scholarly journals Hydrogen Inter-Cage Hopping and Cage Occupancies inside Hydrogen Hydrate: Molecular-Dynamics Analysis

2020 ◽  
Vol 11 (1) ◽  
pp. 282
Author(s):  
Yogeshwaran Krishnan ◽  
Mohammad Reza Ghaani ◽  
Arnaud Desmedt ◽  
Niall J. English
Keyword(s):  
Molecular Dynamics ◽  
Energy Barrier ◽  
Guest Molecule ◽  
Arrhenius Equation ◽  
Dynamics Simulation ◽  
Type Ii ◽  
Large Cage ◽  
Guest Molecules ◽  
Simulation Time ◽  
Average Occupancy

The inter-cage hopping in a type II clathrate hydrate with different numbers of H2 and D2 molecules, from 1 to 4 molecules per large cage, was studied using a classical molecular dynamics simulation at temperatures of 80 to 240 K. We present the results for the diffusion of these guest molecules (H2 or D2) at all of the different occupations and temperatures, and we also calculated the activation energy as the energy barrier for the diffusion using the Arrhenius equation. The average occupancy number over the simulation time showed that the structures with double and triple large-cage H2 occupancy appeared to be the most stable, while the small cages remained with only one guest molecule. A Markov model was also calculated based on the number of transitions between the different cage types.

Nano-Indentation Simulation Study Based on Parallel Computing

2012 ◽  
Vol 500 ◽  
pp. 696-701
Author(s):  
Ying Zhu ◽  
Sen Song ◽  
Ling Ling Xie ◽  
Shun He Qi ◽  
Qian Qian Liu
Keyword(s):  
Molecular Dynamics ◽  
Parallel Computing ◽  
Molecular Dynamics Simulation ◽  
Large Scale ◽  
Dynamics Simulation ◽  
Parallel Computer ◽  
Nano Indentation ◽  
Simulation Results ◽  
The Impact ◽  
Simulation Time

This method of parallel computing into nanoindentation molecular dynamics simulation (MDS), the author uses a nine-node parallel computer and takes the single crystal aluminum as the experimental example, to implement the large-scale process simulation of nanoindentation. Compared the simulation results with experimental results is to verify the reliability of the simulation. The method improves the computational efficiency and shortens the simulation time and the expansion of scale simulation can significantly reduce the impact of boundary conditions, effectively improve the accuracy of the molecular dynamics simulation of nanoindentation.

Molecular dynamics simulation study of cyclohexane guest molecules in the cyclohexane/thiourea inclusion compound

2000 ◽  
Vol 261 (1-2) ◽  
pp. 125-135 ◽  
Author(s):  
Jean-Christophe Soetens ◽  
Arnaud Desmedt ◽  
François Guillaume ◽  
Kenneth D.M. Harris
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Simulation Study ◽  
Inclusion Compound ◽  
Dynamics Simulation ◽  
Guest Molecules

Molecular dynamics simulation studies of hyperbranched polyglycerols and their encapsulation behaviors of small drug molecules

2016 ◽  
Vol 18 (32) ◽  
pp. 22446-22457 ◽  
Author(s):  
Chunyang Yu ◽  
Li Ma ◽  
Ke Li ◽  
Shanlong Li ◽  
Yannan Liu ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Computer Simulation ◽  
Molecular Dynamics Simulation ◽  
Dynamics Simulation ◽  
Simulation Studies ◽  
Guest Molecules ◽  
Drug Molecules

Computer simulation could disclose more details about the conformations of HPGs and their encapsulation behaviors of guest molecules.

scholarly journals Molecular Dynamics Simulation Studies of p-Xylene in OH-free Si-MCM-41

2005 ◽  
Vol 60 (11-12) ◽  
pp. 805-813 ◽  
Author(s):  
Tanin Nanok ◽  
Philippe A. Bopp ◽  
Jumras Limtrakul
Keyword(s):  
Molecular Dynamics ◽  
Electrostatic Interactions ◽  
Zeolite Catalysts ◽  
Van Der Waals Interactions ◽  
Dynamics Simulation ◽  
Guest Molecules ◽  
Self Diffusion ◽  
Order Of Magnitude ◽  
Average Potential Energy ◽  
Mcm 41

We report on modeling efforts and molecular dynamics computer simulations of the structure and self-diffusion of p-xylene in OH-free Si-MCM-41 as a function of loading. Both the guest molecules and Si-MCM-41 are modeled as flexible entities. With this newly developped intermolecular force field the average potential energy of p-xylene in the pore increases with increasing loading. The adsorption of p-xylene in MCM-41 is primarily associated with the van der Waals interactions of the model, whereas the contribution from electrostatic interactions is relatively small (about 2 kcal/mol), in accordance with other aromatic hydrocarbons adsorbed in zeolite catalysts. The calculated selfdiffusion coefficients of p-xylene in Si-MCM-41 are well comparable with diffusion coefficients of pyridine in MCM-41 and of the same order of magnitude as in liquid p-xylene. Increasing the loading results in non-negligible mutual p-xylene interaction, thus leading to a decrease of the self-diffusion coefficient.

Ab Initio Molecular Dynamics Study of Plutonium (IV) Solvation

2012 ◽  
Vol 1475 ◽  
Author(s):  
Ian Kirker ◽  
Nikolas Kaltsoyannis
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Ab Initio ◽  
Gas Phase ◽  
Conclusive Evidence ◽  
Dynamics Simulation ◽  
Ab Initio Molecular Dynamics ◽  
Simulated Environment ◽  
Water Hydrolysis ◽  
Simulation Time

ABSTRACTGas phase-optimized structures are used to assemble an ab initio molecular dynamics simulation of plutonium (IV) solvated in water. Hydrolysis is observed, and results are compared to experimental EXAFS data.While simulation time is insufficient to be conclusive, evidence suggests that the 7-coordinate singly-hydrolysed complex, [Pu (OH) (OH2)6]3+, is most stable in our simulated environment. Energetic differences between the gas-phase optimised structure and the prevalent dynamic simulation structure are shown to be relatively small.

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