Readings

The table below provides information on the course's lecture (L) and exam (E) sessions.

Text Readings

All Text Readings are in Dill, K., and S. Bromberg. Molecular Driving Forces. New York: Garland Press, 2003. ISBN: 0815320515.

Additional References

van Holde = van Holde, K. E., W. C. Johnson, and P. S. Ho. Principles of Physical Biochemistry. Upper Saddle River, NJ: Prentice Hall, 1998. ISBN: 0137204590.

Eisenberg = Eisenberg, D., and D. Crothers. Physical Chemistry with Applications to the Life Sciences. Menlo Park, CA: Benjamin/Cummings, 1979. ISBN: 080532402X.

Kittel = Kittel, C., and H. Kroemer. Thermal Physics. 2nd ed. San Francisco CA: W. H. Freeman, 1980. ISBN: 0716710889.

SES # TOPICS TEXT READINGS ADDITIONAL REFERENCES
L1 Introduction

Purpose of Stat Mech

Probability
Ch. 1 (Ex. 1.1-1.6)
L2 Probability Ch. 1, 2
L3 Equilibrium States Ch. 2 (Through Ex. 2.2)
L4 Equilibrium States – Lattice Model for Diffusion

Rubber Elasticity
Ch. 2
L5 Introduction to Conservation Laws (1st Law, Quantization, 2nd Law) Ch. 3
L6 Boltzmann’s Law and Entropy as an Extensive Property

Law of Increased Entropy
Ch. 6 (Through Ex. 6.2) Kittel, Ch. 2
L7 More Boltzmann’s Law

Partition Functions
Ch. 6
L8 Simulations

PCR
E1 Quiz I
L9 Thermodynamic Systems

Intensive/Extensive Properties

Fundamental Equations for Energy and Entropy

Definitions of Thermodynamic Driving Forces (Part 1) Thermodynamic Forces

Homogeneous Functions

Definition of Equilibrium, Temperature, Pressure
Ch. 7 (To Ex. 7.4)
L10 Introduction to Chemical Potential - Thermo Cycles - First Law Relations between Heat, Work, Energy Ch. 7
L11 Reversible and Irreversible Processes Ch. 7
L12 Introduction to Free Energy

Helmholtz Free energy
Ch. 8
L13 Enthalpy

Gibbs Free Energy
Ch. 8 Kittel Problem, 9.4

van Holde, Ch. 2
L14 Fundamental Equations and their Natural Variables

Heat Capacities

Equilibrium Temperature
Ch. 8
L15 Thermodynamic Cycles

Carnot Cycle and Inequality

Heat Engines

Path Dependence
Ch. 8 Kittel, Ch. 8
L16 Partial Molar Properties Ch. 9
L17 Partial Molar Properties II Ch. 9 Eisenberg, Ch. 7
L18 Simulations

Monte Carlo
E2 Quiz II
L19 Boltzmann Distribution Law Ch. 10
L20 Partition Functions Ch. 10
L21 Prediction of Thermodynamic Properties from Partition Functions

Ensembles
Ch. 10 Eisenberg, Ch. 14
L22 Quantum Partition Function Ch. 10, 11
L23 Equipartition Ch. 11
L24 Equipartition (cont.) Ch. 11
L25 Chemical Equlibria

Le Chatelier’s Principle (Ex. 8, Pressure Denaturation of Proteins)

van’t Hoff
Ch. 13 (To Ex. 13.18) van Holde, Ch. 3
L26 Solid-liquid-gas Equilibrium Ch. 14
L27 Solutions and Mixtures

Polymers
Ch. 15, 31
L28 Solvation – Osmotic Pressure Ch. 16
L29 Solvation – Protein/Macromolecule Adsorption at Interfaces Ch. 16 van Holde, Ch. 2
L30 Polymer Chain Ch. 31
E3 Quiz III
L31 Polymer Chain II Ch. 32
L32 Polymer Chain III Ch. 33
L33 Cooperativity Ch. 26
L34 Cooperativity (cont.) Ch. 28
L35 Protein Folding van Holde, Ch. 2
L36 Review