Free Energy Profile of NaCl in Water: First-Principles Molecular Dynamics with SCAN and ωB97X-V Exchange–Correlation Functionals

2018 ◽  
Vol 14 (2) ◽  
pp. 884-893 ◽  
Author(s):  
Yi Yao ◽  
Yosuke Kanai
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
First Principles ◽  
Energy Profile ◽  
Free Energy Profile ◽  
Exchange Correlation ◽  
First Principles Molecular Dynamics

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

scholarly journals Molecular dynamics simulations and free energy profile of Paracetamol in DPPC and DMPC lipid bilayers

2014 ◽  
Vol 126 (3) ◽  
pp. 637-647 ◽  
Author(s):  
YOUSEF NADEMI ◽  
SEPIDEH AMJAD IRANAGH ◽  
ABBAS YOUSEFPOUR ◽  
SEYEDEH ZAHRA MOUSAVI ◽  
HAMID MODARRESS
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulations ◽  
Lipid Bilayers ◽  
Energy Profile ◽  
Free Energy Profile ◽  
Dynamics Simulations

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.

Energy versus free-energy conservation in first-principles molecular dynamics

1992 ◽  
Vol 45 (19) ◽  
pp. 11372-11374 ◽  
Author(s):  
Renata M. Wentzcovitch ◽  
José Luís Martins ◽  
Philip B. Allen
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Energy Conservation ◽  
First Principles ◽  
First Principles Molecular Dynamics

scholarly journals The transition mechanism of DNA overstretching: a microscopic view using molecular dynamics

2014 ◽  
Vol 11 (97) ◽  
pp. 20140399 ◽  
Author(s):  
L. Bongini ◽  
V. Lombardi ◽  
P. Bianco
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Average Distance ◽  
Sampling Technique ◽  
Energy Difference ◽  
Umbrella Sampling ◽  
Energy Profile ◽  
Structural Explanation ◽  
Free Energy Profile ◽  
Transition Mechanism

The overstretching transition in torsionally unconstrained DNA is studied by means of atomistic molecular dynamics simulations. The free-energy profile as a function of the length of the molecule is determined through the umbrella sampling technique providing both a thermodynamic and a structural characterization of the transition pathway. The zero-force free-energy profile is monotonic but, in accordance with recent experimental evidence, becomes two-state at high forces. A number of experimental results are satisfactorily predicted: (i) the entropic and enthalpic contributions to the free-energy difference between the basic (B) state and the extended (S) state; (ii) the longitudinal extension of the transition state and (iii) the enthalpic contribution to the transition barrier. A structural explanation of the experimental finding that overstretching is a cooperative reaction characterized by elementary units of approximately 22 base pairs is found in the average distance between adenine/thymine-rich regions along the molecule. The overstretched DNA adopts a highly dynamical and structurally disordered double-stranded conformation which is characterized by residual base pairing, formation of non-native intra-strand hydrogen bonds and effective hydrophobic screening of apolar regions.

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