Non-driven polymer translocation through a nanopore: computational evidence that the escape and relaxation processes are coupled

TL;DR

This study uses Molecular Dynamics simulations to challenge the common assumption that polymer chains are always relaxed during nanopore translocation, revealing a coupled escape and relaxation process with accelerated chain dynamics at the end.

Contribution

It provides computational evidence that polymer translocation involves non-equilibrium conformations, especially during the final escape phase, contradicting existing equilibrium-based models.

Findings

Translocation process is not fully in equilibrium despite longer translocation times.

The last half of the chain escapes in less than 12% of total time.

Significant acceleration occurs at the end of the chain escape.

Abstract

Most of the theoretical models describing the translocation of a polymer chain through a nanopore use the hypothesis that the polymer is always relaxed during the complete process. In other words, models generally assume that the characteristic relaxation time of the chain is small enough compared to the translocation time that non-equilibrium molecular conformations can be ignored. In this paper, we use Molecular Dynamics simulations to directly test this hypothesis by looking at the escape time of unbiased polymer chains starting with different initial conditions. We find that the translocation process is not quite in equilibrium for the systems studied, even though the translocation time tau is about 10 times larger than the relaxation time tau_r. Our most striking result is the observation that the last half of the chain escapes in less than ~12% of the total escape time, which implies that there is a large acceleration of the chain at the end of its escape from the channel.