This section contains documents created from scanned original files, which are inaccessible to screen reader software. A "#" symbol is used to denote such documents.
Notes from lectures 3 through 25 are courtesy of Laura Proctor. Used with permission.
Course notes.| 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.)