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Shrestha, S. (author), Dekker, J. (author), Gerritsma, M.I. (author), Hulshoff, S.J. (author), Akkerman, I. (author)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...journal article 2024
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Tišma, M. (author), Bock, Florian Patrick (author), Kerssemakers, J.W.J. (author), Antar, Hammam (author), Japaridze, A. (author), Gruber, Stephan (author), Dekker, C. (author)Bacterial chromosomes are folded into tightly regulated three-dimensional structures to ensure proper transcription, replication, and segregation of the genetic information. Direct visualization of chromosomal shape within bacterial cells is hampered by cell-wall confinement and the optical diffraction limit. Here, we combine cell-shape...journal article 2024
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Nedelcu, Alex (author), Mendes Florindo, A.M. (author), Han, S.H. (author), Dekker, Jaap (author), de Vlieger, M.J. (author), Castro, Saullo G.P. (author), Peeters, D.M.J. (author)Double-curved composite structures that are manufactured via automated fiber placement, such as pressure vessels, can take advantage of tow steering to reduce weight. This design freedom comes with the cost of adding internal normal stresses to the tow, possibly leading to wrinkles or pull up. The present work investigates tow pull up both...journal article 2024
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De Franceschi, N. (author), Hoogenberg, B. (author), Katan, A.J. (author), Dekker, C. (author)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...journal article 2024
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Tišma, M. (author), Bock, Florian Patrick (author), Kerssemakers, J.W.J. (author), Antar, Hammam (author), Japaridze, A. (author), Gruber, Stephan (author), Dekker, C. (author)Correction to: Nature Communicationhttps://doi.org/10.1038/s41467-024-47094-x, published online 28 March 2024 The original version of this article contained an error in the “Acknowledgement “section. The original version read “We also acknowledge funding for the work in S.G. lab by the Swiss National Science Foundation (grant number: 310030L...journal article 2024
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Liu, Z. (author), van Veen, E.N.W. (author), Sanchez González, H. (author), Solano Hermosilla, B.P. (author), Palmero Moya, F.J.P.M. (author), Mc Cluskey, K.A. (author), Ramirez Montero, D.F. (author), van Laar, T. (author), Dekker, N.H. (author)Integrated single-molecule force-fluorescence spectroscopy setups allow for simultaneous fluorescence imaging and mechanical force manipulation and measurements on individual molecules, providing comprehensive dynamic and spatiotemporal information. Dual-beam optical tweezers (OT) combined with a confocal scanning microscope form a force...journal article 2024
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Janissen, R. (author), Barth, R. (author), Polinder, M.L. (author), van der Torre, J. (author), Dekker, C. (author)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 ...journal article 2024
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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 ‑M (author), Dekker, C. (author)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...journal article 2023
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Saccher, M. (author), Kawasaki, S. (author), Klootwijk, Johan (author), van Schaijk, Rob (author), Dekker, R. (author)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,...journal article 2023
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- Dekker, C. (author) journal article 2023
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- Dekker, N.H. (author) 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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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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Sanchez González, H. (author), Liu, Z. (author), van Veen, E.N.W. (author), van Laar, T. (author), Diffley, John F.X. (author), Dekker, N.H. (author)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...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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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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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
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Shi, X. (author), Pumm, Anna Katharina (author), Maffeo, Christopher (author), Kohler, Fabian (author), Feigl, Elija (author), Zhao, W. (author), Verschueren, D.V. (author), Golestanian, Ramin (author), Aksimentiev, Aleksei (author), Dietz, Hendrik (author), Dekker, C. (author)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...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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De Franceschi, N. (author), Barth, R. (author), Meindlhumer, S. (author), Fragasso, A. (author), Dekker, C. (author)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...journal article 2023