Simulation of Semiflexible Cyclic and Linear Chains Moderately and Strongly Confined in Nanochannels

Abstract

The constraints due to the chain closure in combination with the geometrical constraints of a DNA molecule are inevitable for many biological processes. In this work, structural properties of flexible and semiflexible cyclic chains and their linear analogues confined in cylindrical channels were studied using the coarse-grained Metropolis Monte Carlo simulations. The radius of gyration satisfactorily represents the longitudinal stretching of both chain topologies. Transition between the moderate and strong confinement regime of semiflexible cyclic chains is described for the first time. Qualitatively similar response of the chain elongation to the confinement strength variation Rg(D) is obtained in the case of cyclic chains. However, the relative chain extension is stronger, the Odijk strong confinement regime is extended to larger channel diameters D, and under moderate confinement the chain extension declines less steeply for cyclic chains. All three findings are explained in terms of the strong self-av...