Modeling Methods, Molecular Dynamics, Computational Models and Computer
Simulations of Molecular Systems:
Contents:
Articles
1
Molecular Modeling Methods 2
Molecular Modeling 2
Quantum field theory 6
Local quantum field theory 18
Physical chemistry 19
Chemical physics 21
Computational chemistry 22
''n''- body problem 29
Hartree--Fock method 34
Mean field theory 41
Landau theory 43
Flory--“Huggins solution theory 45
Scheutjens- Fleer theory 48
Molecular graphics 48
VRML 58
Molecular design software 61
Computational chemistry 64
Theoretical Quantum Chemistry 71
Quantum chemistry 71
Molecular orbital theory 75
Generalized valence bond 78
Moeller--Plesset perturbation theory 79
List of quantum chemistry and solid state physics software 83
International Academy of Quantum Molecular Science 86
Molecular Dynamics, Theories and Computational Methods 90
Classical mechanics 90
Newton's laws of motion 101
Analytical dynamics 110
Force Fields 112
Molecular mechanics 119
Molecular dynamics 124
NAnoscale Molecular Dynamics 136
CHARMM 138
Charm+ + 142
Assisted Model Building with Energy Refinement 143
Optimized Potentials for Liquid Simulations 146
Abalone (molecular mechanics) 147
Statistical mechanics 148
Statistical field theory 159
Mathematical chemistry 160
Monte Carlo method 161
Quantum Monte Carlo 171
Dynamics of Markovian particles 174
Molecular Modeling Applications to Complex Biomolecules 175
Protein structure prediction 175
Protein folding 182
Protein design 188
Homology modeling 191
Loop modeling 198
MODELLER 199
Molecular models of DNA 200
List of nucleic acid simulation software 213
Molecular Networks and Complex Molecule Dynamics 215
Topological dynamics 215
Proteomics 216
List of protein structure prediction software 222
Protein- DNA interaction site predictor 225
DNA Dynamics 227
DNA nanotechnology 240
Molecular self- assembly 249
Interactome 252
Cell signaling 254
Molecular evolution 260
Molecular phylogenetics 263
Computational phylogenetics 266
References
Article Sources and Contributors 274
Image Sources, Licenses and Contributors 278
Article Licenses
License 280
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contributors listed before the License Statement.
http://en.wikipedia.org/wiki/User:Bci2/Books/Molecular_Modeling_and_Dynamics
Copyright@2009-2010 bci1 and Bci2 : Copyright statement:
Permission is granted to copy, distribute and/or modify
this document under the terms of the GNU Free
Documentation License, Version 1.2 or any later version
;published by the Free Software Foundation, with no
Invariant Sections, no Front-Cover Texts, and no Back-
Cover Texts. A copy of the license is included in the
section entitled "GNU Free Documentation License". Edited
by Bci2, with all contributors listed before the License
statement.
