Driven translocation of a polynucleotide chain through a nanopore--A continuous time Monte-Carlo study

TL;DR

This study uses continuous time Monte-Carlo simulations to analyze polynucleotide translocation through a nanopore under electric field, revealing multi-peak passage time distributions consistent with experimental observations.

Contribution

It introduces a Monte-Carlo simulation approach for nanopore translocation, considering different chain-pore interactions and entry orientations, providing insights into translocation time distributions.

Findings

Distribution of translocation times has three peaks.

Results align with experimental data from KBBD.

Interaction and entry orientation affect translocation dynamics.

Abstract

Using continuous time Monte-Carlo method we simulated the translocation of a polynucleotide chain driven through a nanopore by an electric field. We have used two models of driven diffusion due to the electric field. The chain may have strong interaction with the pore, and depends on which end of the chain first enters the pore. Depending on this interaction, in both cases, the distribution of times for the chain to pass through the pore in our model is found to have three peaks, as observed in the experiment of Kasianowicz, Brandin, Branton and Deamer (KBBD).