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Dekker, F.W. (author), Erkin, Z. (author)
Privacy-preserving data aggregation protocols have been researched widely, but usually cannot guarantee correctness of the aggregate if users are malicious. These protocols can be extended with zero-knowledge proofs and commitments to work in the malicious model, but this incurs a significant computational cost on the end users, making adoption...
conference paper 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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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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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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Birnie, Anthony (author), Dekker, C. (author)
Chromosome structure and dynamics are essential for life, as the way that our genomes are spatially organized within cells is crucial for gene expression, differentiation, and genome transfer to daughter cells. There is a wide variety of methods available to study chromosomes, ranging from live-cell studies to single-molecule biophysics,...
review 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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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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Schmid, S. (author), Dekker, C. (author)
Proteins are the active workhorses in our body. These biomolecules perform all vital cellular functions from DNA replication and general biosynthesis to metabolic signaling and environmental sensing.While static 3D structures are now readily available, observing the functional cycle of proteins-involving conformational changes and...
review 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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Kluba, M.M. (author), Li, J. (author), Parkkinen, Katja (author), Louwerse, Marcus (author), Snijder, Jaap (author), Dekker, R. (author)
Several Silicon on Insulator (SOI) wafer manufacturers are now offering products with customer‐defined cavities etched in the handle wafer, which significantly simplifies the fabrication of MEMS devices such as pressure sensors. This paper presents a novel cavity buried oxide (BOX) SOI substrate (cavity‐BOX) that contains a patterned BOX...
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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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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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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Deshpande, Siddharth (author), Dekker, C. (author)
Cells organize their interior through membrane-bound organelles and through membraneless condensates that are formed by liquid–liquid phase separation (LLPS). The complex process of coacervation that is involved in LLPS is challenging to study in living cells. Hence, studying coacervation in cell-mimicking synthetic containers can yield...
review 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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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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Fragasso, A. (author), de Vries, Hendrik W. (author), Andersson, John (author), van der Sluis, E.O. (author), van der Giessen, Erik (author), Dahlin, Andreas (author), Onck, Patrick R. (author), Dekker, C. (author)
Nuclear Pore Complexes (NPCs) regulate bidirectional transport between the nucleus and the cytoplasm. Intrinsically disordered FG-Nups line the NPC lumen and form a selective barrier, where transport of most proteins is inhibited whereas specific transporter proteins freely pass. The mechanism underlying selective transport through the NPC is...
journal article 2021
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Martins Da Ponte, R. (author), Gaio, N. (author), van Zeijl, H.W. (author), Vollebregt, S. (author), Dijkstra, Paul (author), Dekker, R. (author), Serdijn, W.A. (author), Giagka, Vasiliki (author)
One of the many applications of organ-on-a-chip (OOC) technology is the study of biological processes in human induced pluripotent stem cells (iPSCs) during pharmacological drug screening. It is of paramount importance to construct OOCs equipped with highly compact in situ sensors that can accurately monitor, in real time, the extracellular...
journal article 2021
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