Non-equilibrium effects in chaperone-assisted translocation of a stiff polymer

TL;DR

This study uses simulations to explore how non-equilibrium effects influence chaperone-assisted translocation of stiff polymers, revealing conditions that lead to superdiffusive behavior and confirming the theoretical basis of the equilibration process.

Contribution

It provides a detailed analysis of non-equilibrium effects in polymer translocation, highlighting the impact of chaperone size, binding energy, and distribution on translocation dynamics.

Findings

Non-equilibrium effects cause superdiffusion during translocation.

Equilibration rate varies with chaperone parameters, exceeding 20 times per monomer in some cases.

Theoretical confirmation of the equilibration process.

Abstract

Chaperone-assisted biopolymer translocation is the main model proposed for translocation \textit{in vivo}. A dynamical Monte Carlo method is used to simulate the translocation of a stiff homopolymer through a nanopore driven by chaperones. Chaperones are proteins that bind to the polymer near the wall and prevent its backsliding through Cis side. The important parameters include binding energy, size and the local concentration of the chaperones. The profile of these local concentrations, build up the chaperones distribution. Here we investigate the effects of binding energy, size and the exponential distribution of chaperones in their equilibration in each step of the polymer translocation needed for stable translocation time. The simulation results show that in case of chaperones with the size of a monomer ($\lambda=1$) and/or positive effective binding energy and/or uniform distribution, the chaperones binding equilibration rate/frequency is less than $5$ times per monomer. However, in some special cases in the exponential distribution of chaperones with size $\lambda>1$ and negative effective binding energy the equilibration rate will diverge to more than $20$ times per monomer. We show that this non-equilibrium effect results in supper diffusion, seen before. Moreover, we confirm the equilibration process theoretically.