Lecture Notes

Notes from lectures 3 through 25 are courtesy of Laura Proctor. Used with permission.

LEC # TOPICS
Protein Modeling
1 Introduction and Protein Modeling Questions ( PDF )
2 Models of Proteins ( PDF )
3 Discrete Conformational Search ( PDF )
4 Binding and Docking ( PDF )
5 Molecular Dynamics Simulation ( PDF )
6 Molecular Dynamics and Electrostatics ( PDF )
7 Continuum Electrostatic Modeling I ( PDF )
8 Continuum Electrostatic Modeling II ( PDF )
9 Electrostatic Optimization and Design ( PDF )
10 Electrostatics Modeling ( PDF 1 ) ( PDF 2 )
11 Statistical Mechanics ( PDF )
Network Modeling
12 Statistical Mechanics (cont.) ( PDF )
13 Formulating and Simulating Network Models in Biology ( PDF )
14 Formulating Models ( PDF )
15 Nonlinear Dynamics and Stability ( PDF )
16 Steady-State Problems ( PDF )
17 Parameter Fitting and Estimation ( PDF )
18 Parameter Estimation; Robustness, Fragility, Control ( PDF )
Image Modeling
19 2-D and 3-D Light Microscopy; Image Reconstruction ( PDF )
20 Deconvolution ( PDF )
21 Deconvolution II ( PDF )
22 Blind Deconvolution ( PDF )
23 Optical Flow ( PDF )
24 High-Throughput Data and its Analysis ( PDF )
25 Inference and Statistics ( PDF )
26 Roundup

Supplemental Notes

Adjoint Sensitivity Analysis for Optimization ( PDF ) (Courtesy of Joshua Apgar and Jared Toettcher. Used with permission.)