Related papers: Pore-polymer interaction reveals non-universality …
The effect of sequence heterogeneity on polynucleotide translocation across a pore and on simple models of molecular motors such as helicases, DNA polymerase/exonuclease and RNA polymerase is studied in detail. Pore translocation of RNA or…
The role of active stress on the conformational dynamics of a polymer has drawn significant interest due to its potential applications in understanding the energy landscape of protein structures, buckling of biopolymers, genomic spatial…
We formulate and characterize a model to describe the dynamics of semiflexible polymers in the presence of activity due to motor proteins attached irreversibly to a substrate, and a transverse pulling force acting on one end of the…
Adsorption of polymers to surfaces is crucial for understanding many fundamental processes in nature. Recent experimental studies indicate that the adsorption dynamics is dominated by non-equilibrium effects. We investigate the adsorption…
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…
We investigate the stretching response of a thick polymer model by means of extensive stochastic simulations. The computational results are synthesized in an analytic expression that characterizes how the force versus elongation curve…
This paper studies the features of a homopolymer translocating through a flexible pore. The channel is modeled as a monolayer tube composed by monomers with two elastic parameters: spring-like two body interaction and bending three body…
We consider the response of an adsorbed polymer that is pulled by an AFM within a simple geometric framework. We separately consider the cases of i) fixed polymer-surface contact point, ii) sticky case where the polymer is peeled off from…
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 $E$,…
Theoretical and experimental investigations of water vapor interaction with porous materials are carried out both at the macro level and at the micro level. At the macro level, the influence of the arrangement structure of individual pores…
We study the dynamics of an ideal polymer chain in a crowded, viscoelastic medium and in the presence of active forces. The motion of the centre of mass and of individual monomers is calculated. On time scales that are comparable to the…
We consider a directed walk model of a homopolymer (in two dimensions) which is self-interacting and can undergo a collapse transition, subject to an applied tensile force. We review and interpret all the results already in the literature…
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…
We investigate the effect of hydrodynamic interactions on the non-equilibrium drift dynamics of an ideal flexible polymer pulled by a constant force applied at one end of the polymer using the perturbation theory and the renormalization…
We study unbiased translocation of a flexible polymer chain through a membrane pore under the influence of active noise and steric exclusion using Langevin dynamics simulations. The active noise is incorporated by introducing nonchiral and…
We introduce a fiber bundle model where the interaction among fibers is modeled by an adjustable stress-transfer function which can interpolate between the two limiting cases of load redistribution, the global and the local load sharing…
Fundamental understanding of the effect of microscopic parameters on the dynamics of probe particles in different complex environments has wide implications. Examples include diffusion of proteins in the biological hydrogels, porous media,…
The self-avoid random walk algorithm has been extensively used in the study of polymers. In this work we study the basic properties of the trajectories generated with this algorithm when two interactions are added to it: contact and folding…
These notes are devoted to the statistical mechanics of directed polymers interacting with one-dimensional spatial defects. We are interested in particular in the situation where frozen disorder is present. These polymer models undergo a…
In this paper we compare two polymer stretching experiments. The outcome of both experiments is a force-extension relation. We use a one-dimensional model to show that in general the two quantities are not equal. In certain limits, however,…