Nobuhiko Watari

How accurate are stochastic rotation dynamics simulations of polymer dynamics

We examine carefully the accuracy of stochastic rotational dynamics (SRD) simulations for isolated polymer chains in a solvent, where SRD incorporates hydrodynamic interaction (HI) through momentum exchange (collisions) between polymer beads and solvent beads, both of which are assigned mass. We show that the main error is due to the inertial effect that finite bead mass has on polymer hydrodynamics. We find that the inertial effect is negligible when Rg, the radius of gyration of the polymer chain is much larger than LM, the distance over which bead inertia is lost due to collisions with solvent. For moderate HI, good agreement is found between the rotational relaxation time simulated by SRD with that from normal-mode analysis and from Brownian dynamics (BD) simulations, even for short five-bead chains. For dominant HI, for short chains, we can minimize the inertial effect by varying the ratio of polymer to solvent bead mass. For long chains (Rg≫LM) SRD and BD relaxation times agree, but are larger than ...

Conformation dependence of DNA electrophoretic mobility in a converging channel

The electrophoresis of λ‐DNA is observed in a microscale converging channel where the center‐of‐masses trajectories of DNA molecules are tracked to measure instantaneous electrophoretic (EP) mobilities of DNA molecules of various stretch lengths and conformations. Contrary to the usual assumption that DNA mobility is a constant, independent of field and DNA length in free solution, we find DNA EP mobility varies along the axis in the contracting geometry. We correlate this mobility variation with the local stretch and conformational changes of the DNA, which are induced by the electric field gradient produced by the contraction. A “shish‐kebab” model of a rigid polymer segment is developed, which consists of aligned spheres acting as charge and drag centers. The EP mobility of the shish‐kebab is obtained by determining the electrohydrodynamic interactions of aligned spheres driven by the electric field. Multiple shish‐kebabs are then connected end‐to‐end to form a freely jointed chain model for a flexible DNA chain. DNA EP mobility is finally obtained as an ensemble average over the shish‐kebab orientations that are biased to match the overall stretch of the DNA chain. Using physically reasonable parameters, the model agrees well with experimental results for the dependence of EP mobility on stretch and conformation. We find that the magnitude of the EP mobility increases with DNA stretch, and that this increase is more pronounced for folded conformations.