Polymer translocation through a nanopore in mesoscopic simulations

Abstract

Dissipative particle dynamics (DPD) simulations are carried out to study the translocation of a single polymer chain through a pore under fluid field. The influences of the field strength E, the chain length N, the solvent quality α sp, and the pore size h on the translocation time are evaluated. The translocation time τ, which is defined as the time that the chain moves through the pore completely in the direction of the driving force, scales with the field strength E as τ ∼ E −0.48±0.01. We find that the translocation time is proportional to the chain length, which is in agreement with the experimental results and theoretical predictions. Tracing the variation of the square radius of gyration, R g 2 , and the polymer configuration during translocation, we observe that the chain is elongated when it is passing through the pore, which manifests that the chain is not in equilibrium during the translocation process. We also find that the worse the solvent quality is, the less time it will take to translocate, no matter what the size of the pore is. If the size of the pore is enlarged, the translocation time will be shorter. The information we gain from this study may benefit to the DNA sequencing.