Pulling a folded polymer through a nanopore

TL;DR

This paper extends the iso-flux tension propagation theory to model the translocation of folded polymers through nanopores, validated by molecular dynamics simulations, revealing detailed dynamics including stages, waiting times, and velocity profiles.

Contribution

We generalize the IFTP theory to account for folded polymers with two segments translocating simultaneously, providing analytical and simulation insights.

Findings

Translocation involves two main stages with coupled and independent dynamics.

Equal monomer flux assumption allows analytical derivation of equations of motion.

MD simulations reveal translocation time distribution and monomer velocities.

Abstract

We investigate the translocation dynamics of a folded linear polymer which is pulled through a nanopore by an external force. To this end, we generalize the iso-flux tension propagation (IFTP) theory for end-pulled polymer translocation to include the case of two segments of the folded polymer traversing simultaneously trough the pore. Our theory is extensively benchmarked with corresponding Molecular Dynamics (MD) simulations. The translocation process for a folded polymer can be divided into two main stages. In the first stage, both branches are traversing the pore and their dynamics is coupled. If the branches are not of equal length, there is a second stage where translocation of the shorter branch has been completed. Using the assumption of equal monomer flux of both branches, we analytically derive the equations of motion for both branches and characterise the translocation dynamics in detail from the average waiting time and its scaling form. Moreover, MD simulations are used to study additional details of translocation dynamics such as the translocation time distribution and individual monomer velocities.