Instantaneous normal mode analysis for intermolecular and intramolecular vibrations of water from atomic point of view

2013 ◽  
Vol 139 (20) ◽  
pp. 204505 ◽  
Author(s):  
Yu-Chun Chen ◽  
Ping-Han Tang ◽  
Ten-Ming Wu
Keyword(s):  
Normal Mode ◽  
Normal Mode Analysis ◽  
Point Of View ◽  
Mode Analysis ◽  
Instantaneous Normal Mode ◽  
Intramolecular Vibrations

Instantaneous normal mode analysis of hydrated electron solvation dynamics

2001 ◽  
Vol 114 (8) ◽  
pp. 3598-3611 ◽  
Author(s):  
Chao-Yie Yang ◽  
Kim F. Wong ◽  
Munir S. Skaf ◽  
Peter J. Rossky
Keyword(s):  
Normal Mode ◽  
Normal Mode Analysis ◽  
Hydrated Electron ◽  
Mode Analysis ◽  
Solvation Dynamics ◽  
Electron Solvation ◽  
Instantaneous Normal Mode

scholarly journals ProMode-Oligomer: Database of Normal Mode Analysis in Dihedral Angle Space for a Full-Atom System of Oligomeric Proteins

2012 ◽  
Vol 6 (1) ◽  
pp. 9-19 ◽  
Author(s):  
Hiroshi Wako ◽  
Shigeru Endo
Keyword(s):  
Normal Mode ◽  
Protein Complexes ◽  
Normal Mode Analysis ◽  
Normal Modes ◽  
Point Of View ◽  
Mode Analysis ◽  
Dihedral Angles ◽  
Oligomeric Proteins ◽  
Displacement Vectors ◽  
Atom System

The database ProMode-Oligomer (http://promode.socs.waseda.ac.jp/promode_oligomer) was constructed by collecting normal-mode-analysis (NMA) results for oligomeric proteins including protein-protein complexes. As in the ProMode database developed earlier for monomers and individual subunits of oligomers (Bioinformatics vol. 20, pp. 2035–2043, 2004), NMA was performed for a full-atom system using dihedral angles as independent variables, and we released the results (fluctuations of atoms, fluctuations of dihedral angles, correlations between atomic fluctuations, etc.). The vibrating oligomer is visualized by animation in an interactive molecular viewer for each of the 20 lowest-frequency normal modes. In addition, displacement vectors of constituent atoms for each normal mode were decomposed into two characteristic motions in individual subunits, i.e., internal and external (deformation and rigid-body movements of the individual subunits, respectively), and then the mutual movements of the subunits and the movement of atoms around the interface regions were investigated. These results released in ProMode-Oligomer are useful for characterizing oligomeric proteins from a dynamic point of view. The analyses are illustrated with immunoglobulin light- and heavy-chain variable domains bound to lysozyme and to a 12-residue peptide.

Dynamics of Rare Gases in Zeolites: Instantaneous Normal Mode Analysis

1999 ◽  
Vol 103 (14) ◽  
pp. 2740-2748 ◽  
Author(s):  
Vishal Mehra ◽  
Ritu Basra ◽  
Monika Khanna ◽  
Charusita Chakravarty
Keyword(s):  
Normal Mode ◽  
Normal Mode Analysis ◽  
Mode Analysis ◽  
Rare Gases ◽  
Instantaneous Normal Mode

scholarly journals Instantaneous Normal Mode Analysis of Supercooled Water

2000 ◽  
Vol 84 (20) ◽  
pp. 4605-4608 ◽  
Author(s):  
E. La Nave ◽  
A. Scala ◽  
F. W. Starr ◽  
F. Sciortino ◽  
H. E. Stanley
Keyword(s):  
Normal Mode ◽  
Normal Mode Analysis ◽  
Supercooled Water ◽  
Mode Analysis ◽  
Instantaneous Normal Mode
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