We investigate the conformation and relaxation dynamics of single DNA molecules in strong confinement (smaller than persistence length) with coarse-grained semiflexible chain (SFC) models using overdamped Langevin dynamics simulations. DNA properties in nanochannels and nanoslits are studied in confinement with height (H) ranging from the DNA radius of gyration (R g) to smaller than the persistence length (P). Qualitatively different dependences of chain conformation and relaxation time on H in moderate (P < H < R g) and strong (H < P) confinement are observed for very stiff SFC in the nanochannel but not in the nanoslit. The chain relaxation time (t relax) exhibits strong power-law dependence in H < P nanochannels, verified with and without including hydrodynamic interactions (HI). The inclusion of hydrodynamic interactions affects chain relaxation dynamics even in strong confinement, indicating the intersegmental hydrodynamic interactions affect dominant segmental relaxation mechanisms of strongly confined polymers.

We have studied the effect of chain topology on the structural properties and diffusion of polymers in a dilute solution in a good solvent. Specifically, we have used three different simulation techniques to compare the chain size and diffusion coefficient of linear and ring polymers in solution. The polymer chain is modeled using a bead-spring representation. The solvent is modeled using three different techniques: molecular dynamics (MD) simulations with a particulate solvent in which hydrodynamic interactions are accounted through the intermolecular interactions, multiparticle collision dynamics (MPCD) with a point particle solvent which has stochastic interactions with the polymer, and the lattice Boltzmann method in which the polymer chains are coupled to the lattice fluid through friction. Our results show that the three methods give quantitatively similar results for the effect of chain topology on the conformation and diffusion behavior of the polymer chain in a good solvent. The ratio of diffusivities of ring and linear polymers is observed to be close to that predicted by perturbation calculations based on the Kirkwood hydrodynamic theory.