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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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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, C. (author), Haering, Christian H. (author), Peters, Jan Michael (author), Rowland, B.D. (author)A potential mechanism of DNA loop extrusion by molecular motors is discussed.journal article 2023
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Dekker, Bo (author), Schouten, A.C. (author), Scharenborg, O.E. (author)Silent speech interfaces could enable people who lost the ability to use their voice or gestures to communicate with the external world, e.g., through decoding the person’s brain signals when imagining speech. Only a few and small databases exist that allow for the development and training of brain computer interfaces (BCIs) that can decode...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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Kawasaki, S. (author), Saccher, M. (author), de Wijs, Willem-Jan (author), van den Brand, Jeroen (author), Dekker, R. (author)Capacitive micromachined ultrasonic transducers (CMUTs) with a built-in charge layer are known as a pre-charged CMUT. In our prior work, we have shown how to model and characterize the charges inside the pre-charged collapse-mode CMUT and conducted life-time test that showed that the charges trapped inside the dielectric were stable in the order...conference paper 2023
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Saccher, M. (author), Schaijk, Rob van (author), Kawasaki, Shinnosuke (author), Klootwijk, Johan H. (author), Rashidi, A. (author), Giagka, Vasiliki (author), Savoia, Alessandro Stuart (author), Dekker, R. (author)Capacitive Micromachined Ultrasound Transducers (CMUTs) have many advantages compared to other ultrasonic transducer technologies, especially for implantable devices. However, they require a high bias voltage for efficient operation. To eliminate the need for an external bias voltage, a charge storage layer can be embedded in the dielectric....conference paper 2023
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Ramirez Montero, D.F. (author), Liu, Z. (author), Dekker, N.H. (author)DNA constructs for single-molecule experiments often require specific sequences and/or extrahelical/noncanonical structures to study DNA-processing mechanisms. The precise introduction of such structures requires extensive control of the sequence of the initial DNA substrate. A commonly used substrate in the synthesis of DNA constructs is...journal article 2023
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Rashidi, A. (author), Saccher, M. (author), Karuthedath, Cyril Baby (author), Sebastian, Abhilash Thanniyil (author), Savoia, Alessandro Stuart (author), Lavigne, Frederik (author), Stubbe, Frederic (author), Dekker, R. (author), Giagka, Vasiliki (author)Aluminum Nitride (AlN) Piezoelectric Micromachined Ultrasonic Transducers (PMUTs) are gaining interest for biomedical implant power due to biocompatibility and lowtemperature processing. However, due to the low piezoelectric coefficient of AlN PMUTs, storage capacitors are often used to accumulate ultrasonic power transferred over an extended...conference paper 2023
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Saccher, M. (author), Rashidi, A. (author), Savoia, Alessandro Stuart (author), Giagka, Vasiliki (author), Dekker, R. (author)In the domain of ultrasonically powered biomedical implants, there is an increasing interest in cm-scale ultrasonic receivers (RX). However, when a single-element transducer is used as the RX transducer, an uneven phase distribution across the RX area can significantly reduce the harvestable power. In this paper, we investigate the impact of...conference paper 2023
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Mc Cluskey, K.A. (author), Dekker, N.H. (author)TIRF (Total Internal Reflection Fluorescence) microscopy is a powerful tool for measuring the intra- and intermolecular dynamics of fluorescently-labeled single molecules. As TIRF measurements move to more complex biological systems with more fluorescent probes, the multi-band-pass dichroic that separates excitation from emission becomes...journal article 2023
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Davidson, Iain F. (author), Barth, R. (author), Zaczek, Maciej (author), van der Torre, J. (author), Tang, Wen (author), Nagasaka, Kota (author), Janissen, R. (author), Kerssemakers, J.W.J. (author), Wutz, Gordana (author), Dekker, C. (author), Peters, Jan Michael (author)In eukaryotes, genomic DNA is extruded into loops by cohesin<sup>1</sup>. By restraining this process, the DNA-binding protein CCCTC-binding factor (CTCF) generates topologically associating domains (TADs)<sup>2,3</sup> that have important roles in gene regulation and recombination during development and disease<sup>1,4–7</sup>. How CTCF...journal article 2023
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Ramirez Montero, D.F. (author), Sanchez González, H. (author), van Veen, E.N.W. (author), van Laar, T. (author), Solano Hermosilla, B.P. (author), Diffley, John F.X. (author), Dekker, N.H. (author)The eukaryotic replicative helicase CMG centrally orchestrates the replisome and leads the way at the front of replication forks. Understanding the motion of CMG on the DNA is therefore key to our understanding of DNA replication. In vivo, CMG is assembled and activated through a cell-cycle-regulated mechanism involving 36 polypeptides that...journal article 2023
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Tišma, M. (author), Janissen, R. (author), Antar, Hammam (author), Martin Gonzalez, A. (author), Barth, R. (author), Beekman, T.G.T. (author), van der Torre, J. (author), Michieletto, Davide (author), Gruber, Stephan (author), Dekker, C. (author)In most bacteria, chromosome segregation is driven by the ParABS system where the CTPase protein ParB loads at the parS site to trigger the formation of a large partition complex. Here, we present in vitro studies of the partition complex for Bacillus subtilis ParB, using single-molecule fluorescence microscopy and AFM imaging to show that...journal article 2023
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He, P. (author), Katan, A.J. (author), Tubiana, Luca (author), Dekker, C. (author), Michieletto, Davide (author)Kinetoplast DNA (kDNA) is a two-dimensional Olympic-ring-like network of mutually linked DNA minicircles found in certain parasites called trypanosomes. Understanding the self-assembly and replication of this structure are not only major open questions in biology but can also inform the design of synthetic topological materials. Here, we...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