Out of Equilibrium Characteristics of a Forced Translocating Chain through a Nanopore

TL;DR

This study uses simulations to analyze the out-of-equilibrium conformations of a polymer chain during nanopore translocation, revealing distinct differences between the cis and trans sides and characterizing the chain's dynamic behavior.

Contribution

It provides a detailed simulation-based analysis of the out-of-equilibrium conformations and Flory exponents of a translocating polymer chain, highlighting differences between cis and trans sides.

Findings

Polymer configurations differ significantly between cis and trans sides.

Immediately after translocation, the chain exhibits a Flory exponent of approximately 0.45.

The chain is out of equilibrium during and immediately after translocation.

Abstract

Polymer translocation through a nano-pore in a thin membrane is studied using a coarse-grained bead-spring model and Langevin dynamics simulation with a particular emphasis to explore out of equilibrium characteristics of the translocating chain. We analyze the out of equilibrium chain conformations both at the $cis$ and the $trans$ side separately either as a function of the time during the translocation process or as as function of the monomer index $m$ inside the pore. A detailed picture of translocation emerges by monitoring the center of mass of the translocating chain, longitudinal and transverse components of the gyration radii and the end to end vector. We observe that polymer configurations at the $cis$ side are distinctly different from those at the $trans$ side. During the translocation, and immediately afterwards, the chain is clearly out of equilibrium, as different parts of the chain are characterized by a series of effective Flory exponents. We further notice that immediately after the translocation the last set of beads that have just translocated take a relatively compact structure compared to the first set of beads that translocated earlier, and the chain immediately after translocation is described by an effective Flory exponent $0.45 \pm 0.01$. The analysis of these results is further strengthened by looking at the conformations of chain segments of equal length as they cross from the $cis$ to the $trans$ side, We discuss implications of these results to the theoretical estimates and numerical simulation studies of the translocation exponent reported by various groups.