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Maxim Belkin

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University Of Applied Sciences Van Hall Larenstein

Benjamin Cressiot

CY Cergy Paris Université

David Aarón Estrada

S. Yemenicioglu

Lusine Gasparyan

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Papers by Maxim Belkin

Molecular Dynamics Simulation of DNA Capture and Transport in Heated Nanopores

ACS Applied Materials & Interfaces

The integration of local heat sources with solid-state nanopores offers new means for controlling... more The integration of local heat sources with solid-state nanopores offers new means for controlling the transmembrane transport of charged biomacromolecules. In the case of electrophoretic transport of DNA, recent experimental studies revealed unexpected temperature dependences of the DNA capture rate, the DNA translocation velocity, and the ionic current blockades produced by the presence of DNA in the nanopore. Here, we report the results of all-atom molecular dynamics simulations that elucidated the effect of temperature on the key microscopic processes governing electric field-driven transport of DNA through nanopores. Mimicking the experimental setup, we simulated the capture and subsequent translocation of short DNA duplexes through a locally heated nanopore at several temperatures and electrolyte conditions. The temperature dependence of ion mobility at the DNA surface was found to cause the dependence of the relative conductance blockades on temperature. To the first order, the effective force on DNA in the nanopore was found to be independent of temperature, despite a considerable reduction of solution viscosity. The temperature dependence of the solution viscosity was found to make DNA translocations faster for a uniformly heated system but not in the case of local heating that does not affect viscosity of solution surrounding the untranslocated part of the molecule. Increasing solution temperature was also found to reduce the lifetime of bonds formed between cations and DNA. Using a flow suppression algorithm, we were able to separate the effects of electro-osmotic flow and direct ion binding, finding the reduced durations of DNA−ion bonds to increase, albeit weakly, the effective force experienced by DNA in an electric field. Unexpectedly, our simulations revealed a considerable temperature dependence of solvent velocity at the DNA surfaceslip velocity, an effect that can alter hydrodynamic coupling between the motion of DNA and the surrounding fluid.

Mechanical Trapping of DNA in a Double-Nanopore System

Nano letters, Jan 14, 2016

Nanopores have become ubiquitous components of systems for single-molecule manipulation and detec... more Nanopores have become ubiquitous components of systems for single-molecule manipulation and detection, in particular DNA sequencing where electric field driven translocation of DNA through a nanopore is used to read out the DNA molecule. Here, we present a double-pore system where two nanopores are drilled in parallel through the same solid-state membrane, which offers new opportunities for DNA manipulation. Our experiments and molecular dynamics simulations show that simultaneous electrophoretic capture of a DNA molecule by the two nanopores mechanically traps the molecule, increasing its residence time within the nanopores by orders of magnitude. Remarkably, by using two unequal-sized nanopores, the pore of DNA entry and exit can be discerned from the ionic current blockades, and the translocation direction can be precisely controlled by small differences in the effective force applied to DNA. The mechanical arrest of DNA translocation using a double-pore system can be straightfor...

Emergent Phenomena in Far-From-Equilibrium Magnetic Granular Ensembles at a Liquid-Air Interface

AIP Conference Proceedings, 2009

Remarkable nontrivially ordered self-assembled structures are formed in ensembles of magnetic mic... more Remarkable nontrivially ordered self-assembled structures are formed in ensembles of magnetic microparticles suspended at a liquid/air interface and energized by an alternating magnetic field. These dynamic structures emerge as a result of a competition between magnetic and hydrodynamic forces. Each structure (snake) is accompanied by a hydrodynamic vortex quadrupole. Under certain conditions snakes spontaneously break the symmetry of surface flows and turn into swimmers. Observed phenomena have been successfully described by a phenomenological model.

Large scale surface flow generation in driven suspensions of magnetic microparticles

Formation of Quantum Phase Slip Pairs in Superconducting Nanowires

Physical Review X, 2015

Macroscopic quantum tunneling is a fundamental phenomenon of quantum mechanics related to the act... more Macroscopic quantum tunneling is a fundamental phenomenon of quantum mechanics related to the actively debated topic of quantum-to-classical transition. The ability to realize macroscopic quantum tunneling affects implementation of qubit-based quantum computing schemes and their protection against decoherence. Decoherence in qubits can be reduced by means of topological protection, e.g., by exploiting various parity effects. In particular, paired phase slips can provide such protection for superconducting qubits. Here, we report on the direct observation of quantum paired phase slips in thin-wire superconducting loops. We show that in addition to conventional single phase slips that change the superconducting order parameter phase by 2π, there are quantum transitions that change the phase by 4π. Quantum paired phase slips represent a synchronized occurrence of two macroscopic quantum tunneling events, i.e., cotunneling. We demonstrate the existence of a remarkable regime in which paired phase slips are exponentially more probable than single ones.

Plasmonic Nanopores for Trapping, Controlling Displacement, and Sequencing of DNA

ACS nano, 2015

With the aim of developing a DNA sequencing methodology, we theoretically examine the feasibility... more With the aim of developing a DNA sequencing methodology, we theoretically examine the feasibility of using nanoplasmonics to control the translocation of a DNA molecule through a solid-state nanopore and to read off sequence information using surface-enhanced Raman spectroscopy. Using molecular dynamics simulations, we show that high-intensity optical hot spots produced by a metallic nanostructure can arrest DNA translocation through a solid-state nanopore, thus providing a physical knob for controlling the DNA speed. Switching the plasmonic field on and off can displace the DNA molecule in discrete steps, sequentially exposing neighboring fragments of a DNA molecule to the pore as well as to the plasmonic hot spot. Surface-enhanced Raman scattering from the exposed DNA fragments contains information about their nucleotide composition, possibly allowing the identification of the nucleotide sequence of a DNA molecule transported through the hot spot. The principles of plasmonic nanop...

Magnetically driven surface mixing

Physical review. E, Statistical, nonlinear, and soft matter physics, 2009

Magnetic microparticles suspended on the surface of liquid and energized by vertical alternating ... more Magnetic microparticles suspended on the surface of liquid and energized by vertical alternating magnetic field exhibit complex collective behavior. Various immobile and self-propelled self-assembled structures have been observed. Here, we report on experimental studies of mixing and surface diffusion processes in this system. We show that the pattern-induced surface flows have properties of quasi-two-dimensional turbulence. Correspondingly, the surface advection of tracer particle exhibits properties of Brownian diffusion.

Modeling thermophoretic effects in solid-state nanopores

Journal of computational electronics, 2014

Local modulation of temperature has emerged as a new mechanism for regulation of molecular transp... more Local modulation of temperature has emerged as a new mechanism for regulation of molecular transport through nanopores. Predicting the effect of such modulations on nanopore transport requires simulation protocols capable of reproducing non-uniform temperature gradients observed in experiment. Conventional molecular dynamics (MD) method typically employs a single thermostat for maintaining a uniform distribution of temperature in the entire simulation domain, and, therefore, can not model local temperature variations. In this article, we describe a set of simulation protocols that enable modeling of nanopore systems featuring non-uniform distributions of temperature. First, we describe a method to impose a temperature gradient in all-atom MD simulations based on a boundary-driven non-equilibrium MD protocol. Then, we use this method to study the effect of temperature gradient on the distribution of ions in bulk solution (the thermophoretic effect). We show that DNA nucleotides exhib...

Driven magnetic ensembles on a surface of liquid: emergent phe-nomena and control

Large scale surface flow generation in driven suspensions of magnetic microparticles: Experiment, theoretical model and simulations

Assembly and control of self-propelled structures in driven suspensions of magnetic microparticles

Generation of dynamic self-propelled structures by symmetry breaking mechanism in driven magnetic layers on the surface of liquid

Self-organization of magnetic particles at fluid interfaces

Mixing fluid by self-propelled objects

Fluid dynamics Model for dynamic self-assembled magnetic surface structures (4 pages) 015301 (R)

Method of driving liquid flow at or near the free surface using magnetic microparticles

Thermophoretic Regulation of Molecular Flux through a Nanopore

Macroscopic Quantum Cotunneling of Phase Slips

Self-Assembled Magnetic Surface Swimmers

Physical Review Letters, 2009

We report studies of novel self-assembled magnetic surface swimmers (magnetic snakes), formed fro... more We report studies of novel self-assembled magnetic surface swimmers (magnetic snakes), formed from a dispersion of magnetic microparticles on the liquid/air interface and energized by an alternating magnetic field. We show that under certain conditions the snakes spontaneously break the symmetry of surface flows and turn into self-propelled objects. Parameters of the driving magnetic field tune the propulsion velocity of these snake-like swimmers. We find that the surface flows symmetry can be also broken in a controlled fashion by attaching a large bead to a magnetic snake (bead-snake hybrid), transforming it into a robust self-locomoting entity. Observed phenomena have been successfully described by phenomenological model based on the amplitude equation for surface waves coupled to the large-scale hydrodynamic mean flow equation.

Driven Magnetic Particles on a Fluid Surface: Pattern Assisted Surface Flows

Physical Review Letters, 2007

Magnetic microparticles suspended on the liquid-air interface and subjected to an alternating mag... more Magnetic microparticles suspended on the liquid-air interface and subjected to an alternating magnetic field exhibit spontaneous formation of dynamic localized snake patterns. These patterns are accompanied by four large-scale hydrodynamic vortices located at the opposite ends of the snake patterns. We report detailed studies of these large-scale vortices and their relationship to the collective response of magnetic particles in the presence of an alternating magnetic field. We present a model based on the amplitude equation for surface waves coupled to the large-scale hydrodynamic mean flow equation. The model describes both the formation of the dynamic snake patterns and the induced structure of the experimentally observed hydrodynamic flows.

Molecular Dynamics Simulation of DNA Capture and Transport in Heated Nanopores

ACS Applied Materials & Interfaces

The integration of local heat sources with solid-state nanopores offers new means for controlling... more The integration of local heat sources with solid-state nanopores offers new means for controlling the transmembrane transport of charged biomacromolecules. In the case of electrophoretic transport of DNA, recent experimental studies revealed unexpected temperature dependences of the DNA capture rate, the DNA translocation velocity, and the ionic current blockades produced by the presence of DNA in the nanopore. Here, we report the results of all-atom molecular dynamics simulations that elucidated the effect of temperature on the key microscopic processes governing electric field-driven transport of DNA through nanopores. Mimicking the experimental setup, we simulated the capture and subsequent translocation of short DNA duplexes through a locally heated nanopore at several temperatures and electrolyte conditions. The temperature dependence of ion mobility at the DNA surface was found to cause the dependence of the relative conductance blockades on temperature. To the first order, the effective force on DNA in the nanopore was found to be independent of temperature, despite a considerable reduction of solution viscosity. The temperature dependence of the solution viscosity was found to make DNA translocations faster for a uniformly heated system but not in the case of local heating that does not affect viscosity of solution surrounding the untranslocated part of the molecule. Increasing solution temperature was also found to reduce the lifetime of bonds formed between cations and DNA. Using a flow suppression algorithm, we were able to separate the effects of electro-osmotic flow and direct ion binding, finding the reduced durations of DNA−ion bonds to increase, albeit weakly, the effective force experienced by DNA in an electric field. Unexpectedly, our simulations revealed a considerable temperature dependence of solvent velocity at the DNA surfaceslip velocity, an effect that can alter hydrodynamic coupling between the motion of DNA and the surrounding fluid.

Mechanical Trapping of DNA in a Double-Nanopore System

Nano letters, Jan 14, 2016

Nanopores have become ubiquitous components of systems for single-molecule manipulation and detec... more Nanopores have become ubiquitous components of systems for single-molecule manipulation and detection, in particular DNA sequencing where electric field driven translocation of DNA through a nanopore is used to read out the DNA molecule. Here, we present a double-pore system where two nanopores are drilled in parallel through the same solid-state membrane, which offers new opportunities for DNA manipulation. Our experiments and molecular dynamics simulations show that simultaneous electrophoretic capture of a DNA molecule by the two nanopores mechanically traps the molecule, increasing its residence time within the nanopores by orders of magnitude. Remarkably, by using two unequal-sized nanopores, the pore of DNA entry and exit can be discerned from the ionic current blockades, and the translocation direction can be precisely controlled by small differences in the effective force applied to DNA. The mechanical arrest of DNA translocation using a double-pore system can be straightfor...

Emergent Phenomena in Far-From-Equilibrium Magnetic Granular Ensembles at a Liquid-Air Interface

AIP Conference Proceedings, 2009

Remarkable nontrivially ordered self-assembled structures are formed in ensembles of magnetic mic... more Remarkable nontrivially ordered self-assembled structures are formed in ensembles of magnetic microparticles suspended at a liquid/air interface and energized by an alternating magnetic field. These dynamic structures emerge as a result of a competition between magnetic and hydrodynamic forces. Each structure (snake) is accompanied by a hydrodynamic vortex quadrupole. Under certain conditions snakes spontaneously break the symmetry of surface flows and turn into swimmers. Observed phenomena have been successfully described by a phenomenological model.

Large scale surface flow generation in driven suspensions of magnetic microparticles

Formation of Quantum Phase Slip Pairs in Superconducting Nanowires

Physical Review X, 2015

Macroscopic quantum tunneling is a fundamental phenomenon of quantum mechanics related to the act... more Macroscopic quantum tunneling is a fundamental phenomenon of quantum mechanics related to the actively debated topic of quantum-to-classical transition. The ability to realize macroscopic quantum tunneling affects implementation of qubit-based quantum computing schemes and their protection against decoherence. Decoherence in qubits can be reduced by means of topological protection, e.g., by exploiting various parity effects. In particular, paired phase slips can provide such protection for superconducting qubits. Here, we report on the direct observation of quantum paired phase slips in thin-wire superconducting loops. We show that in addition to conventional single phase slips that change the superconducting order parameter phase by 2π, there are quantum transitions that change the phase by 4π. Quantum paired phase slips represent a synchronized occurrence of two macroscopic quantum tunneling events, i.e., cotunneling. We demonstrate the existence of a remarkable regime in which paired phase slips are exponentially more probable than single ones.

Plasmonic Nanopores for Trapping, Controlling Displacement, and Sequencing of DNA

ACS nano, 2015

With the aim of developing a DNA sequencing methodology, we theoretically examine the feasibility... more With the aim of developing a DNA sequencing methodology, we theoretically examine the feasibility of using nanoplasmonics to control the translocation of a DNA molecule through a solid-state nanopore and to read off sequence information using surface-enhanced Raman spectroscopy. Using molecular dynamics simulations, we show that high-intensity optical hot spots produced by a metallic nanostructure can arrest DNA translocation through a solid-state nanopore, thus providing a physical knob for controlling the DNA speed. Switching the plasmonic field on and off can displace the DNA molecule in discrete steps, sequentially exposing neighboring fragments of a DNA molecule to the pore as well as to the plasmonic hot spot. Surface-enhanced Raman scattering from the exposed DNA fragments contains information about their nucleotide composition, possibly allowing the identification of the nucleotide sequence of a DNA molecule transported through the hot spot. The principles of plasmonic nanop...

Magnetically driven surface mixing

Physical review. E, Statistical, nonlinear, and soft matter physics, 2009

Magnetic microparticles suspended on the surface of liquid and energized by vertical alternating ... more Magnetic microparticles suspended on the surface of liquid and energized by vertical alternating magnetic field exhibit complex collective behavior. Various immobile and self-propelled self-assembled structures have been observed. Here, we report on experimental studies of mixing and surface diffusion processes in this system. We show that the pattern-induced surface flows have properties of quasi-two-dimensional turbulence. Correspondingly, the surface advection of tracer particle exhibits properties of Brownian diffusion.

Modeling thermophoretic effects in solid-state nanopores

Journal of computational electronics, 2014

Local modulation of temperature has emerged as a new mechanism for regulation of molecular transp... more Local modulation of temperature has emerged as a new mechanism for regulation of molecular transport through nanopores. Predicting the effect of such modulations on nanopore transport requires simulation protocols capable of reproducing non-uniform temperature gradients observed in experiment. Conventional molecular dynamics (MD) method typically employs a single thermostat for maintaining a uniform distribution of temperature in the entire simulation domain, and, therefore, can not model local temperature variations. In this article, we describe a set of simulation protocols that enable modeling of nanopore systems featuring non-uniform distributions of temperature. First, we describe a method to impose a temperature gradient in all-atom MD simulations based on a boundary-driven non-equilibrium MD protocol. Then, we use this method to study the effect of temperature gradient on the distribution of ions in bulk solution (the thermophoretic effect). We show that DNA nucleotides exhib...

Driven magnetic ensembles on a surface of liquid: emergent phe-nomena and control

Large scale surface flow generation in driven suspensions of magnetic microparticles: Experiment, theoretical model and simulations

Assembly and control of self-propelled structures in driven suspensions of magnetic microparticles

Generation of dynamic self-propelled structures by symmetry breaking mechanism in driven magnetic layers on the surface of liquid

Self-organization of magnetic particles at fluid interfaces

Mixing fluid by self-propelled objects

Fluid dynamics Model for dynamic self-assembled magnetic surface structures (4 pages) 015301 (R)

Method of driving liquid flow at or near the free surface using magnetic microparticles

Thermophoretic Regulation of Molecular Flux through a Nanopore

Macroscopic Quantum Cotunneling of Phase Slips

Self-Assembled Magnetic Surface Swimmers

Physical Review Letters, 2009

We report studies of novel self-assembled magnetic surface swimmers (magnetic snakes), formed fro... more We report studies of novel self-assembled magnetic surface swimmers (magnetic snakes), formed from a dispersion of magnetic microparticles on the liquid/air interface and energized by an alternating magnetic field. We show that under certain conditions the snakes spontaneously break the symmetry of surface flows and turn into self-propelled objects. Parameters of the driving magnetic field tune the propulsion velocity of these snake-like swimmers. We find that the surface flows symmetry can be also broken in a controlled fashion by attaching a large bead to a magnetic snake (bead-snake hybrid), transforming it into a robust self-locomoting entity. Observed phenomena have been successfully described by phenomenological model based on the amplitude equation for surface waves coupled to the large-scale hydrodynamic mean flow equation.

Driven Magnetic Particles on a Fluid Surface: Pattern Assisted Surface Flows

Physical Review Letters, 2007

Magnetic microparticles suspended on the liquid-air interface and subjected to an alternating mag... more Magnetic microparticles suspended on the liquid-air interface and subjected to an alternating magnetic field exhibit spontaneous formation of dynamic localized snake patterns. These patterns are accompanied by four large-scale hydrodynamic vortices located at the opposite ends of the snake patterns. We report detailed studies of these large-scale vortices and their relationship to the collective response of magnetic particles in the presence of an alternating magnetic field. We present a model based on the amplitude equation for surface waves coupled to the large-scale hydrodynamic mean flow equation. The model describes both the formation of the dynamic snake patterns and the induced structure of the experimentally observed hydrodynamic flows.