MoSDeF-GOMC: Python Software for the Creation of Scientific Workflows for the Monte Carlo Simulation Engine GOMC.

Autor: Crawford B; Department of Chemical Engineering, Wayne State University, Detroit, Michigan 48202-4050, United States., Timalsina U; Institute for Software Integrated Systems (ISIS), Vanderbilt University, Nashville, Tennessee 37212, United States., Quach CD; Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37235-1604, United States.; Multiscale Modeling and Simulation (MuMS) Center, Vanderbilt University, Nashville, Tennessee 37212, United States., Craven NC; Multiscale Modeling and Simulation (MuMS) Center, Vanderbilt University, Nashville, Tennessee 37212, United States.; Interdisciplinary Material Science Program, Vanderbilt University, Nashville, Tennessee 37235-0106, United States., Gilmer JB; Multiscale Modeling and Simulation (MuMS) Center, Vanderbilt University, Nashville, Tennessee 37212, United States.; Interdisciplinary Material Science Program, Vanderbilt University, Nashville, Tennessee 37235-0106, United States., McCabe C; Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37235-1604, United States.; Multiscale Modeling and Simulation (MuMS) Center, Vanderbilt University, Nashville, Tennessee 37212, United States., Cummings PT; Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37235-1604, United States.; Multiscale Modeling and Simulation (MuMS) Center, Vanderbilt University, Nashville, Tennessee 37212, United States., Potoff JJ; Department of Chemical Engineering, Wayne State University, Detroit, Michigan 48202-4050, United States.

Publikováno v: Journal of chemical information and modeling [J Chem Inf Model] 2023 Feb 27; Vol. 63 (4), pp. 1218-1228. Date of Electronic Publication: 2023 Feb 15.

Examining the self-assembly of patchy alkane-grafted silica nanoparticles using molecular simulation.

Autor: Craven NC; Interdisciplinary Materials Science Program, Vanderbilt University, Nashville, Tennessee 37235, USA., Gilmer JB; Interdisciplinary Materials Science Program, Vanderbilt University, Nashville, Tennessee 37235, USA., Spindel CJ; Multiscale Modeling and Simulation (MuMS) Center, Vanderbilt University, Nashville, Tennessee 37235, USA., Summers AZ; Multiscale Modeling and Simulation (MuMS) Center, Vanderbilt University, Nashville, Tennessee 37235, USA., Iacovella CR; Multiscale Modeling and Simulation (MuMS) Center, Vanderbilt University, Nashville, Tennessee 37235, USA., McCabe C; Multiscale Modeling and Simulation (MuMS) Center, Vanderbilt University, Nashville, Tennessee 37235, USA.

Publikováno v: The Journal of chemical physics [J Chem Phys] 2021 Jan 21; Vol. 154 (3), pp. 034903.

Towards Molecular Simulations that are Transparent, Reproducible, Usable By Others, and Extensible (TRUE).

Autor: Thompson MW; Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA.; Multiscale Modeling and Simulation Center, Vanderbilt University, Nashville, TN, USA., Gilmer JB; Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA.; Multiscale Modeling and Simulation Center, Vanderbilt University, Nashville, TN, USA., Matsumoto RA; Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA.; Multiscale Modeling and Simulation Center, Vanderbilt University, Nashville, TN, USA., Quach CD; Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA.; Multiscale Modeling and Simulation Center, Vanderbilt University, Nashville, TN, USA., Shamaprasad P; Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA.; Multiscale Modeling and Simulation Center, Vanderbilt University, Nashville, TN, USA., Yang AH; Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA.; Multiscale Modeling and Simulation Center, Vanderbilt University, Nashville, TN, USA., Iacovella CR; Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA.; Multiscale Modeling and Simulation Center, Vanderbilt University, Nashville, TN, USA., Cabe CM; Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA.; Multiscale Modeling and Simulation Center, Vanderbilt University, Nashville, TN, USA., Cummings PT; Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA.; Multiscale Modeling and Simulation Center, Vanderbilt University, Nashville, TN, USA.

Publikováno v: Molecular physics [Mol Phys] 2020; Vol. 118 (9-10). Date of Electronic Publication: 2020 Apr 08.

Using interactive Jupyter Notebooks and BioConda for FAIR and reproducible biomolecular simulation workflows.

Autor: Bayarri, Genís¹ (AUTHOR), Andrio, Pau² (AUTHOR), Gelpí, Josep Lluís^2,3 (AUTHOR), Hospital, Adam¹ (AUTHOR) adam.hospital@irbbarcelona.org, Orozco, Modesto^1,3 (AUTHOR) adam.hospital@irbbarcelona.org

Publikováno v: PLoS Computational Biology. 6/20/2024, Vol. 20 Issue 6, p1-14. 14p.

Contributions of Molecular Dynamics Simulations to Elastohydrodynamic Lubrication.

Autor: Ewen, James P., Spikes, Hugh A., Dini, Daniele

Publikováno v: Tribology Letters; 2021, Vol. 69 Issue 1, p1-19, 19p