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| Date | Topics | Lecturer |
| 1/6/05 | General Introduction – Plan | Bahar, Tang |
| 1/11/05 |
Fluctuations vs. Rotational Isomeric Transitions in Macromolecules (Chapt
6 in Daune et al) Lecture 2 (Fluctuations and MD Sim.) |
Bahar |
| 1/13/05 | MD simulations (Leach) | Camacho |
| 1/18/05 | Folding Kinetics & Pathways (Chapters 18 and 19 in Fersht) | Zuckerman |
| 1/20/05 | Conformational Changes (Chapt 8 in Daune) + Chapt 10 in Fersht | Bahar |
| 1/25/05 | Chem Reaction Kinetics – Enzyme Kinetics- Michaelis Menten (Chapt 3 in Fersht) | Tang |
| 1/27/05 | Molecular dynamics and spin relaxation | Tang |
| 2/1/05 | Relaxations for motions on ps-ns time scale I | Tang |
| 2/3/05 | Relaxations for motions on ps-ns time scale II | Tang |
| 2/8/05 | Relaxations for motions on ms-ms time scale | Tang |
| 2/10/05 | NMR measurements for extremely slow motions | Tang |
| 2/15/05 | Review | Tang |
| 2/17/05 | 1st Exam | Tang |
| 2/22/05 | Folding of soluble protein model system lysozyme | Klein-Seetharaman |
| 2/24/05 | Folding of membrane protein model system rhodopsin and bacteriorhodopsin | Klein-Seetharaman |
| 3/1/05 | Equilibrium fluctuations in G protein coupled receptors | Klein-Seetharaman |
| 3/3/05 | Functional conformational changes in G protein coupled receptors | Klein-Seetharaman |
| 3/8/05 | Spring Break | |
| 3/10/05 | Spring Break | |
| 3/15/05 | Single-molecule dynamics I | Leuba |
| 3/17/05 | Single-molecule dynamics II | Leuba |
| 3/22/05 | Ion channels and electrophysiology I | Levitan |
| 3/24/05 | Ion channels and electrophysiology II | Levitan |
| 3/29/05 | Motions from EPR (I) | Saxena |
| 3/31/05 | Motions from EPR (II) | Saxena |
| 4/5/05 | Problem Review - 2nd Exam | Tang |
| 4/7/05 | Brownian Motion (Chapt 7 in Daune et al) | Camacho |
| 4/12/05 | Brownian Simulations (Chapt 7 in Daune et al.) | Meirovitch |
| 4/14/05 | Ab initio simulations of folding using coarse-grained models (Rosetta etc.) | Meirovitch |
| 4/19/05 | Essential dynamics and normal mode analysis (Chapter 6 in Daune et al.) | Bahar |
| 4/21/05 | MC simulations – Coarse-grained methods | Zuckerman |
| 4/26/05 | Analytical methods – Elastic Networks – Master equation | Bahar |
| 4/28/05 | Final Exam |