Translocation through conical pores: A direction-dependent process

TL;DR

This study models polymer translocation through conical channels using molecular dynamics, revealing how pore geometry and polymer length influence translocation times and dynamics, with implications for understanding biological transport processes.

Contribution

It provides the first detailed molecular dynamics analysis of direction-dependent polymer translocation through conical pores, highlighting geometry effects and transition to symmetric translocation.

Findings

Translocation time varies significantly with pore geometry and polymer length.

Asymmetry in pore shape causes distinct translocation dynamics from each end.

Polymer rigidity and length affect the translocation process and transition point.

Abstract

The transport of biomolecules across a cell membrane is an important phenomena that plays a pivotal role in the functioning of biological cells. In this paper, we investigate such processes by modeling the translocation of polymers through a conical channel, directed from the wider opening to the narrow end of the conical channel. We use the molecular dynamics approach to study the problem. The effect of the different conical pore geometry and polymer lengths on translocation dynamics is determined from the behavior of the total translocation time, $\tau$, and waiting time distributions, $w(s)$. The escape of polymer segments from the narrow end of the conical channel is tracked by studying their velocity profile ($v_{s}$). To demonstrate the asymmetric pore effects on the translocation dynamics, we compare the translocation process from both the ends of the conical channel. We find striking differences in the translocation dynamics for both processes, which are in agreement with the experimental study. We have accounted the effect of various rigidity, and increasing length of a polymer chain, on both types of processes. The study can be used to find the transition from a directional dependent to a directional independent translocation process through a asymmetric channel.