Are classical molecular dynamics calculations accurate for state-to-state transition probabilities in the atomic hydrogen + deuterium reaction?

1990 ◽  
Vol 94 (17) ◽  
pp. 6696-6706 ◽  
Author(s):  
Meishan. Zhao ◽  
Donald G. Truhlar ◽  
Normand C. Blais ◽  
David W. Schwenke ◽  
Donald J. Kouri
Keyword(s):  
Molecular Dynamics ◽  
Atomic Hydrogen ◽  
State Transition ◽  
Transition Probabilities ◽  
Classical Molecular Dynamics ◽  
Molecular Dynamics Calculations ◽  
Hydrogen Deuterium

How to accurately model IR spectra of nanosized silicate grains

2019 ◽  
Vol 15 (S350) ◽  
pp. 431-433
Author(s):  
Joan Mariñoso Guiu ◽  
Antoni Macià ◽  
Stefan T. Bromley
Keyword(s):  
Molecular Dynamics ◽  
Ir Spectra ◽  
Density Functional ◽  
Effect Of Temperature ◽  
Chemical Compositions ◽  
Functional Theory ◽  
Classical Molecular Dynamics ◽  
Molecular Dynamics Calculations ◽  
Harmonic Oscillator Approximation ◽  
Dynamics Simulations

AbstractWe assess the accuracy of various computational methods for obtaining infrared (IR) spectra of nanosized silicate dust grains directly from their atomistic structure and atomic motions. First, IR spectra for a selection of small nanosilicate clusters with a range of sizes and chemical compositions are obtained within the harmonic oscillator approximation employing density functional theory (DFT) based quantum chemical calculations. To check if anharmonic effects play a significant role in the IR spectra of these nanoclusters, we further obtain their IR spectra from finite temperature DFT-based ab initio molecular dynamics (AIMD). Finally, we also study the effect of temperature on the broadening of the obtained IR spectra peaks in larger nanosilicate grains with a range of crystallinities. In this case, less computationally costly classical molecular dynamics simulations are necessary due to the large number of atoms involved. Generally, we find that although DFT-based methods are more accurate, surprisingly good IR spectra can also be obtained from classical molecular dynamics calculations.

Modeling Radiation Effects on the Fracture Process in Simplified Nuclear Glass

2011 ◽  
Vol 488-489 ◽  
pp. 154-157 ◽  
Author(s):  
Le Hai Kieu ◽  
Jean Marc Delaye ◽  
Claude Stolz
Keyword(s):  
Molecular Dynamics ◽  
Fracture Toughness ◽  
Young’S Modulus ◽  
Radiation Effects ◽  
Fracture Process ◽  
Elastic Limit ◽  
Young's Modulus ◽  
Fracture Mechanisms ◽  
Classical Molecular Dynamics ◽  
Molecular Dynamics Calculations

Experimentally, the evolution of several mechanic properties (hardness, density, Young’s modulus, fracture toughness) is observed in nuclear glasses under irradiation. In this work, classical molecular dynamics calculations are performed to better understand fracture mechanisms in simplified nuclear glasses at atomistic scale and to explain the radiation effects. Fractures are simulated in more disordered glasses, representative of irradiated samples, to reveal radiation effects. We observe a lower elastic limit and a greater plasticity in the irradiated glass that can explain its larger fracture toughness.

MOLECULAR DYNAMICS CALCULATIONS OF NEAR-CRITICAL LIQUID OXYGEN DROPLET SURFACE TENSION

2005 ◽  
Vol 15 (4) ◽  
pp. 413-422 ◽  
Author(s):  
Michael M. Micci ◽  
S. J. Lee ◽  
B. Vieille ◽  
C. Chauveau ◽  
Iskendar Gokalp
Keyword(s):  
Molecular Dynamics ◽  
Surface Tension ◽  
Droplet Surface ◽  
Liquid Oxygen ◽  
Molecular Dynamics Calculations

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.

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