Molecular dynamics and diffusion

Kubicki, J.D. and Lasaga, A.C., Molecular dynamics and diffusion in silicate melts, in Diffusion, Atomic Ordering, and Mass Transport Selected Problems in Geochemistry, Ganguly, J., Ed., Springer-Verlag, New York, 1991, P- L... 

Molecular Dynamics and Diffusion Model of Single Proton Conduction through Gramicidin. 

The numerical modeling methods for polymer blends have been reviewed in this chapter, with different categories such as volume-of-fluid, molecular dynamics and diffusion-controlled methods being introduced. Use of the Cahn-Hilliard method was emphasized for binary and ternary polymer systems with no obvious mechanical flux, while specific factors such as elastic energy and functionalized substrate were considered for purposes of comparison. The diffusion-controlled model described, using the Cahn-Hilliard equation as the constitutive equation, can be used to depict the gradient of the interface as well as the composition profile of partially miscible blends hence, it is feasible to implement this equation in a polymer blend system. It should be noted that although these examples do not consider mechanical flux, additional constitutive equations (e.g., Navier-Stokes) can easily be added to this diffusion-controlled model. 

NMRrelaxation and diffusion experiments provide important insights into both the internal molecular dynamics and the overall hydrodynamic behavior of unfolded and partly folded states. Local variations in backbone dynamics are correlated with propensities for local compaction of the polypeptide chain that results in constriction of backbone motions (Eliezer et al., 1998, 2000). This can occur through formation of... 

Molecular Dynamics and Monte Carlo simulations have been used to predict the adsorption isotherms and transport diffusivities of Xe adsorbed in A1P04-31. The results of these calculations can be used to predict the properties of Xe diffusing through membranes made from A1P04-31 crystals directly from atomic-scale principles. 

Two atomistic approaches have been presented briefly above molecular dynamics and the transition-state approach. They are still not ideal tools for the prediction of diffusion constants because (i) in order to obtain a reliable chain packing with a MD simulation one still needs the experimental density of the polymer and (ii) though TSA does not require classical dynamics it involves a number of simplifying assumptions, i.e. duration of jump mechanism, elastic polymer matrix, size of smearing factor, that impair to a certain degree the ab initio character of the method. However MD and TSA are valuable achievements, they are complementary in several... 

Abstract The chemical activation of light alkanes by acidic zeolites was studied by a combined Classical Mechanics/Quantum Mechanics approach. The diffusion and adsorption steps were investigated by Molecular Mechanics, Molecular Dynamics and Monte Carlo simulations. The chemical reactions step was studied at the DPT (B3LYP) level with 6-31IG basis sets and 3T and 5T clusters to represent the acid site ofthe zeolite. 

The next section gives a brief overview of the main computational techniques currently applied to catalytic problems. These techniques include ab initio electronic structure calculations, (ab initio) molecular dynamics, and Monte Carlo methods. The next three sections are devoted to particular applications of these techniques to catalytic and electrocatalytic issues. We focus on the interaction of CO and hydrogen with metal and alloy surfaces, both from quantum-chemical and statistical-mechanical points of view, as these processes play an important role in fuel-cell catalysis. We also demonstrate the role of the solvent in electrocatalytic bondbreaking reactions, using molecular dynamics simulations as well as extensive electronic structure and ab initio molecular dynamics calculations. Monte Carlo simulations illustrate the importance of lateral interactions, mixing, and surface diffusion in obtaining a correct kinetic description of catalytic processes. Finally, we summarize the main conclusions and give an outlook of the role of computational chemistry in catalysis and electrocatalysis. 

Simulations—isoergic and isothermal, by molecular dynamics and Monte Carlo—as well as analytic theory have been used to study this process. The diagnostics that have been used include study of mean nearest interparticle distances, kinetic energy distributions, pair distribution functions, angular distribution functions, mean square displacements and diffusion coefficients, velocity autocorrelation functions and their Fourier transforms, caloric curves, and snapshots. From the simulations it seems that some clusters, such as Ar, 3 and Ar, 9, exhibit the double-valued equation of state and bimodal kinetic energy distributions characteristic of the phase change just described, but others do not. Another kind of behavior seems to occur with Arss, which exhibits a heterogeneous equilibrium, with part of the cluster liquid and part solid. 

We may look at atomic clusters as particularly apt and useful models to study virtually every aspect of what we call, diffusely, complexity. Simulations are particularly powerful means to carry out such studies. For example, we can follow trajectories for very long times with molecular dynamics and thereby evaluate the global means of the exponential rates of divergence of neighboring trajectories. This is the most common way to evaluate those exponents, the Liapunov exponents. The sum of these is the Kolmogorov entropy, one gross measure of the volume of phase space that the system explores, and hence one... 

R164 N. Chandrakumar, High Resolution NMR as a Probe of Molecular Structure, Dynamics and Diffusion , p. Pl/485... 

Polar carotenoids present in membranes have been shown to limit molecular oxygen penetration into lipid bilayer as demonstrated by the pigment-related decrease of the oxygen diffusion-concentration product (Subczynski et al., 1991). This effect, being most probably a direct consequence of the influence ofthe carotenoids on molecular dynamics and structure of lipid membranes, appears particularly important taking into consideration the deleterious role of active oxygen species with respect to biomembranes. 

These two equations, (50) and (51), illustrate how the macrodynamic theory can give a kinematic framework, which may be of interest in connection with work on the molecular dynamics of diffusion. It is seen that on a fundamental basis it is not possible to express the mutual coefficient in terms of the two selfdiffusion coefficients (of component a) and D (of component b). As a matter of fact, self diffusion of a component in a mixture is a more complicated process than mutual diffusion, as far as frictions are concerned, because according to (50) it depends on two kinds of friction, viz., internal friction within this component... 

NMR spectroscopy is a nondestructive technique, widely used in chemistry, that provides detailed information on molecular structure, both for pure compounds and in complex mixtures [12]. NMR spectroscopic methods can also be used to probe metabolite molecular dynamics and mobility as well as substance concentrations through the interpretation of NMR spin relaxation times and by the determination of molecular diffusion coefficients [13]. 

Theory, Experiment, and Reaction Rates. A Personal View. J. D. Doll and A. F. Voter, Annu. Rev. Phys. Chem., 38, 413 (1987). Recent Develoinnents in the Theory of Surface Diffusion. B. J. Berne, in Multiple Time Scales, J. U. Brackbill and B. I. Cohen, Eds., Academic Press, Orlando, FL, 1987, pp. 419-436, Molecular Dynamics and Monte Carlo Simulation of Rare Events. P. HSnggi, P. Talkner, and M. Borkovec, Rev. Mod. Phys., 62, 251 (1990). Reaction-Rate Theory Fifty Years After Kramers. 

Lefort. R. Toudic. B. Etrillard, J. Bourges. P. Currat. R. Breczewski, T. Dynamical molecular disorder and diffuse scattering in an alkane/urea incommensurate inclusion compound. Eur. Phys. J., B 2001, 24. 51. 

Spectroscopic techniques, in general, are very well suited for investigation into molecular aspects such as local molecular arrangements, molecular dynamics, and molecular interactions. However, for many microemulsions, in particular those that simultaneously contain large amounts of water and oil, these aspects are rather uninteresting. Local molecular dynamics are determined by short-range interactions and are essentially independent of the self-assembly structure. Nuclear magnetic resonance (NMR) is, however, particular as a spectroscopic technique in that it can also provide information on other central matters such as phase behavior and microstructure. In particular, NMR self-diffusion and, to some... 

COSMO-RS is a surprisingly robust method suitable for predictive calculations in a broad range of application areas. For a comprehensive survey we refer to [14]. COSMO-RS has some limitations for instance, it is unable to treat dynamic properties such as viscosities and diffusion coefficients. Therefore COSMO-RS does not provide a complete description of liquid phases. In principle, the more rigorous molecular dynamics and Monte Carlo approaches offer a complete picture, but on the other hand they are several orders of magnitude more computationally demanding. 

Demurov, A., Radhakrishnan, R., Trout, B.L., Computations of diffusivities in ice and CO2 clathrate hydrates via molecular dynamics and Monte Carlo simulations. J. Chem. Phys., 116 (2002) 702-709. 

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