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Foundations of Algorithms and Computational Techniques in Systems Biology >> Content Detail



Syllabus



Syllabus

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Recommended Textbooks


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

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

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

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

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



Grading



ACTIVITIESPERCENTAGES
Homework80%
Class Participation20%



Calendar



LEC #TOPICSKEY DATES
Protein Modeling
1Introduction and Protein Modeling Questions
2Models of Proteins
3Discrete Conformational Search
4Binding and Docking
5Molecular Dynamics SimulationHomework 1 due
6Molecular Dynamics and Electrostatics
7Continuum Electrostatic Modeling I
8Continuum Electrostatic Modeling II
9Electrostatic Optimization and DesignHomework 2 due
10Electrostatics Modeling
11Statistical Mechanics
Network Modeling
12Statistical Mechanics (cont.)
13Formulating and Simulating Network Models in BiologyHomework 3 due
14Formulating Models
15Nonlinear Dynamics and StabilityHomework 4 due
16Steady-State Problems
17Parameter Fitting and Estimation
18Parameter Estimation; Robustness, Fragility, ControlHomework 5 due
Image Modeling
192-D and 3-D Light Microscopy; Image Reconstruction
20Deconvolution
21Deconvolution II
22Blind DeconvolutionHomework 6 due
23Optical Flow
24High-Throughput Data and its Analysis
25Inference and Statistics
26RoundupHomework 7 due

 








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