- document
-
Shi, X. (author), Pumm, Anna Katharina (author), Isensee, Jonas (author), Zhao, W. (author), Verschueren, D.V. (author), Martin Gonzalez, A. (author), Golestanian, Ramin (author), Dietz, Hendrik (author), Dekker, C. (author)Flow-driven rotary motors such as windmills and water wheels drive functional processes in human society. Although examples of such rotary motors also feature prominently in cell biology, their synthetic construction at the nanoscale has remained challenging. Here we demonstrate flow-driven rotary motion of a self-organized DNA nanostructure...journal article 2022
- document
-
Ying, Yi Lun (author), Hu, Zheng Li (author), Zhang, Shengli (author), Qing, Yujia (author), Fragasso, A. (author), Maglia, Giovanni (author), Meller, Amit (author), Bayley, Hagan (author), Dekker, C. (author), Long, Yi Tao (author)Inspired by the biological processes of molecular recognition and transportation across membranes, nanopore techniques have evolved in recent decades as ultrasensitive analytical tools for individual molecules. In particular, nanopore-based single-molecule DNA/RNA sequencing has advanced genomic and transcriptomic research due to the...review 2022
- document
-
Dekker, H.N.J. (author), Ragni, D. (author), Baars, W.J. (author), Scarano, F. (author), Tuinstra, Marthijn (author)An experimental investigation is conducted to study the aerodynamic behavior of a two-rotor system in ground proximity. The counter-rotating rotors are placed side-by-side in the hovering condition. The time-averaged and unsteady flow behavior is studied when the rotor-to-rotor lateral distance and the distance between the rotors and the...journal article 2022
- document
-
Wen, C. (author), Bertosin, E. (author), Shi, X. (author), Dekker, C. (author), Schmid, Sonja (author)Nanopores are versatile single-molecule sensors offering a simple label-free readout with great sensitivity. We recently introduced the nanopore electro-osmotic trap (NEOtrap) which can trap and sense single unmodified proteins for long times. The trapping is achieved by the electro-osmotic flow (EOF) generated from a DNA-origami sphere...journal article 2022
- document
-
Janissen, R. (author), Eslami Mossallam, B. (author), Artsimovitch, Irina (author), Depken, S.M. (author), Dekker, N.H. (author)Pausing by bacterial RNA polymerase (RNAp) is vital in the recruitment of regulatory factors, RNA folding, and coupled translation. While backtracking and intra-structural isomerization have been proposed to trigger pausing, our mechanistic understanding of backtrack-associated pauses and catalytic recovery remains incomplete. Using high...journal article 2022
- document
-
Bengtson, M.L. (author), Bharadwaj, M. (author), Franch, O. (author), van der Torre, J. (author), Meerdink, V.E.E. (author), Schallig, Henk (author), Dekker, C. (author)Nucleic-acid detection is crucial for basic research as well as for applications in medicine such as diagnostics. In resource-limited settings, however, most DNA-detection diagnostic schemes are inapplicable since they rely on expensive machinery, electricity, and trained personnel. Here, we present an isothermal DNA detection scheme for the...journal article 2022
- 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