662 citations · 11.9k across the 197 of their papers we have counts for
24 papers · 1 filter
Driven polymer translocation into a channel: Iso-flux tension propagation theory and Langevin dynamics simulations
Jalal Sarabadani, Ralf Metzler, Tapio Ala-Nissila
Iso-flux tension propagation (IFTP) theory and Langevin dynamics (LD) simulations are employed to study the dynamics of channel-driven polymer translocation in which a polymer tran…
Critical adsorption of polyelectrolytes onto planar and convex highly charged surfaces: the nonlinear Poisson-Boltzmann approach
Sidney J. de Carvalho, Ralf Metzler, Andrey G. Cherstvy
We study the adsorption-desorption transition of polyelectrolyte chains onto planar, cylindrical and spherical surfaces with arbitrarily high surface charge densities by massive Mo…
Facilitation of polymer looping and giant polymer diffusivity in crowded solutions of active particles
J. Shin, A. G. Cherstvy, W. K. Kim +1
We study the dynamics of polymer chains in a bath of self-propelled particles (SPP) by extensive Langevin dynamics simulations in a two dimensional system. Specifically, we analyse…
Self-subdiffusion in solutions of star-shaped crowders: non-monotonic effects of inter-particle interactions
Jaeoh Shin, Andrey G. Cherstvy, Ralf Metzler
We examine by extensive computer simulations the self-diffusion of anisotropic star like particles in crowded two-dimensional solutions. We investigate the implications of the area…
Inverted critical adsorption of polyelectrolytes in confinement
Sidney J. de Carvalho, Ralf Metzler, Andrey G. Cherstvy
What are the fundamental laws for the adsorption of charged polymers onto oppositely charged surfaces, for convex, planar, and concave geometries? This question is at the heart of…
Conformational properties of complex polymers: rosette versus star-like structures
Viktoria Blavatska, Ralf Metzler
Multiple loop formation in polymer macromolecules is an important feature of the chromatin organization and DNA compactification in the nuclei. We analyze the size and shape charac…
Non-universal tracer diffusion in crowded media of non-inert obstacles
Surya K. Ghosh, Andrey G. Cherstvy, Ralf Metzler
We study the diffusion of a tracer particle, which moves in continuum space between a lattice of excluded volume, immobile non-inert obstacles. In particular, we analyse how the st…
Kinetics of polymer looping with macromolecular crowding: effects of volume fraction and crowder size
Jaeoh Shin, Andrey G. Cherstvy, Ralf Metzler
The looping of polymers such as DNA is a fundamental process in the molecular biology of living cells, whose interior is characterised by a high degree of molecular crowding. We he…
Critical adsorption of polyelectrolytes onto charged Janus nanospheres
Sidney J. de Carvalho, Ralf Metzler, Andrey G. Cherstvy
Based on extensive Monte Carlo simulations and analytical considerations we study the electrostatically driven adsorption of flexible polyelectrolyte chains onto charged Janus nano…
Collective dynamics effect transient subdiffusion of inert tracers in gel networks
Aljaz Godec, Maximilian Bauer, Ralf Metzler
Based on extensive Brownian dynamics simulations we study the thermally driven motion of a tracer bead in a cross-linked, dynamic gel network in the limit when the tracer bead's si…
Deformation propagation in responsive polymer network films
Surya K Ghosh, Andrey G Cherstvy, Ralf Metzler
We study the elastic deformations in a cross-linked polymer network film triggered by the binding of submicron particles with a sticky surface, mimicking the interactions of viral…
Mixing and segregation of ring polymers: spatial confinement and molecular crowding effects
Jaeoh Shin, Andrey G Cherstvy, Ralf Metzler
During the life cycle of bacterial cells the non-mixing of the two ring-shaped daughter genomes is an important prerequisite for the cell division process. Mimicking the environmen…
Anomalous diffusion of phospholipids and cholesterols in a lipid bilayer and its origins
Jae-Hyung Jeon, Hector Martinez-Seara Monne, Matti Javanainen +1
Combining extensive molecular dynamics simulations of lipid bilayer systems of varying chemical composition with single-trajectory analyses we systematically elucidate the stochast…
The chain sucker: translocation dynamics of a polymer chain into a long narrow channel driven by longitudinal flow
Kaifu Luo, Ralf Metzler
Using analytical techniques and Langevin dynamics simulations, we investigate the dynamics of polymer translocation into a narrow channel of width embedded in two dimensions, d…
Polymer translocation into a fluidic channel through a nanopore
Kaifu Luo, Ralf Metzler
Using two dimensional Langevin dynamics simulations, we investigate the dynamics of polymer translocation into a fluidic channel with diameter through a nanopore under a drivin…
Polymer translocation into laterally unbounded confined environments
Kaifu Luo, Ralf Metzler
Using Langevin dynamics simulations in three dimensions (3D), we investigate the dynamics of polymer translocation into the regions between two parallel plane walls with separation…
Polymer translocation out of confined environments
Kaifu Luo, Ralf Metzler, Tapio Ala-Nissila +1
We consider the dynamics of polymer translocation out of confined environments. Analytic scaling arguments lead to the prediction that the translocation time scales like $τ\sim N^{…
Diffusion mechanisms of localised knots along a polymer
Ralf Metzler, Walter Reisner, Robert Riehn +3
We consider the diffusive motion of a localized knot along a linear polymer chain. In particular, we derive the mean diffusion time of the knot before it escapes from the chain onc…
Fractal Dimension and Localization of DNA Knots
Erika Ercolini, Francesco Valle, Jozef Adamcik +5
The scaling properties of DNA knots of different complexities were studied by atomic force microscope. Following two different protocols DNA knots are adsorbed onto a mica surface…
Optimal target search on a fast folding polymer chain with volume exchange
Michael A. Lomholt, Tobias Ambjornsson, Ralf Metzler
We study the search process of a target on a rapidly folding polymer (`DNA') by an ensemble of particles (`proteins'), whose search combines 1D diffusion along the chain, Levy type…
Blinking statistics of a molecular beacon triggered by end-denaturation of DNA
Tobias Ambjoernsson, Ralf Metzler
We use a master equation approach based on the Poland-Scheraga free energy for DNA denaturation to investigate the (un)zipping dynamics of a denaturation wedge in a stretch of DNA,…
Sensing DNA - DNA as nanosensor: a perspective towards nanobiotechnology
Ralf Metzler, Tobias Ambjoernsson
Based on modern single molecule techniques, we devise a number of possible experimental setups to probe local properties of DNA such as the presence of DNA-knots, loops or folds, o…
Tight and loose shapes in flat entangled dense polymers
Andreas Hanke, Ralf Metzler, Paul G. Dommersnes +2
We investigate the effects of topological constraints (entanglements) on two dimensional polymer loops in the dense phase, and at the collapse transition (Theta point). Previous st…
Bubble dynamics in DNA
Andreas Hanke, Ralf Metzler
The formation of local denaturation zones (bubbles) in double-stranded DNA is an important example for conformational changes of biological macromolecules. We study the dynamics of…