Difference between revisions of "Supplement: Biomolecular Feedback Systems"

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Biological systems make use of feedback in an extraordinary number of ways, on scales ranging from molecules
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The supplement contains a number of examples and exercises related to some of the molecular mechanisms for feedback within cellsThese examples are being expanded into a set of notes by [http://www.eecs.umich.edu/~ddv/ Domitilla Del Vecchio] and [[User:Murray|Richard Murray]] based on a variety of presentations, lectures and notes.
to cells to organisms to ecosystems.  This page collects information on the analysis of feedback systems in biologyWhat is currently connected here are working notes on the supplement and links to further information. This information is ''in progress''; comments and constructive suggestions are welcome and can be sent to [[User:murray|Richard Murray]].
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== Cell Biology (Del Vecchio and Murray) ==
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=== Outline ===
  
The text 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 [http://www.eecs.umich.edu/~ddv/ Domitilla Del Vecchio] and [[User:Murray|Richard Murray]] based on a variety of presentations, lectures and notes.
 
 
'''Tentative outline'''
 
 
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Some of the examples for this material will be pulled from tutorial presentations on control given at systems biology workshops:
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=== Examples ===
* [http://www.ima.umn.edu/2007-2008/W4.21-25.08/abstracts.html#Murray-Richard Tutorial on control theory], IMA workshop on Design Principles in Biological Systems, 21 April 2008.
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== Microbial Ecosystems ==
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== Integrative Biology ==
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=== Locomotion ===
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Summarize work of Full, Holmes et al showing role of dynamics and feedback in insect locomotion.
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* Low order models to describe locomotion
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* Bifurcations of stable gates, neural pattern generator
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* [http://epubs.siam.org/SIREV/volume-48/art_44513.html The Dynamics of Legged Locomotion: Models, Analyses, and Challenges], Philip Holmes, Robert J. Full, Dan Koditschek, John Guckenheimer.  ''SIAM Review'', 48(2):207-304, 2006.  (requires subscription)
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=== Insect Flight ===
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Summarize work of Dickinson, Srinivasan et al showing mechanisms for visual sensoring processing and sensor fusion in insect flight.
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== Motor Control Systems ==
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Summarize work on Massaquoi from CSHL course.
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=== Additional Information ===
  
== Additional Information ==
 
 
* [http://meetings.cshl.edu/meetings/engine06.shtml Engineering Principles in Biological Systems]: 6-8 December 2006, Cold Spring Harbor Laboratory
 
* [http://meetings.cshl.edu/meetings/engine06.shtml Engineering Principles in Biological Systems]: 6-8 December 2006, Cold Spring Harbor Laboratory
 
* [http://www.ima.umn.edu/2007-2008/W4.21-25.08/ Design Principles in Biological Systems]: 24-28 April 2008, Institute for Mathematics and Its Applications (IMA)
 
* [http://www.ima.umn.edu/2007-2008/W4.21-25.08/ Design Principles in Biological Systems]: 24-28 April 2008, Institute for Mathematics and Its Applications (IMA)

Revision as of 02:51, 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. Introduction
  2. Modeling
    • Review of cell biology basics
    • Chemical kinetics, Michaelis-Menten, Hill functions
    • Signaling cascades
    • Standard elements (repressor, activator, combinatorial promotors, etc)
    • Additional topics (time delays)
  3. Regulation in cells
    • Proportional control: activation and repression (+ demand theory)
    • Integral compensation (chemotaxis)
    • Allosteric regulation
  1. Robustness and limits of performance
    • Autocatalysis and right half plane zeros
  2. Biological switches and oscillators
  3. Multi-cellular signalling
    • Development (notch/delta)
    • Quorum sensing
  4. Modularity and synthetic biology

Examples

Additional Information