Dynamics of Semiflexible Chains and Rings in Confinement

We investigate the dynamics of semiflexible chains, loops, and partial loops in confinement and examine the influence of intra-chain hydrodynamic interactions (HI) on chain dynamics. A hybrid lattice Boltzmann - Brownian dynamics is developed to study chain dynamics in near and sub-Kuhn length channels. It is found that as the channel height decreases below the Kuhn length, the chain exhibit different characteristic relaxation than in larger channels. Furthermore, the gradual screening of HI in smaller channels is found to reduce the difference between linear and circular chain diffusion. Good agreements are found with single molecule DNA measurements in nanoslits.