Momentum Removal to Obtain the Position-Dependent Diffusion Constant in Constrained Molecular Dynamics Simulation

<div>The position-dependent diffusion coefficient along with free energy profile are important parameters needed to study mass transport in heterogeneous systems such as biological and polymer membranes, and molecular dynamics (MD) calculation is a popular tool to obtain them. Among many methodologies, the Marrink-Berendsen (MB) method is often employed to calculate the position-dependent diffusion coefficient, in which the autocorrelation function of the force on a fixed molecule is related to the friction on the molecule. However, the diffusion coefficient is shown to be affected by the period of the removal of the center-of-mass velocity, which is necessary when performing MD calculations using the Ewald method for Coulombic interaction. We have clarified theoretically in this study how this operation affects the diffusion coefficient calculated by the MB method, and the theoretical predictions are proven by MD calculations. Therefore, we succeeded in providing guidance on how to select an appropriate the period of the removal of the center-of-mass velocity in estimating the position-dependent diffusion coefficient by the MB method. This guideline is applicable also to the Woolf-Roux method.</div>

Momentum Removal to Obtain the Position-Dependent Diffusion Constant in Constrained Molecular Dynamics Simulation

<div>The position-dependent diffusion coefficient along with free energy profile are important parameters needed to study mass transport in heterogeneous systems such as biological and polymer membranes, and molecular dynamics (MD) calculation is a popular tool to obtain them. Among many methodologies, the Marrink-Berendsen (MB) method is often employed to calculate the position-dependent diffusion coefficient, in which the autocorrelation function of the force on a fixed molecule is related to the friction on the molecule. However, the diffusion coefficient is shown to be affected by the period of the removal of the center-of-mass velocity, which is necessary when performing MD calculations using the Ewald method for Coulombic interaction. We have clarified theoretically in this study how this operation affects the diffusion coefficient calculated by the MB method, and the theoretical predictions are proven by MD calculations. Therefore, we succeeded in providing guidance on how to select an appropriate the period of the removal of the center-of-mass velocity in estimating the position-dependent diffusion coefficient by the MB method. This guideline is applicable also to the Woolf-Roux method.</div>

White X-ray radiation diffraction in crystals analysis by Ewald method in determining crystal lattice angular parameters

Using the Ewald method, the analysis a diffraction pattern formation in the interaction of white xray radiation with crystals in the process of diffraction shooting by the ω-scanning method using a point counter is carried out. The influence of such parameters as x-ray voltage x-ray tube and the angular the counter position to the number and intensity of reflections on x-rays. It is shown that the angles between the diffraction maxima on the diffractograms obtained by ω-scanning using white x-ray radiation are equal to the angles between the corresponding crystallographic planes. The angles and crystallographic indices of the reflecting crystals planes of some simple substances were measured using the considered x-ray survey.

High throughput identification of Li ion diffusion pathways in typical solid state electrolytes and electrode materials by BV-Ewald method

A new BV-Ewald method was developed to calculate Li-ion diffusion pathways more quickly and correctly.