2,124 research outputs found
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
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