MATLAB® software is required to run the .m files in this section.
Table for Lecture Notes
| 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) |