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Neklyudova, M. (author), Erdamar, A.K. (author), Vicarelli, L. (author), Heerema, S.J. (author), Rehfeldt, T. (author), Pandraud, G. (author), Koladouz Esfahani, Z. (author), Dekker, C. (author), Zandbergen, H.W. (author)
We present a technique to fabricate ultrathin (down to 20 nm) uniform electron transparent windows at dedicated locations in a SiN membrane for in situ transmission electron microscopy experiments. An electron-beam (e-beam) resist is spray-coated on the backside of the membrane in a KOH-etched cavity in silicon which is patterned using...
journal article 2017
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Dekker, M.J. (author)
Research in the field of automated vehicles focuses primarily on technological developments and interactions of the system with other roads users, leaving a knowledge gap of actual user demand for automated vehicles. This study investigates the development of Automated Driving Systems - Dedicated Vehicles (ADS-DVs) from the perspective of the...
master thesis 2017
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Deshpande, S.R. (author), Birnie, A.T.F. (author), Dekker, C. (author)
Due to their cell membrane-mimicking properties, liposomes have served as a versatile research tool in science, from membrane biophysics and drug delivery systems to bottom-up synthetic cells. We recently reported a novel microfluidic method, Octanol-assisted Liposome Assembly (OLA), to form cell-sized, monodisperse, unilamellar liposomes...
journal article 2017
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Dekker, R.C.M. (author)
master thesis 2017
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Nechemia-Arbely, Yael (author), Fachinetti, Daniele (author), Miga, Karen H. (author), Sekulic, Nikolina (author), Soni, G.V. (author), Kim, Dong Hyun (author), Wong, Adeline K. (author), Lee, Ah Young (author), Nguyen, Kristen (author), Dekker, C. (author), Ren, Bing (author), Black, Ben E. (author), Cleveland, Don W. (author)
Chromatin assembled with centromere protein A (CENP-A) is the epigenetic mark of centromere identity. Using new reference models, we now identify sites of CENP-A and histone H3.1 binding within the megabase, α-satellite repeat-containing centromeres of 23 human chromosomes. The overwhelming majority (97%) of α-satellite DNA is found to be...
journal article 2017
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Vlijm, R. (author), Kim, S.H. (author), De Zwart, P. L. (author), Dalal, Y. (author), Dekker, C. (author)
Nucleosomes form the unit structure of the genome in eukaryotes, thereby constituting a fundamental tenet of chromatin biology. In canonical nucleosomes, DNA wraps around the histone octamer in a left-handed toroidal ramp. Here, in single-molecule magnetic tweezers studies of chaperone-assisted nucleosome assembly, we show that the handedness...
journal article 2017
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Dekker, M. (author), Leijnse, T. (author), Simonse, J. (author), Van Westen, B. (author)
This main objective of this report is to find the cause of the erosion problem and to design a solution for the problematic situation in front of the Iberostar Varadero Hotel, Cuba. This hotel is situated in the eastern part of the Peninsula of Hicacos. For almost 40 years erosion problems are present at this location and need direct attention....
student report 2017
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Burnham, D.R. (author), Nijholt, B. (author), de Vlaminck, I. (author), Quan, Jinhua (author), Yusufzai, Timur (author), Dekker, C. (author)
We investigate the mechanistic nature of the Snf2 family protein HARP, mutations of which are responsible for Schimke immuno-osseous dysplasia. Using a single-molecule magnetic tweezers assay, we construct RPA-stabilized DNA bubbles within torsionally constrained DNA to investigate the annealing action of HARP on a physiologically relevant...
journal article 2017
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Shafqat, Salman (author), Hoefnagels, Johan P.M. (author), Savov, A.M. (author), Joshi, S. (author), Dekker, R. (author), Geers, Marc G.D. (author)
The exciting field of stretchable electronics (SE) promises numerous novel applications, particularly in-body and medical diagnostics devices. However, future advanced SE miniature devices will require high-density, extremely stretchable interconnects with micron-scale footprints, which calls for proven standardized (complementary metal-oxide...
journal article 2017
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Kriegel, Franziska (author), Ermann, Niklas (author), Forbes, R.J.G. (author), Dulin, D. (author), Dekker, N.H. (author), Lipfert, J. (author)
The mechanical properties of DNA fundamentally constrain and enable the storage and transmission of genetic information and its use in DNA nanotechnology. Many properties of DNA depend on the ionic environment due to its highly charged backbone. In particular, both theoretical analyses and direct singlemolecule experiments have shown its...
journal article 2017
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van Riessen, B. (author), Negenborn, R.R. (author), Dekker, Rommert (author)
The intermodal hinterland transportation of maritime containers is under pressure from port authorities and shippers to achieve a more integrated, efficient network operation. Current optimisation methods in literature yield limited results in practice, though, as the transportation product structure limits the flexibility to optimise network...
journal article 2017
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Joshi, S. (author), Bagani, R. (author), Beckers, Lucas (author), Dekker, R. (author)
This paper reports the use of rubber—Polybutadiene as an intermediate adhesive layer for improving the adhesion between polyimide (PI) and silicone polydimethylsiloxane (PDMS) which is required for a reliable fabrication of flexible/stretchable body patches for various applications. The adhesive bond initiated by the butyl rubber (BR), apart...
conference paper 2017
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Kluba, M.M. (author), Arslan, A. (author), Stoute, R. (author), Muganda, James (author), Dekker, R. (author)
This paper presents a new method for the CMOS compatible fabrication of microchannels integrated into a silicon substrate. In a single-step DRIE process (Deep Reactive Ion Etching) a network of microchannels with High Aspect Ratio (HAR) up to 10, can be etched in a silicon substrate through a mesh mask. In the same single etching step,...
conference paper 2017
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van Oene, M.M. (author), Dickinson, L.E. (author), Cross, B. (author), Pedaci, F. (author), Lipfert, J. (author), Dekker, N.H. (author)
The bacterial flagellar motor of Escherichia coli is a nanoscale rotary engine essential for bacterial propulsion. Studies on the power output of single motors rely on the measurement of motor torque and rotation under external load. Here, we investigate the use of magnetic tweezers, which in principle allow the application and active control...
journal article 2017
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Dulin, D. (author), Arnold, Jamie J. (author), van Laar, T. (author), Oh, Hyung Suk (author), Lee, Cheri (author), Perkins, Angela L. (author), Harki, Daniel A. (author), Depken, S.M. (author), Cameron, Craig E. (author), Dekker, N.H. (author)
RNA viruses pose a threat to public health that is exacerbated by the dearth of antiviral therapeutics. The RNA-dependent RNA polymerase (RdRp) holds promise as a broad-spectrum, therapeutic target because of the conserved nature of the nucleotide-substrate-binding and catalytic sites. Conventional, quantitative, kinetic analysis of antiviral...
journal article 2017
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Eeftens, J.M. (author), Bisht, Shveta (author), Kerssemakers, J.W.J. (author), Kschonsak, Marc (author), Haering, Christian H. (author), Dekker, C. (author)
Condensin, a conserved member of the SMC protein family of ring-shaped multi-subunit protein complexes, is essential for structuring and compacting chromosomes. Despite its key role, its molecular mechanism has remained largely unknown. Here, we employ single-molecule magnetic tweezers to measure, in real time, the compaction of individual...
journal article 2017
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Movalli, Paola (author), Bode, P. (author), Dekker, René (author), Fornasari, Lorenzo (author), van der Mije, Steven (author), Yosef, Reuven (author)
This study examines the potential to use instrumental neutron activation analysis (INAA) to explore temporal and geographical variation in exposure to heavy metals and other selected elements in common kestrel Falco tinnunculus using feathers from a natural history collection. The study gathered samples of two breast feathers from each of 16...
journal article 2017
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Caspi, Y. (author), Dekker, C. (author)
The bacterial Min protein system provides a major model system for studying reaction-diffusion processes in biology. Here we present the first in vitro study of the Min system in fully confined three-dimensional chambers that are lithography-defined, lipid-bilayer coated and isolated through pressure valves. We identify three typical...
journal article 2016
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Dekker, J.J. (author)
master thesis 2016
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Plesa, C. (author), Verschueren, D.V. (author), Pud, S. (author), van der Torre, J. (author), Ruitenberg, J.W. (author), Witteveen, M.J. (author), Jonsson, P.M. (author), Grosberg, Alexander Y. (author), Rabin, Yitzhak (author), Dekker, C. (author)
Long DNA molecules can self-entangle into knots. Experimental techniques for observing such DNA knots (primarily gel electrophoresis) are limited to bulk methods and circular molecules below 10 kilobase pairs in length. Here, we show that solid-state nanopores can be used to directly observe individual knots in both linear and circular single...
journal article 2016
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