Related papers: Non-driven polymer translocation through a nanopor…
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…
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 analyse bead--spring polymers coupled to Navier--Stokes turbulence in ultra--dilute solutions at Weissenberg number \(Wi\approx 80\). The polymers do not alter the large-scale turbulent structure, but hydrodynamic interactions generate…
Directed transport is a characteristic feature of numerous biological systems in response to signals such as nutrient and chemical gradients. These signals often depend on time owing to the high complexity of interactions in these systems.…
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,…
Stress relaxation following deformation of an entangled polymeric liquid is thought to be affected by transient reforming of chain entanglements. In this work, we use single molecule techniques to study the relaxation of individual polymers…
In this paper we study the tunneling using a background independent (polymer) quantization scheme. We show that at low energies, for the tunneling through a single potential barrier, the polymer transmission coefficient and the polymer…
Motivated by identifying the origin of the bias dependence of tension propagation we investigate methods for measuring tension propagation quantitatively in computer simulations of driven polymer translocation. Here the motion of flexible…
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…
Motivated by the experiments on DNA under torsion, we consider the problem of pulling a polymer out of a potential well by a force applied to one of its ends. If the force is less than a critical value, then the process is activated and has…
Significant challenges exist in the nonlinear extensional rheology of entangled polymers. With simulations, we show that the key to understanding this problem is to recognize the existence and importance of a strain-induced crossover from…
Nonequilibrium molecular dynamics simulations are used to study the deformation behavior of disperse polymer melts by tracking test chains of length N = Mw, the weight average molecular weight, in melts of varying dispersity. At high strain…
Recent measurements of durations of non-equilibrium processes provide valuable information on microscopic mechanisms and energetics. Comprehensive theory for corresponding experiments so far is well developed for single-particle systems…
Recent years have seen a surge of interest in nanopores because such structures show a strong potential for characterizing nanoparticles, proteins, DNA, and even single molecules. These systems have been extensively studied in experiment as…
We investigate the dynamics and the pathways of the collapse of a single, semiflexible polymer in a poor solvent via 3-D Brownian Dynamics simulations. Earlier work indicates that the condensation of semiflexible polymers generically…
Here we report on the translocation of folded polymers through nano-pores using molecular dynamic simulations. Two cases are studied; one in which a folded molecule unfolds upon passage and one in which the folding remains intact as the…
Using an Ising-like model of protein mechanical unfolding, we introduce a diffusive dynamics on its exactly known free energy profile, reducing the nonequilibrium dynamics of the model to a biased random walk. As an illustration, the model…
Recent theoretical modeling offers a unified picture for the description of stochastic processes characterized by a crossover from anomalous to normal behavior. This is particularly welcome, as a growing number of experiments suggest the…
We investigate the translocation of a stiff polymer through a nanopore in a membrane, in the presence of binding particles (chaperones) that bind reversibly to the polymer on both sides of the membrane. A bound chaperone covers one…
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…