Dynamics of driven translocation of semiflexible polymers

TL;DR

This study investigates how the translocation time of semiflexible polymers through nanopores depends on bending rigidity, force, and polymer length, revealing effects of buckling and trans side friction on the dynamics.

Contribution

It introduces a detailed Langevin dynamics model showing how polymer stiffness and buckling influence driven translocation, highlighting differences from flexible polymers.

Findings

Translocation time increases with bending rigidity and force.

Buckling reduces trans side friction, affecting translocation dynamics.

Center of mass diffusion speeds up translocation, especially at low forces.

Abstract

We study translocation of semiflexible polymers driven by force $f_d$ inside a nanometer-scale pore using our three-dimensional Langevin dynamics model. We show that the translocation time $\tau$ increases with increasing bending rigidity $\kappa$. Similarly, the exponent $\beta$ for the scaling of $\tau$ with polymer length $N$, $\tau \sim N^\beta$, increases with increasing $\kappa$ as well as with increasing $f_d$. By comparing waiting times between semiflexible and fully flexible polymers we show that for realistic $f_d$ translocation dynamics is to a large extent, but not completely, determined by the polymer's elastic length measured in number of Kuhn segments $N_{\rm Kuhn}$. Unlike in driven translocation of flexible polymers, friction related to the polymer segment on the trans side has a considerable effect on the resulting dynamics. This friction is intermittently reduced by buckling of the polymer segment in the vicinity of the pore opening on the trans side. We show that in the experimentally relevant regime, where viscosity is higher than in computer simulation models, the probability for this buckling increases with increasing $f_d$, giving rise to larger contribution to trans side friction at small $f_d$. Similarly to flexible polymers, we find significant center of mass diffusion of the cis side polymer segment. This speeds up translocation, which effect is larger for smaller $f_d$. However, this speed-up is smaller than the slowing down due to the trans side friction. At large enough $N_{\rm Kuhn}$, the roles can be seen to be reversed and the dynamics of flexible polymers be reached. However, for example, polymers used in translocation experiments of DNA, are elastically so short, that the finite-length dynamics outlined here applies.