Molecular dynamics simulation, diffusion coefficient estimation

Even conclusions drawn from the different computer simulation studies also do not seem to be consistent. The classic computer simulation study of Alder and Wainwright was performed at low density [173]. In this study they have shown that the long-time diffusion coefficient diverges in 2-D systems due to the existence of persistent hydrodynamic flows. On the other hand, some recent molecular dynamics simulations of 2-D systems have reported estimates of the self-diffusion coefficient [174]. In particular, it appeared from these simulations that a diffusion coefficient might, after all, exist at higher densities due to the absence of the persistent hydrodynamic... 

Molecular Dynamics Simulation Estimation of Diffusion Coefficients... 

Viscosity is related to the self-diffusion coefficient (equation 9.15) and can be estimated by molecular dynamics simulations [8]. 

The size-selectivity factor, which depends on the permeant s volume and the lateral pressure exerted by the membrane, is formulated as the reverse work done required to accommodate the permeant in the membrane. In this sense, it is analogous to the cavitation term in models of water solvation. Based on molecular dynamic simulations of membrane diffusion of small molecules, the calculated diffusion coefficients display small deviations across the membrane barrier. Assuming that the rates of diffusion in the membrane barrier are similar to those of bulk solvent with similar viscosity, or at least that they correlate strongly, the barrier diffusion coefficient is estimated using the size-dependent Stokes-Einstein relation, where kg is the Boltzmann constant, T is temperature, is membrane viscosity and is the radius of the permeant. 

Molecular dynamics simulations were used to estimate the diffusion coefficients of the sorbates in both short- and long-chain models. Four geometry-optimized sor-bates were randomly inserted in the model cells and long NVT simulations were performed. The complete methodology has been described elsewhere and is not detailed... 

M. Meunier. Diffusion coefficients of small gas molecules in amorphous cw-1,4-poly butadiene estimated by molecular dynamics simulations. J. Chem. Phys. 123,2005,134906. 

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