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Contents

Preface ..............................................................................VII
Authors .............................................................................IX

PART - M:
An Introduction to Classical Molecular Dynamics ......... 1
Classical Molecular Mechanics (MM) .................................... 5
Quantum Mechanics (QM) .................................................... 9
Force Fields (FF) ................................................................ 11
Bond and non-bond interactions ........................................ 13
Numerical integration (Verlet) ............................................. 20
Control of system variables: Thermostats and barostats ...... 21
Applications ....................................................................... 23
APPENDIX M-A: Molecular Dynamics Laboratory
(by GROMACS) ................................................ 33

PART - K:
An Introduction to Classical Kinetic Theory ............... 49
Probability and Probability Density Function (PDF) ............. 53
Maxwell-Boltzmann PDF for the kinetic energy (1D) ............ 57
Maxwell-Boltzmann PDF for the velocity vector (3D) ............ 59
Maxwell-Boltzmann equilibrium distribution function (6D) .. 61
Changing paradigm: relaxation towards equilibrium ........... 62
Bhatnagar–Gross–Krook (BGK) model ................................. 70
Irreversible dynamics: H-theorem ....................................... 71
Deriving Euler equations (for matching continuum) ............ 73
APPENDIX K-A: Applied Lighting ............................................... 76
Simplified kinetic theory of photons .................................... 79
Beer-Lambert law............................................................... 80
Radiative Transfer Equation (RTE) ...................................... 81
Human physiology ............................................................. 82
Intensity distribution ......................................................... 87
Artificial light sources ........................................................ 88
APPENDIX K-B: Lattice Boltzmann Method ............................... 90
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Key ingredients of the Lattice Boltzmann Method (LBM) ...... 91

Solutions with multiple time scales .................................... 95
Asymptotic analysis by Chapman – Enskog expansion ...... 105
Applications ..................................................................... 112
APPENDIX K-C: Kinetic Theory/CFD Laboratory
(by PALABOS) ................................................ 115

PART - C:
An Introduction to Continuum Thermo-Mechanics ... 149
Navier–Stokes–Fourier (NSF) system of equations:
Conserved quantities........................................................ 154
Non-conserved quantities ................................................. 168
Compressible limit ........................................................... 173
Incompressible limit ......................................................... 180
Dissipative functions and turbulence ............................... 190
Integral equations ............................................................ 199
Applications ..................................................................... 202
APPENDIX C-A: Tensor notation ............................................. 208
APPENDIX C-B: Applied acoustics ........................................... 222
Linear and non-dissipative theory of sound propagation ... 224
Pure tones, i.e. single sinusoidal waves ............................ 227
Human physiology ........................................................... 232
Sound in enclosed spaces for ensuring acoustic safety
of workers ........................................................................ 235
How to deal with complex sounds ..................................... 240
APPENDIX C-C: Numerical modeling ....................................... 242
APPENDIX C-D: Continuum mechanics/CFD Laboratory
(by OPENFOAM) ............................................ 258

PART - D:
An Introduction to System Analysis and Design ....... 265
Exergy analysis in engineering systems made
of many components ........................................................ 270
Exergy analysis of multi-fluid systems (humid air) ............ 279
Applications .................................................................... 288

PART - R:
An Introduction to Model Reduction ........................ 291
Elementary reactions and detailed chemical kinetics......... 296
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Constrained extrema and equilibrium points .................... 303

Dynamical systems and Lyapunov functions..................... 311
Multiple time scales in homogeneous combustion ............. 318
Low dimensional manifolds, separation of motions
and Quasi-Equilibrium Manifolds (QEM) .......................... 324
Slow Invariant Manifolds (SIM) and their construction ...... 330
Applications ..................................................................... 345
APPENDIX R-A: Model Reduction Laboratory
(by CANTERA) ............................................. 351