Related papers: Reaching large lengths and long times in polymer d…
We employ a three-dimensional molecular dynamics to simulate translocation of a polymer through a nanopore driven by an external force. The translocation is investigated for different three pore diameter and two different external forces.…
We model the behavior of a big (Brazil) nut in a medium of smaller nuts with a stochastic asymmetric simple exclusion dynamics of a polymer-monomer lattice system. The polymer or `rod' can move up or down in an external negative field,…
We study the dynamics of flexible, semiflexible, and self-avoiding polymer chains moving under a Kramers metastable potential. Due to thermal noise, the polymers, initially placed in the metastable well, can cross the potential barrier, but…
Simulations in finite density, beta=0 lattice QCD by means of the Monomer-Dimer-Polymer algorithm show a signal of first order transition at finite temporal size. This behaviour agrees with predictions of the mean field approximation, but…
We study the behavior of classical dimer coverings of the square lattice - a paradigmatic model for systems subject to constraints - evolving under local stochastic dynamics, by means of Monte Carlo simulations and theoretical arguments. We…
Lattice model of directed self avoiding walk is used to investigate adsorption properties of a semiflexible sequential copolymer chain on an impenetrable curved surface on a hexagonal lattice in two dimensions. Walks of the copolymer chains…
Using a mapping of compact polymers on the Manhattan lattice to spanning trees, we calculate exactly the average number of bends at infinite temperature. We then find, in a high temperature approximation, the energy of the system as a…
Using analytical techniques and Langevin dynamics simulations, we investigate the dynamics of polymer translocation into a narrow channel of width $R$ embedded in two dimensions, driven by a force proportional to the number of monomers in…
We study at- and out-of-equilibrium dynamics of a single homopolymer chain at low temperature using molecular dynamics simulations. The main quantities of interest are the average root mean square displacement of the monomers below the…
Almost all the polymer crystals have several polymorphic modifications. Their structure and existence conditions, as well as transitions between them are not understood even in the case of the 'model' polymer polyethylene (PE). For analysis…
The transport of polymers with folded configurations across membrane pores is investigated theoretically by analyzing simple discrete stochastic models. The translocation dynamics is viewed as a sequence of two events: motion of the folded…
The effect of crowding on the run-and-tumble dynamics of swimmers such as bacteria is studied using a discrete lattice model of mutually excluding particles that move with constant velocity along a direction that is randomized at a rate…
We present data of Monte Carlo simulations for monodisperse linear polymer chains in dense melts with degrees of polymerization between N=16 and N=512. The aim of this study is to investigate the crossover from Rouse-like dynamics for short…
We study the static properties of a semiflexible polymer exposed to a quenched random environment by means of computer simulations. The polymer is modeled as two-dimensional Heisenberg chain. For the random environment we consider hard…
We study a model describing some aspects of the dynamics of biopolymers. The models involve either one or two finite chains with a number N of sites that represent the "units" of a biophysical system. The mechanical degrees of freedom of…
We analyze the crystallization and collapse transition of a simple model for flexible polymer chains on simple cubic and face-centered cubic lattices by means of sophisticated chain-growth methods. In contrast to bond-fluctuation polymer…
Active polymers are ubiquitous in nature, and often kicked by persistent noises that break detailed balance. In order to capture the out-of-equilibrium dynamics of such active polymers, we propose a simple yet reliable analytical framework…
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 obtain the solution of models of self-avoiding walks with attractive interactions on Husimi lattices built with squares. Two attractive interactions are considered: between monomers on first-neighbor sites and not consecutive along a…
This study presents an enhanced method for analyzing cluster dynamics, with a particular focus on tracking clusters' continuity over time using time-series data from molecular dynamics (MD) simulation. The proposed method was applied to…