekker, L.","","1966","","Intreerede","nl","public lecture","Uitgevrij Waltman Delft","","","","","","","","Applied Sciences","","","","",""
"uuid:e14fb452-5434-4596-8c5f-8cfc0f59be28","http://resolver.tudelft.nl/uuid:e14fb452-5434-4596-8c5f-8cfc0f59be28","Numerical aspects of the one-dimensional diffusion equation","Dekker, L.","Van Spiegel, E. (promotor)","1964","","","en","doctoral thesis","","","","","","","","","Electrical Engineering, Mathematics and Computer Science","","","","",""
"uuid:94ca35eb-9cbc-4187-b2c1-68ce0c2e5d41","http://resolver.tudelft.nl/uuid:94ca35eb-9cbc-4187-b2c1-68ce0c2e5d41","Phenol fabrikage uit cumeen","Dekker, T.T.","","1959","Document(en) uit de collectie Chemische Procestechnologie","","nl","report","Delft University","","","","","","","","Applied Sciences","DelftChemTech","","","",""
"uuid:4c661535-126d-49f9-bf3a-016a08176c1b","http://resolver.tudelft.nl/uuid:4c661535-126d-49f9-bf3a-016a08176c1b","Verslag fabrieksschema styreen","Dekker, C.W.","","1959","Document(en) uit de collectie Chemische Procestechnologie","","nl","report","Delft University","","","","","","","","Applied Sciences","DelftChemTech","","","",""
"uuid:daff9707-038b-4296-9a5d-198f9fd3cb42","http://resolver.tudelft.nl/uuid:daff9707-038b-4296-9a5d-198f9fd3cb42","Enkele onderzoekingen over de absorptiesnelheid van NO2 in water","Dekker, W.A.","Kramers, H. (promotor)","1958","","","nl","doctoral thesis","","","","","","","","","Applied Sciences","","","","",""
"uuid:3cf614a9-a7fd-49bf-860b-fbb67cb56ede","http://resolver.tudelft.nl/uuid:3cf614a9-a7fd-49bf-860b-fbb67cb56ede","Bereiding van magnesium uit zeewater","Dekker, W.A.; Van Oldenborgh, J.","","1955","Document(en) uit de collectie Chemische Procestechnologie","","nl","report","Delft University","","","","","","","","Applied Sciences","DelftChemTech","","","",""