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van Cranenburgh, S. (author), Dekker, Thijs (author)
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...
contribution to periodical 2018
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Savov, A.M. (author), Joshi, S. (author), Shafqat, Salman (author), Hoefnagels, Johan P.M. (author), Louwerse, M.C. (author), Stoute, R. (author), Dekker, R. (author)
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...
journal article 2018
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Cramer, Sophie J.E. (author), Dekker, Janneke (author), Dankelman, J. (author), Pauws, Steffen C. (author), Hooper, Stuart B. (author), te Pas, Arjan B. (author)
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,...
review 2018
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van Driel, B.A. (author), van den Berg, K. J. (author), Smout, M. (author), Dekker, N (author), Kooyman, P.J. (author), Dik, J. (author)
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...
journal article 2018
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Wiktor, J.M. (author), Sherratt, David J. (author), Dekker, C. (author)
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...
journal article 2018
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Quiros Solano, W.F. (author), Gaio, N. (author), Stassen, O.M.J.A. (author), Arik, Y.B. (author), Silvestri, C. (author), Van Engeland, N.C.A. (author), van der Meer, A.D. (author), Passier, R. (author), Sahlgren, C.M. (author), Bouten, C.V.C. (author), van den Berg, A. (author), Dekker, R. (author), Sarro, P.M. (author)
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...
journal article 2018
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Dekker, Mark M. (author), van Lieshout, Rolf N. (author), Ball, Robin C. (author), Bouman, Paul C. (author), Dekker, Stefan C. (author), Dijkstra, Henk A. (author), Goverde, R.M.P. (author), Huisman, Dennis (author), Panja, Deb (author), Schaafsma, Alfons A.M. (author), van den Akker, Marjan (author)
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...
conference paper 2018
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Deshpande, S.R. (author), Spoelstra, W.K. (author), Kerssemakers, J.W.J. (author), Dekker, C. (author)
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...
journal article 2018
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Restrepo Perez, L. (author), Joo, C. (author), Dekker, C. (author)
Proteins are major building blocks of life. The protein content of a cell and an organism provides key information for the understanding of biological processes and disease. Despite the importance of protein analysis, only a handful of techniques are available to determine protein sequences, and these methods face limitations, for example,...
review 2018
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Shi, X. (author), Verschueren, D.V. (author), Dekker, C. (author)
Plasmon resonance biosensors provide ultimate sensitivity at the single-molecule level. This sensitivity is, however, associated with a nanometer-sized confined hotspot, and molecular transport toward the sensor relies on inefficient diffusion. Here, we combine a plasmonic nanoantenna with a solid-state nanopore and demonstrate that single...
journal article 2018
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Spoelstra, W.K. (author), Deshpande, S.R. (author), Dekker, C. (author)
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...
review 2018
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Caspi, Y. (author), Dekker, C. (author)
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...
journal article 2018
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Ordu, O. (author), Kremser, Leopold (author), Lusser, Alexandra (author), Dekker, N.H. (author)
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...
journal article 2018
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Heerema, S.J. (author), Vicarelli, L. (author), Pud, S. (author), Schouten, R.N. (author), Zandbergen, H.W. (author), Dekker, C. (author)
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...
journal article 2018
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Ananth, A.N. (author), Mishra, Ankur (author), Frey, Steffen (author), Dwarkasing, A. (author), Versloot, Roderick (author), van der Giessen, Erik (author), Görlich, Dirk (author), Onck, Patrick (author), Dekker, C. (author)
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...
journal article 2018
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Verschueren, D.V. (author), Yang, W.W.W. (author), Dekker, C. (author)
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...
journal article 2018
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Kim, S.H. (author), Ganji, M. (author), Kim, E. (author), van der Torre, J. (author), Abbondanzieri, E. (author), Dekker, C. (author)
The three-dimensional organization of DNA is increasingly understood to play a decisive role in vital cellular processes. Many studies focus on the role of DNA-packaging proteins, crowding, and confinement in arranging chromatin, but structural information might also be directly encoded in bare DNA itself. Here, we visualize plectonemes ...
journal article 2018
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Verschueren, D.V. (author), Pud, S. (author), Shi, X. (author), de Angelis, L. (author), Kuipers, L. (author), Dekker, C. (author)
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,...
journal article 2018
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Caneva, S.L. (author), Gehring, P. (author), Suárez, Víctor García (author), García-Fuente, Amador (author), Stefani, D. (author), Olavarria Contreras, I.J. (author), Ferrer, Jaime (author), Dekker, C. (author), van der Zant, H.S.J. (author)
. Consistent with the principles of subwavelength optics, the wave nature of...
journal article 2018
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Yang, W.W.W. (author), Restrepo Perez, L. (author), Bengtson, M.L. (author), Heerema, S.J. (author), Birnie, A.T.F. (author), van der Torre, J. (author), Dekker, C. (author)
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...
journal article 2018
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