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

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.