Photophysics of BODIPY-Based Photosensitizer for Photodynamic Therapy: Surface Hopping and Classical Molecular Dynamics

2019 ◽  
Vol 15 (9) ◽  
pp. 5046-5057 ◽  
Author(s):  
Marek Pederzoli ◽  
Mirza Wasif Baig ◽  
Mojmír Kývala ◽  
Jiří Pittner ◽  
Lukasz Cwiklik
Keyword(s):  
Molecular Dynamics ◽  
Photodynamic Therapy ◽  
Surface Hopping ◽  
Classical Molecular Dynamics

scholarly journals Bodipy-Based Photosensitizer for Photodynamic Therapy - Photophysics and Membrane Localisation Via Classical Molecular Dynamics and Surface Hopping

2020 ◽  
Vol 118 (3) ◽  
pp. 79a
Author(s):  
Lukasz Cwiklik ◽  
Marek Pederzoli ◽  
Mirza Wasif Baig ◽  
Mojmír Kývala ◽  
Jiří Jiří Pittner
Keyword(s):  
Molecular Dynamics ◽  
Photodynamic Therapy ◽  
Surface Hopping ◽  
Classical Molecular Dynamics

Evaluation of Mixed Quantum-Classical Molecular Dynamics on cis‐Azobenzene Photoisomerization

2021 ◽  
Author(s):  
Diandong Tang ◽  
Lin Shen ◽  
Wei-hai Fang
Keyword(s):  
Molecular Dynamics ◽  
Electronic State ◽  
Quantitative Prediction ◽  
Surface Hopping ◽  
Ultrafast Processes ◽  
Nonadiabatic Transitions ◽  
Classical Molecular Dynamics ◽  
Molecular Dynamics Methods

The quantitative prediction on nonadiabatic transitions between different electronic state is important to understand ultrafast processes in photochemistry. A variety of mixed quantum-classical molecular dynamics methods such as surface hopping...

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.

Nonadiabatic molecular dynamics simulation for the ultrafast photoisomerization of dMe-OMe-NAIP based on TDDFT on-the-fly potential energy surfaces

2021 ◽  
Vol 23 (9) ◽  
pp. 5236-5243
Author(s):  
Ying Hu ◽  
Chao Xu ◽  
Linfeng Ye ◽  
Feng Long Gu ◽  
Chaoyuan Zhu
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Potential Energy ◽  
Potential Energy Surfaces ◽  
Dynamics Simulation ◽  
Surface Hopping ◽  
Nonadiabatic Molecular Dynamics ◽  
Energy Surfaces

Global switching on-the-fly trajectory surface hopping molecular dynamics simulation was performed on the accurate TD-B3LYP/6-31G* potential energy surfaces for E-to-Z and Z-to-E photoisomerization of dMe-OMe-NAIP up to S1(ππ*) excitation.

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
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