Lecture Notes

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)

Course Info

Learning Resource Types

notes Lecture Notes
assignment Problem Sets