Course Meeting Times
Lectures: 2 sessions / week, 1.5 hours / session
Recommended Textbooks
Schlick, T. Molecular Modeling and Simulation: An Interdisciplinary Guide. New York, NY: Springer, 2002. ISBN: 9780387954042.
Allen, M. P., and D. J. Tildesley. Computer Simulation of Liquids. New York, NY: Oxford University Press, 1989. ISBN: 9780198556459.
Trefethen, L. N., and D. Bau, III. Numerical Linear Algebra. Philadelphia, PA: SIAM, 1997. ISBN: 9780898713619.
Branden, C.-I., and J. Tooze. Introduction to Protein Structure. 2nd ed. New York, NY: Routledge, 1999. ISBN: 9780815323051.
Bertero, M., and P. Boccacci. Introduction to Inverse Problems in Imaging. New York, NY: Taylor & Francis, 1998. ISBN: 9780750304399.
Grading
| ACTIVITIES | PERCENTAGES |
|---|---|
| Homework | 80% |
| Class Participation | 20% |
Calendar
| LEC # | TOPICS | KEY DATES |
|---|---|---|
| Protein Modeling | ||
| 1 | Introduction and Protein Modeling Questions | |
| 2 | Models of Proteins | |
| 3 | Discrete Conformational Search | |
| 4 | Binding and Docking | |
| 5 | Molecular Dynamics Simulation | Homework 1 due |
| 6 | Molecular Dynamics and Electrostatics | |
| 7 | Continuum Electrostatic Modeling I | |
| 8 | Continuum Electrostatic Modeling II | |
| 9 | Electrostatic Optimization and Design | Homework 2 due |
| 10 | Electrostatics Modeling | |
| 11 | Statistical Mechanics | |
| Network Modeling | ||
| 12 | Statistical Mechanics (cont.) | |
| 13 | Formulating and Simulating Network Models in Biology | Homework 3 due |
| 14 | Formulating Models | |
| 15 | Nonlinear Dynamics and Stability | Homework 4 due |
| 16 | Steady-State Problems | |
| 17 | Parameter Fitting and Estimation | |
| 18 | Parameter Estimation; Robustness, Fragility, Control | Homework 5 due |
| Image Modeling | ||
| 19 | 2-D and 3-D Light Microscopy; Image Reconstruction | |
| 20 | Deconvolution | |
| 21 | Deconvolution II | |
| 22 | Blind Deconvolution | Homework 6 due |
| 23 | Optical Flow | |
| 24 | High-Throughput Data and its Analysis | |
| 25 | Inference and Statistics | |
| 26 | Roundup | Homework 7 due |