scholarly journals Adaptive-Partitioning QM/MM for Molecular Dynamics Simulations: 4. Proton Hopping in Bulk Water

2015 ◽  
Vol 11 (6) ◽  
pp. 2398-2411 ◽  
Author(s):  
Soroosh Pezeshki ◽  
Hai Lin
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Bulk Water ◽  
Adaptive Partitioning ◽  
Dynamics Simulations

Absorption of Mechanical Energy via Formation of Ice Nanotubes in Zeolite

2021 ◽  
Author(s):  
Kenji Mochizuki
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Heterogeneous System ◽  
Mechanical Energy ◽  
Bulk Water ◽  
Pure Silica ◽  
Dynamics Simulations ◽  
First Time

Abstract Molecular dynamics simulations are carried out for a heterogeneous system composed of bulk water and pure-silica zeolites of the AFI type. Our simulations show, for the first time, the...

Molecular dynamics simulations predict an accelerated dissociation of H2CO3 at the air–water interface

2014 ◽  
Vol 16 (46) ◽  
pp. 25573-25582 ◽  
Author(s):  
Mirza Galib ◽  
Gabriel Hanna
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Molecular Dynamics Simulations ◽  
Carbonic Acid ◽  
Bulk Water ◽  
Water Interface ◽  
Air Water Interface ◽  
Dynamics Simulations ◽  
Dissociation Barrier

Ab initio molecular dynamics simulations of carbonic acid (H2CO3) at the air–water interface yield a lower dissociation barrier than in bulk water.

scholarly journals Reactivity of an Excess Electron with Monovalent Cations in Bulk Water by Mixed Quantum Classical Molecular Dynamics Simulations

2004 ◽  
Vol 30 (11-12) ◽  
pp. 749-754 ◽  
Author(s):  
Riccardo Spezia ◽  
Cédric Nicolas ◽  
François-Xavier Coudert ◽  
Pierre Archirel ◽  
Rodolphe Vuilleumier ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Bulk Water ◽  
Excess Electron ◽  
Monovalent Cations ◽  
Classical Molecular Dynamics ◽  
Dynamics Simulations

Molecular dynamics simulations of the Ag+ or Na+ cation with an excess electron in bulk water

2004 ◽  
Vol 120 (11) ◽  
pp. 5261-5268 ◽  
Author(s):  
Riccardo Spezia ◽  
Cédric Nicolas ◽  
Pierre Archirel ◽  
Anne Boutin
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Bulk Water ◽  
Excess Electron ◽  
Dynamics Simulations

scholarly journals Molecular Dynamics Simulations of Electron−Alkali Cation Pairs in Bulk Water

2006 ◽  
Vol 110 (1) ◽  
pp. 607-615 ◽  
Author(s):  
François-Xavier Coudert ◽  
Pierre Archirel ◽  
Anne Boutin
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Bulk Water ◽  
Alkali Cation ◽  
Dynamics Simulations

Molecular dynamics study of wetting of alkanes on water: From high temperature to the supercooled region and the influence of second inflection points of interfacial tensions

2021 ◽  
Author(s):  
Pauf Neupane ◽  
Gerald Wilemski
Keyword(s):  
Molecular Dynamics ◽  
Surface Tension ◽  
High Temperature ◽  
Temperature Dependence ◽  
Molecular Dynamics Simulations ◽  
Bulk Water ◽  
Interfacial Tensions ◽  
Inflection Points ◽  
Dynamics Simulations ◽  
Supercooled Region

To explore the wetting behavior of alkanes on bulk water interfaces, molecular dynamics simulations were carried out to determine the temperature dependence of (1) the surface tension of alkanes (octane,...

Adaptive Partitioning QM/MM for Molecular Dynamics Simulations: 6. Proton Transport through a Biological Channel

2019 ◽  
Vol 15 (2) ◽  
pp. 892-905 ◽  
Author(s):  
Adam W. Duster ◽  
Christina M. Garza ◽  
Baris O. Aydintug ◽  
Mikias B. Negussie ◽  
Hai Lin
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Proton Transport ◽  
Adaptive Partitioning ◽  
Dynamics Simulations

scholarly journals Adaptive QM/MM for Molecular Dynamics Simulations: 5. On the Energy-Conserved Permuted Adaptive-Partitioning Schemes

Molecules ◽  
2018 ◽  
Vol 23 (9) ◽  
pp. 2170 ◽  
Author(s):  
Adam Duster ◽  
Chun-Hung Wang ◽  
Hai Lin
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Model System ◽  
Water Model ◽  
Quantum Mechanical ◽  
Many Body ◽  
Adaptive Partitioning ◽  
Pap Method ◽  
Dynamics Simulations

In combined quantum-mechanical/molecular-mechanical (QM/MM) dynamics simulations, the adaptive-partitioning (AP) schemes reclassify atoms on-the-fly as QM or MM in a smooth manner. This yields a mobile QM subsystem with contents that are continuously updated as needed. Here, we tailor the Hamiltonian adaptive many-body correction (HAMBC) proposed by Boreboom et al. [J. Chem. Theory Comput. 2016, 12, 3441] to the permuted AP (PAP) scheme. The treatments lead to the HAMBC-PAP method (HPAP), which both conserves energy and produces accurate solvation structures in the test of “water-in-water” model system.

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