We study the translocation of a semiflexible polymer through a conical channel with attractive surface interactions and a driving force which varies spatially inside the channel. Using the results of the translocation dynamics of a flexible polymer through an extended channel as control, we first show that the asymmetric shape of the channel gives rise to non-monotonic features in the total translocation time as a function of the apex angle of the channel. The waiting time distributions of individual monomer beads inside the channel show unique features strongly dependent on the driving force and the surface interactions. Polymer stiffness results in longer translocation times for all angles of the channel. Further, non-monotonic features in the translocation time as a function of the channel angle changes substantially as the polymer becomes stiffer, which is reflected in the changing features of the waiting time distributions. We construct a free energy description of the system incorporating entropic and energetic contributions in the low force regime to explain the simulation results.

The transport of biomolecules across a cell membrane is an important phenomena 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 waiting time distributions, w(s). The escape of polymer segments from the narrow end of the conical channel is tracked by studying their velocity profile (vs). To demonstrate the asymmetric pore effects on the translocatin dynamics, we compare the translocation process from both the ends 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 the effect of various rigidity, and increasing length of a polymer chain, on both types of processes. The study can be used to find the transition from a directional dependent to a directional independent translocation process through a asymmetric channel.

We study the translocation of a semiflexible polymer through a conical channel with attractive surface interactions and a driving force which varies spatially inside the channel. Using the results of the translocation dynamics of a flexible polymer through an extended channel as control, we first show that the asymmetric shape of the channel gives rise to non-monotonic features in the total translocation time as a function of the apex angle of the channel. The waiting time distributions of individual monomer beads inside the channel show unique features strongly dependent on the driving force and the surface interactions. Polymer stiffness results in longer translocation times for all angles of the channel. Further, non-monotonic features in the translocation time as a function of the channel angle changes substantially as the polymer becomes stiffer, which is reflected in the changing features of the waiting time distributions. We construct a free energy description of the system incorporating entropic and energetic contributions in the low force regime to explain the simulation results.