Investigation of tracer diffusion in crowded cylindrical channel

TL;DR

This study uses molecular dynamics simulations to explore how tracer particles diffuse within crowded cylindrical channels, revealing transient subdiffusive behavior influenced by interactions and the mobility of surrounding polymers, relevant to biological systems.

Contribution

It introduces a coarse-grained simulation model to analyze tracer diffusion in crowded cylindrical channels, highlighting the effects of polymer grafting, mobility, and attraction on diffusion behavior.

Findings

Transient subdiffusion occurs at high attraction levels.

Long-term diffusion remains normal despite transient subdiffusion.

Mobility of background particles significantly affects diffusion dynamics.

Abstract

Based on a coarse-grained model, we carry out molecular dynamics simulations to analyze the diffusion of a small tracer particle inside a cylindrical channel whose inner wall is covered with randomly grafted short polymeric chains. We observe an interesting transient subdiffusive behavior along the cylindrical axis at high attraction between the tracer and the chains, however, the long time diffusion is always normal. This process is found to be enhanced for the case that we immobilize the grafted chains, i.e. the sub-diffusive behavior sets in at an earlier time and spans over a longer time period before becoming diffusive. Even if the grafted chains are replaced with a frozen sea of repulsive, non-connected particles in the background, the transient subdiffusion is observed. The intermediate subdiffusive behavior only disappears when the grafted chains are replaced with a mobile background sea of mutually repulsive particles. Overall, the long time diffusion coefficient of the tracer along the cylinder axis decreases with the increase in system volume fraction, strength of attraction between the tracer and the background and also on freezing the background. We believe that the simple model presented here could be useful for a qualitative understanding of the process of macromolecular diffusion inside the nuclear pore complex.