Course Meeting Times

Lectures: 2 sessions / week, 1.5 hours / session

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.


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