Lectures On Statistical Physics And Protein Folding

Kerson Huang9812561439, 9789812561435, 9789812569387, 9812561501

This book introduces an approach to protein folding from the point of view of kinetic theory. There is an abundance of data on protein folding, but few proposals are available on the mechanism driving the process. Here, presented for the first time, are suggestions on possible research directions, as developed by the author in collaboration with C. C. Lin.

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Table of contents :
Contents……Page 8
Foreword……Page 6
Introduction……Page 12
1.1 Statistical Ensembles……Page 16
1.2 Microcanonical Ensemble and Entropy……Page 18
1.4 Principle of Maximum Entropy……Page 20
1.5 Example: Defects in Solid……Page 22
2.1 Classical Gas of Atoms……Page 26
2.2 The Most Probable Distribution……Page 27
2.3 The Distribution Function……Page 28
2.4 Thermodynamic Properties……Page 31
3.1 Canonical Ensemble……Page 32
3.3 The Free Energy……Page 35
3.4 Maxwell’s Relations……Page 38
3.5 Example: Unwinding of DNA……Page 39
4.1 Changing the Particle Number……Page 42
4.2 Grand Canonical Ensemble……Page 43
4.4 Critical Fluctuations……Page 45
4.5 Example: Ideal Gas……Page 46
5.1 First-Order Phase Transitions……Page 48
5.2 Second-Order Phase Transitions……Page 49
5.3 Van der Waals Equation of State……Page 52
5.4 Maxwell Construction……Page 55
6.1 Nucleation and Spinodal Decomposition……Page 58
6.2 The Freezing of Water……Page 60
7.1 Ginsburg–Landau Theory……Page 64
7.2 Second-Order Phase Transition……Page 65
7.3 First-Order Phase Transition……Page 66
7.4 Cahn–Hilliard Equation……Page 68
8.2 Large-Distance Correlations……Page 70
8.3 Universality Classes……Page 72
8.5 Scaling Properties……Page 73
9.1 Brownian Motion……Page 76
9.2 Random Walk……Page 78
9.3 Diffusion……Page 79
9.5 Diffusion Equation……Page 80
10.1 The Equation……Page 82
10.2 Solution……Page 83
10.4 Power Spectrum and Correlation……Page 84
10.5 Causality……Page 85
10.6 Energy Balance……Page 87
11.1 Life……Page 90
11.2 Cell Structure……Page 91
11.3 Molecular Interactions……Page 93
11.4 Primary Protein Structure……Page 94
11.5 Secondary Protein Structure……Page 96
11.6 Tertiary Protein Structure……Page 97
11.7 Denatured State of Protein……Page 99
12.1 Hydrophobic Effect……Page 100
12.2 Micelles and Bilayers……Page 102
12.3 Cell Membrane……Page 103
12.4 Kinetics of Self-Assembly……Page 105
12.5 Kinetic Arrest……Page 107
13.1 The Statistical View……Page 110
13.2 Denatured State……Page 111
13.3 Molten Globule……Page 112
13.5 Convergent Evolution……Page 116
14.1 The Universal Range……Page 120
14.2 Collapse and Annealing……Page 121
14.3 Self-Avoiding Walk (SAW)……Page 123
15.2 Vortex Model……Page 128
15.3 Quantum Turbulence……Page 131
15.4 Convergent Evolution in Turbulence……Page 132
16.1 Mechanism of Convergent Evolution……Page 134
16.3 Energy Cascade in the Polymer Chain……Page 135
16.4 Energy Cascade in the Molten Globule……Page 137
16.5 Secondary and Tertiary Structures……Page 138
A.1 Brownian Motion of a Forced Harmonic Oscillator……Page 140
A.2.1 Equations of Motion……Page 142
A.2.2 Energy Balance……Page 144
A.2.4 Perturbation Theory……Page 145
A.2.5 Weak-Damping Approximation……Page 146
A.3 Model of Protein Dynamics……Page 147
A.4 Fluctuation–Dissipation Theorem……Page 150
A.5 The Cascade Time……Page 151
A.6 Numerical Example……Page 152
Index……Page 156