Diffraction on a crystalline slab formed by point-like scattering centres is treated as a multiple scattering problem based on the Ewald equations. Using general results expressed in a lucid matrix form, the two-beam solution for both coplanar and non-coplanar cases valid near and far from Bragg peaks is found and a detailed comparison of the final formulae obtained with those following from Laue's theory is performed.
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http://dx.doi.org/10.1107/S0108767304034452 | DOI Listing |
J Chem Theory Comput
January 2025
Chemical and Materials Physics Graduate Program, Departments of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering, University of California, Irvine, Irvine, California 92697, United States.
Molecular dynamics (MD) simulations are essential for understanding molecular phenomena at the atomic level, with their accuracy largely dependent on both the employed force field and sampling. Polarizable force fields, which incorporate atomic polarization effects, represent a significant advancement in simulation technology. The polarizable Gaussian multipole (pGM) model has been noted for its accurate reproduction of ab initio electrostatic interactions.
View Article and Find Full Text PDFArthritis Res Ther
December 2024
Department of Hematology, Oncology and Rheumatology, Internal Medicine V, University Hospital Heidelberg, Im Neuenheimer Feld 410, 69120, Heidelberg, Germany.
Objective: The high potential of CD19.CAR-T cells to treat autoimmune diseases such as Systemic Sclerosis (SSc) supposedly relies on the disappearance of autoantibodies. Here we investigated effects of CAR-T cells on the innate immune system which is an important contributor to pathology in SSc.
View Article and Find Full Text PDFJ Phys Chem B
November 2024
Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, United States.
All-atom constant pH molecular dynamics simulations offer a powerful tool for understanding pH-mediated and proton-coupled biological processes. As the protonation equilibria of protein side chains are shifted by electrostatic interactions and desolvation energies, p values calculated from the constant pH simulations may be sensitive to the underlying protein force field and water model. Here we investigated the force field dependence of the all-atom particle mesh Ewald (PME) continuous constant pH (PME-CpHMD) simulations of a mini-protein BBL.
View Article and Find Full Text PDFJ Chem Phys
October 2024
Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, USA.
We develop a computational method for modeling electrostatic interactions of arbitrarily shaped, polarizable objects on colloidal length scales, including colloids/nanoparticles, polymers, and surfactants, dispersed in explicit ion electrolytes and nonionic solvents. Our method computes the nonuniform polarization charge distribution induced in a colloidal particle by both externally applied electric fields and local electric fields arising from other charged objects in the dispersion. This leads to expressions for electrostatic energies, forces, and torques that enable efficient molecular dynamics and Brownian dynamics simulations of colloidal dispersions in electrolytes, which can be harnessed to accurately predict structural and transport properties.
View Article and Find Full Text PDFAging (Albany NY)
October 2024
Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Denmark.
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