Supplement: Biomolecular Feedback Systems

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Domitilla Del Vecchio (U. Mich) and Richard M. Murray (Caltech)

The supplement contains a number of examples and exercises related to some of the molecular mechanisms for feedback within cells. These examples are being expanded into a set of notes by Domitilla Del Vecchio and Richard Murray based on a variety of presentations, lectures and notes.


  1. Review of Core Processes
    • Modeling of transcription and translation
      • ODE models (coming from chemical reactions and thermodynamics)
      • time constants
      • cell affects (dilution, degradation)
    • Transcriptional Regulation
      • repression
      • activation
      • (Thermodynamics → chemical kinetics →Hill functions, Michaelis-Menten)
    • Intracellular sensing
    • Intracellular communication
    • Intracellular computation
  2. Dynamic behavior
    • Steady state analysis (log/log diagrams)
    • Phase plane analysis
    • Time response
    • Limit cycles
  3. Feedback examples
    • Lactose metabolism
    • Heat shock
    • Chemotaxis
  1. Stochastic behavior
    • Noise modeling (intrinsic/extrinsic), spectrum
    • Stochastic simulation analysis (SSA)
    • Markov modeling and analysis
    • Linearized modeling and analysis: include disturbance attenuation in freq domain (?)
  2. Biological circuit design
    • DNA-protein, vs protein-protein, etc.
    • Feedforward loops
    • PID in biocircuits
    • Activation vs repression (demand theory)
    • Modularity and retroactivity
    • Logical functions: AND, switches, inverters, toggles, etc.
  3. Design examples
  4. Robustness and evolvability
  5. Multicellular systems
    • Additional core processes
    • Quorum Sensing
    • Development


Additional Information