Related papers: Tracer dynamics in polymer networks: generalized L…
The general problem of tracer diffusion in non-equilibrium baths is important in a wide range of systems, from the cellular level to geographical lengthscales. In this paper, we revisit the archetypical example of such a system: 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 consider a driven tracer particle (TP) in a bath of hard-core particles undergoing continuous exchanges with a reservoir. We develop an analytical framework which allows us to go beyond the standard force-velocity relation used for this…
The generalized Langevin equation (GLE), derived by projection from a general many-body Hamiltonian, exactly describes the dynamics of an arbitrary coarse-grained variable in a complex environment. However, analysis and prediction of…
The Langevin Equation for cooperative dynamics represents the dynamics of polymer melts with chains of increasing degree of polymerization, covering the full range of behavior from the unentangled to the entangled regime. This equation…
Langevin Dynamics simulations of polymer translocation are performed where the polymer is stretched via two opposing forces applied on the first and last monomer before and during translocation. In this setup, polymer translocation is…
We perform large scale three-dimensional molecular dynamics simulations of unlinked and unknotted ring polymers diffusing through a background gel, here a three-dimensional cubic lattice. Taking advantage of this architecture, we propose a…
Single file translocation of a homopolymer through an active channel under the presence of a driving force is studied using Langevin dynamics simulation. It is shown that a channel with sticky walls and oscillating width could lead to…
A generalized Langevin equation is suggested to describe a system with memory($u(t,t') = \frac{1}{\Gamma (\nu )}(t - t')^\nu $) as well as with positive and negative damping. The equation can be transformed into the Fokker-Planck equation…
The mechanical properties of polymer gels based on cytoskeleton proteins (e.g. actin) have been studied extensively due to their significant role in biological cell motility and in maintaining the cell's structural integrity. Microrheology…
We use stochastic computer simulations to study the transport of a spherical cargo particle along a microtubule-like track on a planar substrate by several kinesin-like processive motors. Our newly developed adhesive motor dynamics…
Active transport of biomolecules assisted by motor proteins is imperative for the proper functioning of cellular activities. Inspired by the diffusion of active agents in crowded cellular channels, we computationally investigate the…
The dynamics of polymer-nanoparticle (NP) mixtures, which involves multiple scales and system-specific variables, has posed a long-standing challenge on its theoretical description. In this paper, we construct a microscopic theory for…
The paper addresses the single-file diffusion in the presence of an absorbing boundary. The emphasis is on an interplay between the hard-core interparticle interaction and the absorption process. The resulting dynamics exhibits several…
We study the driven translocation of polymers under time-dependent driving forces using $N$-particle Langevin dynamics simulations. We consider the force to be either sinusoidally oscillating in time or dichotomic noise with exponential…
The Zimm equation for the position vector of a polymer segment is generalized taking into account the effect of viscous memory. The Oseen tensor is built on the basis of the nonstationary Navier-Stokes equation. After the preliminary…
We derive an analytical expression for the intermediate scattering function of a particle on a flat surface obeying the Generalised Langevin Equation, with exponential memory friction. Numerical simulations based on an extended phase space…
Memory effects, sometimes, can not be neglected. In the framework of continuous time random walk, memory effect is modeled by the correlated waiting times. In this paper, we derive the two-point probability distribution of the stochastic…
Several experiments on tagged molecules or particles in living systems suggest that they move anomalously slow - their mean squared displacement (MSD) increase slower than linearly with time. Leading models aimed at understanding these…
We analyze the dynamics of an active tracer particle embedded in a thermal lattice gas. All particles are subject to exclusion up to third nearest neighbors on the square lattice, which leads to slow dynamics at high densities. For the case…