Free energy and structure of polyproline peptides: An ab initio and classical molecular dynamics investigation

2010 ◽  
Vol 110 (15) ◽  
pp. 2865-2879 ◽  
Author(s):  
Mahmoud Moradi ◽  
Jung-Goo Lee ◽  
Volodymyr Babin ◽  
Christopher Roland ◽  
Celeste Sagui
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Ab Initio ◽  
Classical Molecular Dynamics

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.

Combined ab initio and classical molecular dynamics simulations of alkyl-lithium aggregates in ethereal solutions

2008 ◽  
Vol 121 (5-6) ◽  
pp. 321-326 ◽  
Author(s):  
Hassan K. Khartabil ◽  
Marilia T. C. Martins-Costa ◽  
Philippe C. Gros ◽  
Yves Fort ◽  
Manuel F. Ruiz-López
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Molecular Dynamics Simulations ◽  
Classical Molecular Dynamics ◽  
Dynamics Simulations

Structure of layered C60 on Si(100) surface studied by ab initio and classical molecular dynamics simulations

1993 ◽  
Vol 19 (1-2) ◽  
pp. 165-171 ◽  
Author(s):  
Yoshiyuki Kawazoe ◽  
Yutaka Maruyama ◽  
Hashem Rafii-Tabar ◽  
Makoto Ikeda ◽  
Hiroshi Kamiyama ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Molecular Dynamics Simulations ◽  
Classical Molecular Dynamics ◽  
Dynamics Simulations

scholarly journals Molecular dynamics and charge transport in organic semiconductors: a classical approach to modeling electron transfer

2017 ◽  
Vol 8 (4) ◽  
pp. 2597-2609 ◽  
Author(s):  
Kenley M. Pelzer ◽  
Álvaro Vázquez-Mayagoitia ◽  
Laura E. Ratcliff ◽  
Sergei Tretiak ◽  
Raymond A. Bair ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Electron Transfer ◽  
Charge Transfer ◽  
Charge Transport ◽  
Ab Initio ◽  
Organic Semiconductors ◽  
Multiscale Approach ◽  
Classical Approach ◽  
Classical Molecular Dynamics

Using ab initio calculations of charges in PCBM fullerenes, a multiscale approach applies classical molecular dynamics to model charge transfer.

Classical versus ab initio structural relaxation: electronic excitations and optical properties of Ge nanocrystals embedded in a SiC matrix

2004 ◽  
Vol 832 ◽  
Author(s):  
Giancarlo Cappellini ◽  
H.-Ch. Weissker ◽  
D. De Salvator ◽  
J. Furthmüller ◽  
F. Bechstedt ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Optical Properties ◽  
Ab Initio ◽  
First Principles ◽  
Electronic Excitation ◽  
First Principle ◽  
Electronic Excitations ◽  
Combined Method ◽  
Classical Molecular Dynamics ◽  
Ge Nanocrystals

ABSTRACTWe discuss and test a combined method to efficiently perform ground- and excited-state calculations for relaxed structures using both a quantum first-principles approach and a classical molecular-dynamics scheme. We apply this method to calculate the ground state, the optical properties, and the electronic excitations of Ge nanoparticles embedded in a cubic SiC matrix. Classical molecular dynamics is used to relax the large-supercell system. First-principles quantum techniques are then used to calculate the electronic structure and, in turn, the electronic excitation and optical properties. The proposed procedure is tested with data resulting from a full first-principles scheme. The agreement is quantitatively discussed between the results after the two computational paths with respect to the structure, the optical properties, and the electronic excitations. The combined method is shown to be applicable to embedded nanocrystals in large simulation cells for which the first-principle treatment of the ionic relaxation is presently out of reach, whereas the electronic, optical and excitation properties can already be obtained ab initio. The errors incurred from the relaxed structure are found to be non-negligible but controllable.

Displacement of carbonates in Ca2UO2(CO3)3 by amidoxime-based ligands from free-energy simulations

2018 ◽  
Vol 47 (5) ◽  
pp. 1604-1613 ◽  
Author(s):  
Bo Li ◽  
Chad Priest ◽  
De-en Jiang
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulations ◽  
Umbrella Sampling ◽  
Nacl Solution ◽  
Classical Molecular Dynamics ◽  
Energy Profiles ◽  
Energy Simulations ◽  
Dynamics Simulations ◽  
Free Energy Profiles

Classical molecular dynamics simulations coupled with umbrella sampling reveal the atomistic processes and free-energy profiles of the displacement of carbonate groups in the Ca2UO2(CO3)3 complex by amidoxime-based ligands in a 0.5 M NaCl solution.

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