Complex networks

Keywords: complex networks, complexity, robustness, biology, feedback, internet

This page copied from "http://www.cds.caltech.edu/~doyle/CmplxNets/"

NEED TO TRANSFER slides and more papers from old page to this page and also to other pages for sub-topics.

Introductory slides

Introductory and review slides on complex networks, biological complexity and robustness.

• Physics talk (slides) Nov 11, 2004
• Emergent complexity (slides) Nov 22, 2004 Georgia Tech
• Old IPAM slides

Slides from old talks on Complexity and Robustness

1. CDC plenary slides (ppt)

2. Introduction to complex networks (ppt)

3. Allerton plenary (ppt)

4. Introduction to HOT (ppt)

Review papers

Complexity and robustness,
Carlson JM, Doyle J,
Proc. Natl. Acad. Sci. USA 99: 2538-2545 Suppl. 1 Feb 19, 2002.

Reverse Engineering of Biological Complexity
Csete M and Doyle J,
Science 295 (5560): 1664-1669 Mar 1, 2002. (1.2MB pdf)

• See also introductory papers on HOT

Papers

Bow ties, metabolism, and disease,
Csete M.E. and J.C. Doyle,
Trends in Biotechnology 22(9):446-50 Sept 2004. (121K)

Robustness of cellular functions,
J. Stelling, U. Sauer, Z. Szallasi, F. J. Doyle III, and J. Doyle,
Cell 118: 675–685, Sept 17 2004. (244K)

Surviving Heat Shock: Control Strategies for Robustness and Performance,
H. El-Samad, H. Kurata , J.C. Doyle , C.A. Gross, and M. Khammash,
Proc. Natl. Acad. Sci. USA 102(8): 2736-2741 Feb 22, 2005. (390K)

A First-principles Approach to Understanding the Internet's Router-level TopologyAbstract
Lun Li, David Alderson, W. Willinger and John C. Doyle
in Proceedings of ACM SIGCOMM, Portland, OR, Aug 2004 (1.5MB)

Mutation, specialization, and hypersensitivity in highly optimized tolerance,
Zhou T, Carlson JM, Doyle J,
Proc. Natl. Acad. Sci. USA 99 (4): 2049-2054 Feb 19, 2002.

Power Laws, Highly Optimized Tolerance and Generalized Source Coding,
J. Doyle and J.M. Carlson,
Phys. Rev. Let., 84(24):5656-5659, 2000.

Robust perfect adaptation in bacterial chemotaxis through integral feedback control.
Yi T-M, Huang Y, Simon MI, Doyle J.
Proc. Natl. Acad. Sci. USA 97(9):4649-4653, 2000.

PhD theses & Drafts

• Robust Flow Stability: Theory, Computations and Experiments in Near Wall Turbulence,

PhD thesis by Kumar Bobba (pdf)

• Structured semidefinite programs and semialgebraic geometry methods in robustness and optimization,

Pablo Parrilo,

PhD Thesis, Control and Dynamical Systems, Caltech, (Gzipped postscript)

• Feedback regulation of the heat shock response in E. Coli,

Kurata, El-Samad, Yi, Khammash, and Doyle, draft, (PS (7M) or Zipped (300k))

• Highly Optimized Tolerance: A Mechanism for Power Laws in Designed Systems,
  

Carlson and Doyle,
PRE, (pdf)

Related reading

Supplementary material

• Biological examples (pdf)
• Feedback examples (pdf)
• Legos and protocols: Notes and Pictures
• Biology and protocols: Slides
• Integral feedback: Proofs and Notes

Additional recommended books

A course in Robust Control Theory: A Convex Approach, Dullerud and Paganini, Springer

Essentials of Robust Control, Zhou, Prentice-Hall

Cells, Embryos, and Evolution, Gerhart and Kirschner

Related topics

• network architecture and protocols
• General complexity
• Complexity and robustness

Links

• [Feedback Control Theory, by Doyle, Francis and Tannenbaum]
• [Internet Protocols, Evolution, and Theory]
• [Systems Biology Workbench (SBW) and Markup Language (SBML)]

Related news and commentary items

• Highly Optimized Tolerance. in American Institute of Physics (AIP) Physics News Update
  

Number 474 (Story #1), March 10, 2000 by Phillip F. Schewe and Ben Stein [1]

• Applied mathematics: The power of design
  

Nature 405, 6785, pp 412-413 (25 May 2000) Mark Newman [2]

• This link is broken (Aug 2008) for International Science News, as the author is deceased. [3]

• Cell signaling pathways as control modules: Complexity for simplicity?
  

Douglas A. Lauffenburger,
Proc. Natl. Acad. Sc. May 9, 2000 vol. 97 no. 10 5031-5033 [4]