Translocation of polymers through a wide-open conical pore

Abstract

Abstract The transport of biomolecules across a cell membrane is an important phenomenon that plays a pivotal role in the functioning of biological cells. In this paper, we investigate such processes by modeling the translocation of polymers through a conical channel, directed from the wider opening to the narrow end of the conical channel. We use the molecular dynamics approach to study the problem. The effect of the different conical pore geometry and polymer lengths on translocation dynamics is determined from the behavior of the total translocation time, τ, and the waiting time distributions, w(s). The escape of polymer segments from the narrow end of the conical channel is tracked by studying the escape velocity profile (〈v i 〉). To demonstrate the asymmetric pore effects on the translocation dynamics, we compare the translocation process from both the terminals: the wider-opening and the narrow-end of the conical channel. We find striking differences in the translocation dynamics for both processes, which are in agreement with the experimental study. We have accounted for the effect of various rigidity, and increasing length of a polymer chain, on both types of processes. This computational study can be used to underline the translocation process from different conical pores.