Highly driven polymer translocation from a cylindrical cavity with a finite length.

Abstract

We present a computer simulation study of polymer translocation in a situation where the chain is initially confined to a closed cylindrical cavity in order to reduce the impact of conformational diversity on the translocation times. In particular, we investigate how the coefficient of variation of the distribution of translocation times can be minimized by optimizing both the volume and the aspect ratio of the cavity. Interestingly, this type of confinement sometimes increases the number and impact of hairpin conformations such that the fluctuations in the translocation process do not follow a power law in time (for instance, these fluctuations can even vary non-monotonically with time). We develop a tension-propagation model for a polymer compressed into such a confining volume and find that its predictions are in good agreement with our simulation results in the experimentally relevant strongly driven limit. Both the theoretical calculations and the simulation data yield a minimum in the coefficient of variation of the distribution of translocation times for a cylindrical cavity with an aspect ratio that makes it similar to a hemisphere. This provides guidance for the design of new devices based on the preconfinement of the target polymer into cavities.