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.

20 pages, 6 figures

References in corpus (3)

• Effects of electrostatic screening on the conformation of single DNA molecules confined in a nanochannel
• Diffusion mechanisms of localised knots along a polymer
• Orientational correlations in confined DNA

Cited by in corpus (7)

• Nanoconfined circular and linear DNA - equilibrium conformations and unfolding kinetics
• Confined polymers in the extended de Gennes regime
• One-parameter scaling theory for DNA extension in a nanochannel
• Scaling regimes of a semi-flexible polymer in a rectangular channel
• How nanochannel confinement affects the DNA melting transition within the Poland-Scheraga model
• A model for melting of confined DNA
• Electrophoretic Mobility of Polyelectrolytes within a Confining Well