Self-diffusion in two-dimensional hard ellipsoid suspensions

We studied the self-diffusion of colloidal ellipsoids in a monolayer near a flat wall by video microscopy. The image processing algorithm can track the positions and orientations of ellipsoids with sub-pixel resolution. The translational and rotational diffusions were measured in both the lab frame and the body frame along the long and short axes. The long-time and short-time diffusion coefficients of translational and rotational motions were measured as functions of the particle concentration. We observed sub-diffusive behavior in the intermediate time regime due to the caging of neighboring particles. Both the beginning and the ending times of the intermediate regime exhibit power-law dependence on concentration. The long-time and short-time diffusion anisotropies change non-monotonically with concentration and reach minima in the semi-dilute regime because the motions along long axes are caged at lower concentrations than the motions along short axes. The effective diffusion coefficients change with time t as a linear function of (lnt)/t for the translational and rotational diffusions at various particle densities. This indicates that their relaxation functions decay according to 1/t which provides new challenges in theory. The effects of coupling between rotational and translational Brownian motions were demonstrated and the two time scales corresponding to anisotropic particle shape and anisotropic neighboring environment were measured

Efficient multiple time scale molecular dynamics: using colored noise thermostats to stabilize resonances

Multiple time scale molecular dynamics enhances computational efficiency by updating slow motions less frequently than fast motions. However, in practice the largest outer time step possible is limited not by the physical forces but by resonances between the fast and slow modes. In this paper we show that this problem can be alleviated by using a simple colored noise thermostatting scheme which selectively targets the high frequency modes in the system. For two sample problems, flexible water and solvated alanine dipeptide, we demonstrate that this allows the use of large outer time steps while still obtaining accurate sampling and minimizing the perturbation of the dynamics. Furthermore, this approach is shown to be comparable to constraining fast motions, thus providing an alternative to molecular dynamics with constraints.Comment: accepted for publication by the Journal of Chemical Physic