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, NY: Routledge, 2002. ISBN: 9780815320517.
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: 9780137204595.
Eisenberg = Eisenberg, D., and D. Crothers. Physical Chemistry with Applications to the Life Sciences. Menlo Park, CA: Benjamin/Cummings, 1979. ISBN: 9780805324020.
Kittel = Kittel, C., and H. Kroemer. Thermal Physics. 2nd ed. New York, NY: W.H. Freeman, 1980. ISBN: 9780716710882.
| 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 |
