Monomer distributions and intra-chain collisions of a polymer confined to a channel

TL;DR

This study uses Monte Carlo simulations to analyze how self-avoiding polymers confined in channels distribute their monomers and how intra-chain collisions influence their conformations, with implications for DNA in nanofluidic channels.

Contribution

It provides detailed insights into monomer distributions and collision frequencies in confined polymers, highlighting the weak dependence on spatial position and explaining deviations from mean-field predictions.

Findings

Most intra-chain collisions occur between neighboring monomers.

Collision probability depends weakly on monomer position.

Self-avoidance effects are weaker than mean-field theory suggests.

Abstract

We study the conformations of a self-avoiding polymer confined to a channel by computing the cross-sectional distributions of the positions of its monomers. By means of Monte-Carlo simulations for a self-avoiding, freely-jointed chain we determine how the cross-sectional distribution for a given monomer depends on its location in the polymer, and how strongly this distribution is affected by self avoidance. To this end we analyze how the frequency of intra-chain collisions between monomers depends on their spatial position in the channel and on their location within the polymer. We show that most collisions occur between closely neighboring monomers. As a consequence the collision probability depends only weakly on the spatial position of the monomers. Our results explain why the effect of self-avoidance on the monomer distributions is weaker than predicted by mean-field theory. We discuss the relevance of our results for studies of DNA conformations in nanofluidic channels.