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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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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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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
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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
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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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Dekker, H.N.J. (author), Baars, W.J. (author), Scarano, F. (author), Tuinstra, Marthijn (author), Ragni, D. (author)The unsteady flow behaviour of two side-by-side rotors in ground proximity is experimentally investigated. The rotors induce a velocity distribution interacting with the ground causing the radial expansion of the rotor wakes. In between the rotors, an interaction of the two wakes takes place, resulting in an upward flow similar to a fountain....journal article 2023
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Ördög, Balázs (author), De Coster, Tim (author), Dekker, Sven O. (author), Bart, Cindy I. (author), Zhang, Juan (author), Boink, Gerard J.J. (author), Bax, Wilhelmina H. (author), Deng, Shanliang (author), den Ouden, B.L. (author), de Vries, Antoine A.F. (author), Pijnappels, Daniël A. (author)To unlock new research possibilities by acquiring control of action potential (AP) morphologies in excitable cells, we developed an opto-electronic feedback loop-based system integrating cellular electrophysiology, real-time computing, and optogenetic approaches and applied it to monolayers of heart muscle cells. This allowed accurate...journal article 2023
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Dekker, Ruben (author)Supporting designers working with AI is important, yet the tools they have at their disposal are in many ways not satisfactory. The aim of this project was to design a digital canvas tool which lets designers explore AI and ML, adopt the affordances that AI and ML as a design material give, and which can be used to map out and design integrated...master thesis 2022
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Dekker, Joey (author)Advection is at the heart of fluid dynamics and is responsible for many interesting phenomena. Unfortunately, it is also the source of the non-linearity of fluid dynamics. As such, its numerical treatment is challenging and often suboptimal. One way to more effectively deal with advection is by using a Lagrangian formulation instead of the...master thesis 2022
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Dekker, Joanne (author)This study is about young adults who cannot work or study due to mental health problems. When they turn 18, they have to wait for new care because of the transition from youth care to the adult social domain. This is why they are referred to as the W18 (waiteen) in this report.<br/><br/>Besides waiting time, this study outlines four other...master thesis 2022
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Dekker, Bo (author)To enable communication for patients who have lost the ability to speak due to severe neuromuscular diseases, covert speech based brain-computer interfaces (BCIs) might be used. These system use neural signals arising from covert speech and translate them into text or synthesised speech. Covert speech is imagining to speak without moving any of...master thesis 2022
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Dekker, Diewertje (author)Accurate short term rain predictions are important for flood early warning systems, emergency services, energy management and other services that that make weather dependent decisions. Recently introduced machine learning models suffer from blurry and unrealistic predictions at longer lead times, causing poor performance on the rarer heavy...master thesis 2022
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Dekker, M.C. (author)Repetitive Strain Injuries (RSI), also known as Work-Related Upper Limb Disorders (WRULD), surged in the early years of this millennium due to computer work. In this thesis, the magnitude, causes and consequences of this phenomenon for the student population of the Faculty of Industrial Design Engineering (IDE) at the Delft University of...doctoral thesis 2022
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Dekker, Madelief (author)A guide for the landscape architectural design of an urban forest that helps create realms of experience in order to make people more aware of our connection to nature.<br/><br/>The imbalance between how we live and how the natural world around us works leads to a disconnected relationship with nature. Because of this many people see nature that...master thesis 2022
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Dekker, Abram (author)Due to the continuously increasing volume of road freight transportation, there is a need to aid or automate truck-trailer driving. Truck docking, the process of parking a truck-trailer combination at a loading dock, is one of the most difficult manoeuvres for professional drivers. In this work, we propose a Model Predictive Control (MPC)-based...master thesis 2022
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Dekker, Diewertje (author)This additional thesis project is performed as preliminary research for a bigger project that they are going to start at Lund University, to investigate whether the use of a different interpolation methods, to link the precipitation data to the sub-basins centers of the HYPE model, lead to improved model performance. In this report, previously...student report 2022