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Yang, Sora (author), Klughammer, N. (author), Barth, A. (author), Tanenbaum, M. (author), Dekker, C. (author)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...journal article 2023
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Kolbeck, Pauline J. (author), Tišma, M. (author), Analikwu, B.T. (author), Vanderlinden, Willem (author), Dekker, C. (author), Lipfert, Jan (author)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...journal article 2023
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Ramirez Montero, D.F. (author), Sanchez González, H. (author), van Veen, E.N.W. (author), van Laar, T. (author), Solano Hermosilla, B.P. (author), Diffley, John F.X. (author), Dekker, N.H. (author)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...journal article 2023
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Roslon, I.E. (author), Japaridze, A. (author), Rodenhuis, Stef (author), Hamoen, Lieke (author), Ghatkesar, M.K. (author), Steeneken, P.G. (author), Dekker, C. (author), Alijani, F. (author)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...journal article 2023
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Ramirez Montero, D.F. (author), Liu, Z. (author), Dekker, N.H. (author)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...journal article 2023
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Dekker, Mark M. (author), Daioglou, Vassilis (author), Pietzcker, Robert (author), Rodrigues, Renato (author), de Boer, Harmen Sytze (author), Dalla Longa, Francesco (author), Drouet, Laurent (author), Emmerling, Johannes (author), Fattahi, Amir (author), Fotiou, Theofano (author), Fragkos, Panagiotis (author), Fricko, Oliver (author), Gusheva, E. (author), Harmsen, Mathijs (author), Huppmann, Daniel (author), Kannavou, Maria (author), Krey, Volker (author), Lombardi, F. (author), Luderer, Gunnar (author), Pfenninger, Stefan (author), Tsiropoulos, Ioannis (author), Zakeri, Behnam (author), van der Zwaan, Bob (author), Usher, Will (author), van Vuuren, Detlef (author)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...journal article 2023
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Dekker, Bo (author), Schouten, A.C. (author), Scharenborg, O.E. (author)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...conference paper 2023
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Kawasaki, S. (author), Saccher, M. (author), de Wijs, Willem-Jan (author), van den Brand, Jeroen (author), Dekker, R. (author)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...conference paper 2023
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Saccher, M. (author), Schaijk, Rob van (author), Kawasaki, Shinnosuke (author), Klootwijk, Johan H. (author), Rashidi, A. (author), Giagka, Vasiliki (author), Savoia, Alessandro Stuart (author), Dekker, R. (author)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....conference paper 2023
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Saccher, M. (author), Rashidi, A. (author), Savoia, Alessandro Stuart (author), Giagka, Vasiliki (author), Dekker, R. (author)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...conference paper 2023
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Rashidi, A. (author), Saccher, M. (author), Karuthedath, Cyril Baby (author), Sebastian, Abhilash Thanniyil (author), Savoia, Alessandro Stuart (author), Lavigne, Frederik (author), Stubbe, Frederic (author), Dekker, R. (author), Giagka, Vasiliki (author)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...conference paper 2023
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Akyüz, M. Hakan (author), Dekker, Rommert (author), Sharif Azadeh, S. (author)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...journal article 2023
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Meindlhumer, S. (author), Brauns, Fridtjof (author), Finžgar, Jernej Rudi (author), Kerssemakers, J.W.J. (author), Dekker, C. (author), Frey, Erwin (author)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...journal article 2023
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Blanch Jover, A. (author), Dekker, C. (author)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...review 2023
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Barth, R. (author), Pradhan, B. (author), Kim, E. (author), Davidson, Iain F. (author), van der Torre, J. (author), Peters, Jan Michael (author), Dekker, C. (author)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...journal article 2023
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van Loo, N. (author), Mazur, G.P. (author), Dvir, T. (author), Wang, Guanzhong (author), Dekker, R.C. (author), Lemang, M.F. (author), Sfiligoj, C. (author), Bordin, A. (author), van Driel, D. (author), Kouwenhoven, Leo P. (author)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...journal article 2023
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Nova, I.C. (author), Ritmejeris, J. (author), Brinkerhoff, H.D. (author), Koenig, T.J.R. (author), Gundlach, Jens H. (author), Dekker, C. (author)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...journal article 2023
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Fan, D. (author), Cnossen, J.P. (author), Hung, S. (author), Kromm, D. (author), Dekker, N.H. (author), Verbiest, G.J. (author), Smith, C.S. (author)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...journal article 2023
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Kim, Eugene (author), Barth, R. (author), Dekker, C. (author)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...review 2023
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Diameter Dependence of Transport through Nuclear Pore Complex Mimics Studied Using Optical NanoporesKlughammer, N. (author), Barth, A. (author), Dekker, Maurice (author), Fragasso, A. (author), Onck, Patrick R. (author)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...journal article 2023