Molecular Dynamics diffusion coefficient

Monte Carlo simulations require less computer time to execute each iteration than a molecular dynamics simulation on the same system. However, Monte Carlo simulations are more limited in that they cannot yield time-dependent information, such as diffusion coefficients or viscosity. As with molecular dynamics, constant NVT simulations are most common, but constant NPT simulations are possible using a coordinate scaling step. Calculations that are not constant N can be constructed by including probabilities for particle creation and annihilation. These calculations present technical difficulties due to having very low probabilities for creation and annihilation, thus requiring very large collections of molecules and long simulation times. 

Molecular dynamics calculations are more time-consuming than Monte Carlo calculations. This is because energy derivatives must be computed and used to solve the equations of motion. Molecular dynamics simulations are capable of yielding all the same properties as are obtained from Monte Carlo calculations. The advantage of molecular dynamics is that it is capable of modeling time-dependent properties, which can not be computed with Monte Carlo simulations. This is how diffusion coefficients must be computed. It is also possible to use shearing boundaries in order to obtain a viscosity. Molec-... 

The non-bonded interaction energy, the van-der-Waals and electrostatic part of the interaction Hamiltonian are best determined by parametrizing a molecular liquid that contains the same chemical groups as the polymers against the experimentally measured thermodynamical and dynamical data, e.g., enthalpy of vaporization, diffusion coefficient, or viscosity. The parameters can then be transferred to polymers, as was done in our case, for instance in polystyrene (from benzene) [19] or poly (vinyl alcohol) (from ethanol) [20,21]. 

FIQ. 3 Diffusion coefficient of benzene molecules in benzene-polystyrene mixtures normalized by the diffusion coefficient of neat benzene molecular dynamics results, NMR measurements and prediction by the Mackie-Meares model [26]. 

Here the vector rj represents the centre of mass position, and D is usually averaged over several time origins to to improve statistics. Values for D can be resolved parallel and perpendicular to the director to give two components (D//, Dj ), and actual values are summarised for a range of studies in Table 3 of [45]. Most studies have found diffusion coefficients in the 10 m s range with the ratio D///Dj between 1.59 and 3.73 for calamitic liquid crystals. Yakovenko and co-workers have carried out a detailed study of the reorientational motion in the molecule PCH5 [101]. Their results show that conformational molecular flexibility plays an important role in the dynamics of the molecule. They also show that cage models can be used to fit the reorientational correlation functions of the molecule. 

Self-diffusion coefficients are dynamic properties that can be easily obtained by molecular dynamics simulation. The properties are obtained from mean-square displacement by the Einstein equation ... 

Monte Carlo heat flow simulation, nonequilibrium molecular dynamics, 73-74, 77-81 multiparticle collision dynamics hydrodynamic equations, 105-107 macroscopic laws and transport coefficients, 102-104 single-particle friction and diffusion, 114-118... 

Molecular dynamics simulations [183] have suggested that the diffusion coefficient increases with increasing ratio in the layers, which can... 

The above experimental results largely relate to spectroscopic techniques, which do not give direct information about the spatial scale of the molecular motions. The size of the spatial heterogeneities is estimated by indirect methods such as sensitivity of the dynamics to the probe size or from the differences between translational and rotational diffusion coefficients (rotation-translation paradox). It might be expected that the additional spatial information provided by neutron scattering could help to discriminate between the two scenarios proposed. 

An indirect indication of the presence of interactions between micellar phase and drugs is given by molecular and dynamic parameters of the drug and the micelles (ionic mobility, diffusion coefficient, hydrodynamic radius, apparent molecular mass), which are altered by the solubilization of lipophilic substances in a significant manner. 

Not only does anion-1 differ from the molecular anions of acetonitrile in its absorption properties, but its dynamic properties are also anomalous. While anion-2 has normal mobility, anion-1 is a high-mobility anion whose room temperature diffusion coefficient is more than three times higher than that of solute ions and anion-2 [30]. The activation energy for this migration is just 3.2 kJ/mol while the value for normal ions (including anion-2) is 7.6 kJ/mol [30]. Electron-transfer reactions that involve anion-1... 

The computational efficiency of a FF approach also enables simulations of dynamical behavior—molecular dynamics (MD). In MD, the classical equations of motion for a system of N atoms are solved to generate a search in phase space, or trajectory, under specified thermodynamic conditions (e.g., constant temperature or constant pressure). The trajectory provides configurational and momentum information for each atom from which thermodynamic properties such as the free energy, or time-dependent properties such as diffusion coefficients, can be calculated. 

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