Free-Energy Profiles for A-/B-DNA Conformational Transitions in Isolated and Aggregated States from All-Atom Molecular Dynamics Simulation

2018 ◽  
Vol 122 (33) ◽  
pp. 7990-7996 ◽  
Author(s):  
Cheng-Tsung Lai ◽  
George C. Schatz
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulation ◽  
Conformational Transitions ◽  
Dynamics Simulation ◽  
Energy Profiles ◽  
Free Energy Profiles

Energetics of nonpolar and polar compounds in cationic, anionic, and nonionic micelles studied by all-atom molecular dynamics simulation combined with a theory of solutions

2016 ◽  
Vol 18 (19) ◽  
pp. 13223-13231 ◽  
Author(s):  
Atsushi Date ◽  
Ryosuke Ishizuka ◽  
Nobuyuki Matubayasi
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulation ◽  
Polar Compounds ◽  
Dynamics Simulation ◽  
Energy Profiles ◽  
Polar Solutes ◽  
Free Energy Profiles

Free-energy profiles of binding nonpolar and polar solutes in cationic, anionic, and nonionic micelles.

Li deposition and desolvation with electron transfer at a silicon/propylene-carbonate interface: transition-state and free-energy profiles by large-scale first-principles molecular dynamics

2018 ◽  
Vol 20 (17) ◽  
pp. 11586-11591 ◽  
Author(s):  
Tsukuru Ohwaki ◽  
Taisuke Ozaki ◽  
Yukihiro Okuno ◽  
Tamio Ikeshoji ◽  
Hideto Imai ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
First Principles ◽  
Large Scale ◽  
Dynamics Simulation ◽  
Charge Transfer Process ◽  
Energy Profiles ◽  
Process Coupling ◽  
Free Energy Profiles ◽  
First Principles Molecular Dynamics

We report the result of a large-scale first-principles molecular dynamics simulation under different electric biases performed to understand the charge transfer process coupling with lithium deposition and desolvation processes.

scholarly journals Free Energy Profile of APOBEC3G Protein Calculated by a Molecular Dynamics Simulation

Biology ◽  
2012 ◽  
Vol 1 (2) ◽  
pp. 245-259
Author(s):  
Yoshifumi Fukunishi ◽  
Saki Hongo ◽  
Masami Lintuluoto ◽  
Hiroshi Matsuo
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulation ◽  
Dynamics Simulation ◽  
Energy Profile ◽  
Free Energy Profile

On the use of the adiabatic molecular dynamics technique in the calculation of free energy profiles

2002 ◽  
Vol 116 (11) ◽  
pp. 4389-4402 ◽  
Author(s):  
Lula Rosso ◽  
Peter Mináry ◽  
Zhongwei Zhu ◽  
Mark E. Tuckerman
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Energy Profiles ◽  
Free Energy Profiles
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