Translocation Dynamics with Attractive Nanopore-Polymer Interactions

TL;DR

This study uses Langevin dynamics simulations to explore how attractive interactions between polymers and nanopores influence translocation dynamics, revealing a transition from non-activated to activated pore emptying and explaining different experimental scaling behaviors.

Contribution

It introduces a detailed analysis of the three-stage translocation process under attractive interactions, highlighting the dominant role of pore emptying in strong attraction regimes.

Findings

Attractive interactions significantly alter translocation times.

Pore emptying transitions from non-activated to activated with increased attraction.

Results align with experimental observations and explain different scaling behaviors.

Abstract

Using Langevin dynamics simulations, we investigate the influence of polymer-pore interactions on the dynamics of biopolymer translocation through nanopores. We find that an attractive interaction can significantly change the translocation dynamics. This can be understood by examining the three components of the total translocation time $\tau \approx \tau_1+\tau_2+\tau_3$ corresponding to the initial filling of the pore, transfer of polymer from the \textit{cis} side to the \textit{trans} side, and emptying of the pore, respectively. We find that the dynamics for the last process of emptying of the pore changes from non-activated to activated in nature as the strength of the attractive interaction increases, and $\tau_3$ becomes the dominant contribution to the total translocation time for strong attraction. This leads to a new dependence of $\tau$ as a function of driving force and chain length. Our results are in good agreement with recent experimental findings, and provide a possible explanation for the different scaling behavior observed in solid state nanopores {\it vs.} that for the natural $\alpha$-hemolysin channel.