Here you can download pdf versions of recent lecture notes, and other course information.

- Course syllabus.
- Notes on thermodynamics, from J.C.
Slater,
*Introduction to Chemical Physics*, chapters 1-3. - Entropy and the Boltzmann distribution.
**Homework #1**, due in class, Feb. 1: Problems 1.15, 4.5, 5.6 and 6.2.- Build-up procedure for partition
functions, by Herschbach, Johnston and Rapp.
**Homework #2**, due in class, Feb. 8: Problems 10.7, 10.18, 11.6, 11.11 and 11.16.**Homework #3**, due in class, Feb. 20: Problems 8.18, 10.16, 12.3, 13.2, and 13.8.- Getting free energies from
simulation (revised, 24 Feb.)..
- Proton binding to proteins: pKa calculations
with explicit and implicit solvent models, by Simonson, Carlsson and
Case.
**Homework #4/#5**, due in class on March 1 and March 8.- Dynamics of ligand escape from the heme
pocket of myoglobin, by Kottalam and Case.
- Notes on molecular dynamics and force fields..
- Notes on electrostatics and
continuum solvent models.
**Homework #6**, due in class, Mar. 29: Problems 20.11, 22.6, 22.13, 23.2 and 23.13.**Homework #7**, due in class on April 5.- Notes on ligand binding and
allostery (revised on 5 April).
**Homework #8**, due in class, Apr. 12: Problems 26.12, 28.2, 28.3 and 29.1.- Notes on ligand binding kinetics to
myoglobin.
- Classical derivation of transition state
theory.
- Fitting models to data.
- Instructions for the final
project.

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