Short-time Fourier transform analysis ofab initio molecular dynamics simulation: Collision reaction between CN and C4H6

2005 ◽  
Vol 26 (5) ◽  
pp. 436-442 ◽  
Author(s):  
Mari Tamaoki ◽  
Yusuke Yamauchi ◽  
Hiromi Nakai
Keyword(s):  
Molecular Dynamics ◽  
Fourier Transform ◽  
Molecular Dynamics Simulation ◽  
Dynamics Simulation ◽  
Short Time Fourier Transform ◽  
Short Time

scholarly journals Short-time correlations in liquids: Molecular-dynamics simulation of hard spheroids

1990 ◽  
Vol 65 (22) ◽  
pp. 2828-2831 ◽  
Author(s):  
Julian Talbot ◽  
Daniel Kivelson ◽  
Gilles Tarjus ◽  
Michael P. Allen ◽  
Glenn T. Evans ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Dynamics Simulation ◽  
Time Correlations ◽  
Short Time

scholarly journals Flavodoxin in a binary surfactant system consisting of the nonionic 1-decanoyl-rac-glycerol and the zwitterionic lauryldimethylamine-N-oxide: molecular dynamics simulation approach

2020 ◽  
Vol 12 ◽  
pp. 120004
Author(s):  
Behnaz Bazaziyan ◽  
Mohammad Reza Bozorgmehr ◽  
Mohammad Momen-Heravi ◽  
S. Ali Beyramabadi
Keyword(s):  
Molecular Dynamics ◽  
Diffusion Coefficient ◽  
Molecular Dynamics Simulation ◽  
Dynamics Simulation ◽  
Radius Of Gyration ◽  
Surfactant Mixture ◽  
Surfactant Mixtures ◽  
Protein Activity ◽  
Experimental Conditions ◽  
Short Time

Due to the short time constant of the spin-spin relaxation process, there is a limitation in the preparation of NMR sample solution for large proteins. To overcome this problem, reverse micelle systems are used.  Here, molecular dynamics simulation was used to study the structure of flavodoxin in a quaternary mixture of 1-decanoyl-rac-glycerol, lauryldimethylamine-N-oxide, pentane and hexanol.  Hexanol was used as co-solvent. Simulations were performed at three different co-solvent concentrations.  The proportion of components in the mixture was selected according to experimental conditions.  For comparison, simulation of flavodoxin in water was also performed.  The simulation results show that the C$$\alpha$$-RMSD for the protein in water is less than for the surfactant mixture.  Also, the radius of gyration of flavodoxin increased in the presence of surfactants.  The distance between the two residues trp-57 and phe-94, as a measure of protein activity, was obtained from the simulations.  The results showed that in the surfactant mixtures this distance increases.  Analysis of the secondary structure of the protein shows that the N-terminal part of the flavodoxin is more affected by surfactants.  The flavodoxin diffusion coefficient in the surfactant mixture decreased in relation to its diffusion coefficient in water.

scholarly journals Vibrational energy redistribution in crystalline nitromethane simulated by ab initio molecular dynamics

RSC Advances ◽  
2021 ◽  
Vol 11 (16) ◽  
pp. 9557-9567
Author(s):  
Meilin Lu ◽  
Zhaoyang Zheng ◽  
Gangbei Zhu ◽  
Yuxiao Wang ◽  
Yanqiang Yang
Keyword(s):  
Molecular Dynamics ◽  
Fourier Transform ◽  
Ab Initio ◽  
Vibrational Energy ◽  
Ab Initio Molecular Dynamics ◽  
Short Time Fourier Transform ◽  
Energy Redistribution ◽  
Mode Decomposition ◽  
Dynamics Simulations ◽  
Short Time

Ab initio molecular dynamics simulations (AIMD) are systematically performed to study the Vibrational Energy Redistribution (VER) in solid nitromethane (NM) by combining normal mode decomposition and short-time Fourier transform technique.

Sign in / Sign up

Export Citation Format

Share Document