Polymer translocation into and out of an ellipsoidal cavity

TL;DR

This study uses Monte Carlo simulations to analyze how polymer translocation into and out of ellipsoidal cavities depends on shape, interactions, and driving forces, revealing faster translocation in ellipsoids compared to spheres.

Contribution

It introduces a detailed free energy analysis of polymer translocation in ellipsoidal cavities, incorporating shape effects and interaction forces, with comparison to Langevin dynamics results.

Findings

Faster polymer ejection and insertion in ellipsoidal cavities compared to spherical ones.

Qualitative agreement with Langevin dynamics for ejection, but not for insertion.

Translocation times depend on cavity shape, interactions, and driving forces.

Abstract

Monte Carlo simulations are used to study the translocation of a polymer into and out of a ellipsoidal cavity through a narrow pore. We measure the polymer free energy F as a function of a translocation coordinate, s, defined to be the number of bonds that have entered the cavity. To study polymer insertion, we consider the case of a driving force acting on monomers inside the pore, as well as monomer attraction to the cavity wall. We examine the changes to F(s) upon variation in the shape anisometry and volume of the cavity, the polymer length, and the strength of the interactions driving the insertion. For athermal systems, the free energy functions are analyzed using a scaling approach, where we treat the confined portion of the polymer to be in the semi-dilute regime. The free energy functions are used with the Fokker-Planck equation to measure mean translocation times, as well as translocation time distributions. We find that both polymer ejection and insertion is faster for ellipsoidal cavities than for spherical cavities. The results are in qualitative agreement with those of a Langevin dynamics study in the case of ejection but not for insertion. The discrepancy is likely due to out-of-equilibrium conformational behaviour that is not accounted for in the FP approach