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Electrostatic control of the proximity effect in the bulk of semiconductor-superconductor hybrids

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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Three-dimensional localization microscopy with increased axial precision through TIRF angle modulation

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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Looping the Genome with SMC Complexes

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 Nanopores

Klughammer, 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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A DNA turbine powered by a transmembrane potential across a nanopore

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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Modeling and Characterization of Pre-Charged Collapse-Mode CMUTs

Saccher, M. (author), Kawasaki, S. (author), Klootwijk, Johan (author), van Schaijk, Rob (author), Dekker, R. (author)

Recently, the applications of ultrasound transducers expanded from high-end diagnostic tools to point of care diagnostic devices and wireless power receivers for implantable devices. These new applications additionally require that the transducer technology must comply to biocompatibility and manufacturing scalability. In this respect,...

journal article 2023

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Nanopores as versatile single-molecule tools: From DNA turbines to protein sequencing

Dekker, C. (author)

journal article 2023

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Optimizing single-molecule experimental approaches for the study of complex protein assemblies on DNA

Dekker, N.H. (author)

journal article 2023

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Aeropropulsive Performance Modelling of Over-The-Wing Propulsion at Incidence

Dekker, H.N.J. (author), Tuinstra, M (author), Baars, W.J. (author), Scarano, F. (author), Ragni, D. (author)

A semi-emperical model is developed, able to capture the aeropropulsive performance characteristics of Over-The-Wing propellers at incidence. The model is based on an hypothesis on the interactions of the propeller- and wing-induced flow fields. Effects of these interactions on the both the thrust and lift are written in a form in which the...

conference paper 2023

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Correction: Aeropropulsive Performance Modelling of Over-The-Wing Propulsion at Incidence

Dekker, H.N.J. (author), Tuinstra, Marthijn (author), Baars, W.J. (author), Scarano, F. (author), Ragni, D. (author)

conference paper 2023

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Supercoiling-dependent DNA binding: quantitative modeling and applications to bulk and single-molecule experiments

Kolbeck, Pauline J. (author), Tišma, M. (author), Analikwu, B.T. (author), Vanderlinden, Willem (author), Dekker, C. (author), Lipfert, Jan (author)

DNA stores our genetic information and is ubiquitous in applications, where it interacts with binding partners ranging from small molecules to large macromolecular complexes. Binding is modulated by mechanical strains in the molecule and can change local DNA structure. Frequently, DNA occurs in closed topological forms where topology and...

journal article 2023

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Dynamin A as a one-component division machinery for synthetic cells

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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Testing pseudotopological and nontopological models for SMC-driven DNA loop extrusion against roadblock-traversal experiments

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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A new setup to study the influence of plant growth on the consolidation of dredged cohesive sediment

Barciela Rial, M. (author), Saaltink, Remon M. (author), van Kessel, Thijs (author), Chassagne, C. (author), Dekker, Stefan C. (author), de Boer, Hugo J. (author), Griffioen, Jasper (author), Wassen, Martin J. (author), Winterwerp, J.C. (author)

Dredged cohesive sediment is progressively being used for wetland construction. However, little is known about the effect of plant growth during the self-weight consolidation of this sediment. In order to check the feasibility of such a study, a new experimental setup has been constructed. As an example, the effect of Phragmites australis on the...

journal article 2023

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Unsteady flow behaviour of multi-rotors in ground proximity

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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MukBEF-dependent chromosomal organization in widened Escherichia coli

Japaridze, A. (author), van Wee, R.G. (author), Gogou, C. (author), Kerssemakers, J.W.J. (author), van den Berg, D.F. (author), Dekker, C. (author)

The bacterial chromosome is spatially organized through protein-mediated compaction, supercoiling, and cell-boundary confinement. Structural Maintenance of Chromosomes (SMC) complexes are a major class of chromosome-organizing proteins present throughout all domains of life. Here, we study the role of the Escherichia coli SMC complex MukBEF...

journal article 2023

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Detection of phosphorylation post-translational modifications along single peptides with nanopores

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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Directing Min protein patterns with advective bulk flow

Meindlhumer, S. (author), Brauns, Fridtjof (author), Finžgar, Jernej Rudi (author), Kerssemakers, J.W.J. (author), Dekker, C. (author), Frey, Erwin (author)

The Min proteins constitute the best-studied model system for pattern formation in cell biology. We theoretically predict and experimentally show that the propagation direction of in vitro Min protein patterns can be controlled by a hydrodynamic flow of the bulk solution. We find downstream propagation of Min wave patterns for low MinE:MinD...

journal article 2023

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Zero-Mode Waveguide Nanowells for Single-Molecule Detection in Living Cells

Yang, Sora (author), Klughammer, N. (author), Barth, A. (author), Tanenbaum, M. (author), Dekker, C. (author)

Single-molecule fluorescence imaging experiments generally require sub-nanomolar protein concentrations to isolate single protein molecules, which makes such experiments challenging in live cells due to high intracellular protein concentrations. Here, we show that single-molecule observations can be achieved in live cells through a drastic...

journal article 2023

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Microwell-enhanced optical rapid antibiotic susceptibility testing of single bacteria

Roslon, I.E. (author), Japaridze, A. (author), Rodenhuis, Stef (author), Hamoen, Lieke (author), Ghatkesar, M.K. (author), Steeneken, P.G. (author), Dekker, C. (author), Alijani, F. (author)

Bacteria that are resistant to antibiotics present an increasing burden on healthcare. To address this emerging crisis, novel rapid antibiotic susceptibility testing (AST) methods are eagerly needed. Here, we present an optical AST technique that can determine the bacterial viability within 1 h down to a resolution of single bacteria. The...

journal article 2023