Difference between revisions of "Supplement: Biomolecular Feedback Systems"

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{{supheader|Biological Systems}}
 
{{supheader|Biological Systems}}
<font size="+1" color=blue>Domitilla Del Vecchio (U. Mich) and Richard M. Murray (Caltech)</font>
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<font size="+1">Domitilla Del Vecchio (U. Mich) and Richard M. Murray (Caltech)</font>
  
 
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| width=50% |
 
| width=50% |
 
<ol type="I">
 
<ol type="I">
<li> Introduction</li>
+
<li> Review of Core Processes
<li> Modeling  
+
* Modeling of transcription and translation
* Review of cell biology basics
+
** ODE models (coming from chemical reactions and thermodynamics)
* Chemical kinetics, Michaelis-Menten, Hill functions
+
** time constants
* Signaling cascades
+
** cell affects (dilution, degradation)
* Standard elements (repressor, activator, combinatorial promotors, etc)
+
* Transcriptional Regulation
* Additional topics (time delays)
+
** repression
 +
** activation
 +
** (Thermodynamics &rarr; chemical kinetics &rarr;Hill functions, Michaelis-Menten)
 +
* Intracellular sensing
 +
* Intracellular communication
 +
* Intracellular computation
 
</li>
 
</li>
<li> Regulation in cells
+
<li> Dynamic behavior
* Proportional control: activation and repression (+ demand theory)
+
* Steady state analysis (log/log diagrams)
* Integral compensation (chemotaxis)
+
* Phase plane analysis
* Allosteric regulation
+
* Time response
 +
* Limit cycles
 +
</li>
 +
<li> Feedback examples
 +
* Lactose metabolism
 +
* Heat shock
 +
* Chemotaxis
 
</li>
 
</li>
 
</ol>  
 
</ol>  
 
|  
 
|  
 
<ol type="I" start=4>
 
<ol type="I" start=4>
<li> Robustness and limits of performance
+
<li> Stochastic behavior 
* Autocatalysis and right half plane zeros
+
* Noise modeling (intrinsic/extrinsic), spectrum
 +
* Stochastic simulation analysis (SSA)
 +
* Markov modeling and analysis
 +
* Linearized modeling and analysis: include disturbance attenuation in freq domain (?)
 +
</li>
 +
<li> 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.
 +
</li>
 +
<li> Design examples
 +
</li>
 +
<li> Robustness and evolvability
 +
</li>
 +
<li> Multicellular systems
 +
* Additional core processes
 +
* Quorum Sensing
 +
* Development
 
</li>
 
</li>
<li> Biological switches and oscillators </li>
 
<li> Multi-cellular signalling </li>
 
* Development (notch/delta)
 
* Quorum sensing
 
<li> Modularity and synthetic biology </li>
 
 
</ol>
 
</ol>
 
|}
 
|}

Revision as of 02:59, 15 June 2008

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.

Outline

  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

Examples

Additional Information