Dynamics and Conformation of Semiflexible Polymers in Strong Quasi-1D and -2D Confinement

Abstract

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.

Hydrodynamics of DNA confined in nanoslits and nanochannels

“…This is not the only possibility, and every method has intrinsic advantages and shortcomings. An alternate approach while maintaining an implicit solvent is coupling a lattice Boltzmann (LB) solution for the fluid flow to the polymer model [48, 107–112], where random fluctuations are added to the stress tensor directly [113] to introduce Brownian fluctuations. As this method solves the Boltzmann equation rather than the Stokes equation, it leads to some approximations.…”

Kirkwood Diffusivity of Long Semiflexible Chains in Nanochannel Confinement

“…28 The coarse-grained nature of these models allows simulation of experimentally relevant molecular weights with a small number of beads for a sufficiently long time. 29 Because such bead-spring models do not have the necessary resolution when the confinement size is of the order of the persistence length of the polymer, finer models have been used recently for Metropolis Monte Carlo 6,22 and lattice Boltzmann-based simulations 30 of semiflexible chains in confinement. Models with adequate resolution used in conjunction with these methods, however, require hundreds or even thousands of beads to reach the length scales relevant to scaling theories and experiments, making such simulations infeasible.…”

Evaluation of the Kirkwood approximation for the diffusivity of channel-confined DNA chains in the de Gennes regime

“…8 While hydrodynamic screening by the walls greatly simplifies scaling theories 9 for the dynamics by removing hydrodynamic interactions between blobs, obtaining the prefactors for the scaling laws is complicated by the absence of a Green's function for the Stokes equation in confinement 8 and the cost of incorporating hydrodynamic interactions in general. Consequently, dynamic simulations of DNA in a nanochannel that incorporate hydrodynamic interactions [10][11][12] are restricted to relatively short chains or rather coarse models. The results thus obtained are informative, but the computational cost required to obtain them makes these methods prohibitive for studying DNA diffusion with the sub-persistence length resolution and long chains 13 A possible alternative to dynamic simulations is the Kirkwood-Riseman 14,15 approach, commonly referred to as the Kirkwood approximation, which leads to a computationally efficient simulation method at the expense of an error in the computation of the diffusion coefficient.…”