Translocation is a nonequilibrium process at all stages: Simulating the capture and translocation of a polymer by a...

Langevin dynamics simulations of the capture of polymers by a nanopore and the subsequent translocation through the nanopore are performed. These simulations are conducted for several polymer lengths at two different values for the Péclet number, which quantifies the drift-diffusion balance of the system. The capture-translocation process is divided into several stages, and the dynamics of translocation are characterized by measuring the average time for each stage and also the average conformation of the polymer at each stage. Comparison to the standard simulation approach of simulating only the translocation process reveals several important differences. While in the standard protocol, the polymer is essentially equilibrated at the start of translocation, simulations of the capture process reveal a polymer that is elongated when it approaches the pore and either remains elongated or becomes compressed at the start of translocation depending on the drift-diffusion balance. These results demonstrate that translocation is a non-equilibrium process at all stages and that simulations assuming equilibration could yield improper results, even at a qualitative level. The scaling of the translocation time with polymer length is found to be significantly different between the two simulation protocols thus demonstrating that the capture step is an essential part of modeling the translocation process.