MATLAB® software is required to run the .m files in this section.
| LEC # | TOPICS |
|---|---|
| Part I: Systems Microbiology - 'The Cell as a Well-stirred Bioreactor' | |
| 1 | Introduction (PDF) Michaelis-Menten Kinetics |
| 2 | Equilibrium Binding Cooperativity |
| 3 | Lambda Phage (PDF) Multistability Associated MATLAB® Code File (M) |
| 4 | Multistability (cont.) (PDF) |
| 5 | Synthetic Genetic Switches |
| 6 | Stability Analysis (PDF) |
| 7 | Introduction E. coli Chemotaxis (PDF - 1.3 MB) |
| 8 | Fine-tuned versus Robust Chemotaxis Models (PDF) Associated MATLAB® Code File (M) |
| 9 | Wrapping up Chemotaxis (PDF) |
| 10 | Genetic Oscillators (PDF) Associated MATLAB® Code File (M) |
| 11 | Genetic Oscillators (cont.) |
| 12 | Stochastic Chemical Kinetics |
| 13 | Stochastic Chemical Kinetics (cont.) |
| Part II: Cell Systems Biology - 'The Importance of Diffusion and Gradients for Cellular Regulation' | |
| 14 | Introduction Cell Systems Biology (PDF) Fick's Laws |
| 15 | Local Excitation Global Inhibition Theory |
| 16 | Local Excitation (cont.) (PDF) Global Inhibition Theory (cont.) |
| 17 | Rapid Pole-to-pole Oscillations in E. coli (PDF) Associated MATLAB® Code File (M - 1 of 2) (M - 2 of 2) |
| 18 | Rapid Pole-to-pole Oscillations in E. coli (cont.) (PDF) |
| 19 | Models for Eukaryotic Gradient Sensing |
| 20 | Models for Eukaryotic Gradient Sensing (cont.) (PDF) |
| 21 | Modeling Cytoskeleton Dynamics |
| 22 | Modeling Cytoskeleton Dynamics (cont.) |
| Part III: Developmental Systems Biology - 'Building an Organism Starting From a Single Cell' | |
| 23 | Quorum Sensing (PDF) |
| 24 | Final Problem Set Question Hour |
| 25 | Drosophila Development (PDF) |