Langevin dynamics simulation of single-stranded DNA translocation though nanopore in external non-uniform electric field

Abstract

Nanopore sequencers for deoxyribonucleic acid (DNA) have attracted significant attention to achieve high speed analysis with lower cost. Translocation mechanisms of DNA through a nanopore are not only essential in polymer physics but also critical in single-molecule detection. We address the electrokinetic transport of single-stranded DNA (ssDNA) through a nanopore in the presence of external nonuniform electric fields. Herein, a long-chain DNA molecule is represented by a coarse-grained bead-spring model consisting of 400 beads connected with harmonic springs. Langevin dynamics simulations are performed to investigate the electrokinetic transport dynamics in solution. In the whole structure of a nanofluidic device consisting of microchannel, nanochannel, and nanopore, non-uniform electric fields are numerically analyzed by using the finite element method. Conformation changes of the DNA chain during the translocation process is analyzed and we can predict a waiting time of ssDNA at the entrance of nanochannel before entering a nanopore, which is of great interest but difficult to observe in experiments. Our simulation results are expected to provide useful information to design an advanced nanopore devices for DNA sequencing.