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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
Grading criteria.
| ACTIVITIES |
PERCENTAGES |
| Homework |
80% |
| Class Participation |
20% |
Calendar
Course schedule.
| 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 |