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Register a new userComparative classical and ab initio Molecular Dynamics study of molten and glassy germanium dioxide
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A Molecular Dynamics (MD) study of static and dynamic properties of molten and glassy germanium dioxide is presented. The interactions between the atoms are modelled by the classical pair potential proposed by Oeffner and Elliott (OE) [Oeffner R D and Elliott S R 1998, Phys. Rev. B, 58, 14791]. We compare our results to experiments and previous simulations. In addition, an ab initio method, the so-called Car-Parrinello Molecular Dynamics (CPMD), is applied to check the accuracy of the structural properties, as obtained by the classical MD simulations with the OE potential. As in a similar study for SiO2, the structure predicted by CPMD is only slightly softer than that resulting from the classical MD. In contrast to earlier simulations, both the static structure and dynamic properties are in very good agreement with pertinent experimental data. MD simulations with the OE potential are also used to study the relaxation dynamics. As previously found for SiO2, for high temperatures the dynamics of molten GeO2 is compatible with a description in terms of mode coupling theory.
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We report the first measurements of the dynamics of liquid germanium (l-Ge) by quasi-elastic neutron scattering on time-of-flight and triple-axis spectrometers. These results are compared with simulation data of the structure and dynamics of l-Ge which have been obtained with ab initio density functional theory methods. The simulations accurately reproduce previous results from elastic and inelastic scattering experiments, as well as the q-dependence of the width of the quasi-elastic signal of the new experimental data. In order to understand some special features of the structure of the liquid we have also simulated amorphous Ge. Overall we find that the atomistic model represents accurately the average structure of real l-Ge as well as the time dependent structural fluctuations. The new quasi-elastic neutron scattering data allows us to investigate to what extent simple theoretical models can be used to describe diffusion in l-Ge.
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In serine proteases (SPs), the H-bond between His-57 and Asp-102, and that between Gly-193 and the transition state intermediate play a crucial role for enzymatic function. To shed light on the nature of these interactions, we have carried out ab initio molecular dynamics simulations on complexes representing adducts between the reaction intermediate and elastase (one protein belonging to the SP family). Our calculations indicate the presence of a low--barrier H-bond between His-57 and Asp-102, in complete agreement with NMR experiments on enzyme--transition state analog complexes. Comparison with an ab initio molecular dynamics simulation on a model of the substrate--enzyme adduct indicates that the Gly-193--induced strong stabilization of the intermediate is accomplished by charge/dipole interactions and not by H-bonding as previously suggested. Inclusion of the protein electric field in the calculations does not affect significantly the charge distribution.
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