Simulated Diffusion Coefficients Research Articles

Smart Monte Carlo for accurate simulation of rare-event dynamics: Diffusion of adsorbed species on solid surfaces

We introduce a dynamical Smart Monte Carlo algorithm and assess its applicability for simulating the rare-event dynamics of adsorbate diffusion. Using the dynamical Smart Monte Carlo method, we simulate the self-diffusion of an adatom in the Cu/Cu(001) and Rh/Rh(111) systems and we compare the simulated diffusion coefficients to values arising from molecular dynamics and transition-state theory. We find that the accuracy of Smart Monte Carlo is sensitive to details of the potential-energy surface. For Cu/Cu(001), the agreement between dynamical Smart Monte Carlo, molecular dynamics, and transition-state theory is excellent. A similar comparison for the Rh/Rh(111) systems shows discrepancies between these three techniques. We find that the origins of the discrepancies in the Rh/Rh(111) system are transition-state recrossings, for small simulation time steps, and low escape rates of the adatom from the binding sites, at large time steps. We examine the sampling and dynamics in trajectories using a smaller time step for motion perpendicular to the surface than that for parallel motion. These studies show that low Smart Monte Carlo escape rates in the Rh/Rh(111) system can be correlated to excessive sampling, beyond the configurational space of the potential-energy minimum, at large time steps. Recrossings can be understood to arise from the absence of velocity correlations in the low-friction, transition-state region and can be minimized through the use of a large time step for parallel motion. With the appropriate choice of simulation time steps it is possible to improve the agreement between dynamical Smart Monte Carlo and more rigorous dynamical techniques.

Permeability of lysozyme tetragonal crystals to water

Diffusion of water within cross-linked tetragonal crystals of hen egg-white lysozyme has been measured and simulated on a computer using the X-ray structure of water-filled channels within the crystal lattice. Relative to the self-diffusion coefficient of bulk water molecules, the experimental diffusion coefficient of water within the crystal was found to be 13 times reduced in the (001) crystallographic plane and 5 times reduced in the [001] direction. Comparison of the experimental and computer simulated diffusion coefficients shows that steric limitations for water diffusion are mostly responsible for this reduction of the water diffusion in the crystal, with the self-diffusion coefficient of intracrystalline water reduced by no more than 30–40% as compared to that of bulk water.

Cation dependence of the ionic dynamics in computer simulated molten nitrates

In order to study the cation dependence of the ionic dynamics in molten nitrates, molecular dynamics simulations including vibrational degrees of freedom were carried out for molten LiNO3, NaNO3, and RbNO3. Coulomb pair potential with Born-type repulsion was adopted for the interionic interaction. The simulated diffusion coefficient was smaller for a larger cation, and that of nitrate ions did not change with changing cation species. The mean squared charge displacements showed that the static conductivity decreased considerably as the cation size increased from Li+ to Rb+. The simulated orientational correlation function of nitrate ions decayed more quickly as the cation size increased. Far infrared absorption spectrum simulated from the time evolution of the dipole moment (or the current) of the system showed that the peak shifted to the low energy side and the intensity decreased as the cation size increased. Results of the simulation were compared with the experimental diffusion constants, static and dynamic conductivities, and rotational behavior revealed by Raman spectroscopy. The simulated vibrational correlation functions and the power spectra of NO3− could reproduce the observed cation dependence of the peak frequencies of the ν1(A′1) and ν2(A″2) modes. However, the assumed interionic potentials in the present simulation were found to result in too slow vibrational dephasing of the ν1 mode and too fast dephasing of the ν2 mode as compared with the infrared and isotropic Raman spectra. Strong correlation between radial and angular distributions of cations was found in the first coordination spheres of nitrate ions in the simulated molten nitrates.

Comparison of computer simulated and theoretical tracer diffusion coefficients for a strictly regular solution model of a concentrated alloy

Abstract The tracer diffusion coefficients for a strictly regular solution model of a binary f.c.c. alloy with a very small vacancy content have been calculated by Monte Carlo simulations of the tracer correlation factors, mean jump frequencies and vacancy availability factors. Results have been compared with a theoretical expression due to Stolwijk for the correlation factor, expressions due to Kikuchi and Sato for the jump frequency and vacancy availability factor and the expression for the diffusion coefficient obtained by combining these theoretical results. The agreement is good above critical solution temperature. At the lower temperatures studied isotherms of tracer diffusion coefficient versus concentration show a maximum for both simulated and theoretical results.

Molecular dynamics studies of hydrocarbon diffusion in zeolites

Molecular dynamics simulation techniques have been used to investigate behaviour of sorbed CH4 and C2H4 in zeolite ZSM-5. Our calculations allowed for framework in addition to molecular motions. Diffusion trajectories were obtained for the sorbed molecules. Simulated diffusion coefficients were in acceptable agreement with experiment.

The quantum simulation of hydrogen in metals

Abstract Realistic quantitative calculations on atomistic models for hydrogen in metals are difficult because quantum effects must be included. We show that quantum simulation based on Feynman's path-integral formulation of quantum mechanics gives a powerful way of making such calculations. After summarizing some essential facts about metal-hydrogen systems, we explain the principles of pathintegral simulation. We present the results of classical molecular-dynamics and quantum path-integral simulations of hydrogen in Pd and Nb based on simple empirical interaction models. Results are given for the probability density ρ(r) of hydrogen as a function of position r in the unit cell, and for a quantity proportional to the diffusion coefficient. We point out that diffraction measurements of ρ(r) would allow an important test of the interaction models. The simulated diffusion coefficient for H in Nb shows the experimentally observed break in Arrhenius slope at ∼250 K, which we argue represents a cross-over from ...

Electrophoresis of interacting proteins II. A simple method of simulation

Goad's method for the numerical solution of the conservation-of-mass equation of a system of migrating and simultaneously interacting macromolecules is simplified by taking into account the velocity fluxes between adjacent boxes only. The error introduced in this way is used to advantage to simulate the effect of the diffusional flux. It is shown that this procedure is essentially the same as the counter-current analog method developed by Bethune and Kegeles to account for the effect of diffusion on transport patterns of interacting proteins. The adjustment of the simulated diffusion coefficients to their actual values is discussed and the results of different calculations are compared. It is shown that diffusional spreading has only a secondary influence on the development of a reaction boundary.