Free energy of a folded semiflexible polymer confined to a nanochannel of various geometries

TL;DR

This study uses Monte Carlo simulations to analyze the free energy and conformational behavior of folded semiflexible polymers in nanochannels of various geometries, exploring scaling laws and comparing with theoretical predictions.

Contribution

It provides new insights into the scaling of free energies and entropic forces for polymers in different channel geometries, validating theoretical models with simulation data.

Findings

Entropic force scaling matches second virial level predictions.

Hairpin fold free energy aligns with recent theoretical calculations.

Polymer behavior consistent with previous simulation studies in Odijk regimes.

Abstract

Monte Carlo simulations are used to study the conformational properties of a folded semiflexible polymer confined to a long channel. We measure the variation in the conformational free energy with respect to the end-to-end distance of the polymer, and from these functions we extract the free energy of the hairpin fold, as well as the entropic force arising from interactions between the portions of the polymer that overlap along the channel. We consider the scaling of the free energies with respect to varying the persistence length of the polymer, as well as the channel dimensions for confinement in cylindrical, rectangular and triangular channels. We focus on polymer behaviour in both the classic Odijk and back folded Odijk regimes. We find the scaling of the entropic force to be close to that predicted from a scaling argument that treats interactions between deflection segments at the second virial level. In addition, the measured hairpin fold free energy is consistent with that obtained directly from a recent theoretical calculation for cylindrical channels. It is also consistent with values determined from measurements of the global persistence length of a polymer in the backfolded Odijk regime in recent simulation studies.