Course Meeting Times

Lectures: 2 sessions / week, 1.5 hours / session

Recommended Textbooks

Buy at Amazon Schlick, T. Molecular Modeling and Simulation: An Interdisciplinary Guide. New York, NY: Springer, 2002. ISBN: 9780387954042.

Buy at Amazon Allen, M. P., and D. J. Tildesley. Computer Simulation of Liquids. New York, NY: Oxford University Press, 1989. ISBN: 9780198556459.

Buy at Amazon Trefethen, L. N., and D. Bau, III. Numerical Linear Algebra. Philadelphia, PA: SIAM, 1997. ISBN: 9780898713619.

Buy at Amazon Branden, C.-I., and J. Tooze. Introduction to Protein Structure. 2nd ed. New York, NY: Routledge, 1999. ISBN: 9780815323051.

Buy at Amazon Bertero, M., and P. Boccacci. Introduction to Inverse Problems in Imaging. New York, NY: Taylor & Francis, 1998. ISBN: 9780750304399.


Homework 80%
Class Participation 20%


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