Related papers: Comment on ``Passage Times for Unbiased Polymer Tr…
Polymers confined in corrugated channels, i.e. channels of varying amplitude, display {multiple local maxima and minima of the diffusion coefficient upon increasing their degree of polymerization $N$}. We propose a theoretical effective…
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 $R$ under a driving force $F$, respectively. Compared with…
We study voltage driven translocation of a single stranded (ss) DNA through a membrane channel. Our model, based on a master equation (ME) approach, investigates the probability density function (pdf) of the translocation times, and shows…
We employ a multiscale approach to model the translocation of biopolymers through nanometer size pores. Our computational scheme combines microscopic Langevin molecular dynamics (MD) with a mesoscopic lattice Boltzmann (LB) method for the…
We report grand canonical Monte Carlo simulations of the critical point properties of homopolymers within the Bond Fluctuation model. By employing Configurational Bias Monte Carlo methods, chain lengths of up to N=60 monomers could be…
We study the conformation and dynamics of a single polymer chain that is pulled by a constant force applied at its one end with the other end free. Such a situation is relevant to the growing technology of manipulating individual…
We present exact spatio-temporal correlation functions of a Rouse polymer chain submerged in a fluid having planar mixed flow, in the steady state. Using these correlators, determination of the time scale distribution functions associated…
We study the driven translocation of a flexible polymer through an interacting conical pore using Langevin dynamics simulations. We find that, for a fixed value of externally applied force and pore polymer interaction strength, the mean…
The translocation of structured RNA or DNA molecules through narrow pores necessitates the opening of all base pairs. Here, we study the interplay between the dynamics of translocation and base-pairing theoretically, using kinetic Monte…
The Rouse model can be regarded as the standard model to describe the dynamics of a short polymer chain under melt conditions. In this contribution, we explicitly check one of the fundamental assumptions of this model, namely that of a…
We present a Brownian dynamics model of driven polymer translocation, in which non-equilibrium memory effects arising from tension propagation (TP) along the cis side subchain are incorporated as a time-dependent friction. To solve the…
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…
How much time does it take for a fluctuating system, such as a polymer chain, to reach a target configuration that is rarely visited -- typically because of a high energy cost ? This question generally amounts to the determination of the…
In this work we study the assisted translocation of a polymer across a membrane nanopore, inside which a molecular motor exerts a force fuelled by the hydrolysis of ATP molecules. In our model the motor switches to its active state for a…
Chaperones are binding proteins which work as a driving force to bias the biopolymer translocation by binding to it near the pore and preventing its backsliding. Chaperones may have different spatial distribution. Recently we show the…
We study the jamming transition in a model of elastic particles under shear at zero temperature, with a focus on the relaxation time $\tau_1$. This relaxation time is from two-step simulations where the first step is the ordinary shearing…
Polymer-coated pores play a crucial role in nucleo-cytoplasmic transport and in a number of biomimetic and nanotechnological applications. Here we present Monte Carlo and Density Functional Theory approaches to identify different collective…
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 investigate the translocation of a single stranded DNA through a pore which fluctuates between two conformations, using coupled master equations. The probability density function of the first passage times (FPT) of the translocation…
We study escape dynamics of a double-stranded DNA (dsDNA) through an idealized double nanopore (DNP) geometry subject to two equal and opposite forces (tug-of-war) using Brownian dynamics (BD) simulation. In addition to the geometrical…