Effect of Inhomogeneity in Translocation of Polymers through Nanopores

TL;DR

This paper presents a theoretical analysis of how inhomogeneous polymer structures, specifically double- and single-stranded segments, affect translocation times through nanopores, highlighting the impact of entrance order and external conditions.

Contribution

It introduces a simple analytical model to study the translocation of inhomogeneous polymers, considering different entrance orientations and their effects on dynamics.

Findings

Entrance order significantly influences translocation times.

External fields and interaction energies affect translocation dynamics.

Theoretical insights are supported by free-energy landscape analysis.

Abstract

The motion of polymers with inhomogeneous structure through nanopores is discussed theoretically. Specifically, we consider the translocation dynamics of polymers consisting of double-stranded and single-stranded blocks. Since only the single-stranded chain can go through the nanopore the double-stranded segment has to unzip before the translocation. Utilizing a simple analytical model, translocation times are calculated explicitly for different polymer orientations, i.e., when the single-stranded block enters the pore first and when the double-stranded segment is a leading one. The dependence of the translocation dynamics on external fields, energy of interaction in the double-stranded segment, size of the polymer and the fraction of double-stranded monomers is analyzed. It is found that the order of entrance into the pore has a significant effect on the translocation dynamics. The theoretical results are discussed using free-energy landscape arguments.