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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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Tišma, M. (author), Kaljević, Jovana (author), Gruber, Stephan (author), Le, Tung B.K. (author), Dekker, C. (author)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...review 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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Rouillon, Clément (author), Eckhardt, Bruna V. (author), Kollenstart, Leonie (author), Gruss, Fabian (author), Verkennis, Alexander E.E. (author), Rondeel, Inge (author), van Laar, T. (author), Albanese, Pascal (author), Dekker, N.H. (author)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...journal article 2023
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Dekker, H.N.J. (author), Tuinstra, M (author), Baars, W.J. (author), Scarano, F. (author), Ragni, D. (author)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...conference paper 2023
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Kuijpers, L.C. (author), van Veen, E.N.W. (author), Van der Pol, Leo (author), Dekker, N.H. (author)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...journal article 2023
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- Dekker, H.N.J. (author), Tuinstra, Marthijn (author), Baars, W.J. (author), Scarano, F. (author), Ragni, D. (author) conference paper 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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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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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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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