Polymer translocation through a nanopore assisted by an environment of active rods

Hamidreza Khalilian,Jalal Sarabadani,Tapio Ala-Nissila

doi:10.1103/physrevresearch.3.013080

Abstract

We use a combination of computer simulations and iso-flux tension propagation (IFTP) theory to investigate translocation dynamics of a flexible linear polymer through a nanopore into an environment composed of repulsive active rods in 2D. We demonstrate that the rod activity induces a crowding effect on the polymer, leading to a time-dependent net force that facilitates translocation into the active environment. Incorporating this force into the IFTP theory for pore-driven translocation allows us to characterise translocation dynamics in detail and derive a scaling form for the average translocation time as $\tilde{\tau} \sim \tilde{L}_{\textrm{r}}^{\nu} / \tilde{F}_{\textrm{SP}} $, where $\tilde{L}_{\textrm{r}}$ and $\tilde{F}_{\textrm{SP}}$ are the rod length and self-propelling force acting on the rods, respectively, and $\nu$ is the Flory exponent.

Highlights

Translocation dynamics of biopolymers through nanopores has been one of the most active research areas in soft matter during the past few decades
The simulation data show that the trans-side subchain (0 < s N02) contributes to the waiting time (WT) due to the small magnitude of f(t) at the beginning of translocation process because a short section of the trans-side subchain is temporarily retracted to the cis side
We have used a combination of Langevin dynamics (LD) simulations and isoflux tension propagation (IFTP) theory in the strong stretching (SS) regime to characterize the waiting time distribution w and the average translocation time τ

Summary

INTRODUCTION

Translocation dynamics of biopolymers through nanopores has been one of the most active research areas in soft matter during the past few decades (see, e.g., Refs. [1–4] and references therein). Pore-driven polymer translocation in the presence of spherical APs has been considered using computer simulation methods [77] and it was found that with high activity, there is a crowding effect in two dimensions (2D) that leads to a speed-up of translocation. This scaling form for the translocation time is valid in the limit of long chains (N01 1) and its dependence on Lr and FSP comes from the effective net force acting on the monomer(s) at the pore induced by the APs with the trans-side subchain. This leads to scaling of τwith N01 identical to that of a pore-driven chain without APs. The structure of the paper is as follows.

LANGEVIN DYNAMICS SIMULATIONS

ISOFLUX TENSION PROPAGATION THEORY

Waiting time distribution

Scaling of translocation time

CONCLUSION