Related papers: Polymer translocation into laterally unbounded con…
We theoretically investigate the kinetics of the folding transition of a single semiflexible polymer. In the folding transition, the growth rate decrease with an increase in the number of monomers in a collapsed domain, suggesting that the…
We investigate the dynamics of polymer translocation through a nanopore under an externally applied field using the 2D fluctuating bond model with single-segment Monte Carlo moves. We concentrate on the influence of the field strength $E$,…
By analyzing the real space nonequilibrium dynamics of polymers, we elucidate the physics of driven translocation and propose its dynamical scaling scenario analogous to that in the surface growth phenomena. We provide a detailed account of…
Here using LAMMPS molecular dynamics (MD) software, we simulate polymer translocation in 2 dimensions. We do the simulations for weak and moderate forces and for different pore diameters. Our results show that in both non-equilibrium and…
We study analytically a model of a two dimensional, partially directed, flexible or semiflexible polymer, attached to an attractive wall which is perpendicular to the preferred direction. In addition, the polymer is stretched by an…
Motivated by recent nanofluidics experiments, we use Brownian dynamics and Monte Carlo simulations to study the conformation, organization and dynamics of two polymer chains confined to a single box-like cavity. The polymers are modeled as…
Translocation dynamics of an active semi-flexible polymer through a nano-pore into a rigid two dimensional circular cavity, and the polymer packing dynamics have been studied by using Langevin dynamics (LD) simulations. The results show…
Monte Carlo simulations are used to study the translocation of a polymer into and out of a ellipsoidal cavity through a narrow pore. We measure the polymer free energy F as a function of a translocation coordinate, s, defined to be the…
DNA translocation through nanopores is one of the most promising strategies for the next-generation sequencing technologies. Most part of experimental and numerical works has focused on polymer translocation biased by electrophoresis, where…
We investigate by Monte Carlo simulations the zipping and unzipping dynamics of two polymers connected by one end and subject to an attractive interaction between complementary monomers. In zipping, the polymers are quenched from a high…
I did off-lattice 3D Monte Carlo simulations for polymer translocation through a narrow pore at low external field, trying to be as close to a direct approach as possible. The process was found non equilibrium globally, but dynamics of the…
Polymer transport is investigated for two paradigmatic laminar flows having open and closed streamlines, respectively. For both types of flows we find transport depletion owing to the action of the polymers elastic degree of freedom. For…
Dimerization and subsequent aggregation of polymers and biopolymers often occur under nonequilibrium conditions. When the initial state of the polymer is not collapsed or the final folded native state, the dynamics of dimerization can…
We use Langevin dynamics (LD) simulations to investigate single-file diffusion (SFD) in a dilute solution of flexible linear polymers inside a narrow tube with periodic boundary conditions (a torus). The transition from SFD, where the time…
Polymers confined to a narrow channel are subject to strong entropic forces that tend to drive the molecules apart. In this study, we use Monte Carlo computer simulations to study the segregation behavior of two flexible hard-sphere…
Brownian dynamics (BD) simulations are used to study the translocation dynamics of a coarse-grained polymer through a cylindrical nanopore. We consider the case of short polymers, with a polymer length, N, in the range N=21-61. The rate of…
Motivated by identifying the origin of the bias dependence of tension propagation we investigate methods for measuring tension propagation quantitatively in computer simulations of driven polymer translocation. Here the motion of flexible…
Single three dimensional polymers confined to a slab, i.e. to the region between two parallel plane walls, are studied by Monte Carlo simulations. They are described by $N$-step walks on a simple cubic lattice confined to the region $1 \le…
We study the translocation of a semiflexible polymer through extended pores with patterned stickiness, using Langevin dynamics simulations. We find that the consequence of pore patterning on the translocation time dynamics is dramatic and…
Using molecular dynamics simulation, we investigate the effect of confinement on a system that comprises several stiff segmented polymer chains where each chain has similar segments, but length and stiffness of the segments vary among the…