The diffusion and relaxation of Gaussian chains in narrow rectangular slits

Abstract

The confinement of a polymer to volumes whose characteristic linear dimensions are comparable to or smaller than its bulk radius of gyration R(G,bulk) can produce significant changes in its static and dynamic properties, with important implications for the understanding of single-molecule processes in biology and chemistry. In this paper, we present calculations of the effects of a narrow rectangular slit of thickness d on the scaling behavior of the diffusivity D and relaxation time τr of a Gaussian chain of polymerization index N and persistence length l0. The calculations are based on the Rouse-Zimm model of chain dynamics, with the pre-averaged hydrodynamic interaction being obtained from the solutions to Stokes equations for an incompressible fluid in a parallel plate geometry in the limit of small d. They go beyond de Gennes' purely phenomenological analysis of the problem based on blobs, which has so far been the only analytical route to the determination of chain scaling behavior for this particular geometry. The present model predicts that D ∼ dN(-1)ln (N∕d(2)) and τr ∼ N(2)d(-1)[ln (N∕d(2))](-1) in the regime of moderate confinement, where l0 ≪ d < R(G,bulk). The corresponding results for the blob model have exactly the same power law behavior, but contain no logarithmic corrections; the difference suggests that segments within a blob may actually be partially draining and not non-draining as generally assumed.

Hydrodynamics of DNA confined in nanoslits and nanochannels

“…In fact, their analysis showed that ζ ~ L (ln L ) −1 for ideal chains in slits, indicating partial draining of blobs [40]. This result was later substantiated theoretically via the pre-averaging approximation [67]. Nonetheless, Doyle and coworkers [40] found that, for slit-confined polymers in good solvent conditions, ζ is indeed proportional to L , in agreement with the somewhat fortuitously obtained outcome of blob theory, where the hydrodynamic interactions were assumed to decay exponentially outside of a distance H for both channels and slits [49].…”