A Classical Molecular Dynamics Study on the Effect of Si/Al Ratio and Silanol Nest Defects on Water Diffusion in Zeolite HY

2021 ◽  
Author(s):  
A. J. Porter ◽  
A. J. O’Malley
Keyword(s):  
Molecular Dynamics ◽  
Water Diffusion ◽  
Classical Molecular Dynamics

A Conserved Asparagine in a Ubiquitin Conjugating Enzyme Positions the Substrate for Nucleophilic Attack

2018 ◽  
Author(s):  
Walker M. Jones ◽  
Aaron G. Davis ◽  
R. Hunter Wilson ◽  
Katherine L. Elliott ◽  
Isaiah Sumner
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Molecular Mechanics ◽  
Reaction Rates ◽  
Nucleophilic Attack ◽  
Classical Molecular Dynamics ◽  
Ubiquitin Conjugating Enzyme ◽  
Conjugating Enzyme

We present classical molecular dynamics (MD), Born-Oppenheimer molecular dynamics (BOMD), and hybrid quantum mechanics/molecular mechanics (QM/MM) data. MD was performed using the GPU accelerated pmemd module of the AMBER14MD package. BOMD was performed using CP2K version 2.6. The reaction rates in BOMD were accelerated using the Metadynamics method. QM/MM was performed using ONIOM in the Gaussian09 suite of programs. Relevant input files for BOMD and QM/MM are available.

scholarly journals Ab initio molecular dynamics of hydrogen on tungsten surfaces

2021 ◽  
Author(s):  
Alberto Rodríguez-Fernández ◽  
Laurent Bonnet ◽  
Pascal Larrégaray ◽  
Ricardo Díez Muiño
Keyword(s):  
Molecular Dynamics ◽  
Density Functional Theory ◽  
Ab Initio ◽  
Density Functional ◽  
Ab Initio Molecular Dynamics ◽  
Dissociation Process ◽  
Functional Theory ◽  
Classical Molecular Dynamics ◽  
Hydrogen Molecules

The dissociation process of hydrogen molecules on W(110) was studied using density functional theory and classical molecular dynamics.

scholarly journals Unveiling the Interplay Between Diffusing CO2 and Ethanol Molecules in Champagne Wines by Classical Molecular Dynamics and 13C NMR Spectroscopy

2014 ◽  
Vol 5 (24) ◽  
pp. 4232-4237 ◽  
Author(s):  
David A. Bonhommeau ◽  
Alexandre Perret ◽  
Jean-Marc Nuzillard ◽  
Clara Cilindre ◽  
Thibaud Cours ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Nmr Spectroscopy ◽  
13C Nmr ◽  
13C Nmr Spectroscopy ◽  
Classical Molecular Dynamics

On the structure of biomedical silver-doped phosphate-based glasses from molecular dynamics simulations

2014 ◽  
Vol 16 (39) ◽  
pp. 21135-21143 ◽  
Author(s):  
Richard I. Ainsworth ◽  
Jamieson K. Christie ◽  
Nora H. de Leeuw
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
First Principles ◽  
Classical Molecular Dynamics ◽  
Dynamics Simulations

First-principles and classical molecular dynamics simulations have been carried out on undoped and silver-doped phosphate-based glasses with 50 mol% P2O5, 0–20 mol% Ag2O, and varying amounts of Na2O and CaO.

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