scholarly journals Free energy profiles for penetration of methane and water molecules into spherical sodium dodecyl sulfate micelles obtained using the thermodynamic integration method combined with molecular dynamics calculations

2012 ◽  
Vol 136 (1) ◽  
pp. 014511 ◽  
Author(s):  
K. Fujimoto ◽  
N. Yoshii ◽  
S. Okazaki
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Sodium Dodecyl Sulfate ◽  
Integration Method ◽  
Sodium Dodecyl ◽  
Thermodynamic Integration ◽  
Water Molecules ◽  
Energy Profiles ◽  
Molecular Dynamics Calculations ◽  
Free Energy Profiles

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

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.

Unveiling conformational dynamics changes of H-Ras induced by mutations based on accelerated molecular dynamics

2020 ◽  
Vol 22 (37) ◽  
pp. 21238-21250
Author(s):  
Jianzhong Chen ◽  
Wei Wang ◽  
Laixue Pang ◽  
Weiliang Zhu
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Conformational Dynamics ◽  
Conformational Transformation ◽  
Accelerated Molecular Dynamics ◽  
Energy Profiles ◽  
Free Energy Profiles

The conformational transformation of two switches caused by mutations induces different free energy profiles of H-Ras.

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.

The molecular mechanism of ligand unbinding from the human telomeric G-quadruplex by steered molecular dynamics and umbrella sampling simulations

2015 ◽  
Vol 17 (19) ◽  
pp. 12857-12869 ◽  
Author(s):  
Jia-Kai Zhou ◽  
Dah-Yen Yang ◽  
Sheh-Yi Sheu
Keyword(s):  
Mechanical Properties ◽  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Mechanism ◽  
Steered Molecular Dynamics ◽  
Umbrella Sampling ◽  
Energy Profiles ◽  
G Quadruplex ◽  
Free Energy Profiles

The mechanical properties and kinetic pathways of the ligand BMVC unbinding from the G-quadruplex were investigated via the computation of free energy profiles.

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