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 (This resource may not render correctly in a screen reader.PDF)
4 Binding and Docking (This resource may not render correctly in a screen reader.PDF)
5 Molecular Dynamics Simulation (This resource may not render correctly in a screen reader.PDF)
6 Molecular Dynamics and Electrostatics (This resource may not render correctly in a screen reader.PDF)
7 Continuum Electrostatic Modeling I (This resource may not render correctly in a screen reader.PDF)
8 Continuum Electrostatic Modeling II (This resource may not render correctly in a screen reader.PDF)
9 Electrostatic Optimization and Design (This resource may not render correctly in a screen reader.PDF)
10 Electrostatics Modeling (This resource may not render correctly in a screen reader.PDF 1) (This resource may not render correctly in a screen reader.PDF 2)
11 Statistical Mechanics (This resource may not render correctly in a screen reader.PDF)
Network Modeling
12 Statistical Mechanics (cont.) (This resource may not render correctly in a screen reader.PDF)
13 Formulating and Simulating Network Models in Biology (This resource may not render correctly in a screen reader.PDF)
14 Formulating Models (This resource may not render correctly in a screen reader.PDF)
15 Nonlinear Dynamics and Stability (This resource may not render correctly in a screen reader.PDF)
16 Steady-State Problems (This resource may not render correctly in a screen reader.PDF)
17 Parameter Fitting and Estimation (This resource may not render correctly in a screen reader.PDF)
18 Parameter Estimation; Robustness, Fragility, Control (This resource may not render correctly in a screen reader.PDF)
Image Modeling
19 2-D and 3-D Light Microscopy; Image Reconstruction (This resource may not render correctly in a screen reader.PDF)
20 Deconvolution (This resource may not render correctly in a screen reader.PDF)
21 Deconvolution II (This resource may not render correctly in a screen reader.PDF)
22 Blind Deconvolution (This resource may not render correctly in a screen reader.PDF)
23 Optical Flow (This resource may not render correctly in a screen reader.PDF)
24 High-Throughput Data and its Analysis (This resource may not render correctly in a screen reader.PDF)
25 Inference and Statistics (This resource may not render correctly in a screen reader.PDF)
26 Roundup

Supplemental Notes

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