Related papers: Noise driven translocation of short polymers in cr…
We study the dynamics of a polymer, described as a variant of a Rouse chain, driven by an active terminal monomer (head). The local active force induces a transition from a globule-like to an elongated state, as revealed by the study of the…
We consider the barotropic Navier--Stokes system driven by a physically well-motivated transport noise in both continuity as well as momentum equation. We focus on three different situations: (i) the noise is smooth in time and the…
We investigate the problem of polymer translocation through a nanopore in the absence of an external driving force. To this end, we use the two-dimensional (2D) fluctuating bond model with single-segment Monte Carlo moves. To overcome the…
During polymer translocation driven by e.g. voltage drop across a nanopore, the segments in the cis-side is incessantly pulled into the pore, which are then pushed out of it into the trans-side. This pulling and pushing polymer segments are…
We extend the Rouse model of polymer dynamics to situations of non-stationary chain growth. For a dragged polymer chain of length $N(t) = t^\alpha$, we find two transitions in conformational dynamics. At $\alpha= 1/2$, the propagation of…
The effect of the microscopic structure of a pore on polymer translocation is studied using Langevin dynamics simulation, and the consequence of introducing patterned stickiness inside the pore is investigated. It is found that the…
We study the diffusion of a linear polymer in the presence of permeable membranes without excluded volume interactions, using scaling theory and Monte Carlo simulations. We find that the average time it takes for a chain with polymerization…
A general approach to consider spatially extended stochastic systems with correlations between additive and multiplicative noises subject to nonlinear damping is developed. Within modified cumulant expansion method, we derive an effective…
In this work we study the transport properties of non-interacting overdamped particles, moving on tilted disordered potentials, subjected to Gaussian white noise. We give exact formulas for the drift and diffusion coefficients for the case…
We study the dynamics of a Brownian particle in Morse potential under thermal fluctuations, modeled by Gaussian white noise whose amplitude depends on absolute temperature. Dynamics of such a particle is investigated by numerically…
Polymer translocation is a promising strategy for the next-generation DNA sequencing technologies. The use of biological and synthetic nano-pores, however, still suffers from serious drawbacks. In particular, the width of the membrane layer…
We consider the motion of a particle in a force field subjected to adiabatic, fluctuations of external origin. We do not put the restriction on the type of stochastic process that the noise is Gaussian. Based on a method developed earlier…
We study the dynamics of a simple adaptive system in the presence of noise and periodic damping. The system is composed by two paths connecting a source and a sink, the dynamics is governed by equations that usually describe food search of…
The local dynamical features of a PEO melt studied by MD simulations are compared to two model chain systems, namely the well-known Rouse model as well as the semiflexible chain model (SFCM) that additionally incorporates chain stiffness.…
A simple one-dimensional model is constructed for polymer motion. It exhibits the crossover from reptation to Rouse dynamics through gradually allowing hernia creation and annihilation. The model is treated by the density matrix technique…
This paper reports the force spectroscopy analysis of a polymer that translocates from one side of a membrane to the other side through an extended pore, pulled by a cantilever that moves with constant velocity against the damping and the…
While the characteristics of the driven translocation for asymptotically long polymers are well understood, this is not the case for finite-sized polymers, which are relevant for real-world experiments and simulation studies. Most notably,…
We present results from our simulations of biopolymer translocation in a solvent which explain the main experimental findings. The forced translocation can be described by simple force balance arguments for the relevant range of pore…
We consider a model of active Brownian agents interacting via a harmonic attractive potential in a two-dimensional system in the presence of noise. By numerical simulations, we show that this model possesses a noise-induced transition…
By means of computer simulations, we investigate the relaxation of the Rouse modes in a simple bead-spring model for non-entangled polymer blends. Two different models are used for the fast component, namely fully-flexible and semiflexible…