(244g) Monte Carlo Diffusivity Calculation of Semiflexible Polymers Confined in Nanochannels

Bead-spring models have been used previously to investigate the dynamics of polymers in confinement with Brownian Dynamics (BD) simulations. However, the long length and time scales involved render BD simulations unsuitable for studying the dynamics of confined semiflexible polymers, such as DNA. In this talk, we demonstrate that the diffusion coefficient of confined polymers can be estimated by combining CFD solutions of the Stokes equation with the Pruned-Enriched Rosenbluth Method (PERM), a Monte Carlo chain growth technique. The diffusion coefficient obtained by the Kirkwood approximation shows good agreement with theoretical predictions both in the Odijk regime (extreme confinement) and the de Gennes regime (moderate confinement). Our simulations of long chains, up to 20,000 beads, indicate that the diffusivity reaches the asymptotic limit much quicker than other properties like the extension, underscoring the importance of rapid screening of hydrodynamic interactions due to channel walls. Our results yet again manifest the superiority of the discrete wormlike chain model for simulation of confined polymers over a wide range of channel sizes.