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.)
