Part 1. Basic principles

Chapter 1. Thermodynamics

Chapter 2. Four basic quantum mechanical models of nuclear & electronic motion: a synopsis.

Chapter 3. Molecular structure and interactions

Chapter 4. Water and the hydrophobic effect

Part 2. Statistical mechanics: The molecular basis of thermodynamics

Chapter 5. The molecular partition function

Chapter 6. System ensembles and partition functions

Chapter 7. Sampling molecular systems with simulations

Part 3. Binding to macromolecules

Chapter 8. Binding equilibria

Chapter 9. Thermodynamics of molecular interactions

Chapter 10. Elements of statistical mechanics of liquids and solutions

Chapter 11. Analysis of binding equilibria in terms of partition functions

Chapter 12. Coupled equilibria

Chapter 13. Allosteric function

Chapter 14. Charged groups: Binding of hydrogen ions, solvation and charge-charge interactions

Part 4. Conformational stability and conformation change

Chapter 15. Some elements of polymer physics

Chapter 16. Helix-coil equilibria

Chapter 17. Protein unfolding equilibria

Chapter 18. Elasticity of biological materials

Part 5. Kinetics and irreversible processes

Chapter 19. Kinetics

Chapter 20. Kinetics of protein folding

Chapter 21. Irreversible and stochastic processes

Appendices

Appendix 1: Probability

Appendix 2: Random walk and central limit theorem

Appendix 3: The grand partition function: derivation and relation to other types of partition functions

Appendix 4: Methods to compute a PMF

Appendix 5: Theory of the helix-coil transition

Appendix 6: Laplace transform

Appendix 7: Poisson equation

Appendix 8: Defining molecular boundaries

Appendix 9: Equations

Appendix 10: Useful facts