Complex networks
Keywords: complex networks, complexity, robustness, biology, feedback, internet
Introductory slides 2002-2004
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 2002
Slides from old talks on Complexity and Robustness
- CDC plenary slides (ppt)
- Introduction to complex networks (ppt)
- Allerton plenary (ppt)
- 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, http://www.cds.caltech.edu/~doyle/CmplxNets/heat_shock.ps (PS 7MB) ] 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 pdf) and (Pictures)
- Biology and protocols: Slides ppt
- Integral feedback pdf: 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
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
by Phillip F. Schewe and Ben Stein
in American Institute of Physics (AIP) Physics News Update
Number 474 (Story #1), March 10, 2000
Applied mathematics: The power of design
Mark Newman
Nature 405, 6785, pp 412-413 (25 May 2000)
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
- This link is broken (Aug 2008) for International Science News, as the author is deceased. [1]
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See also
- This page copied and re-formatted from "http://www.cds.caltech.edu/~doyle/CmplxNets/"
- To Do