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 |