Polymer translocation: a nonequilibrium process

Abstract

3D Langevin dynamics simulations of the capture and translocation of polymers through a nanopore are conducted for several polymer lengths and two different Péclet values (that quantify the drift-diffusion balance of the system). By measuring the average conformation of the polymer and the average duration of each stage, simulations of the capture process reveal an elongated polymer approaching the nanopore and either remains elongated or becomes compressed just prior to translocation depending on the drift-diffusion balance. This is in direct contrast with the standard approach of simulating only the translocation process where the polymer is assumed to start translocation in an equilibrated state. The conformational differences directly impact scaling results of the translocation time by polymer length, where, even on a qualitative level, simulations that assume equilibration may yield incorrect results. The capture process is therefore an essential step for modelling and establishes the nonequilibrium nature of the translocation process.