- document
-
Kim, E. (author), Martin Gonzalez, A. (author), Pradhan, B. (author), van der Torre, J. (author), Dekker, C. (author)Condensin, a structural maintenance of chromosomes (SMC) complex, has been shown to be a molecular motor protein that organizes chromosomes by extruding loops of DNA. In cells, such loop extrusion is challenged by many potential conflicts, for example, the torsional stresses that are generated by other DNA-processing enzymes. It has so far...journal article 2022
- document
-
Mazur, G.P. (author), van Loo, N. (author), Wang, J. (author), Dvir, T. (author), Wang, Guanzhong (author), Korneychuk, S. (author), Borsoi, F. (author), Dekker, R.C. (author), Badawy, G.H.A. (author), Vinke, Peter (author), Quintero Perez, M. (author), Heedt, S. (author), Kouwenhoven, Leo P. (author)In superconducting quantum circuits, aluminum is one of the most widely used materials. It is currently also the superconductor of choice for the development of topological qubits. However, aluminum-based devices suffer from poor magnetic field compatibility. Herein, this limitation is resolved by showing that adatoms of heavy elements (e.g.,...journal article 2022
- document
-
Kawasaki, S. (author), Yeh, Jia-Jun (author), Saccher, M. (author), Li, Jian (author), Dekker, R. (author)The main limitation of acoustic particle separation for microfluidic application is its low sorting efficiency. This is due to the weak coupling of surface acoustic waves (SAWs) into the microchannel. In this work, we demonstrate bulk acoustic wave (BAW) particle sorting using capacitive micromachined ultrasonic transducers (CMUTs) for the first...conference paper 2022
- document
-
Fragasso, A. (author), de Vries, Hendrik W. (author), Andersson, John (author), van der Sluis, E.O. (author), van der Giessen, Erik (author), Onck, Patrick R. (author), Dekker, C. (author)Nuclear pore complexes (NPCs) regulate all molecular transport between the nucleus and the cytoplasm in eukaryotic cells. Intrinsically disordered Phe-Gly nucleoporins (FG-Nups) line the central conduit of NPCs to impart a selective barrier where large proteins are excluded unless bound to a transport receptor (karyopherin; Kap). Here, we...journal article 2022
- document
-
Chardon, Florian (author), Japaridze, A. (author), Witt, Hannes (author), Velikovsky, Leonid (author), Chakraborty, Camellia (author), Wilhelm, Therese (author), Dumont, Marie (author), Yang, W.W.W. (author), Dekker, C. (author)Chromosome inheritance depends on centromeres, epigenetically specified regions of chromosomes. While conventional human centromeres are known to be built of long tandem DNA repeats, much of their architecture remains unknown. Using single-molecule techniques such as AFM, nanopores, and optical tweezers, we find that human centromeric DNA...journal article 2022
- document
-
Fayezioghani, A. (author), Dekker, R. (author), Sluys, Lambertus J. (author)Structural components in corrosive environments such as pipelines, bridges, aircrafts, and turbines are imposed to stress corrosion. A stress corrosion model for pit growth should a) accurately consider the electrochemistry of the corrosion process, b) properly deal with the moving interface between solid and electrolyte, and c) effectively...journal article 2022
- document
-
Boskeljon-Horst, Leonie (author), J. de Boer, Robert (author), Sillem, S. (author), Dekker, Sidney W. A. (author)In this study we identify the differences in goal realisation when applying two conflicting paradigms regarding rule perception and management. We gathered more than 30 scenarios where goal conflicts were apparent in a military operational unit. We found that operators repetitively utilized certain routines in executing their tasks in an effort...journal article 2022
- document
-
Fayezioghani, A. (author), Dekker, R. (author), Sluys, Lambertus J. (author)Corrosion is a phenomenon observed in structural components in corrosive environments such as pipelines, bridges, aircrafts, turbines, etc. The computational model of corrosion should enjoy two features: a) accurately considering the electrochemistry of corrosion and b) properly dealing with the moving interface between solid and electrolyte....journal article 2022
- document
-
Pradhan, B. (author), Barth, R. (author), Kim, E. (author), van Laar, T. (author), Yang, W.W.W. (author), Ryu, J.K. (author), van der Torre, J. (author), Peters, Jan Michael (author), Dekker, C. (author)Ring-shaped structural maintenance of chromosomes (SMC) complexes like condensin and cohesin extrude loops of DNA. It remains, however, unclear how they can extrude DNA loops in chromatin that is bound with proteins. Here, we use in vitro single-molecule visualization to show that nucleosomes, RNA polymerase, and dCas9 pose virtually no...journal article 2022
- document
-
Kuijpers, L.C. (author), van Laar, T. (author), Janissen, R. (author), Dekker, N.H. (author)Multiplexed single-molecule magnetic tweezers (MT) have recently been employed to probe the RNA synthesis dynamics of RNA-dependent RNA polymerases (RdRp). Here, we present a protocol for simultaneously probing the RNA synthesis dynamics of hundreds of single polymerases with MT. We describe the preparation of a dsRNA construct for probing...journal article 2022
- document
-
Dekker, S.W.A. (author), Tooma, Michael (author)The shortcomings of incident-based metrics for worker safety such as total recordable incident frequency rate (TRIFR) are well documented. In particular, a low TRIFR is no assurance against legal liability. There is considerable overlap between the literature on safety as the presence of capacities to make things go well, and jurisprudence in...journal article 2022
- document
-
Meindlhumer, S. (author), Kerssemakers, J.W.J. (author), Dekker, C. (author)The Min protein system is arguably the best-studied model system for biological pattern formation. It exhibits pole-to-pole oscillations in E. coli bacteria as well as a variety of surface wave patterns in in vitro reconstitutions. Such Min surface wave patterns pose particular challenges to quantification as they are typically only semi...journal article 2022
- document
-
Saccher, M. (author), Lolla, Sai Sandeep (author), Kawasaki, S. (author), Dekker, R. (author)Ultrasound (US) has recently gained attention for powering and communication with implantable devices due to its short wavelength and low attenuation. However, beam mis-alignments cause a sharp decrease in the amount of transferred power and quality of communication. This work investigates a telemetry protocol that relies on the difference in...conference paper 2022
- document
-
Holub, M. (author), Birnie, A.T.F. (author), Japaridze, A. (author), van der Torre, J. (author), Ridder, Maxime den (author), de Ram, C. (author), Pabst, Martin (author), Dekker, C. (author)Chromosome structure and function is studied using various cell-based methods as well as with a range of in vitro single-molecule techniques on short DNA substrates. Here, we present a method to obtain megabase-pair-length deproteinated DNA for in vitro studies. We isolated chromosomes from bacterial cells and enzymatically digested the...journal article 2022
- document
-
Dekker, W.J.C. (author), Jürgens, H. (author), Ortiz Merino, R.A. (author), Mooiman, C. (author), van den Berg, Remon (author), Kaljouw, Astrid (author), Mans, R. (author), Pronk, J.T. (author)While thermotolerance is an attractive trait for yeasts used in industrial ethanol production, oxygen requirements of known thermotolerant species are incompatible with process requirements. Analysis of oxygen-sufficient and oxygen-limited chemostat cultures of the facultatively fermentative, thermotolerant species Ogataea parapolymorpha...journal article 2022
- document
-
Mc Cluskey, K.A. (author), van Veen, E.N.W. (author), Cnossen, J.P. (author), Wesselink, W.J. (author), Asscher, F.M. (author), Smith, C.S. (author), Dekker, N.H. (author)Accurate image alignment is critical in multicolor single-molecule fluorescence microscopy. Global alignment using affine transformations leaves residual errors due to the nonlinearity of the distortions, which decreases the effective field of view. Subsequent local refinement demands either large amounts of reference data and processing time...journal article 2021
- document
-
Dekker, Levi (author)In this thesis, a ground structure based thermofluid topology optimization (TO) method is presented which is applicable to problems with creeping flow. Fluid channels with creeping flow are found in a variety of engineering applications, primarily in the field of microfluidics. Current fluid channel TO is typically done with density-based TO and...master thesis 2021
- document
-
Dekker, R. (author)The world is currently in a severe man-made climate crisis, creating the need for using renewable energy sources such as offshore wind farms. Offshore wind turbines do not take up any valuable space on land and can use the greater wind resource at sea. The downside is, however, that they are exposed to a much harsher environment at sea, which...doctoral thesis 2021
- document
-
Dekker, W.J.C. (author)Saccharomyces cerevisiae is a natural producer of ethanol and industrial strains can produce ethanol at high volumetric rates and near-theoretical yields. In addition to its fast fermentative metabolism, its GRAS (generally recognized as safe) status, ease of genetic engineering, tolerance to low pH and high ethanol concentrations contribute to...doctoral thesis 2021
- document
-
Dekker, Loek (author)In the Netherlands, one of the government bodies solving complex problems is the Netherlands Enterprise Agency (‘Rijksdienst Voor Ondernemers’; RVO). Within RVO, X-lab is developing new ways of working to be better prepared to deal with these complex problems. In short, X-lab is RVO’s internal innovation lab that creates and collects different...master thesis 2021