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Lecture Notes



Lecture Notes

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'
1Introduction (PDF)

Michaelis-Menten Kinetics
2Equilibrium Binding

Cooperativity
3Lambda Phage (PDF)

Multistability

Associated MATLAB® Code File (M)
4Multistability (cont.) (PDF)
5Synthetic Genetic Switches
6Stability Analysis (PDF)
7Introduction E. coli Chemotaxis (PDF - 1.3 MB)
8Fine-tuned versus Robust Chemotaxis Models (PDF)

Associated MATLAB® Code File (M)
9Wrapping up Chemotaxis (PDF)
10Genetic Oscillators (PDF)

Associated MATLAB® Code File (M)
11Genetic Oscillators (cont.)
12Stochastic Chemical Kinetics
13Stochastic Chemical Kinetics (cont.)
Part II: Cell Systems Biology - 'The Importance of Diffusion and Gradients for Cellular Regulation'
14Introduction Cell Systems Biology (PDF)

Fick's Laws
15Local Excitation

Global Inhibition Theory
16Local Excitation (cont.) (PDF)

Global Inhibition Theory (cont.)
17Rapid Pole-to-pole Oscillations in E. coli (PDF)

Associated MATLAB® Code File (M - 1 of 2) (M - 2 of 2)

18Rapid Pole-to-pole Oscillations in E. coli (cont.) (PDF)
19Models for Eukaryotic Gradient Sensing
20Models for Eukaryotic Gradient Sensing (cont.) (PDF)
21Modeling Cytoskeleton Dynamics
22Modeling Cytoskeleton Dynamics (cont.)
Part III: Developmental Systems Biology - 'Building an Organism Starting From a Single Cell'
23Quorum Sensing (PDF)
24Final Problem Set Question Hour
25Drosophila Development (PDF)

 








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