Lecture Notes

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

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.)