arXiv subjects

Cees Dekker

Publications and source records attributed to Cees Dekker.

At least 19 recordsLinked to original sources

arXiv2024

Synchronization of E. coli bacteria moving in coupled wells

Synchronization plays a crucial role in the dynamics of living organisms, from fireflies flashing in unison to pacemaker cells that jointly generate heartbeats. Uncovering the mechanism behind these phenomena requires an understanding of individual biological oscillators and the coupling forces between them. Here, we develop a single-cell assay that studies rhythmic behavior in the motility of individual E.coli cells that can be mutually synchronized. Circular microcavities are used to isolate E.coli cells that swim along the cavity wall, resulting in self-sustained oscillations. Upon connecting these cavities by microchannels the bacterial motions can be coupled, yielding nonlinear dynamic synchronization patterns with phase slips. We demonstrate that the coordinated movement observed in coupled E. coli oscillators follows mathematical rules of synchronization which we use to quantify the coupling strength. These findings advance our understanding of motility in confinement, and lay the foundation for engineering desired dynamics in microbial active matter.

nlin.AO↗

arXiv2022

Single-Molecule Structure and Topology of Kinetoplast DNA Networks

The Kinetoplast DNA (kDNA) is a two-dimensional Olympic-ring-like network of mutually linked 2.5 kb-long 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 report the first high-resolution, single-molecule study of kDNA network topology using AFM and steered molecular dynamics simulations. We map out the DNA density within the network and the distribution of linking number and valence of the minicircles. We also characterise the DNA hubs that surround the network and show that they cause a buckling transition akin to that of a 2D elastic thermal sheet in the bulk. Intriguingly, we observe a broad distribution of density and valence of the minicircles, indicating heterogeneous network structure and individualism of different kDNA structures. Our findings explain outstanding questions in the field and offer single-molecule insights into the properties of a unique topological material.

cond-mat.soft↗

arXiv2022

Bridging scales in a multiscale pattern-forming system

Self-organized pattern formation is vital for many biological processes. Reaction-diffusion models have advanced our understanding of how biological systems develop spatial structures, starting from homogeneity. However, biological processes inherently involve multiple spatial and temporal scales and transition from one pattern to another over time, rather than progressing from homogeneity to a pattern. To deal with such multiscale systems, coarse-graining methods are needed that allow the dynamics to be reduced to the relevant degrees of freedom at large scales, but without losing information about the patterns at the small scales. Here, we present a semi-phenomenological approach which exploits mass-conservation in pattern formation, and enables to reconstruct information about patterns from the large-scale dynamics. The basic idea is to partition the domain into distinct regions (coarse-grain) and determine instantaneous dispersion relations in each region, which ultimately inform about local pattern-forming instabilities. We illustrate our approach by studying the Min system, a paradigmatic model for protein pattern formation. By performing simulations, we first show that the Min system produces multiscale patterns in a spatially heterogeneous geometry. This prediction is confirmed experimentally by in vitro reconstitution of the Min system. Using a recently developed theoretical framework for mass-conserving reaction-diffusion systems, we show that the spatiotemporal evolution of the total protein densities on large-scales reliably predicts the pattern-forming dynamics. Our approach provides an alternative and versatile theoretical framework for complex systems where analytical coarse-graining methods are not applicable, and can in principle be applied to a wide range of systems with an underlying conservation law.

physics.bio-ph↗

arXiv2022

A DNA turbine powered by a transmembrane potential across a nanopore

Rotary motors play key roles in energy transduction, from macroscale windmills to nanoscale turbines such as ATP synthase in cells. Despite our capabilities to construct engines at many scales, developing functional synthetic turbines at the nanoscale has remained challenging. Here, we experimentally demonstrate rationally designed nanoscale DNA-origami turbines with three chiral blades. These DNA nanoturbines are 24-27 nm in height and diameter and can utilise transmembrane electrochemical potentials across nanopores to drive DNA bundles into sustained unidirectional rotations of up to 10 revolutions/s. The rotation direction is set by the designed chirality of the turbine. All-atom molecular dynamics simulations show how hydrodynamic flows drive this turbine. At high salt concentrations, the rotation direction of turbines with the same chirality is reversed, which is explained by a change in the anisotropy of the electrophoretic mobility. Our artificial turbines operate autonomously in physiological conditions, converting energy from naturally abundant electrochemical potentials into mechanical work. The results open new possibilities for engineering active robotics at the nanoscale.

physics.bio-ph↗

arXiv2022

Sustained unidirectional rotation of a self-organized DNA rotor on a nanopore

Flow-driven rotary motors drive functional processes in human society such as windmills and water wheels. Although examples of such rotary motors also feature prominently in cell biology, their synthetic construction at the nanoscale has thus far remained elusive. Here, we demonstrate flow-driven rotary motion of a self-organized DNA nanostructure that is docked onto a nanopore in a thin solid-state membrane. An elastic DNA bundle self assembles into a chiral conformation upon phoretic docking onto the solid-state nanopore, and subsequently displays a sustained unidirectional rotary motion of up to 20 revolutions/s. The rotors harness energy from a nanoscale water and ion flow that is generated by a static (electro)chemical potential gradient in the nanopore that is established through a salt gradient or applied voltage. These artificial nanoengines self-organize and operate autonomously in physiological conditions, paving a new direction in constructing energy-transducing motors at nanoscale interfaces.

physics.bio-ph↗

arXiv2020

Nanopores -- a Versatile Tool to Study Protein Dynamics

Proteins are the active working horses in our body. These biomolecules perform all vital cellular functions from DNA replication and general biosynthesis to metabolic signaling and environmental sensing. While static 3D structures are now readily available, observing the functional cycle of proteins - involving conformational changes and interactions - remains very challenging, e.g., due to ensemble averaging. However, time-resolved information is crucial to gain a mechanistic understanding of protein function. Single-molecule techniques such as FRET and force spectroscopies provide answers but can be limited by the required labelling, a narrow time bandwidth, and more. Here, we describe electrical nanopore detection as a tool for probing protein dynamics. With a time bandwidth ranging from microseconds to hours, it covers an exceptionally wide range of timescales that is very relevant for protein function. First, we discuss the working principle of label-free nanopore experiments, various pore designs, instrumentation, and the characteristics of nanopore signals. In the second part, we review a few nanopore experiments that solved research questions in protein science, and we compare nanopores to other single-molecule techniques. We hope to make electrical nanopore sensing more accessible to the biochemical community, and to inspire new creative solutions to resolve a variety of protein dynamics - one molecule at a time.

q-bio.QM↗

arXiv2020

Palladium Zero-Mode Waveguides for Optical Single Molecule Detection with Nanopores

Holes in metal films block any transmitting light if the wavelength is much larger than the hole diameter, establishing such nanopores as so-called Zero Mode Waveguides (ZMWs). Molecules on the other hand, can still passage through these holes. We use this to detect individual fluorophore-labelled molecules as they travel through a ZMW and thereby traverse from the dark region to the illuminated side, upon which they emit fluorescent light. This is beneficial both for background suppression and to prevent premature bleaching. We use palladium as a novel metal-film material for ZMWs, which is advantageous compared to conventionally used metals. We demonstrate that it is possible to simultaneously detect translocations of individual free fluorophores of different colors. Labeled DNA and protein biomolecules can be detected as well at the single-molecule level with a high signal-to-noise ratio and at high bandwidth, which opens the door to a variety of single-molecule biophysics studies.

physics.app-ph↗

arXiv2020

A Mechanically Tunable Quantum Dot in a Graphene Break Junction

Graphene quantum dots (QDs) are intensively studied as platforms for the next generation of quantum electronic devices. Fine tuning of the transport properties in monolayer graphene QDs, in particular with respect to the independent modulation of the tunnel barrier transparencies, remains challenging and is typically addressed using electrostatic gating. We investigate charge transport in back-gated graphene mechanical break junctions and reveal Coulomb blockade physics characteristic of a single, high-quality QD when a nanogap is opened in a graphene constriction. By mechanically controlling the distance across the newly-formed graphene nanogap, we achieve reversible tunability of the tunnel coupling to the drain electrode by five orders of magnitude, while keeping the source-QD tunnel coupling constant. These findings indicate that the tunnel coupling asymmetry can be significantly modulated with a mechanical tuning knob and has important implications for the development of future graphene-based devices, including energy converters and quantum calorimeters.

cond-mat.mes-hall↗

arXiv2018

Mechanically Controlled Quantum Interference in Graphene Break Junctions

The ability to detect and distinguish quantum interference signatures is important for both fundamental research and for the realization of devices including electron resonators, interferometers and interference-based spin filters. Consistent with the principles of subwavelength optics, the wave nature of electrons can give rise to various types of interference effects, such as Fabry-Pérot resonances, Fano resonances and the Aharonov-Bohm effect. Quantum-interference conductance oscillations have indeed been predicted for multiwall carbon nanotube shuttles and telescopes, and arise from atomic-scale displacements between the inner and outer tubes. Previous theoretical work on graphene bilayers indicates that these systems may display similar interference features as a function of the relative position of the two sheets. Experimental verification is, however, still lacking. Graphene nanoconstrictions represent an ideal model system to study quantum transport phenomena due to the electronic coherence and the transverse confinement of the carriers. Here, we demonstrate the fabrication of bowtie-shaped nanoconstrictions with mechanically controlled break junctions (MCBJs) made from a single layer of graphene. We find that their electrical conductance displays pronounced oscillations at room temperature, with amplitudes that modulate over an order of magnitude as a function of sub-nanometer displacements. Surprisingly, the oscillations exhibit a period larger than the graphene lattice constant. Charge-transport calculations show that the periodicity originates from a combination of quantum-interference and lattice-commensuration effects of two graphene layers that slide across each other. Our results provide direct experimental observation of Fabry-Pérot-like interference of electron waves that are partially reflected/transmitted at the edges of the graphene bilayer overlap region.

cond-mat.mes-hall↗

arXiv2011

Atomic-scale electron-beam sculpting of defect-free graphene nanostructures

In order to harvest the many promising properties of graphene in (electronic) applications, a technique is required to cut, shape or sculpt the material on a nanoscale without damage to its atomic structure, as this drastically influences the electronic properties of the nanostructure. Here, we reveal a temperature-dependent self-repair mechanism allowing damage-free atomic-scale sculpting of graphene using a focused electron beam. We demonstrate that by sculpting at temperatures above 600 °C, an intrinsic self-repair mechanism keeps the graphene single-crystalline during cutting, even thought the electron beam induces considerable damage. Self-repair is mediated by mobile carbon ad-atoms constantly repairing the defects caused by the electron beam. Our technique allows reproducible fabrication and simultaneous imaging of single-crystalline free-standing nanoribbons, nanotubes, nanopores, and single carbon chains.

cond-mat.mtrl-sci↗

arXiv2010

DNA Translocation through Graphene Nanopores

Nanopores -- nanosized holes that can transport ions and molecules -- are very promising devices for genomic screening, in particular DNA sequencing. Both solid-state and biological pores suffer from the drawback, however, that the channel constituting the pore is long, viz. 10-100 times the distance between two bases in a DNA molecule (0.5 nm for single-stranded DNA). Here, we demonstrate that it is possible to realize and use ultrathin nanopores fabricated in graphene monolayers for single-molecule DNA translocation. The pores are obtained by placing a graphene flake over a microsize hole in a silicon nitride membrane and drilling a nanosize hole in the graphene using an electron beam. As individual DNA molecules translocate through the pore, characteristic temporary conductance changes are observed in the ionic current through the nanopore, setting the stage for future genomic screening.

physics.bio-ph↗

arXiv2010

Wedging Transfer of Nanostructures

We report a versatile water-based method for transferring nanostructures onto surfaces of various shapes and compositions. The transfer occurs through the intercalation of a layer of water between a hydrophilic substrate and a hydrophobic nanostructure (for example, graphene flakes, carbon nanotubes, metallic nanostructures, quantum dots, etc) locked within a hydrophobic polymer thin film. As a result, the film entrapping the nanostructure is lifted off and floats at the air-water interface. The nanostructure can subsequently be deposited onto a target substrate by the removal of the water and the dissolution of the polymeric film. We show examples where graphene flakes and patterned metallic nanostructures are precisely transferred onto a specific location on a variety of patterned substrates, even on top of curved objects such as microspheres. The method is simple to use, fast, and does not require advanced equipment.

cond-mat.mes-hall↗

arXiv2005

Orbital Kondo effect in carbon nanotubes

Progress in the fabrication of nanometer-scale electronic devices is opening new opportunities to uncover the deepest aspects of the Kondo effect, one of the paradigmatic phenomena in the physics of strongly correlated electrons. Artificial single-impurity Kondo systems have been realized in various nanostructures, including semiconductor quantum dots, carbon nanotubes and individual molecules. The Kondo effect is usually regarded as a spin-related phenomenon, namely the coherent exchange of the spin between a localized state and a Fermi sea of electrons. In principle, however, the role of the spin could be replaced by other degrees of freedom, such as an orbital quantum number. Here we demonstrate that the unique electronic structure of carbon nanotubes enables the observation of a purely orbital Kondo effect. We use a magnetic field to tune spin-polarized states into orbital degeneracy and conclude that the orbital quantum number is conserved during tunneling. When orbital and spin degeneracies are simultaneously present, we observe a strongly enhanced Kondo effect, with a multiple splitting of the Kondo resonance at finite field and predicted to obey a so-called SU(4) symmetry.

cond-mat.mes-hall↗

arXiv2004

Electron-hole symmetry in a semiconducting carbon nanotube quantum dot

Optical and electronic phenomena in solids arise from the behaviour of electrons and holes (unoccupied states in a filled electron sea). Electron-hole symmetry can often be invoked as a simplifying description, which states that electrons with energy above the Fermi sea behave the same as holes below the Fermi energy. In semiconductors, however, electron-hole symmetry is generally absent since the energy band structure of the conduction band differs from the valence band. Here we report on measurements of the discrete, quantized-energy spectrum of electrons and holes in a semiconducting carbon nanotube. Through a gate, an individual nanotube is filled controllably with a precise number of either electrons or holes, starting from one. The discrete excitation spectrum for a nanotube with N holes is strikingly similar to the corresponding spectrum for N electrons. This observation of near perfect electron-hole symmetry demonstrates for the first time that a semiconducting nanotube can be free of charged impurities, even in the limit of few-electrons or holes. We furthermore find an anomalously small Zeeman spin splitting and an excitation spectrum indicating strong electron-electron interactions.

cond-mat.mes-hall↗

arXiv2004

Fast DNA translocation through a solid-state nanopore

We report translocation experiments on double-strand DNA through a silicon oxide nanopore. Samples containing DNA fragments with seven different lengths between 2000 to 96000 basepairs have been electrophoretically driven through a 10 nm pore. We find a power-law scaling of the translocation time versus length, with an exponent of 1.26 $\pm$ 0.07. This behavior is qualitatively different from the linear behavior observed in similar experiments performed with protein pores. We address the observed nonlinear scaling in a theoretical model that describes experiments where hydrodynamic drag on the section of the polymer outside the pore is the dominant force counteracting the driving. We show that this is the case in our experiments and derive a power-law scaling with an exponent of 1.18, in excellent agreement with our data.

q-bio.BM↗

arXiv2002

Transport through the Interface between a Semiconducting Carbon Nanotube and a Metal Electrode

We report a numerical study of the tunnel conductance through the Schottky barrier at the contact between a semiconducting carbon nanotube and a metal electrode. In a planar gate model the asymmetry between the p--doped and the n--doped region is shown to depend mainly on the difference between the electrode Fermi level and the band gap of carbon nanotubes. We quantitatively show how the gate/nanotube distance is important to get large on--off ratios. We explain the bend of the current versus gate voltage as the transition from a thermal--activation region to a tunneling region. A good agreement is obtained with experimental results for carbon nanotubes field--effect transistors.

cond-mat.mes-hall↗

arXiv2000

Electrical transport through carbon nanotube junctions created by mechanical manipulation

Using an atomic force microscope we have created nanotube junctions such as buckles and crossings within individual single-wall metallic carbon nanotubes connected to metallic electrodes. The electronic transport properties of these manipulated structures show that they form electronic tunnel junctions. The conductance shows power-law behavior as a function of bias voltage and temperature, which can be well modeled by a Luttinger liquid model for tunneling between two nanotube segments separated by the manipulated junction.

cond-mat.mes-hall↗

arXiv2000

A Mechanism for Cutting Carbon Nanotubes with a Scanning Tunneling Microscope

We discuss the local cutting of single-walled carbon nanotubes by a voltage pulse to the tip of a scanning tunneling microscope. The tip voltage ($\mid V \mid \ge $~3.8 eV) is the key physical quantity in the cutting process. After reviewing several possible physical mechanisms we conclude that the cutting process relies on the weakening of the carbon-carbon bonds through a combination of localized particle-hole excitations induced by inelastically tunneling electrons and elastic deformation due to the electric field between tip and sample. The carbon network releases part of the induced mechanical stress by forming topological defects that act as nucleation centers for the formation of dislocations that dynamically propagate towards bond-breaking.

cond-mat.mtrl-sci↗