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Dekker, W.J.C. (author), Ortiz Merino, R.A. (author), Kaljouw, Astrid (author), Battjes, Julius (author), Wiering, Frank W. (author), Mooiman, C. (author), de la Torre, P. (author), Pronk, J.T. (author)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,...journal article 2021
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Ryu, J.K. (author), Bouchoux, Céline (author), Liu, Hon Wing (author), Kim, E. (author), Minamino, Masashi (author), de Groot, Ralph (author), Katan, A.J. (author), Bonato, Andrea (author), Marenduzzo, Davide (author), Michieletto, Davide (author), Uhlmann, Frank (author), Dekker, C. (author)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...journal article 2021
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Loeff, L. (author), Kerssemakers, J.W.J. (author), Joo, C. (author), Dekker, C. (author)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...journal article 2021
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Dekker, R. (author), van der Meer, F.P. (author), Maljaars, J. (author), Sluys, Lambertus J. (author)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...journal article 2021
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Mouter, N. (author), Koster, Paul (author), Dekker, Thijs (author)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...journal article 2021
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Schmid, S. (author), Stömmer, Pierre (author), Dietz, Hendrik (author), Dekker, C. (author)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...journal article 2021
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Whitley, K.D. (author), Jukes, Calum (author), Tregidgo, Nicholas (author), Karinou, Eleni (author), Almada, Pedro (author), Cesbron, Yann (author), Henriques, Ricardo (author), Dekker, C. (author), Holden, Séamus (author)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...journal article 2021
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Klughammer, N. (author), Dekker, C. (author)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...journal article 2021
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Dekker, R. (author), van der Meer, F.P. (author), Maljaars, Johan (author), Sluys, Lambertus J. (author)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...journal article 2021
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Japaridze, A. (author), Yang, W.W.W. (author), Dekker, C. (author), Nasser, William (author), Muskhelishvili, Georgi (author)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...journal article 2021
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Mouter, N. (author), Koster, Paul (author), Dekker, Thijs (author)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...journal article 2021
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Brauns, Fridtjof (author), Pawlik, G. (author), Halatek, Jacob (author), Kerssemakers, J.W.J. (author), Frey, Erwin (author), Dekker, C. (author)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...journal article 2021
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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, Debabrata (author), Schaafsma, Alfons A.M. (author), van den Akker, Marjan (author)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...journal article 2021
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Sanchez González, H. (author), Mc Cluskey, K.A. (author), van Laar, T. (author), van Veen, E.N.W. (author), Asscher, F.M. (author), Solano Hermosilla, B.P. (author), Diffley, John F.X. (author), Dekker, N.H. (author)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...journal article 2021
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Boogaard, Bob (author), Tas, Ali (author), Nijssen, J.P.A. (author), Broeren, F.G.J. (author), van den Dobbelsteen, J.J. (author), Verhoeven, Vincent (author), Pluim, Jip (author), Dekker, Sing (author), Snijder, Eric J. (author), van Hemert, Martijn J. (author), Herfst, Sander (author)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...journal article 2021
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Yang, W.W.W. (author), Radha, Boya (author), Choudhary, Adnan (author), You, Yi (author), Mettela, Gangaiah (author), Geim, Andre K. (author), Aksimentiev, Aleksei (author), Keerthi, Ashok (author), Dekker, C. (author)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...journal article 2021
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Brinkerhoff, H.D. (author), Kang, A.S.W. (author), Liu, Jingqian (author), Aksimentiev, Aleksei (author), Dekker, C. (author)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...journal article 2021
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Ryu, J.K. (author), Katan, A.J. (author), van der Sluis, E.O. (author), Wisse, T. (author), de Groot, Ralph (author), Haering, Christian H. (author), Dekker, C. (author)An amendment to this paper has been published and can be accessed via a link at the top of the paper.journal article 2020
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de Wit, S.I. (author), Dekker, Andre (author)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...journal article 2020
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Tang, Y. (author), Ha, S. (author), Begou, Thomas (author), Lumeau, Julien (author), Urbach, Paul (author), Dekker, N.H. (author), Adam, A.J.L. (author)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...journal article 2020