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.)