Wagner, "Visualization of MD and MC Simulations for Atomistic Modeling", Computer Physics Communications, (2002) 147, p. 665-9.J. Adler, A. Hashibon, N. Schreiber, A. Sorkin, S. Sorkin, and G. Wagner, "Visualization of MD and MC simulations for atomistic modeling", Computer Physics ...
(OKMC) was used to simulate the evolution of defects in Ni under annealing.In each annealing stage,the recombination mechanism was discussed and evolution of the defects under different cascade conditions was compared.It was found that the defects generated in high-temperature cascades are more ...
The MD results agree well with the equilibrium crystal structure, while significant differences between the MD and MC simulations are attributed to various sources. Both the MD and MC simulated melt structures do not confirm Gilbert's dissociation scheme for the hexafluoroaluminate anion....
the compliance and stiffness tensors, and the elastic moduli derived therefrom, at zero temperature. In order to access non-zero temperatures, it is necessary to use either the quasi-harmonic approximation for the vibrational free energy or molecular dynamics (MD) simulations. In the present work...
Teng (with MC) is underway by Ram Dynamics Steady states in fjc=1 and 1 gradient case Funtionalities SCF module summer 2022. Gradients: one, (classical) two (cylindrical and spherical geometry) treee (limited system sizes due to storage of large arrays) Geometries: planar (in 1, 2, 3...
The lack of technology transfer from academia to industry is caused by important gaps between its fundamental basis and the process design. Herein, we explore critical disconnections by conducting coupled mass and heat transfer modeling and MD simulations; we use well-known MD mass and heat ...
Performing both simple and advanced MD simulations interactively, QwikMD automates as many steps as necessary for preparing, carrying out, and analyzing simulations while checking for common errors and enabling reproducibility. QwikMD meets also the needs of experts in the field, increasing the ...
While tRNA and aminoacyl-tRNA synthetases are classes of biomolecules that have been extensively studied for decades, the finer details of how they carry out their fundamental biological functions in protein synthesis remain a challenge. Recent molecular dynamics (MD) simulations are verifying experimental...
recently introduced methods, namely, MDSPACE and MDTOMO, to obtain continuous conformational landscapes of biomolecules by analyzing in vitro and in situ cryo-EM data (single particle images and subtomograms) based on molecular dynamics simulations of an available atomic model of one of the ...
JAX, MD is a research project that is currently under development. Expect sharp edges and possibly some API breaking changes as we continue to support a broader set of simulations. JAX MD is a functional and data driven library. Data is stored in arrays or tuples of arrays and functions tr...