Contents
Foreword
Introduction
1. Entropy
1.1 Statistical Ensembles
1.2 Microcanonical Ensemble and Entropy
1.3 Thermodynamics
1.4 Principle of Maximum Entropy
1.5 Example: Defects in Solid
2. Maxwell-Boltzmann Distribution
2,1 Classical Gas of Atoms
2.2 The Most Probable Distribution
2.3 The Distribution Function
2.4 Thermodynamic Properties
3. Free Energy
3.1 Canonical Ensemble
3.2 Energy Fluctuations
3.3 The Free Energy
3.4 Maxwell's Relations
3.5 Example: Unwinding of DNA
4. Chemical Potential
4.1 Changing the Particle Number
4.2 Grand Canonical Ensemble
4.3 Thermodynamics
4.4 Critical Fluctuations
4.5 Example: Ideal Gas
5. Phase Transitions
5.1 First-Order Phase Transitions
5.2 Second-Order Phase Transitions
5.3 Van der Waals Equation of State
5.4 Maxwell Construction
6. Kinetics of Phase Transitions
6.1 Nucleation and Spinodal Decomposition
6.2 The Freezing of Water
7. The Order Parameter
7 1 Ginsburg-Landau Theory
7.2 Second-Order Phase Transition
7.3 First-Order Phase Transition
7.4 Cahn-Hilliard Equation
8. Correlation Function
8.1 Correlation Length
8.2 Large-Distance Correlations
8.3 Universality Classes
8.4 Compactness Index
8.5 Scaling Properties
9. Stochastic Processes
9.1 Brownian Motion
9.2 Random Walk
9.3 Diffusion
9.4 Central Limit Theorem
9.5 Diffusion Equation
10. Langevin Equation
10.1 The Equation
10.2 Solution
10.3 Fluctuation-Dissipation Theorem
10.4 Power Spectrum and Correlation
10.5 Causality
10.6 Energy Balance
11. The Life Process
11.1 Life
11.2 Cell Structure
11.3 Molecular Interactions
11.4 Primary Protein Structure
11.5 Secondary Protein Structure
11.6 Tertiary Protein Structure
11.7 Denatured State of Protein
12. Self-Assembly
12.1 Hydrophobic Effect
12.2 Micelles and Bilayers
12.3 Cell Membrane
12.4 Kinetics of Self-Assembly
12.5 Kinetic Arrest
13. Kinetics of Protein Folding
13.1 The Statistical View
13.2 Denatured State
13.3 Molten Globule
13.4 Folding Funnel
13.5 Convergent Evolution
14. Power Laws in Protein Folding
14.1 The Universal Range
14.2 Collapse and Annealing
14.3 Self-Avoiding Walk (SAW)
15. Self-Avoiding Walk and Turbulence
15.1 Kolmogorov's Law
15.2 Vortex Model
15.3 Quantum Turbulence
15.4 Convergent Evolution in Turbulence
16. Convergent Evolution in Protein Folding
16.1 Mechanism of Convergent Evolution
16.2 Energy Cascade in Turbulence
16.3 Energy Cascade in the Polymer Chain
16.4 Energy Cascade in the Molten Globule
16.5 Secondary and Tertiary Structures
A. Model of Energy Cascade in a Protein Molecule
A.1 Brownian Motion of a Forced
Harmonic Oscillator
A.2 Coupled Oscillators
A.2.1 Equations of Motion
A.2.2 Energy Balance
A.2.3 Fluctuation-Dissipation Theorem
A.2.4 Perturbation Theory
A.2.5 Weak-Damping Approximation
A.3 Model of Protein Dynamics
A.4 Fluctuation-Dissipation Theorem
A.5 The Cascade Time
A.6 Numerical Example
Index |
