Translocation of Polymers through Nanopores at Weak External Field, Direct Approach with Monte Carlo Simulations

TL;DR

This study uses off-lattice 3D Monte Carlo simulations to investigate polymer translocation through a narrow pore under weak external fields, revealing non-equilibrium global behavior but quasi-equilibrium near the pore, with tension buildup and subdiffusive dynamics.

Contribution

It provides a direct simulation approach to analyze polymer translocation at low fields, highlighting local quasi-equilibrium and tension effects not captured by fractional diffusion models.

Findings

Global non-equilibrium translocation process.

Quasi-equilibrium dynamics near the pore.

Observation of tension buildup and subdiffusive behavior.

Abstract

I did off-lattice 3D Monte Carlo simulations for polymer translocation through a narrow pore at low external field, trying to be as close to a direct approach as possible. The process was found non equilibrium globally, but dynamics of the monomers close to the pore (the fold) was found close to quasi equilibrium. I observed a tension (or pressure) buildup near the pore, and subdiffusion for the displacement of the middle monomer in the pore, as reported in the literature. I did not find the distribution of the reaction coordinate after some time of free diffusion predicted by the fractional diffusion equation.