John C. Doyle - User contributions [en]

Systems biology

2012-05-04T16:39:53Z

Fiona: /* 2011 */

Intro: We study fundamental constraints and trade-offs in biological systems using analytical tools from control theory, information theory, and graph theory. There are hard trade-offs between complexity and robustness in every system, which is worse in systems with particular architecture. We are interested in pinpointing these problems and analyzing how nature manages these trade-offs.

Keywords: '''systems biology''', SBML mark-up, robustness, complexity, networks, biology, proteins.

A few papers were copied from <http://www.cds.caltech.edu/~doyle/RecentPapers/ >

==Systems biology==
Keywords: '''systems biology''', biological networks, complexity, control, heat-shock, protein, robustness, metabolism.

===2011===
[http://www.cds.caltech.edu/~doyle/wiki/images/8/82/OnlineFinalPNASSackler2011.pdf Architecture, constraints, and behavior] 
JC Doyle, MC Csete 
P Natl Acad Sci USA, vol. 108, Sup 3 15624-15630 (2011)

[http://cds-web1.cds.caltech.edu/~doyle2/wiki/images/b/b6/Science-2011-Chandra-187-92.pdf Glycolytic Oscillations and Limits on Robust Efficiency] 
Fiona Chandra, Gentian Buzi, and John Doyle 
Science 333(6039):187-192, July 2011

[http://cds-web1.cds.caltech.edu/~doyle2/wiki/images/a/a2/6.AutomaticaJune2011.pdf Analysis of autocatalytic networks in biology] 
G Buzi, U Topcu, J Doyle 
Automatica 47:1123-1130 (2011)

===2009===
[http://www.nt.ntnu.no/users/skoge/prost/proceedings/acc09/data/papers/0207.pdf ''Linear control analysis of the autocatalytic glycolysis system''] 
Fiona Chandra, Gentian Buzi, John Doyle 
In Proc. American Control Conf, 319-324 JUN 2009

===2007===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/4/43/Nature_Connections07.pdf ''Rules of engagement''] 
John Doyle and Marie Csete 
Nature Vol 446:860 April 19 2007 (142K)

===2006===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/7/74/IEEEProc_Bio.pdf ''Advanced Methods and Algorithms for Biological Networks Analysis''], 
H El-Samad , A Papachristodoulou, S Prajna, J Doyle, and M Khammash 
In Proc. IEEE, 94 (4): 832-853 APR 2006 (900K)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/1/1f/PlosCompBio_HS06.pdf ''Module-Based Analysis of Robustness Tradeoffs in the Heat Shock Response System ''] 
Hiroyuki Kurata, Hana El-Samad, Rei Iwasaki, Hisao Ohtake, John C Doyle, Irina Grigorova, Carol A. Gross, Mustafa Khammash, 
[http://compbiol.plosjournals.org/ PLoS Comput Biol] 2(7): July 2006 (1.1MB)

===2005===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/9/98/FEBS_PPI05.pdf ''Some protein interaction data do not exhibit power law statistics''], 
R. Tanaka, T-M Yi, and J. Doyle 
FEBS letters, 579 (23): 5140-5144 Sept 26 2005 (221K)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/f/f2/IEESysBio05.pdf ''Highly optimised global organisation of metabolic networks''], 
R. Tanaka, M. Csete and J. Doyle, 
IEE Proc.-Syst. Biol. 152(4): 179, Dec 2005 (820K)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/a/a7/PLOS_Primer05.pdf ''Motifs, control, and stability''] (including ''Supplementary Notes: Elementary Feedback Concepts'') 
Doyle J and Csete M 
[http://www.plosbiology.org PLoS Biol] 3(11): e392; 2005. (387K)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/b/b4/PNAS_HeatShock05.pdf ''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)

===2004===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/1/13/Cell04.pdf ''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)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/8/82/Trends04.pdf ''Bow ties, metabolism, and disease''], 
Csete M.E. and J.C. Doyle, 
Trends in Biotechnology 22(9):446-50 Sept 2004. (121K)

===2002===
[http://www.cds.caltech.edu/~doyle2/wiki/skins/common/images/icons/fileicon-pdf.png ''Reverse Engineering of Biological Complexity''] 
Csete M and Doyle J, 
Science 295 (5560): 1664-1669 Mar 1, 2002. (1.2MB)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/1/12/JtheorBiol2002.pdf ''Robustness as a measure of plausibility in models of biochemical networks''], 
Morohashi M, Winn AE, Borisuk MT, Bolouri H, Doyle J, Kitano H, 
Journal Of Theoretical Biology 216 (1): 19-30 May 7, 2002.

===2000===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/f/f0/PNAS4649-2000.full.pdf ''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.

==SBML==
Keywords: '''SBML''', systems biology mark-up language, computer software, biochemical reaction networks

===2004===
[http://scitation.aip.org/dbt/dbt.jsp?KEY=IPSBDJ&Volume=1 '' Evolving a lingua franca and associated software infrastructure for computational systems biology: theSystemsBiologyMarkupLanguage(SBML) project''], 
M. Hucka; A. Finney; B.J. Bornstein; S.M. Keating; B.E. Shapiro; J. Matthews; B.L. Kovitz; M.J. Schilstra; A. Funahashi; J.C. Doyle; and H. Kitano 
IEE Systems Biology. 1:41-53, 2004

*''MathSBML: a package for manipulating SBML-based biological models'', 
Shapiro BE, Hucka M, Finney A, Doyle J. 
Bioinformatics, Nov 1, 2004

===2002===
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11928498&dopt=Abstract ''The ERATO Systems Biology Workbench: enabling interaction and exchange between software tools for computational biology'' (Abstract)] 
Hucka, M., Finney, A., Sauro, H. M., Bolouri, H., Doyle, J., and Kitano,H. 
in Proc. Pac Symp Biocomput. 450-61, 2002.

===2001===
*''The Systems Biology Markup Language'' 
Finney AM, Hucka M, Sauro HM, Doyle J, Kitano H, Bolouri H, 
Molecular Biology of the Cell 12: 708 Suppl. S NOV 2001.

==More Biology==
Keywords: '''biology''', cell, HOT (highly optimized tolerance), SOSTOOLS (sums of squares optimization), robustness
===2005===
''Evolutionary dynamics and highly optimized tolerance,''
Zhou T, Carlson JM, Doyle J 
Journal of Theoretical Biology 236 (4): 438-447 Oct 21 2005

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/0/01/PNAS_HOTFire05.pdf ''Wildfires, complexity, and highly optimized tolerance''], 
MA Moritz, ME Morais, LA Summerell, JM Carlson, J Doyle 
Proc. Natl. Acad. Sci. USA, December 13, 2005; 102 (50):17912–17917 (403K)

===2003===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/f/f8/CDC2003.pdf ''Model validation and robust stability analysis of the bacterial heat shock response using SOSTOOLS.''] 
H. El-Samad, S. Prajna, A. Papachristodoulou, M. Khammash and J. C. Doyle 
in Proc. IEEE CDC, vol. 4:3766 - 3771; Maui, Hawaii, 9-12 Dec. 2003.

===2002===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/7/72/PNAS2538-2002.full.pdf ''Complexity and robustness''], 
Carlson JM, Doyle J, 
Proc. Natl. Acad. Sci. USA 99: 2538-2545 Suppl. 1 Feb 19, 2002.

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/8/85/PNAS2049-2002.full.pdf ''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.

===2001===
*''Oxygen-mediated regulation of skeletal muscle satellite cell proliferation and adipogenesis in culture'' 
Csete M, Walikonis J, Slawny N, Wei Y, Korsnes S , Doyle JC, Wold B, 
Journal of Cellular Physiology, Volume 189, Issue 2, Nov. 2001. 189-196

==Related reading==
[[Papers]]

[[Research]]

[[Tips: Research papers, Publishing and Other Trivia]]

===Other===

===External links===
*[http://sbml.org/Main_Page SBML Definition and homepage]
*[http://sbml.org/Documents SBML documents]
*[http://www.systems-biology.org/ Systems Biology Portal]
*[http://www.hot.caltech.edu/ HOT : Highly Optimized/Organized Tradeoffs/Tolerance, A unified theory of complex networks ]
*[http://www.cds.caltech.edu/sostools/ SOSTOOLS : Software for analysis of complex systems]

[[Category:Research]]
[[Category:Papers by topic]]
[[Category:Papers]]

2010-2011

2012-05-04T16:39:22Z

Fiona: /* Journals */

==2011==
===Journals===
[http://www.cds.caltech.edu/~doyle/wiki/images/8/82/OnlineFinalPNASSackler2011.pdf Architecture, constraints, and behavior] 
JC Doyle, MC Csete 
P Natl Acad Sci USA, vol. 108, Sup 3 15624-15630

[http://www.sciencemag.org/cgi/rapidpdf/333/6039/187?ijkey=V1W0wT80JT9Nk&keytype=ref&siteid=sci Gycolytic oscillations and limits on robust efficiency] 
FA Chandra, G Buzi, JC Doyle 
Science 333(6039):187-192, July 2011

[http://www.cds.caltech.edu/~doyle2/wiki/images/8/87/PhysFluids_23_065108.pdf Amplification and nonlinear mechanisms in plane Couette flow.] 
D Gayme, B McKeon, B Bamieh, A Papachristodolou, and J Doyle. 
Physics of Fluids v23:6:065108 (2011)

[http://www.cds.caltech.edu/~doyle2/wiki/images/a/a2/6.AutomaticaJune2011.pdf Analysis of autocatalytic networks in biology] 
G Buzi, U Topcu, J Doyle 
Automatica 47:1123-1130 (2011)

[http://www.cds.caltech.edu/~doyle2/wiki/images/c/c4/2.IEEE_TransAutoCtrl_Feb_2011_.pdf On Lossless Approximations, the Fluctuation-Dissipation Theorem, and Limitations of Measurements] 
H Sandberg, JC Delvenne, JC Doyle 
IEE Trans Auto Control, v56:2, 293-308 (2011)

[http://www.cds.caltech.edu/~doyle2/wiki/images/6/62/9.ComputerNetworksFeb2011.pdf Cross-layer design in multihop wireless networks] 
L Chen, SH Low, and JC Doyle 
Computer Networks 55:480–496 (2011)

Javad Lavaei, Aydin Babakhani, Ali Hajimiri and John C. Doyle, "Solving
Large-Scale Hybrid Circuit-Antenna Problems," IEEE Transactions on Circuits
and Systems I, vol. 58, no. 2, pp. 374-387, Feb. 2011.

===Conferences===

Effects of Buffers on Stability of Internet Congestion Controllers 
Somayeh Sojoudi, Steven Low and John Doyle 
IEEE International Conference on Computer Communications (INFOCOM), mini conference, China, 2011.

==2010==
===Journals===
[http://www.cds.caltech.edu/~doyle2/wiki/images/a/ab/8.IEEETransNetworkingAug2010.pdf Random access game and medium access control design] 
Lijun Chen, Steven Low, and John Doyle 
IEEE Trans Networking 18:4:1303-1316, AUG 2010.

[http://www.cds.caltech.edu/~doyle2/wiki/images/d/de/1.IEEE_TransSysMCyber_AldersonDoyle-July2010.pdf Contrasting views of complexity and their implications for network-centric infrastructures] 
David Alderson and John Doyle 
IEEE Trans Systems Man Cybernetics—Part A: Syst Humans 40:839-852, JUL 2010.

[http://www.cds.caltech.edu/~dennice/PublishedVersionJFM2010.pdf A streamwise constant model of turbulence in plane Couette flow] 
Gayme DF, McKeon BJ, Papachristodoulou A, Bamieh B, and Doyle JC 
Journal of Fluid Mechanics 665:99-119 (2010)

===Conferences===
Performance Limitations in Autocatalytic Networks in Biology 
Motee N, Chandra F, Bamieh B, Khammash M, and Doyle J 
In Proc 49th IEEE Conf Decision and Control, 4715-4720, Dec 2010.

Passively Controllable Smart Antennas 
Javad Lavaei, Aydin Babakhani, Ali Hajimiri and John C. Doyle 
IEEE Global Communications Conference (GLOBECOM), Miami, Florida, 2010.

Finding Globally Optimum Solutions in Antenna Optimization Problems 
Aydin Babakhani, Javad Lavaei, John C. Doyle and Ali Hajimiri 
IEEE International Symposium on Antennas and Propagation, Toronto, Canada, 2010.

Programmable Antenna Design Using Convex Optimization 
Javad Lavaei, Aydin Babakhani, Ali Hajimiri and John C. Doyle 
19th International Symposium on Mathematical Theory of Networks and Systems, Budapest, Hungary, 2010.

Javad Lavaei, Aydin Babakhani, Ali Hajimiri and John C. Doyle, "A Study of
Near-Field Direct Antenna Modulation Systems Using Convex Optimization," in
American Control Conference, Baltimore, 2010.

Javad Lavaei, John C. Doyle and Steven Low, "Utility Functionals Associated
With Available Congestion Control Algorithms," IEEE International
Conference on Computer Communications (INFOCOM), San Diego, California,
2010.

CDS213

2012-05-04T16:37:39Z

Fiona: /* Readings */

==Readings==

*[http://www.cds.caltech.edu/~doyle/wiki/images/8/84/DoyleRantOnTuring.pdf Doyle's Rant on Turing]
*Willinger W, Alderson D, and Doyle JC (2009) [http://www.cds.caltech.edu/~doyle/wiki/images/f/f8/AMSNoticesInternet.pdf Mathematics and the internet: A source of enormous confusion and great potential]. Notices Amer Math Soc 56:586-599.
*Alderson DL, Doyle JC (2010) [http://www.cds.caltech.edu/~doyle2/wiki/images/d/de/1.IEEE_TransSysMCyber_AldersonDoyle-July2010.pdf Contrasting views of complexity and their implications for network-centric infrastructures]. IEEE Trans Systems Man Cybernetics—Part A: Syst Humans 40:839-852.
*H. Sandberg, J. C. Delvenne, J. C. Doyle. [http://www.cds.caltech.edu/~doyle2/wiki/images/c/c4/2.IEEE_TransAutoCtrl_Feb_2011_.pdf On Lossless Approximations, the Fluctuation-Dissipation Theorem, and Limitations of Measurements, IEEE Trans Auto Control], Feb 2011
*G. Buzi, U. Topcu, J. Doyle. [http://www.cds.caltech.edu/~doyle2/wiki/images/a/a2/6.AutomaticaJune2011.pdf Analysis of autocatalytic networks in biology], Automatica, vol. 47, pp. 1123--1130, 2011
*Chandra F, Buzi G, Doyle JC (2011) [http://www.cds.caltech.edu/~doyle2/wiki/images/b/b6/Science-2011-Chandra-187-92.pdf Glycolytic oscillations and limits on robust efficiency]. Science, Vol 333, pp 187-192.
*JC Doyle, ME Csete (2011) [http://www.cds.caltech.edu/~doyle/wiki/images/8/82/OnlineFinalPNASSackler2011.pdf Architecture, Constraints, and Behavior], P Natl Acad Sci USA, vol. 108, Sup 3 15624-15630
*Gayme DF, McKeon BJ, Bamieh B, Papachristodoulou P, Doyle JC (2011) [http://www.cds.caltech.edu/~doyle2/wiki/images/8/87/PhysFluids_23_065108.pdf Amplification and Nonlinear Mechanisms in Plane Couette Flow], Physics of Fluids, V23, Issue 6, 065108
*Page, M. T., D. Alderson, and J. Doyle (2011), [http://www.cds.caltech.edu/~doyle/wiki/images/a/a1/EarthquakesCalFaults.pdf The magnitude distribution of earthquakes near Southern California faults], J. Geophys. Res., 116, B12309, doi:10.1029/2010JB007933.
*Topcu U, et al. [http://www.cds.caltech.edu/~doyle/wiki/images/d/df/ROA.pdf Robust Region-of-Attraction Estimation]
*Lam, H.K. [http://www.cds.caltech.edu/~doyle/wiki/images/1/13/AutomaticaOutputFeedback.pdf Output-feedback sampled-data polynomial controller of nonlinear systems.] Automatica 47, 2011
*Papachristodoulou, A., Prajna, S. [http://www.cds.caltech.edu/~doyle/wiki/images/9/9c/0475_ThB13_1.pdf A tutorial of on Sum of Squares analysis techniques for systems analysis.]
*[http://www.cds.caltech.edu/~doyle/wiki/images/c/c9/CtrlSysMagHelpSOS.pdf Help on SOS]
 

==Other Reading==
*[http://www.cds.caltech.edu/~doyle/wiki/images/4/4a/ScienceFire.pdf Fire in the Earth System]
 
==Slides==
*April 3, 2012
**[http://www.its.caltech.edu/~fiona/1_IntroTuringCDS213_Apr3_2012.pptx Intro to Turing]
**[http://www.its.caltech.edu/~fiona/4_RedoStatMechCDS213_Apr3_2012.pptx Stat Mech]
**[http://www.its.caltech.edu/~fiona/3_LayeringPhysicsCDS213_Apr3_2012.pptx Layering and Physics]
**[http://www.its.caltech.edu/~fiona/2_ShannonCDS213_Apr3_2012.pptx Shannon]
 
==Resources==
*[http://www.cds.caltech.edu/sostools SOS Tools]
*[http://junction.stanford.edu/~lall/mtns06/ Sanjay Lall's Semidefinite Programming and Algebraic Optimization in Control]

 
Go to the [http://www.cds.caltech.edu/~doyle/wiki/index.php?title=OldCDS213 old CDS 213 page]

File:OnlineFinalPNASSackler2011.pdf

2012-05-04T16:37:13Z

Fiona:

J. Doyle’s Bio

2012-04-24T06:11:41Z

Fiona: /* First Journal Paper */

'''John Doyle''' is the John G Braun Professor of [http://www.cds.caltech.edu Control & Dynamical Systems], [http://www.ee2.caltech.edu/ Electrical Engineering], and [http://www.be.caltech.edu/ BioEngineering] at [http://www.caltech.edu Caltech].

==Recent Adventures==
[http://discovermagazine.com/2007/nov/this-man-wants-to-control-the-internet Discover magazine interviews] Prof. Doyle.

in "This man wants to control the internet" by Carl Zimmer, Discover magazine, 10/25/2007.

===Aug-Sept 2007 ===
[[Recent Adventures in Robustness and Fragility: Travels to Panama and back]]

[http://www.cds.caltech.edu/~murray/wiki/Main_Page Prof. Murray]'s version of [[John Doyle's Panamanian Adventure]]

==Academic summary==

===University===
*BS, MS EE [http://web.mit.edu/ MIT], 1977.
*Ph.D. Math, [http://www.berkeley.edu/ UC Berkeley], 1984.
*Assoc Prof with tenure at [http://www.caltech.edu Caltech], 1986.
*Prof at Caltech, 1991 - present.

===Awards===
====Projects and Grants====
Grants for various projects have been listed on the following pages:

*[[Research#Current_Projects|Research awards for projects]]
*[[Research#Past_Projects|Research awards for past projects]]

====Individual awards====
*[http://www.ieee.org/portal/pages/about/awards/pr/cntrlpr.html IEEE Control Systems Field Award recipient] for "For fundamental contributions to the analysis and control of uncertain systems" in 2004
*[http://www.ieee-centennial.org/ IEEE Centennial] Outstanding Young Engineer Award 
(as the top young researcher under 40 from the IEEE Controls Systems Society, 1984).
*[http://www.ieee.org/portal/pages/about/awards/bios/2004controlsystems.html IEEE Hickernell Award], 1976
*[http://a2c2.org/index.php?option=com_content&task=view&id=32&Itemid=46 American Automatic Control Council (AACC) Eckman Award], 1983
*[http://math.berkeley.edu/aboutus_gifts_funds.html Bernard Friedman Award] (from UC Berkeley)1984
*[http://www.onr.navy.mil/ ONR] Presidential Young Investigator 1986
*[http://www.nsf.gov/index.jsp NSF] Presidential Young Investigator 1986

===Prize papers===
*[http://www.ieee.org/web/publications/journmag/index.html IEEE Transactions] [http://www.ieeecss.org/main.php?levelsecid=171&secid=171&expandsecid=24 George S. Axelby Outstanding Paper Awards] 1990 (two papers)
*[http://www.ieee.org/portal/pages/about/awards/pr/bakepr.html IEEE Baker prize] paper, 1991 
was also ranked in the top 10 ``most important'' papers world-wide in pure and applied mathematics from 1981-1993 in a bibliometric analysis and survey conducted by CTWS-Leiden. It was the most recently published paper to be so ranked.
This prize is awarded once each year to the outstanding paper reporting new research results among all of the IEEE's over 50 technical journals,
*[http://www.a2c2.org/awards/schuck/index.php AACC Hugo Schuck Award], 1994

===Patents===
*[http://www.patentstorm.us/patents/6414827.html US Patent 6414827 - Closed-loop scaling for discrete-time servo controller in a disc drive] Issued July 2, 2002

*[http://www.patentstorm.us/patents/5978752/claims.html US Patent 5978752 - Model validation algorithm for characterizing parameters and uncertainty in a disc drive] Issued Nov 2, 1999

===First Journal Paper===
[http://www.cds.caltech.edu/~doyle/wiki/images/6/62/GuaranteedMarginsLQGRegs.pdf Guaranteed margins for LQG regulators] 
John Doyle 
IEEE Transactions on Automatic Control, Aug 1978, Volume: 23, Issue: 4, Pgs: 756 - 757
 
Abstract: "There are none."
 
[http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=1101812 Link]

===Academic Bio 1990's===
*[http://www.cds.caltech.edu/~doyle/CV.html Academic Bio 1990's]

==Industry summary==
*Served as a consultant to Honeywell Technology Center since 1976

==Research interests==
His research interests are in theoretical foundations for complex networks in engineering and biology, as well as multiscale physics, and include integrating modeling, ID, analysis and design of uncertain nonlinear systems, and computation in analysis and simulation, including complexity theory to guide algorithm development.

Research applications interests are motivated by the interplay between control, dynamical systems, and design and analysis of large, complex systems.

==Athletics==
John Doyle is an athlete in his spare time.

===Some athletic achievements from 1990's:===
*World champion, [http://www.ihpva.org/ IHPVA] speed championships time trial.
*US Record, indoor rowing (former world record).
*2 Gold medals, [http://hosting2.sportingpulse.com/www.imga-masters.com/ World Masters Games].
*Member, Duathlon Team USA.
*Age group wins:
**Duathlon in Exile (world championship qualifier),
**Fall Showdown Duathlon,
**Big Bear Duathlon,
**Powerman Chicago Sprint,
**Steamboat Triathlon,
**USCF District 6 cycling time trial...

*[http://www.cds.caltech.edu/~doyle/CVath.html Athletics 1990's]
*See [[J. Doyle's Bio Athletics]] for details and photos!

==Portraits==
{| class="wikitable"
|-
|[[Image:John-and-marie.jpg]] ||[[Image:bike2.jpg]]||http://discovermagazine.com/2007/nov/this-man-wants-to-control-the-internet/doyle2.jpg
|-
|John and Marie||Cycling||From " This Man Wants To Control the Internet 
This man wants to control the Internet. And you should let him. 
by Carl Zimmer, Photographs by Trujillo/Paumier 
published online October 25, 2007
|}

==See also==
*[http://www.ieee.org/portal/pages/about/awards/bios/2004controlsystems.html 2004 IEEE bio and photo of J Doyle]
*[http://www.cds.caltech.edu/people/ J Doyle's bio at CDS, Caltech]
===older webpages===
*[http://www.cds.caltech.edu/~doyle/CV.html Academic Bio 1990's]
*[http://www.cds.caltech.edu/~doyle/CVath.html Athletics 1990's]

J. Doyle’s Bio

2012-04-24T06:11:03Z

Fiona: /* First Paper */

'''John Doyle''' is the John G Braun Professor of [http://www.cds.caltech.edu Control & Dynamical Systems], [http://www.ee2.caltech.edu/ Electrical Engineering], and [http://www.be.caltech.edu/ BioEngineering] at [http://www.caltech.edu Caltech].

==Recent Adventures==
[http://discovermagazine.com/2007/nov/this-man-wants-to-control-the-internet Discover magazine interviews] Prof. Doyle.

in "This man wants to control the internet" by Carl Zimmer, Discover magazine, 10/25/2007.

===Aug-Sept 2007 ===
[[Recent Adventures in Robustness and Fragility: Travels to Panama and back]]

[http://www.cds.caltech.edu/~murray/wiki/Main_Page Prof. Murray]'s version of [[John Doyle's Panamanian Adventure]]

==Academic summary==

===University===
*BS, MS EE [http://web.mit.edu/ MIT], 1977.
*Ph.D. Math, [http://www.berkeley.edu/ UC Berkeley], 1984.
*Assoc Prof with tenure at [http://www.caltech.edu Caltech], 1986.
*Prof at Caltech, 1991 - present.

===Awards===
====Projects and Grants====
Grants for various projects have been listed on the following pages:

*[[Research#Current_Projects|Research awards for projects]]
*[[Research#Past_Projects|Research awards for past projects]]

====Individual awards====
*[http://www.ieee.org/portal/pages/about/awards/pr/cntrlpr.html IEEE Control Systems Field Award recipient] for "For fundamental contributions to the analysis and control of uncertain systems" in 2004
*[http://www.ieee-centennial.org/ IEEE Centennial] Outstanding Young Engineer Award 
(as the top young researcher under 40 from the IEEE Controls Systems Society, 1984).
*[http://www.ieee.org/portal/pages/about/awards/bios/2004controlsystems.html IEEE Hickernell Award], 1976
*[http://a2c2.org/index.php?option=com_content&task=view&id=32&Itemid=46 American Automatic Control Council (AACC) Eckman Award], 1983
*[http://math.berkeley.edu/aboutus_gifts_funds.html Bernard Friedman Award] (from UC Berkeley)1984
*[http://www.onr.navy.mil/ ONR] Presidential Young Investigator 1986
*[http://www.nsf.gov/index.jsp NSF] Presidential Young Investigator 1986

===Prize papers===
*[http://www.ieee.org/web/publications/journmag/index.html IEEE Transactions] [http://www.ieeecss.org/main.php?levelsecid=171&secid=171&expandsecid=24 George S. Axelby Outstanding Paper Awards] 1990 (two papers)
*[http://www.ieee.org/portal/pages/about/awards/pr/bakepr.html IEEE Baker prize] paper, 1991 
was also ranked in the top 10 ``most important'' papers world-wide in pure and applied mathematics from 1981-1993 in a bibliometric analysis and survey conducted by CTWS-Leiden. It was the most recently published paper to be so ranked.
This prize is awarded once each year to the outstanding paper reporting new research results among all of the IEEE's over 50 technical journals,
*[http://www.a2c2.org/awards/schuck/index.php AACC Hugo Schuck Award], 1994

===Patents===
*[http://www.patentstorm.us/patents/6414827.html US Patent 6414827 - Closed-loop scaling for discrete-time servo controller in a disc drive] Issued July 2, 2002

*[http://www.patentstorm.us/patents/5978752/claims.html US Patent 5978752 - Model validation algorithm for characterizing parameters and uncertainty in a disc drive] Issued Nov 2, 1999

===First Journal Paper===
[http://www.cds.caltech.edu/~doyle/wiki/images/6/62/GuaranteedMarginsLQGRegs.pdf Guaranteed margins for LQG regulators]
John Doyle
IEEE Transactions on Automatic Control, Aug 1978, Volume: 23, Issue: 4, Pgs: 756 - 757

Abstract: "There are none."

[http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=1101812 Link]

===Academic Bio 1990's===
*[http://www.cds.caltech.edu/~doyle/CV.html Academic Bio 1990's]

==Industry summary==
*Served as a consultant to Honeywell Technology Center since 1976

==Research interests==
His research interests are in theoretical foundations for complex networks in engineering and biology, as well as multiscale physics, and include integrating modeling, ID, analysis and design of uncertain nonlinear systems, and computation in analysis and simulation, including complexity theory to guide algorithm development.

Research applications interests are motivated by the interplay between control, dynamical systems, and design and analysis of large, complex systems.

==Athletics==
John Doyle is an athlete in his spare time.

===Some athletic achievements from 1990's:===
*World champion, [http://www.ihpva.org/ IHPVA] speed championships time trial.
*US Record, indoor rowing (former world record).
*2 Gold medals, [http://hosting2.sportingpulse.com/www.imga-masters.com/ World Masters Games].
*Member, Duathlon Team USA.
*Age group wins:
**Duathlon in Exile (world championship qualifier),
**Fall Showdown Duathlon,
**Big Bear Duathlon,
**Powerman Chicago Sprint,
**Steamboat Triathlon,
**USCF District 6 cycling time trial...

*[http://www.cds.caltech.edu/~doyle/CVath.html Athletics 1990's]
*See [[J. Doyle's Bio Athletics]] for details and photos!

==Portraits==
{| class="wikitable"
|-
|[[Image:John-and-marie.jpg]] ||[[Image:bike2.jpg]]||http://discovermagazine.com/2007/nov/this-man-wants-to-control-the-internet/doyle2.jpg
|-
|John and Marie||Cycling||From " This Man Wants To Control the Internet 
This man wants to control the Internet. And you should let him. 
by Carl Zimmer, Photographs by Trujillo/Paumier 
published online October 25, 2007
|}

==See also==
*[http://www.ieee.org/portal/pages/about/awards/bios/2004controlsystems.html 2004 IEEE bio and photo of J Doyle]
*[http://www.cds.caltech.edu/people/ J Doyle's bio at CDS, Caltech]
===older webpages===
*[http://www.cds.caltech.edu/~doyle/CV.html Academic Bio 1990's]
*[http://www.cds.caltech.edu/~doyle/CVath.html Athletics 1990's]

J. Doyle’s Bio

2012-04-24T06:07:45Z

Fiona:

'''John Doyle''' is the John G Braun Professor of [http://www.cds.caltech.edu Control & Dynamical Systems], [http://www.ee2.caltech.edu/ Electrical Engineering], and [http://www.be.caltech.edu/ BioEngineering] at [http://www.caltech.edu Caltech].

==Recent Adventures==
[http://discovermagazine.com/2007/nov/this-man-wants-to-control-the-internet Discover magazine interviews] Prof. Doyle.

in "This man wants to control the internet" by Carl Zimmer, Discover magazine, 10/25/2007.

===Aug-Sept 2007 ===
[[Recent Adventures in Robustness and Fragility: Travels to Panama and back]]

[http://www.cds.caltech.edu/~murray/wiki/Main_Page Prof. Murray]'s version of [[John Doyle's Panamanian Adventure]]

==Academic summary==

===University===
*BS, MS EE [http://web.mit.edu/ MIT], 1977.
*Ph.D. Math, [http://www.berkeley.edu/ UC Berkeley], 1984.
*Assoc Prof with tenure at [http://www.caltech.edu Caltech], 1986.
*Prof at Caltech, 1991 - present.

===Awards===
====Projects and Grants====
Grants for various projects have been listed on the following pages:

*[[Research#Current_Projects|Research awards for projects]]
*[[Research#Past_Projects|Research awards for past projects]]

====Individual awards====
*[http://www.ieee.org/portal/pages/about/awards/pr/cntrlpr.html IEEE Control Systems Field Award recipient] for "For fundamental contributions to the analysis and control of uncertain systems" in 2004
*[http://www.ieee-centennial.org/ IEEE Centennial] Outstanding Young Engineer Award 
(as the top young researcher under 40 from the IEEE Controls Systems Society, 1984).
*[http://www.ieee.org/portal/pages/about/awards/bios/2004controlsystems.html IEEE Hickernell Award], 1976
*[http://a2c2.org/index.php?option=com_content&task=view&id=32&Itemid=46 American Automatic Control Council (AACC) Eckman Award], 1983
*[http://math.berkeley.edu/aboutus_gifts_funds.html Bernard Friedman Award] (from UC Berkeley)1984
*[http://www.onr.navy.mil/ ONR] Presidential Young Investigator 1986
*[http://www.nsf.gov/index.jsp NSF] Presidential Young Investigator 1986

===Prize papers===
*[http://www.ieee.org/web/publications/journmag/index.html IEEE Transactions] [http://www.ieeecss.org/main.php?levelsecid=171&secid=171&expandsecid=24 George S. Axelby Outstanding Paper Awards] 1990 (two papers)
*[http://www.ieee.org/portal/pages/about/awards/pr/bakepr.html IEEE Baker prize] paper, 1991 
was also ranked in the top 10 ``most important'' papers world-wide in pure and applied mathematics from 1981-1993 in a bibliometric analysis and survey conducted by CTWS-Leiden. It was the most recently published paper to be so ranked.
This prize is awarded once each year to the outstanding paper reporting new research results among all of the IEEE's over 50 technical journals,
*[http://www.a2c2.org/awards/schuck/index.php AACC Hugo Schuck Award], 1994

===Patents===
*[http://www.patentstorm.us/patents/6414827.html US Patent 6414827 - Closed-loop scaling for discrete-time servo controller in a disc drive] Issued July 2, 2002

*[http://www.patentstorm.us/patents/5978752/claims.html US Patent 5978752 - Model validation algorithm for characterizing parameters and uncertainty in a disc drive] Issued Nov 2, 1999

===First Paper===
J. Doyle, [[http://www.cds.caltech.edu/~doyle/wiki/images/6/62/GuaranteedMarginsLQGRegs.pdf Guaranteed margins for LQG regulators], IEEE Transactions on Automatic
Control, Aug 1978, Volume: 23, Issue: 4, Pgs: 756 - 757

Abstract: "There are none."

[http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=1101812 Link]

===Academic Bio 1990's===
*[http://www.cds.caltech.edu/~doyle/CV.html Academic Bio 1990's]

==Industry summary==
*Served as a consultant to Honeywell Technology Center since 1976

==Research interests==
His research interests are in theoretical foundations for complex networks in engineering and biology, as well as multiscale physics, and include integrating modeling, ID, analysis and design of uncertain nonlinear systems, and computation in analysis and simulation, including complexity theory to guide algorithm development.

Research applications interests are motivated by the interplay between control, dynamical systems, and design and analysis of large, complex systems.

==Athletics==
John Doyle is an athlete in his spare time.

===Some athletic achievements from 1990's:===
*World champion, [http://www.ihpva.org/ IHPVA] speed championships time trial.
*US Record, indoor rowing (former world record).
*2 Gold medals, [http://hosting2.sportingpulse.com/www.imga-masters.com/ World Masters Games].
*Member, Duathlon Team USA.
*Age group wins:
**Duathlon in Exile (world championship qualifier),
**Fall Showdown Duathlon,
**Big Bear Duathlon,
**Powerman Chicago Sprint,
**Steamboat Triathlon,
**USCF District 6 cycling time trial...

*[http://www.cds.caltech.edu/~doyle/CVath.html Athletics 1990's]
*See [[J. Doyle's Bio Athletics]] for details and photos!

==Portraits==
{| class="wikitable"
|-
|[[Image:John-and-marie.jpg]] ||[[Image:bike2.jpg]]||http://discovermagazine.com/2007/nov/this-man-wants-to-control-the-internet/doyle2.jpg
|-
|John and Marie||Cycling||From " This Man Wants To Control the Internet 
This man wants to control the Internet. And you should let him. 
by Carl Zimmer, Photographs by Trujillo/Paumier 
published online October 25, 2007
|}

==See also==
*[http://www.ieee.org/portal/pages/about/awards/bios/2004controlsystems.html 2004 IEEE bio and photo of J Doyle]
*[http://www.cds.caltech.edu/people/ J Doyle's bio at CDS, Caltech]
===older webpages===
*[http://www.cds.caltech.edu/~doyle/CV.html Academic Bio 1990's]
*[http://www.cds.caltech.edu/~doyle/CVath.html Athletics 1990's]

File:GuaranteedMarginsLQGRegs.pdf

2012-04-24T06:06:52Z

Fiona:

CDS213

2012-04-05T21:16:15Z

Fiona: /* Readings */

==Readings==

*[http://www.cds.caltech.edu/~doyle/wiki/images/8/84/DoyleRantOnTuring.pdf Doyle's Rant on Turing]
*Willinger W, Alderson D, and Doyle JC (2009) [http://www.cds.caltech.edu/~doyle/wiki/images/f/f8/AMSNoticesInternet.pdf Mathematics and the internet: A source of enormous confusion and great potential]. Notices Amer Math Soc 56:586-599.
*Alderson DL, Doyle JC (2010) [http://www.cds.caltech.edu/~doyle2/wiki/images/d/de/1.IEEE_TransSysMCyber_AldersonDoyle-July2010.pdf Contrasting views of complexity and their implications for network-centric infrastructures]. IEEE Trans Systems Man Cybernetics—Part A: Syst Humans 40:839-852.
*H. Sandberg, J. C. Delvenne, J. C. Doyle. [http://www.cds.caltech.edu/~doyle2/wiki/images/c/c4/2.IEEE_TransAutoCtrl_Feb_2011_.pdf On Lossless Approximations, the Fluctuation-Dissipation Theorem, and Limitations of Measurements, IEEE Trans Auto Control], Feb 2011
*G. Buzi, U. Topcu, J. Doyle. [http://www.cds.caltech.edu/~doyle2/wiki/images/a/a2/6.AutomaticaJune2011.pdf Analysis of autocatalytic networks in biology], Automatica, vol. 47, pp. 1123--1130, 2011
*Chandra F, Buzi G, Doyle JC (2011) [http://www.cds.caltech.edu/~doyle2/wiki/images/b/b6/Science-2011-Chandra-187-92.pdf Glycolytic oscillations and limits on robust efficiency]. Science, Vol 333, pp 187-192.
*JC Doyle, ME Csete (2011) [http://www.cds.caltech.edu/~doyle2/wiki/images/4/4e/7.PNAS_InPress_June_2011.pdf Architecture, Constraints, and Behavior], P Natl Acad Sci USA, vol. 108, Sup 3 15624-15630
*Gayme DF, McKeon BJ, Bamieh B, Papachristodoulou P, Doyle JC (2011) [http://www.cds.caltech.edu/~doyle2/wiki/images/8/87/PhysFluids_23_065108.pdf Amplification and Nonlinear Mechanisms in Plane Couette Flow], Physics of Fluids, V23, Issue 6, 065108
*Page, M. T., D. Alderson, and J. Doyle (2011), [http://www.cds.caltech.edu/~doyle/wiki/images/a/a1/EarthquakesCalFaults.pdf The magnitude distribution of earthquakes near Southern California faults], J. Geophys. Res., 116, B12309, doi:10.1029/2010JB007933.
*Topcu U, et al. [http://www.cds.caltech.edu/~doyle/wiki/images/d/df/ROA.pdf Robust Region-of-Attraction Estimation]
*Lam, H.K. [http://www.cds.caltech.edu/~doyle/wiki/images/1/13/AutomaticaOutputFeedback.pdf Output-feedback sampled-data polynomial controller of nonlinear systems.] Automatica 47, 2011
*Papachristodoulou, A., Prajna, S. [http://www.cds.caltech.edu/~doyle/wiki/images/9/9c/0475_ThB13_1.pdf A tutorial of on Sum of Squares analysis techniques for systems analysis.]
*[http://www.cds.caltech.edu/~doyle/wiki/images/c/c9/CtrlSysMagHelpSOS.pdf Help on SOS]
 

==Other Reading==
*[http://www.cds.caltech.edu/~doyle/wiki/images/4/4a/ScienceFire.pdf Fire in the Earth System]
 
==Slides==
*April 3, 2012
**[http://www.its.caltech.edu/~fiona/1_IntroTuringCDS213_Apr3_2012.pptx Intro to Turing]
**[http://www.its.caltech.edu/~fiona/4_RedoStatMechCDS213_Apr3_2012.pptx Stat Mech]
**[http://www.its.caltech.edu/~fiona/3_LayeringPhysicsCDS213_Apr3_2012.pptx Layering and Physics]
**[http://www.its.caltech.edu/~fiona/2_ShannonCDS213_Apr3_2012.pptx Shannon]
 
==Resources==
*[http://www.cds.caltech.edu/sostools SOS Tools]
*[http://junction.stanford.edu/~lall/mtns06/ Sanjay Lall's Semidefinite Programming and Algebraic Optimization in Control]

 
Go to the [http://www.cds.caltech.edu/~doyle/wiki/index.php?title=OldCDS213 old CDS 213 page]

File:0475 ThB13 1.pdf

2012-04-05T21:15:26Z

Fiona:

File:CtrlSysMagHelpSOS.pdf

2012-04-05T21:14:26Z

Fiona:

CDS213

2012-04-05T21:12:53Z

Fiona: /* Readings */

==Readings==

*[http://www.cds.caltech.edu/~doyle/wiki/images/8/84/DoyleRantOnTuring.pdf Doyle's Rant on Turing]
*Willinger W, Alderson D, and Doyle JC (2009) [http://www.cds.caltech.edu/~doyle/wiki/images/f/f8/AMSNoticesInternet.pdf Mathematics and the internet: A source of enormous confusion and great potential]. Notices Amer Math Soc 56:586-599.
*Alderson DL, Doyle JC (2010) [http://www.cds.caltech.edu/~doyle2/wiki/images/d/de/1.IEEE_TransSysMCyber_AldersonDoyle-July2010.pdf Contrasting views of complexity and their implications for network-centric infrastructures]. IEEE Trans Systems Man Cybernetics—Part A: Syst Humans 40:839-852.
*H. Sandberg, J. C. Delvenne, J. C. Doyle. [http://www.cds.caltech.edu/~doyle2/wiki/images/c/c4/2.IEEE_TransAutoCtrl_Feb_2011_.pdf On Lossless Approximations, the Fluctuation-Dissipation Theorem, and Limitations of Measurements, IEEE Trans Auto Control], Feb 2011
*G. Buzi, U. Topcu, J. Doyle. [http://www.cds.caltech.edu/~doyle2/wiki/images/a/a2/6.AutomaticaJune2011.pdf Analysis of autocatalytic networks in biology], Automatica, vol. 47, pp. 1123--1130, 2011
*Chandra F, Buzi G, Doyle JC (2011) [http://www.cds.caltech.edu/~doyle2/wiki/images/b/b6/Science-2011-Chandra-187-92.pdf Glycolytic oscillations and limits on robust efficiency]. Science, Vol 333, pp 187-192.
*JC Doyle, ME Csete (2011) [http://www.cds.caltech.edu/~doyle2/wiki/images/4/4e/7.PNAS_InPress_June_2011.pdf Architecture, Constraints, and Behavior], P Natl Acad Sci USA, vol. 108, Sup 3 15624-15630
*Gayme DF, McKeon BJ, Bamieh B, Papachristodoulou P, Doyle JC (2011) [http://www.cds.caltech.edu/~doyle2/wiki/images/8/87/PhysFluids_23_065108.pdf Amplification and Nonlinear Mechanisms in Plane Couette Flow], Physics of Fluids, V23, Issue 6, 065108
*Page, M. T., D. Alderson, and J. Doyle (2011), [http://www.cds.caltech.edu/~doyle/wiki/images/a/a1/EarthquakesCalFaults.pdf The magnitude distribution of earthquakes near Southern California faults], J. Geophys. Res., 116, B12309, doi:10.1029/2010JB007933.
*Topcu U, et al. [http://www.cds.caltech.edu/~doyle/wiki/images/d/df/ROA.pdf Robust Region-of-Attraction Estimation]
*Lam, H.K. [http://www.cds.caltech.edu/~doyle/wiki/images/1/13/AutomaticaOutputFeedback.pdf Output-feedback sampled-data polynomial controller of nonlinear systems.] Automatica 47, 2011
 

==Other Reading==
*[http://www.cds.caltech.edu/~doyle/wiki/images/4/4a/ScienceFire.pdf Fire in the Earth System]
 
==Slides==
*April 3, 2012
**[http://www.its.caltech.edu/~fiona/1_IntroTuringCDS213_Apr3_2012.pptx Intro to Turing]
**[http://www.its.caltech.edu/~fiona/4_RedoStatMechCDS213_Apr3_2012.pptx Stat Mech]
**[http://www.its.caltech.edu/~fiona/3_LayeringPhysicsCDS213_Apr3_2012.pptx Layering and Physics]
**[http://www.its.caltech.edu/~fiona/2_ShannonCDS213_Apr3_2012.pptx Shannon]
 
==Resources==
*[http://www.cds.caltech.edu/sostools SOS Tools]
*[http://junction.stanford.edu/~lall/mtns06/ Sanjay Lall's Semidefinite Programming and Algebraic Optimization in Control]

 
Go to the [http://www.cds.caltech.edu/~doyle/wiki/index.php?title=OldCDS213 old CDS 213 page]

File:AutomaticaOutputFeedback.pdf

2012-04-05T21:11:54Z

Fiona:

File:ROA.pdf

2012-04-05T21:10:32Z

Fiona:

CDS213

2012-04-05T19:03:13Z

Fiona:

==Readings==

*[http://www.cds.caltech.edu/~doyle/wiki/images/8/84/DoyleRantOnTuring.pdf Doyle's Rant on Turing]
*Willinger W, Alderson D, and Doyle JC (2009) [http://www.cds.caltech.edu/~doyle/wiki/images/f/f8/AMSNoticesInternet.pdf Mathematics and the internet: A source of enormous confusion and great potential]. Notices Amer Math Soc 56:586-599.
*Alderson DL, Doyle JC (2010) [http://www.cds.caltech.edu/~doyle2/wiki/images/d/de/1.IEEE_TransSysMCyber_AldersonDoyle-July2010.pdf Contrasting views of complexity and their implications for network-centric infrastructures]. IEEE Trans Systems Man Cybernetics—Part A: Syst Humans 40:839-852.
*H. Sandberg, J. C. Delvenne, J. C. Doyle. [http://www.cds.caltech.edu/~doyle2/wiki/images/c/c4/2.IEEE_TransAutoCtrl_Feb_2011_.pdf On Lossless Approximations, the Fluctuation-Dissipation Theorem, and Limitations of Measurements, IEEE Trans Auto Control], Feb 2011
*G. Buzi, U. Topcu, J. Doyle. [http://www.cds.caltech.edu/~doyle2/wiki/images/a/a2/6.AutomaticaJune2011.pdf Analysis of autocatalytic networks in biology], Automatica, vol. 47, pp. 1123--1130, 2011
*Chandra F, Buzi G, Doyle JC (2011) [http://www.cds.caltech.edu/~doyle2/wiki/images/b/b6/Science-2011-Chandra-187-92.pdf Glycolytic oscillations and limits on robust efficiency]. Science, Vol 333, pp 187-192.
*JC Doyle, ME Csete (2011) [http://www.cds.caltech.edu/~doyle2/wiki/images/4/4e/7.PNAS_InPress_June_2011.pdf Architecture, Constraints, and Behavior], P Natl Acad Sci USA, vol. 108, Sup 3 15624-15630
*Gayme DF, McKeon BJ, Bamieh B, Papachristodoulou P, Doyle JC (2011) [http://www.cds.caltech.edu/~doyle2/wiki/images/8/87/PhysFluids_23_065108.pdf Amplification and Nonlinear Mechanisms in Plane Couette Flow], Physics of Fluids, V23, Issue 6, 065108
*Page, M. T., D. Alderson, and J. Doyle (2011), [http://www.cds.caltech.edu/~doyle/wiki/images/a/a1/EarthquakesCalFaults.pdf The magnitude distribution of earthquakes near Southern California faults], J. Geophys. Res., 116, B12309, doi:10.1029/2010JB007933.
 
==Other Reading==
*[http://www.cds.caltech.edu/~doyle/wiki/images/4/4a/ScienceFire.pdf Fire in the Earth System]
 
==Slides==
*April 3, 2012
**[http://www.its.caltech.edu/~fiona/1_IntroTuringCDS213_Apr3_2012.pptx Intro to Turing]
**[http://www.its.caltech.edu/~fiona/4_RedoStatMechCDS213_Apr3_2012.pptx Stat Mech]
**[http://www.its.caltech.edu/~fiona/3_LayeringPhysicsCDS213_Apr3_2012.pptx Layering and Physics]
**[http://www.its.caltech.edu/~fiona/2_ShannonCDS213_Apr3_2012.pptx Shannon]
 
==Resources==
*[http://www.cds.caltech.edu/sostools SOS Tools]
*[http://junction.stanford.edu/~lall/mtns06/ Sanjay Lall's Semidefinite Programming and Algebraic Optimization in Control]

 
Go to the [http://www.cds.caltech.edu/~doyle/wiki/index.php?title=OldCDS213 old CDS 213 page]

CDS213

2012-04-04T00:49:50Z

Fiona: /* Slides */

==Readings==

*[http://www.cds.caltech.edu/~doyle/wiki/images/8/84/DoyleRantOnTuring.pdf Doyle's Rant on Turing]
*Willinger W, Alderson D, and Doyle JC (2009) [http://www.cds.caltech.edu/~doyle/wiki/images/f/f8/AMSNoticesInternet.pdf Mathematics and the internet: A source of enormous confusion and great potential]. Notices Amer Math Soc 56:586-599.
*Alderson DL, Doyle JC (2010) [http://www.cds.caltech.edu/~doyle2/wiki/images/d/de/1.IEEE_TransSysMCyber_AldersonDoyle-July2010.pdf Contrasting views of complexity and their implications for network-centric infrastructures]. IEEE Trans Systems Man Cybernetics—Part A: Syst Humans 40:839-852.
*H. Sandberg, J. C. Delvenne, J. C. Doyle. [http://www.cds.caltech.edu/~doyle2/wiki/images/c/c4/2.IEEE_TransAutoCtrl_Feb_2011_.pdf On Lossless Approximations, the Fluctuation-Dissipation Theorem, and Limitations of Measurements, IEEE Trans Auto Control], Feb 2011
*G. Buzi, U. Topcu, J. Doyle. [http://www.cds.caltech.edu/~doyle2/wiki/images/a/a2/6.AutomaticaJune2011.pdf Analysis of autocatalytic networks in biology], Automatica, vol. 47, pp. 1123--1130, 2011
*Chandra F, Buzi G, Doyle JC (2011) [http://www.cds.caltech.edu/~doyle2/wiki/images/b/b6/Science-2011-Chandra-187-92.pdf Glycolytic oscillations and limits on robust efficiency]. Science, Vol 333, pp 187-192.
*JC Doyle, ME Csete (2011) [http://www.cds.caltech.edu/~doyle2/wiki/images/4/4e/7.PNAS_InPress_June_2011.pdf Architecture, Constraints, and Behavior], P Natl Acad Sci USA, vol. 108, Sup 3 15624-15630
*Gayme DF, McKeon BJ, Bamieh B, Papachristodoulou P, Doyle JC (2011) [http://www.cds.caltech.edu/~doyle2/wiki/images/8/87/PhysFluids_23_065108.pdf Amplification and Nonlinear Mechanisms in Plane Couette Flow], Physics of Fluids, V23, Issue 6, 065108
*Page, M. T., D. Alderson, and J. Doyle (2011), [http://www.cds.caltech.edu/~doyle/wiki/images/a/a1/EarthquakesCalFaults.pdf The magnitude distribution of earthquakes near Southern California faults], J. Geophys. Res., 116, B12309, doi:10.1029/2010JB007933.
 
==Other Reading==
*[http://www.cds.caltech.edu/~doyle/wiki/images/4/4a/ScienceFire.pdf Fire in the Earth System]
 
==Slides==
*April 3, 2012
**[http://www.its.caltech.edu/~fiona/1_IntroTuringCDS213_Apr3_2012.pptx Intro to Turing]
**[http://www.its.caltech.edu/~fiona/4_RedoStatMechCDS213_Apr3_2012.pptx Stat Mech]
**[http://www.its.caltech.edu/~fiona/3_LayeringPhysicsCDS213_Apr3_2012.pptx Layering and Physics]
**[http://www.its.caltech.edu/~fiona/2_ShannonCDS213_Apr3_2012.pptx Shannon]

 
Go to the [http://www.cds.caltech.edu/~doyle/wiki/index.php?title=OldCDS213 old CDS 213 page]

CDS213

2012-04-04T00:42:59Z

Fiona:

==Readings==

*[http://www.cds.caltech.edu/~doyle/wiki/images/8/84/DoyleRantOnTuring.pdf Doyle's Rant on Turing]
*Willinger W, Alderson D, and Doyle JC (2009) [http://www.cds.caltech.edu/~doyle/wiki/images/f/f8/AMSNoticesInternet.pdf Mathematics and the internet: A source of enormous confusion and great potential]. Notices Amer Math Soc 56:586-599.
*Alderson DL, Doyle JC (2010) [http://www.cds.caltech.edu/~doyle2/wiki/images/d/de/1.IEEE_TransSysMCyber_AldersonDoyle-July2010.pdf Contrasting views of complexity and their implications for network-centric infrastructures]. IEEE Trans Systems Man Cybernetics—Part A: Syst Humans 40:839-852.
*H. Sandberg, J. C. Delvenne, J. C. Doyle. [http://www.cds.caltech.edu/~doyle2/wiki/images/c/c4/2.IEEE_TransAutoCtrl_Feb_2011_.pdf On Lossless Approximations, the Fluctuation-Dissipation Theorem, and Limitations of Measurements, IEEE Trans Auto Control], Feb 2011
*G. Buzi, U. Topcu, J. Doyle. [http://www.cds.caltech.edu/~doyle2/wiki/images/a/a2/6.AutomaticaJune2011.pdf Analysis of autocatalytic networks in biology], Automatica, vol. 47, pp. 1123--1130, 2011
*Chandra F, Buzi G, Doyle JC (2011) [http://www.cds.caltech.edu/~doyle2/wiki/images/b/b6/Science-2011-Chandra-187-92.pdf Glycolytic oscillations and limits on robust efficiency]. Science, Vol 333, pp 187-192.
*JC Doyle, ME Csete (2011) [http://www.cds.caltech.edu/~doyle2/wiki/images/4/4e/7.PNAS_InPress_June_2011.pdf Architecture, Constraints, and Behavior], P Natl Acad Sci USA, vol. 108, Sup 3 15624-15630
*Gayme DF, McKeon BJ, Bamieh B, Papachristodoulou P, Doyle JC (2011) [http://www.cds.caltech.edu/~doyle2/wiki/images/8/87/PhysFluids_23_065108.pdf Amplification and Nonlinear Mechanisms in Plane Couette Flow], Physics of Fluids, V23, Issue 6, 065108
*Page, M. T., D. Alderson, and J. Doyle (2011), [http://www.cds.caltech.edu/~doyle/wiki/images/a/a1/EarthquakesCalFaults.pdf The magnitude distribution of earthquakes near Southern California faults], J. Geophys. Res., 116, B12309, doi:10.1029/2010JB007933.
 
==Other Reading==
*[http://www.cds.caltech.edu/~doyle/wiki/images/4/4a/ScienceFire.pdf Fire in the Earth System]
 
==Slides==
*April 3, 2012
**[http://www.its.caltech.edu/~fiona/1_IntroTuringCDS213_Apr3_2012.pptx Intro to Turing]
**Stat Mech
**Layering and Physics
**Shannon

 
Go to the [http://www.cds.caltech.edu/~doyle/wiki/index.php?title=OldCDS213 old CDS 213 page]

CDS213

2012-04-02T23:06:54Z

Fiona:

TuringRant

2012-04-02T23:06:31Z

Fiona: /* Doyle's Rant on Turing */

==Doyle's Rant on Turing: Readings==

*[http://www.cds.caltech.edu/~doyle/wiki/images/8/84/DoyleRantOnTuring.pdf Doyle's Rant on Turing]

*Willinger W, Alderson D, and Doyle JC (2009) [http://www.cds.caltech.edu/~doyle/wiki/images/f/f8/AMSNoticesInternet.pdf Mathematics and the internet: A source of enormous confusion and great potential]. Notices Amer Math Soc 56:586-599.
*Alderson DL, Doyle JC (2010) [http://www.cds.caltech.edu/~doyle2/wiki/images/d/de/1.IEEE_TransSysMCyber_AldersonDoyle-July2010.pdf Contrasting views of complexity and their implications for network-centric infrastructures]. IEEE Trans Systems Man Cybernetics—Part A: Syst Humans 40:839-852.
*H. Sandberg, J. C. Delvenne, J. C. Doyle. [http://www.cds.caltech.edu/~doyle2/wiki/images/c/c4/2.IEEE_TransAutoCtrl_Feb_2011_.pdf On Lossless Approximations, the Fluctuation-Dissipation Theorem, and Limitations of Measurements, IEEE Trans Auto Control], Feb 2011
*G. Buzi, U. Topcu, J. Doyle. [http://www.cds.caltech.edu/~doyle2/wiki/images/a/a2/6.AutomaticaJune2011.pdf Analysis of autocatalytic networks in biology], Automatica, vol. 47, pp. 1123--1130, 2011
*Chandra F, Buzi G, Doyle JC (2011) [http://www.cds.caltech.edu/~doyle2/wiki/images/b/b6/Science-2011-Chandra-187-92.pdf Glycolytic oscillations and limits on robust efficiency]. Science, Vol 333, pp 187-192.
*JC Doyle, ME Csete (2011) [http://www.cds.caltech.edu/~doyle2/wiki/images/4/4e/7.PNAS_InPress_June_2011.pdf Architecture, Constraints, and Behavior], P Natl Acad Sci USA, vol. 108, Sup 3 15624-15630
*Gayme DF, McKeon BJ, Bamieh B, Papachristodoulou P, Doyle JC (2011) [http://www.cds.caltech.edu/~doyle2/wiki/images/8/87/PhysFluids_23_065108.pdf Amplification and Nonlinear Mechanisms in Plane Couette Flow], Physics of Fluids, V23, Issue 6, 065108
*Page, M. T., D. Alderson, and J. Doyle (2011), [http://www.cds.caltech.edu/~doyle/wiki/images/a/a1/EarthquakesCalFaults.pdf The magnitude distribution of earthquakes near Southern California faults], J. Geophys. Res., 116, B12309, doi:10.1029/2010JB007933.

 

==Other Readings==
*[http://www.cds.caltech.edu/~doyle/wiki/images/4/4a/ScienceFire.pdf Fire in the Earth System]

File:DoyleRantOnTuring.pdf

2012-04-02T23:05:49Z

Fiona:

Main Page

2012-04-02T22:46:18Z

Fiona: /* Teaching */

<table border=1 width=100% style="color:black; " cellpadding="20" cellspacing="0">
<tr>
<td align=center width=20%> [[Image:Smallpic.JPG]]</td>
<td width=60% align=center>
John C. Doyle 

John G Braun Professor 
of Control and Dynamical Systems 
Electrical Engineering 
and BioEngineering 
Division of Engineering and Applied Science 
California Institute of Technology 

</td>
<td align=center width=20%>


[[J. Doyle’s Bio]]

[[News]]

[[Calendar]]

[[#Contact|Contact]]

[https://www.cds.caltech.edu/squirrelmail/src/login.php CDS Webmail]
</td>
</tr></table>
{| align=center
|[[Image:Blossoms900strip.jpg]]||[[Image:Blossoms900strip.jpg]]||[[Image:Blossoms900strip.jpg]]||[[Image:Blossoms900strip.jpg]]
|}
<hr>

==News==
*Visiting this week: Ioannis Lestas
*[[Research|MURI 2008]]
*[http://discovermagazine.com/2007/nov/this-man-wants-to-control-the-internet Discover magazine] interviews Prof. Doyle.

"This man wants to control the internet" by Carl Zimmer, Discover magazine, 10/25/2007.

==Recent Papers==
*[http://www.cds.caltech.edu/~doyle2/wiki/images/4/4e/7.PNAS_InPress_June_2011.pdf Architecture, constraints, and behavior.] JC Doyle, MC Csete. PNAS, in press, July 2011
*[http://www.cds.caltech.edu/~doyle2/wiki/images/b/b6/Science-2011-Chandra-187-92.pdf Glycolytic oscillations and limits on robust efficiency.] FA Chandra, G Buzi, JC Doyle Science 333(6039):187-192, July 2011
*[http://www.cds.caltech.edu/~doyle2/wiki/images/c/c4/2.IEEE_TransAutoCtrl_Feb_2011_.pdf On Lossless Approximations, the Fluctuation-Dissipation Theorem, and Limitations of Measurements] H Sandberg, JC Delvenne, JC Doyle IEEE Trans Auto Control, v56:2, 293-308 (2011)
*[[Papers|'''More Papers''']]

== Research ==
John Doyle's '''[[research]]''' interests are in theoretical foundations for complex networks in engineering and biology, as well as multiscale physics, and include integrating modeling, ID, analysis and design of uncertain nonlinear systems, and computation in analysis and simulation, including complexity theory to guide algorithm development. Applications interests are motivated by the interplay between: control, dynamical systems, and design and analysis of large, complex systems.

*[[Research|Research projects and grants list]]

== Teaching ==

*[http://www.cds.caltech.edu/~doyle/wiki/index.php?title=CDS213 CDS 213, Robust Control (Spring 2012)]
*[http://www.cds.caltech.edu/~murray/wiki/CDS_212_Fall_2010 CDS 212, Feedback Control Theory (Fall 2010)]
*[[CDS 213|The Architecture of Robust, Evolvable Networks (Wi10)]]

== Contact ==
{| width=100%
|- valign=top
| width=50% |

'''Mailing Address'''

John Doyle 
California Institute of Technology 
Control and Dynamical Systems, MC 107-81 
1200 E. California Blvd 
Pasadena, CA 91125 USA
| width=50% |

'''Contact information'''

E-mail: doyle AT cds dot caltech dot edu 
Office: 109 Steele, 
Phone: 626.395.4808 Fax: 626.395.6170 

'''Admin Assistant''': Anissa Scott 
Office: 107 Steele, 
Email: anissa AT caltech dot edu 
Phone: 626.395.4140 
Labs: 12 STL, 110 GUG (x2319)
|-
|

===Other Caltech links===

*[http://www.caltech.edu California Institute of Technology]
**[http://www.eas.caltech.edu Engineering and Applied Science Division]
***[http://www.be.caltech.edu/ Bioengineering Department]
***[http://www.cds.caltech.edu Control and Dynamical Systems Department]
***[http://www.ee2.caltech.edu/ Electrical Engineering Department]
|}

CDS213

2012-04-02T22:42:22Z

Fiona:

==Readings==

*Willinger W, Alderson D, and Doyle JC (2009) [http://www.cds.caltech.edu/~doyle/wiki/images/f/f8/AMSNoticesInternet.pdf Mathematics and the internet: A source of enormous confusion and great potential]. Notices Amer Math Soc 56:586-599.
*Alderson DL, Doyle JC (2010) [http://www.cds.caltech.edu/~doyle2/wiki/images/d/de/1.IEEE_TransSysMCyber_AldersonDoyle-July2010.pdf Contrasting views of complexity and their implications for network-centric infrastructures]. IEEE Trans Systems Man Cybernetics—Part A: Syst Humans 40:839-852.
*H. Sandberg, J. C. Delvenne, J. C. Doyle. [http://www.cds.caltech.edu/~doyle2/wiki/images/c/c4/2.IEEE_TransAutoCtrl_Feb_2011_.pdf On Lossless Approximations, the Fluctuation-Dissipation Theorem, and Limitations of Measurements, IEEE Trans Auto Control], Feb 2011
*G. Buzi, U. Topcu, J. Doyle. [http://www.cds.caltech.edu/~doyle2/wiki/images/a/a2/6.AutomaticaJune2011.pdf Analysis of autocatalytic networks in biology], Automatica, vol. 47, pp. 1123--1130, 2011
*Chandra F, Buzi G, Doyle JC (2011) [http://www.cds.caltech.edu/~doyle2/wiki/images/b/b6/Science-2011-Chandra-187-92.pdf Glycolytic oscillations and limits on robust efficiency]. Science, Vol 333, pp 187-192.
*JC Doyle, ME Csete (2011) [http://www.cds.caltech.edu/~doyle2/wiki/images/4/4e/7.PNAS_InPress_June_2011.pdf Architecture, Constraints, and Behavior], P Natl Acad Sci USA, vol. 108, Sup 3 15624-15630
*Gayme DF, McKeon BJ, Bamieh B, Papachristodoulou P, Doyle JC (2011) [http://www.cds.caltech.edu/~doyle2/wiki/images/8/87/PhysFluids_23_065108.pdf Amplification and Nonlinear Mechanisms in Plane Couette Flow], Physics of Fluids, V23, Issue 6, 065108
*Page, M. T., D. Alderson, and J. Doyle (2011), [http://www.cds.caltech.edu/~doyle/wiki/images/a/a1/EarthquakesCalFaults.pdf The magnitude distribution of earthquakes near Southern California faults], J. Geophys. Res., 116, B12309, doi:10.1029/2010JB007933.
 
==Other Reading==
*[http://www.cds.caltech.edu/~doyle/wiki/images/4/4a/ScienceFire.pdf Fire in the Earth System]

 
Go to the [http://www.cds.caltech.edu/~doyle/wiki/index.php?title=OldCDS213 old CDS 213 page]

TuringRant

2012-04-02T22:41:39Z

Fiona:

==Doyle's Rant on Turing==

*Willinger W, Alderson D, and Doyle JC (2009) [http://www.cds.caltech.edu/~doyle/wiki/images/f/f8/AMSNoticesInternet.pdf Mathematics and the internet: A source of enormous confusion and great potential]. Notices Amer Math Soc 56:586-599.
*Alderson DL, Doyle JC (2010) [http://www.cds.caltech.edu/~doyle2/wiki/images/d/de/1.IEEE_TransSysMCyber_AldersonDoyle-July2010.pdf Contrasting views of complexity and their implications for network-centric infrastructures]. IEEE Trans Systems Man Cybernetics—Part A: Syst Humans 40:839-852.
*H. Sandberg, J. C. Delvenne, J. C. Doyle. [http://www.cds.caltech.edu/~doyle2/wiki/images/c/c4/2.IEEE_TransAutoCtrl_Feb_2011_.pdf On Lossless Approximations, the Fluctuation-Dissipation Theorem, and Limitations of Measurements, IEEE Trans Auto Control], Feb 2011
*G. Buzi, U. Topcu, J. Doyle. [http://www.cds.caltech.edu/~doyle2/wiki/images/a/a2/6.AutomaticaJune2011.pdf Analysis of autocatalytic networks in biology], Automatica, vol. 47, pp. 1123--1130, 2011
*Chandra F, Buzi G, Doyle JC (2011) [http://www.cds.caltech.edu/~doyle2/wiki/images/b/b6/Science-2011-Chandra-187-92.pdf Glycolytic oscillations and limits on robust efficiency]. Science, Vol 333, pp 187-192.
*JC Doyle, ME Csete (2011) [http://www.cds.caltech.edu/~doyle2/wiki/images/4/4e/7.PNAS_InPress_June_2011.pdf Architecture, Constraints, and Behavior], P Natl Acad Sci USA, vol. 108, Sup 3 15624-15630
*Gayme DF, McKeon BJ, Bamieh B, Papachristodoulou P, Doyle JC (2011) [http://www.cds.caltech.edu/~doyle2/wiki/images/8/87/PhysFluids_23_065108.pdf Amplification and Nonlinear Mechanisms in Plane Couette Flow], Physics of Fluids, V23, Issue 6, 065108
*Page, M. T., D. Alderson, and J. Doyle (2011), [http://www.cds.caltech.edu/~doyle/wiki/images/a/a1/EarthquakesCalFaults.pdf The magnitude distribution of earthquakes near Southern California faults], J. Geophys. Res., 116, B12309, doi:10.1029/2010JB007933.

 
==Other Readings==
*[http://www.cds.caltech.edu/~doyle/wiki/images/4/4a/ScienceFire.pdf Fire in the Earth System]

File:ScienceFire.pdf

2012-04-02T22:40:18Z

Fiona:

CDS213

2012-04-02T22:37:57Z

Fiona:

==Reading==

*Willinger W, Alderson D, and Doyle JC (2009) [http://www.cds.caltech.edu/~doyle/wiki/images/f/f8/AMSNoticesInternet.pdf Mathematics and the internet: A source of enormous confusion and great potential]. Notices Amer Math Soc 56:586-599.
*Alderson DL, Doyle JC (2010) [http://www.cds.caltech.edu/~doyle2/wiki/images/d/de/1.IEEE_TransSysMCyber_AldersonDoyle-July2010.pdf Contrasting views of complexity and their implications for network-centric infrastructures]. IEEE Trans Systems Man Cybernetics—Part A: Syst Humans 40:839-852.
*H. Sandberg, J. C. Delvenne, J. C. Doyle. [http://www.cds.caltech.edu/~doyle2/wiki/images/c/c4/2.IEEE_TransAutoCtrl_Feb_2011_.pdf On Lossless Approximations, the Fluctuation-Dissipation Theorem, and Limitations of Measurements, IEEE Trans Auto Control], Feb 2011
*G. Buzi, U. Topcu, J. Doyle. [http://www.cds.caltech.edu/~doyle2/wiki/images/a/a2/6.AutomaticaJune2011.pdf Analysis of autocatalytic networks in biology], Automatica, vol. 47, pp. 1123--1130, 2011
*Chandra F, Buzi G, Doyle JC (2011) [http://www.cds.caltech.edu/~doyle2/wiki/images/b/b6/Science-2011-Chandra-187-92.pdf Glycolytic oscillations and limits on robust efficiency]. Science, Vol 333, pp 187-192.
*JC Doyle, ME Csete (2011) [http://www.cds.caltech.edu/~doyle2/wiki/images/4/4e/7.PNAS_InPress_June_2011.pdf Architecture, Constraints, and Behavior], P Natl Acad Sci USA, vol. 108, Sup 3 15624-15630
*Gayme DF, McKeon BJ, Bamieh B, Papachristodoulou P, Doyle JC (2011) [http://www.cds.caltech.edu/~doyle2/wiki/images/8/87/PhysFluids_23_065108.pdf Amplification and Nonlinear Mechanisms in Plane Couette Flow], Physics of Fluids, V23, Issue 6, 065108
*Page, M. T., D. Alderson, and J. Doyle (2011), [http://www.cds.caltech.edu/~doyle/wiki/images/a/a1/EarthquakesCalFaults.pdf The magnitude distribution of earthquakes near Southern California faults], J. Geophys. Res., 116, B12309, doi:10.1029/2010JB007933.

 
Go to the [http://www.cds.caltech.edu/~doyle/wiki/index.php?title=OldCDS213 old CDS 213 page]

File:EarthquakesCalFaults.pdf

2012-04-02T22:37:39Z

Fiona:

CDS213

2012-04-02T22:35:02Z

Fiona:

==Reading==

*Willinger W, Alderson D, and Doyle JC (2009) [[http://www.cds.caltech.edu/~doyle/wiki/images/f/f8/AMSNoticesInternet.pdf Mathematics and the internet: A source of enormous confusion and great potential]. Notices Amer Math Soc 56:586-599.
*Alderson DL, Doyle JC (2010) Contrasting views of complexity and their implications for network-centric infrastructures. IEEE Trans Systems Man Cybernetics—Part A: Syst Humans 40:839-852.
*H. Sandberg, J. C. Delvenne, J. C. Doyle. [http://www.cds.caltech.edu/~doyle2/wiki/images/c/c4/2.IEEE_TransAutoCtrl_Feb_2011_.pdf On Lossless Approximations, the Fluctuation-Dissipation Theorem, and Limitations of Measurements, IEEE Trans Auto Control], Feb 2011
*G. Buzi, U. Topcu, J. Doyle. [http://www.cds.caltech.edu/~doyle2/wiki/images/a/a2/6.AutomaticaJune2011.pdf Analysis of autocatalytic networks in biology], Automatica, vol. 47, pp. 1123--1130, 2011
*Chandra F, Buzi G, Doyle JC (2011) [http://www.cds.caltech.edu/~doyle2/wiki/images/b/b6/Science-2011-Chandra-187-92.pdf Glycolytic oscillations and limits on robust efficiency]. Science, Vol 333, pp 187-192.
*JC Doyle, ME Csete (2011) [http://www.cds.caltech.edu/~doyle2/wiki/images/4/4e/7.PNAS_InPress_June_2011.pdf Architecture, Constraints, and Behavior], P Natl Acad Sci USA, vol. 108, Sup 3 15624-15630
*Gayme DF, McKeon BJ, Bamieh B, Papachristodoulou P, Doyle JC (2011) [http://www.cds.caltech.edu/~doyle2/wiki/images/8/87/PhysFluids_23_065108.pdf Amplification and Nonlinear Mechanisms in Plane Couette Flow], Physics of Fluids, V23, Issue 6, 065108
*Page, M. T., D. Alderson, and J. Doyle (2011), The magnitude distribution of earthquakes near Southern California faults, J. Geophys. Res., 116, B12309, doi:10.1029/2010JB007933.

 
Go to the [http://www.cds.caltech.edu/~doyle/wiki/index.php?title=OldCDS213 old CDS 213 page]

OldCDS213

2012-04-02T22:18:58Z

Fiona:

Lectures are held Mondays 3pm & Thursdays 4 pm in Annenberg 107.

==Lecture Schedule + Slides==
*Jan 14: [http://www.cds.caltech.edu/~doyle/213/OlderSlides/NetArchIntro.pptx Intro to Architecture]
**[http://www.cds.caltech.edu/~doyle/213/OlderSlides/NetArchOS.pptx Architecture in Operating Systems]
*Jan19: [http://www.cds.caltech.edu/~doyle/213/OlderSlides/NetArchBio.pptx Architecture in Biology]
*Jan 21:
**[http://www.cds.caltech.edu/~doyle/213/OlderSlides/BioJan21.pptx Glycolysis]
**[http://www.cds.caltech.edu/~doyle/213/OlderSlides/StatMechJan21.pptx Stat Mech]
*Jan 25:[http://www.cds.caltech.edu/~doyle/213/Jan25SlidesReading/ Layering in Biology & Glycolysis + Clothing]

==Further Reading==
*Biology
**[http://www.cds.caltech.edu/~doyle/213/Jan25SlidesReading/PNASHeatShock.pdf Heat Shock Paper (PNAS)]
*Operating Systems

2010-2011

2011-08-24T20:04:26Z

Fiona: /* Journals */

==2011==
===Journals===
[http://www.cds.caltech.edu/~doyle2/wiki/images/4/4e/7.PNAS_InPress_June_2011.pdf Architecture, constraints, and behavior] 
JC Doyle, MC Csete 
PNAS, in press, July 2011

[http://www.sciencemag.org/cgi/rapidpdf/333/6039/187?ijkey=V1W0wT80JT9Nk&keytype=ref&siteid=sci Gycolytic oscillations and limits on robust efficiency] 
FA Chandra, G Buzi, JC Doyle 
Science 333(6039):187-192, July 2011

[http://www.cds.caltech.edu/~doyle2/wiki/images/8/87/PhysFluids_23_065108.pdf Amplification and nonlinear mechanisms in plane Couette flow.] 
D Gayme, B McKeon, B Bamieh, A Papachristodolou, and J Doyle. 
Physics of Fluids v23:6:065108 (2011)

[http://www.cds.caltech.edu/~doyle2/wiki/images/a/a2/6.AutomaticaJune2011.pdf Analysis of autocatalytic networks in biology] 
G Buzi, U Topcu, J Doyle 
Automatica 47:1123-1130 (2011)

[http://www.cds.caltech.edu/~doyle2/wiki/images/c/c4/2.IEEE_TransAutoCtrl_Feb_2011_.pdf On Lossless Approximations, the Fluctuation-Dissipation Theorem, and Limitations of Measurements] 
H Sandberg, JC Delvenne, JC Doyle 
IEE Trans Auto Control, v56:2, 293-308 (2011)

[http://www.cds.caltech.edu/~doyle2/wiki/images/6/62/9.ComputerNetworksFeb2011.pdf Cross-layer design in multihop wireless networks] 
L Chen, SH Low, and JC Doyle 
Computer Networks 55:480–496 (2011)

Javad Lavaei, Aydin Babakhani, Ali Hajimiri and John C. Doyle, "Solving
Large-Scale Hybrid Circuit-Antenna Problems," IEEE Transactions on Circuits
and Systems I, vol. 58, no. 2, pp. 374-387, Feb. 2011.

===Conferences===

Effects of Buffers on Stability of Internet Congestion Controllers 
Somayeh Sojoudi, Steven Low and John Doyle 
IEEE International Conference on Computer Communications (INFOCOM), mini conference, China, 2011.

==2010==
===Journals===
[http://www.cds.caltech.edu/~doyle2/wiki/images/a/ab/8.IEEETransNetworkingAug2010.pdf Random access game and medium access control design] 
Lijun Chen, Steven Low, and John Doyle 
IEEE Trans Networking 18:4:1303-1316, AUG 2010.

[http://www.cds.caltech.edu/~doyle2/wiki/images/d/de/1.IEEE_TransSysMCyber_AldersonDoyle-July2010.pdf Contrasting views of complexity and their implications for network-centric infrastructures] 
David Alderson and John Doyle 
IEEE Trans Systems Man Cybernetics—Part A: Syst Humans 40:839-852, JUL 2010.

[http://www.cds.caltech.edu/~dennice/PublishedVersionJFM2010.pdf A streamwise constant model of turbulence in plane Couette flow] 
Gayme DF, McKeon BJ, Papachristodoulou A, Bamieh B, and Doyle JC 
Journal of Fluid Mechanics 665:99-119 (2010)

===Conferences===
Performance Limitations in Autocatalytic Networks in Biology 
Motee N, Chandra F, Bamieh B, Khammash M, and Doyle J 
In Proc 49th IEEE Conf Decision and Control, 4715-4720, Dec 2010.

Passively Controllable Smart Antennas 
Javad Lavaei, Aydin Babakhani, Ali Hajimiri and John C. Doyle 
IEEE Global Communications Conference (GLOBECOM), Miami, Florida, 2010.

Finding Globally Optimum Solutions in Antenna Optimization Problems 
Aydin Babakhani, Javad Lavaei, John C. Doyle and Ali Hajimiri 
IEEE International Symposium on Antennas and Propagation, Toronto, Canada, 2010.

Programmable Antenna Design Using Convex Optimization 
Javad Lavaei, Aydin Babakhani, Ali Hajimiri and John C. Doyle 
19th International Symposium on Mathematical Theory of Networks and Systems, Budapest, Hungary, 2010.

Javad Lavaei, Aydin Babakhani, Ali Hajimiri and John C. Doyle, "A Study of
Near-Field Direct Antenna Modulation Systems Using Convex Optimization," in
American Control Conference, Baltimore, 2010.

Javad Lavaei, John C. Doyle and Steven Low, "Utility Functionals Associated
With Available Congestion Control Algorithms," IEEE International
Conference on Computer Communications (INFOCOM), San Diego, California,
2010.

2010-2011

2011-08-24T20:03:19Z

Fiona: /* Journals */

==2011==
===Journals===
[http://www.cds.caltech.edu/~doyle2/wiki/images/4/4e/7.PNAS_InPress_June_2011.pdf Architecture, constraints, and behavior] 
JC Doyle, MC Csete 
PNAS, in press, July 2011

[http://www.sciencemag.org/cgi/rapidpdf/333/6039/187?ijkey=V1W0wT80JT9Nk&keytype=ref&siteid=sci Gycolytic oscillations and limits on robust efficiency] 
FA Chandra, G Buzi, JC Doyle 
Science 333(6039):187-192, July 2011

[http://www.cds.caltech.edu/~doyle2/wiki/images/8/87/PhysFluids_23_065108.pdf Amplification and nonlinear mechanisms in plane Couette flow.] 
D Gayme, B McKeon, B Bamieh, A Papachristodolou, and J Doyle. 
Physics of Fluids v23:6:065108 (2011)

[http://www.cds.caltech.edu/~doyle2/wiki/images/a/a2/6.AutomaticaJune2011.pdf Analysis of autocatalytic networks in biology] 
G Buzi, U Topcu, J Doyle 
Automatica 47:1123-1130 (2011)

[http://www.cds.caltech.edu/~doyle2/wiki/images/c/c4/2.IEEE_TransAutoCtrl_Feb_2011_.pdf On Lossless Approximations, the Fluctuation-Dissipation Theorem, and Limitations of Measurements] 
H Sandberg, JC Delvenne, JC Doyle 
IEE Trans Auto Control, v56:2, 293-308 (2011)

[http://www.cds.caltech.edu/~doyle2/wiki/images/6/62/9.ComputerNetworksFeb2011.pdf Cross-layer design in multihop wireless networks] 
L Chen, SH Low, and JC Doyle 
Computer Networks 55:480–496 (2011)

Javad Lavaei, Aydin Babakhani, Ali Hajimiri and John C. Doyle, "Solving
Large-Scale Hybrid Circuit-Antenna Problems," IEEE Transactions on Circuits
and Systems I, vol. 58, no. 2, pp. 374-387, Feb. 2011.

===Conferences===

Effects of Buffers on Stability of Internet Congestion Controllers 
Somayeh Sojoudi, Steven Low and John Doyle 
IEEE International Conference on Computer Communications (INFOCOM), mini conference, China, 2011.

==2010==
===Journals===
[http://cds-web1.cds.caltech.edu/~doyle2/wiki/images/a/ab/8.IEEETransNetworkingAug2010.pdf Random access game and medium access control design] 
Lijun Chen, Steven Low, and John Doyle 
IEEE Trans Networking 18:4:1303-1316, AUG 2010.

[http://cds-web1.cds.caltech.edu/~doyle2/wiki/images/d/de/1.IEEE_TransSysMCyber_AldersonDoyle-July2010.pdf Contrasting views of complexity and their implications for network-centric infrastructures] 
David Alderson and John Doyle 
IEEE Trans Systems Man Cybernetics—Part A: Syst Humans 40:839-852, JUL 2010.

[http://www.cds.caltech.edu/~dennice/PublishedVersionJFM2010.pdf A streamwise constant model of turbulence in plane Couette flow] 
Gayme DF, McKeon BJ, Papachristodoulou A, Bamieh B, and Doyle JC 
Journal of Fluid Mechanics 665:99-119 (2010)

===Conferences===
Performance Limitations in Autocatalytic Networks in Biology 
Motee N, Chandra F, Bamieh B, Khammash M, and Doyle J 
In Proc 49th IEEE Conf Decision and Control, 4715-4720, Dec 2010.

Passively Controllable Smart Antennas 
Javad Lavaei, Aydin Babakhani, Ali Hajimiri and John C. Doyle 
IEEE Global Communications Conference (GLOBECOM), Miami, Florida, 2010.

Finding Globally Optimum Solutions in Antenna Optimization Problems 
Aydin Babakhani, Javad Lavaei, John C. Doyle and Ali Hajimiri 
IEEE International Symposium on Antennas and Propagation, Toronto, Canada, 2010.

Programmable Antenna Design Using Convex Optimization 
Javad Lavaei, Aydin Babakhani, Ali Hajimiri and John C. Doyle 
19th International Symposium on Mathematical Theory of Networks and Systems, Budapest, Hungary, 2010.

Javad Lavaei, Aydin Babakhani, Ali Hajimiri and John C. Doyle, "A Study of
Near-Field Direct Antenna Modulation Systems Using Convex Optimization," in
American Control Conference, Baltimore, 2010.

Javad Lavaei, John C. Doyle and Steven Low, "Utility Functionals Associated
With Available Congestion Control Algorithms," IEEE International
Conference on Computer Communications (INFOCOM), San Diego, California,
2010.

Main Page

2011-08-24T20:00:01Z

Fiona: /* Recent Papers */

<table border=1 width=100% style="color:black; " cellpadding="20" cellspacing="0">
<tr>
<td align=center width=20%> [[Image:Smallpic.JPG]]</td>
<td width=60% align=center>
John C. Doyle 

John G Braun Professor 
of Control and Dynamical Systems 
Electrical Engineering 
and BioEngineering 
Division of Engineering and Applied Science 
California Institute of Technology 

</td>
<td align=center width=20%>


[[J. Doyle’s Bio]]

[[News]]

[[Calendar]]

[[#Contact|Contact]]

[https://www.cds.caltech.edu/squirrelmail/src/login.php CDS Webmail]
</td>
</tr></table>
{| align=center
|[[Image:Blossoms900strip.jpg]]||[[Image:Blossoms900strip.jpg]]||[[Image:Blossoms900strip.jpg]]||[[Image:Blossoms900strip.jpg]]
|}
<hr>

==News==
*Visiting this week: Ioannis Lestas
*[[Research|MURI 2008]]
*[http://discovermagazine.com/2007/nov/this-man-wants-to-control-the-internet Discover magazine] interviews Prof. Doyle.

"This man wants to control the internet" by Carl Zimmer, Discover magazine, 10/25/2007.

==Recent Papers==
*[http://www.cds.caltech.edu/~doyle2/wiki/images/4/4e/7.PNAS_InPress_June_2011.pdf Architecture, constraints, and behavior.] JC Doyle, MC Csete. PNAS, in press, July 2011
*[http://www.cds.caltech.edu/~doyle2/wiki/images/b/b6/Science-2011-Chandra-187-92.pdf Glycolytic oscillations and limits on robust efficiency.] FA Chandra, G Buzi, JC Doyle Science 333(6039):187-192, July 2011
*[http://www.cds.caltech.edu/~doyle2/wiki/images/c/c4/2.IEEE_TransAutoCtrl_Feb_2011_.pdf On Lossless Approximations, the Fluctuation-Dissipation Theorem, and Limitations of Measurements] H Sandberg, JC Delvenne, JC Doyle IEEE Trans Auto Control, v56:2, 293-308 (2011)
*[[Papers|'''More Papers''']]

== Research ==
John Doyle's '''[[research]]''' interests are in theoretical foundations for complex networks in engineering and biology, as well as multiscale physics, and include integrating modeling, ID, analysis and design of uncertain nonlinear systems, and computation in analysis and simulation, including complexity theory to guide algorithm development. Applications interests are motivated by the interplay between: control, dynamical systems, and design and analysis of large, complex systems.

*[[Research|Research projects and grants list]]

== Teaching ==

*[http://www.cds.caltech.edu/~murray/wiki/CDS_212_Fall_2010 CDS 212, Feedback Control Theory (Fall 2010)]
*[[CDS 213|The Architecture of Robust, Evolvable Networks (Wi10)]]

== Contact ==
{| width=100%
|- valign=top
| width=50% |

'''Mailing Address'''

John Doyle 
California Institute of Technology 
Control and Dynamical Systems, MC 107-81 
1200 E. California Blvd 
Pasadena, CA 91125 USA
| width=50% |

'''Contact information'''

E-mail: doyle AT cds dot caltech dot edu 
Office: 109 Steele, 
Phone: 626.395.4808 Fax: 626.395.6170 

'''Admin Assistant''': Anissa Scott 
Office: 107 Steele, 
Email: anissa AT caltech dot edu 
Phone: 626.395.4140 
Labs: 12 STL, 110 GUG (x2319)
|-
|

===Other Caltech links===

*[http://www.caltech.edu California Institute of Technology]
**[http://www.eas.caltech.edu Engineering and Applied Science Division]
***[http://www.be.caltech.edu/ Bioengineering Department]
***[http://www.cds.caltech.edu Control and Dynamical Systems Department]
***[http://www.ee2.caltech.edu/ Electrical Engineering Department]
|}

2010-2011

2011-07-15T21:40:58Z

Fiona: /* Journals */

==2011==
===Journals===
[http://cds-web1.cds.caltech.edu/~doyle2/wiki/images/4/4e/7.PNAS_InPress_June_2011.pdf Architecture, constraints, and behavior] 
JC Doyle, MC Csete 
PNAS, in press, July 2011

[http://www.sciencemag.org/cgi/rapidpdf/333/6039/187?ijkey=V1W0wT80JT9Nk&keytype=ref&siteid=sci Gycolytic oscillations and limits on robust efficiency] 
FA Chandra, G Buzi, JC Doyle 
Science 333(6039):187-192, July 2011

[http://cds-web1.cds.caltech.edu/~doyle2/wiki/images/8/87/PhysFluids_23_065108.pdf Amplification and nonlinear mechanisms in plane Couette flow.] 
D Gayme, B McKeon, B Bamieh, A Papachristodolou, and J Doyle. 
Physics of Fluids v23:6:065108 (2011)

[http://cds-web1.cds.caltech.edu/~doyle2/wiki/images/a/a2/6.AutomaticaJune2011.pdf Analysis of autocatalytic networks in biology] 
G Buzi, U Topcu, J Doyle 
Automatica 47:1123-1130 (2011)

[http://cds-web1.cds.caltech.edu/~doyle2/wiki/images/c/c4/2.IEEE_TransAutoCtrl_Feb_2011_.pdf On Lossless Approximations, the Fluctuation-Dissipation Theorem, and Limitations of Measurements] 
H Sandberg, JC Delvenne, JC Doyle 
IEE Trans Auto Control, v56:2, 293-308 (2011)

[http://cds-web1.cds.caltech.edu/~doyle2/wiki/images/6/62/9.ComputerNetworksFeb2011.pdf Cross-layer design in multihop wireless networks] 
L Chen, SH Low, and JC Doyle 
Computer Networks 55:480–496 (2011)

Javad Lavaei, Aydin Babakhani, Ali Hajimiri and John C. Doyle, "Solving
Large-Scale Hybrid Circuit-Antenna Problems," IEEE Transactions on Circuits
and Systems I, vol. 58, no. 2, pp. 374-387, Feb. 2011.

===Conferences===

Effects of Buffers on Stability of Internet Congestion Controllers 
Somayeh Sojoudi, Steven Low and John Doyle 
IEEE International Conference on Computer Communications (INFOCOM), mini conference, China, 2011.

==2010==
===Journals===
[http://cds-web1.cds.caltech.edu/~doyle2/wiki/images/a/ab/8.IEEETransNetworkingAug2010.pdf Random access game and medium access control design] 
Lijun Chen, Steven Low, and John Doyle 
IEEE Trans Networking 18:4:1303-1316, AUG 2010.

[http://cds-web1.cds.caltech.edu/~doyle2/wiki/images/d/de/1.IEEE_TransSysMCyber_AldersonDoyle-July2010.pdf Contrasting views of complexity and their implications for network-centric infrastructures] 
David Alderson and John Doyle 
IEEE Trans Systems Man Cybernetics—Part A: Syst Humans 40:839-852, JUL 2010.

[http://www.cds.caltech.edu/~dennice/PublishedVersionJFM2010.pdf A streamwise constant model of turbulence in plane Couette flow] 
Gayme DF, McKeon BJ, Papachristodoulou A, Bamieh B, and Doyle JC 
Journal of Fluid Mechanics 665:99-119 (2010)

===Conferences===
Performance Limitations in Autocatalytic Networks in Biology 
Motee N, Chandra F, Bamieh B, Khammash M, and Doyle J 
In Proc 49th IEEE Conf Decision and Control, 4715-4720, Dec 2010.

Passively Controllable Smart Antennas 
Javad Lavaei, Aydin Babakhani, Ali Hajimiri and John C. Doyle 
IEEE Global Communications Conference (GLOBECOM), Miami, Florida, 2010.

Finding Globally Optimum Solutions in Antenna Optimization Problems 
Aydin Babakhani, Javad Lavaei, John C. Doyle and Ali Hajimiri 
IEEE International Symposium on Antennas and Propagation, Toronto, Canada, 2010.

Programmable Antenna Design Using Convex Optimization 
Javad Lavaei, Aydin Babakhani, Ali Hajimiri and John C. Doyle 
19th International Symposium on Mathematical Theory of Networks and Systems, Budapest, Hungary, 2010.

Javad Lavaei, Aydin Babakhani, Ali Hajimiri and John C. Doyle, "A Study of
Near-Field Direct Antenna Modulation Systems Using Convex Optimization," in
American Control Conference, Baltimore, 2010.

Javad Lavaei, John C. Doyle and Steven Low, "Utility Functionals Associated
With Available Congestion Control Algorithms," IEEE International
Conference on Computer Communications (INFOCOM), San Diego, California,
2010.

Main Page

2011-07-14T17:00:11Z

Fiona: /* Recent Papers */

<table border=1 width=100% style="color:black; " cellpadding="20" cellspacing="0">
<tr>
<td align=center width=20%> [[Image:Smallpic.JPG]]</td>
<td width=60% align=center>
John C. Doyle 

John G Braun Professor 
of Control and Dynamical Systems 
Electrical Engineering 
and BioEngineering 
Division of Engineering and Applied Science 
California Institute of Technology 

</td>
<td align=center width=20%>


[[J. Doyle’s Bio]]

[[News]]

[[Calendar]]

[[#Contact|Contact]]

[https://www.cds.caltech.edu/squirrelmail/src/login.php CDS Webmail]
</td>
</tr></table>
{| align=center
|[[Image:Blossoms900strip.jpg]]||[[Image:Blossoms900strip.jpg]]||[[Image:Blossoms900strip.jpg]]||[[Image:Blossoms900strip.jpg]]
|}
<hr>

==News==
*Visiting this week: Ioannis Lestas
*[[Research|MURI 2008]]
*[http://discovermagazine.com/2007/nov/this-man-wants-to-control-the-internet Discover magazine] interviews Prof. Doyle.

"This man wants to control the internet" by Carl Zimmer, Discover magazine, 10/25/2007.

==Recent Papers==
*[http://cds-web1.cds.caltech.edu/~doyle2/wiki/images/4/4e/7.PNAS_InPress_June_2011.pdf Architecture, constraints, and behavior.] JC Doyle, MC Csete. PNAS, in press, July 2011
*[http://cds-web1.cds.caltech.edu/~doyle2/wiki/images/b/b6/Science-2011-Chandra-187-92.pdf Gycolytic oscillations and limits on robust efficiency.] FA Chandra, G Buzi, JC Doyle Science 333(6039):187-192, July 2011
*[http://cds-web1.cds.caltech.edu/~doyle2/wiki/images/c/c4/2.IEEE_TransAutoCtrl_Feb_2011_.pdf On Lossless Approximations, the Fluctuation-Dissipation Theorem, and Limitations of Measurements] H Sandberg, JC Delvenne, JC Doyle IEEE Trans Auto Control, v56:2, 293-308 (2011)
*[[Papers|'''More Papers''']]

== Research ==
John Doyle's '''[[research]]''' interests are in theoretical foundations for complex networks in engineering and biology, as well as multiscale physics, and include integrating modeling, ID, analysis and design of uncertain nonlinear systems, and computation in analysis and simulation, including complexity theory to guide algorithm development. Applications interests are motivated by the interplay between: control, dynamical systems, and design and analysis of large, complex systems.

*[[Research|Research projects and grants list]]

== Teaching ==

*[http://www.cds.caltech.edu/~murray/wiki/CDS_212_Fall_2010 CDS 212, Feedback Control Theory (Fall 2010)]
*[[CDS 213|The Architecture of Robust, Evolvable Networks (Wi10)]]

== Contact ==
{| width=100%
|- valign=top
| width=50% |

'''Mailing Address'''

John Doyle 
California Institute of Technology 
Control and Dynamical Systems, MC 107-81 
1200 E. California Blvd 
Pasadena, CA 91125 USA
| width=50% |

'''Contact information'''

E-mail: doyle AT cds dot caltech dot edu 
Office: 109 Steele, 
Phone: 626.395.4808 Fax: 626.395.6170 

'''Admin Assistant''': Anissa Scott 
Office: 107 Steele, 
Email: anissa AT caltech dot edu 
Phone: 626.395.4140 
Labs: 12 STL, 110 GUG (x2319)
|-
|

===Other Caltech links===

*[http://www.caltech.edu California Institute of Technology]
**[http://www.eas.caltech.edu Engineering and Applied Science Division]
***[http://www.be.caltech.edu/ Bioengineering Department]
***[http://www.cds.caltech.edu Control and Dynamical Systems Department]
***[http://www.ee2.caltech.edu/ Electrical Engineering Department]
|}

Systems biology

2011-07-14T16:59:55Z

Fiona: /* 2011 */

Intro: We study fundamental constraints and trade-offs in biological systems using analytical tools from control theory, information theory, and graph theory. There are hard trade-offs between complexity and robustness in every system, which is worse in systems with particular architecture. We are interested in pinpointing these problems and analyzing how nature manages these trade-offs.

Keywords: '''systems biology''', SBML mark-up, robustness, complexity, networks, biology, proteins.

A few papers were copied from <http://www.cds.caltech.edu/~doyle/RecentPapers/ >

==Systems biology==
Keywords: '''systems biology''', biological networks, complexity, control, heat-shock, protein, robustness, metabolism.

===2011===
[http://cds-web1.cds.caltech.edu/~doyle2/wiki/images/4/4e/7.PNAS_InPress_June_2011.pdf Architecture, constraints, and behavior] 
JC Doyle, MC Csete 
PNAS, in press, July 2011

[http://cds-web1.cds.caltech.edu/~doyle2/wiki/images/b/b6/Science-2011-Chandra-187-92.pdf Glycolytic Oscillations and Limits on Robust Efficiency] 
Fiona Chandra, Gentian Buzi, and John Doyle 
Science 333(6039):187-192, July 2011

[http://cds-web1.cds.caltech.edu/~doyle2/wiki/images/a/a2/6.AutomaticaJune2011.pdf Analysis of autocatalytic networks in biology] 
G Buzi, U Topcu, J Doyle 
Automatica 47:1123-1130 (2011)

===2009===
[http://www.nt.ntnu.no/users/skoge/prost/proceedings/acc09/data/papers/0207.pdf ''Linear control analysis of the autocatalytic glycolysis system''] 
Fiona Chandra, Gentian Buzi, John Doyle 
In Proc. American Control Conf, 319-324 JUN 2009

===2007===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/4/43/Nature_Connections07.pdf ''Rules of engagement''] 
John Doyle and Marie Csete 
Nature Vol 446:860 April 19 2007 (142K)

===2006===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/7/74/IEEEProc_Bio.pdf ''Advanced Methods and Algorithms for Biological Networks Analysis''], 
H El-Samad , A Papachristodoulou, S Prajna, J Doyle, and M Khammash 
In Proc. IEEE, 94 (4): 832-853 APR 2006 (900K)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/1/1f/PlosCompBio_HS06.pdf ''Module-Based Analysis of Robustness Tradeoffs in the Heat Shock Response System ''] 
Hiroyuki Kurata, Hana El-Samad, Rei Iwasaki, Hisao Ohtake, John C Doyle, Irina Grigorova, Carol A. Gross, Mustafa Khammash, 
[http://compbiol.plosjournals.org/ PLoS Comput Biol] 2(7): July 2006 (1.1MB)

===2005===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/9/98/FEBS_PPI05.pdf ''Some protein interaction data do not exhibit power law statistics''], 
R. Tanaka, T-M Yi, and J. Doyle 
FEBS letters, 579 (23): 5140-5144 Sept 26 2005 (221K)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/f/f2/IEESysBio05.pdf ''Highly optimised global organisation of metabolic networks''], 
R. Tanaka, M. Csete and J. Doyle, 
IEE Proc.-Syst. Biol. 152(4): 179, Dec 2005 (820K)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/a/a7/PLOS_Primer05.pdf ''Motifs, control, and stability''] (including ''Supplementary Notes: Elementary Feedback Concepts'') 
Doyle J and Csete M 
[http://www.plosbiology.org PLoS Biol] 3(11): e392; 2005. (387K)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/b/b4/PNAS_HeatShock05.pdf ''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)

===2004===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/1/13/Cell04.pdf ''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)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/8/82/Trends04.pdf ''Bow ties, metabolism, and disease''], 
Csete M.E. and J.C. Doyle, 
Trends in Biotechnology 22(9):446-50 Sept 2004. (121K)

===2002===
[http://www.cds.caltech.edu/~doyle2/wiki/skins/common/images/icons/fileicon-pdf.png ''Reverse Engineering of Biological Complexity''] 
Csete M and Doyle J, 
Science 295 (5560): 1664-1669 Mar 1, 2002. (1.2MB)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/1/12/JtheorBiol2002.pdf ''Robustness as a measure of plausibility in models of biochemical networks''], 
Morohashi M, Winn AE, Borisuk MT, Bolouri H, Doyle J, Kitano H, 
Journal Of Theoretical Biology 216 (1): 19-30 May 7, 2002.

===2000===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/f/f0/PNAS4649-2000.full.pdf ''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.

==SBML==
Keywords: '''SBML''', systems biology mark-up language, computer software, biochemical reaction networks

===2004===
[http://scitation.aip.org/dbt/dbt.jsp?KEY=IPSBDJ&Volume=1 '' Evolving a lingua franca and associated software infrastructure for computational systems biology: theSystemsBiologyMarkupLanguage(SBML) project''], 
M. Hucka; A. Finney; B.J. Bornstein; S.M. Keating; B.E. Shapiro; J. Matthews; B.L. Kovitz; M.J. Schilstra; A. Funahashi; J.C. Doyle; and H. Kitano 
IEE Systems Biology. 1:41-53, 2004

*''MathSBML: a package for manipulating SBML-based biological models'', 
Shapiro BE, Hucka M, Finney A, Doyle J. 
Bioinformatics, Nov 1, 2004

===2002===
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11928498&dopt=Abstract ''The ERATO Systems Biology Workbench: enabling interaction and exchange between software tools for computational biology'' (Abstract)] 
Hucka, M., Finney, A., Sauro, H. M., Bolouri, H., Doyle, J., and Kitano,H. 
in Proc. Pac Symp Biocomput. 450-61, 2002.

===2001===
*''The Systems Biology Markup Language'' 
Finney AM, Hucka M, Sauro HM, Doyle J, Kitano H, Bolouri H, 
Molecular Biology of the Cell 12: 708 Suppl. S NOV 2001.

==More Biology==
Keywords: '''biology''', cell, HOT (highly optimized tolerance), SOSTOOLS (sums of squares optimization), robustness
===2005===
''Evolutionary dynamics and highly optimized tolerance,''
Zhou T, Carlson JM, Doyle J 
Journal of Theoretical Biology 236 (4): 438-447 Oct 21 2005

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/0/01/PNAS_HOTFire05.pdf ''Wildfires, complexity, and highly optimized tolerance''], 
MA Moritz, ME Morais, LA Summerell, JM Carlson, J Doyle 
Proc. Natl. Acad. Sci. USA, December 13, 2005; 102 (50):17912–17917 (403K)

===2003===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/f/f8/CDC2003.pdf ''Model validation and robust stability analysis of the bacterial heat shock response using SOSTOOLS.''] 
H. El-Samad, S. Prajna, A. Papachristodoulou, M. Khammash and J. C. Doyle 
in Proc. IEEE CDC, vol. 4:3766 - 3771; Maui, Hawaii, 9-12 Dec. 2003.

===2002===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/7/72/PNAS2538-2002.full.pdf ''Complexity and robustness''], 
Carlson JM, Doyle J, 
Proc. Natl. Acad. Sci. USA 99: 2538-2545 Suppl. 1 Feb 19, 2002.

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/8/85/PNAS2049-2002.full.pdf ''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.

===2001===
*''Oxygen-mediated regulation of skeletal muscle satellite cell proliferation and adipogenesis in culture'' 
Csete M, Walikonis J, Slawny N, Wei Y, Korsnes S , Doyle JC, Wold B, 
Journal of Cellular Physiology, Volume 189, Issue 2, Nov. 2001. 189-196

==Related reading==
[[Papers]]

[[Research]]

[[Tips: Research papers, Publishing and Other Trivia]]

===Other===

===External links===
*[http://sbml.org/Main_Page SBML Definition and homepage]
*[http://sbml.org/Documents SBML documents]
*[http://www.systems-biology.org/ Systems Biology Portal]
*[http://www.hot.caltech.edu/ HOT : Highly Optimized/Organized Tradeoffs/Tolerance, A unified theory of complex networks ]
*[http://www.cds.caltech.edu/sostools/ SOSTOOLS : Software for analysis of complex systems]

[[Category:Research]]
[[Category:Papers by topic]]
[[Category:Papers]]

2010-2011

2011-07-14T16:59:40Z

Fiona: /* Journals */

==2011==
===Journals===
[http://cds-web1.cds.caltech.edu/~doyle2/wiki/images/4/4e/7.PNAS_InPress_June_2011.pdf Architecture, constraints, and behavior] 
JC Doyle, MC Csete 
PNAS, in press, July 2011

[http://cds-web1.cds.caltech.edu/~doyle2/wiki/images/b/b6/Science-2011-Chandra-187-92.pdf Gycolytic oscillations and limits on robust efficiency] 
FA Chandra, G Buzi, JC Doyle 
Science 333(6039):187-192, July 2011

[http://cds-web1.cds.caltech.edu/~doyle2/wiki/images/8/87/PhysFluids_23_065108.pdf Amplification and nonlinear mechanisms in plane Couette flow.] 
D Gayme, B McKeon, B Bamieh, A Papachristodolou, and J Doyle. 
Physics of Fluids v23:6:065108 (2011)

[http://cds-web1.cds.caltech.edu/~doyle2/wiki/images/a/a2/6.AutomaticaJune2011.pdf Analysis of autocatalytic networks in biology] 
G Buzi, U Topcu, J Doyle 
Automatica 47:1123-1130 (2011)

[http://cds-web1.cds.caltech.edu/~doyle2/wiki/images/c/c4/2.IEEE_TransAutoCtrl_Feb_2011_.pdf On Lossless Approximations, the Fluctuation-Dissipation Theorem, and Limitations of Measurements] 
H Sandberg, JC Delvenne, JC Doyle 
IEE Trans Auto Control, v56:2, 293-308 (2011)

[http://cds-web1.cds.caltech.edu/~doyle2/wiki/images/6/62/9.ComputerNetworksFeb2011.pdf Cross-layer design in multihop wireless networks] 
L Chen, SH Low, and JC Doyle 
Computer Networks 55:480–496 (2011)

Javad Lavaei, Aydin Babakhani, Ali Hajimiri and John C. Doyle, "Solving
Large-Scale Hybrid Circuit-Antenna Problems," IEEE Transactions on Circuits
and Systems I, vol. 58, no. 2, pp. 374-387, Feb. 2011.

===Conferences===

Effects of Buffers on Stability of Internet Congestion Controllers 
Somayeh Sojoudi, Steven Low and John Doyle 
IEEE International Conference on Computer Communications (INFOCOM), mini conference, China, 2011.

==2010==
===Journals===
[http://cds-web1.cds.caltech.edu/~doyle2/wiki/images/a/ab/8.IEEETransNetworkingAug2010.pdf Random access game and medium access control design] 
Lijun Chen, Steven Low, and John Doyle 
IEEE Trans Networking 18:4:1303-1316, AUG 2010.

[http://cds-web1.cds.caltech.edu/~doyle2/wiki/images/d/de/1.IEEE_TransSysMCyber_AldersonDoyle-July2010.pdf Contrasting views of complexity and their implications for network-centric infrastructures] 
David Alderson and John Doyle 
IEEE Trans Systems Man Cybernetics—Part A: Syst Humans 40:839-852, JUL 2010.

[http://www.cds.caltech.edu/~dennice/PublishedVersionJFM2010.pdf A streamwise constant model of turbulence in plane Couette flow] 
Gayme DF, McKeon BJ, Papachristodoulou A, Bamieh B, and Doyle JC 
Journal of Fluid Mechanics 665:99-119 (2010)

===Conferences===
Performance Limitations in Autocatalytic Networks in Biology 
Motee N, Chandra F, Bamieh B, Khammash M, and Doyle J 
In Proc 49th IEEE Conf Decision and Control, 4715-4720, Dec 2010.

Passively Controllable Smart Antennas 
Javad Lavaei, Aydin Babakhani, Ali Hajimiri and John C. Doyle 
IEEE Global Communications Conference (GLOBECOM), Miami, Florida, 2010.

Finding Globally Optimum Solutions in Antenna Optimization Problems 
Aydin Babakhani, Javad Lavaei, John C. Doyle and Ali Hajimiri 
IEEE International Symposium on Antennas and Propagation, Toronto, Canada, 2010.

Programmable Antenna Design Using Convex Optimization 
Javad Lavaei, Aydin Babakhani, Ali Hajimiri and John C. Doyle 
19th International Symposium on Mathematical Theory of Networks and Systems, Budapest, Hungary, 2010.

Javad Lavaei, Aydin Babakhani, Ali Hajimiri and John C. Doyle, "A Study of
Near-Field Direct Antenna Modulation Systems Using Convex Optimization," in
American Control Conference, Baltimore, 2010.

Javad Lavaei, John C. Doyle and Steven Low, "Utility Functionals Associated
With Available Congestion Control Algorithms," IEEE International
Conference on Computer Communications (INFOCOM), San Diego, California,
2010.

Research

2011-07-12T21:42:15Z

Fiona: /* Past Projects */

"Professor Doyle's current '''research''' interests are in theoretical foundations for complex networks, primarily in network engineering and biology." He is also "interested in multiscale physics and financial markets, and the interplay between robustness, feedback, control, dynamical systems, computation, communications, and statistical physics." <http://www.cds.caltech.edu/people/> Aug 2008

Prof. Doyle has "applied complex ideas of robust design and control to many fields and is working on a unified theory of control in engineering, physics and biology." <http://www.ieee.org/portal/pages/about/awards/bios/2004controlsystems.html> Aug 2008

==Current Projects==
*[http://cds-web1.cds.caltech.edu/~doyle2/wiki/index.php?title=Systems_biology Systems Biology] ([http://www.its.caltech.edu/~fiona Fiona Chandra], Genti Buzi)
**Fundamental constraints and trade-offs of autocatalytic networks.
**Collaborators: [http://biochemistry.ucsf.edu/labs/elsamad/home/index.html Hana El-Samad], [http://sysos.eng.ox.ac.uk/control/sysos/index.php/User:Antonis Antonis Papachristodoulou]
*Fluids: [http://cds-web1.cds.caltech.edu/~doyle2/wiki/index.php?title=Turbulence Turbulence Modeling] ([https://www.cds.caltech.edu/~dennice/ Dennice Gayme])
**Collaborators: [http://engineering.ucsb.edu/~bamieh/ Bassam Bamieh], [http://www.mckeon.caltech.edu/ Beverly McKeon]
*[http://openwetware.org/wiki/Doyle Physiology]: Dynamic Modeling of Heart Rate Variability (Li Na, Jerry Cruz)
**Heart rate (HR) in healthy humans has high variability, and loss of this HR variability (HRV) is a signature of stress, fatigue, aging, or disease1-9. Correlating health and high HRV using time series analyses is popular in clinical and athletic training10 research, but its practical impact has been limited by lack of specific physiological mechanisms explaining HRV patterns. Conjectures attributing the cryptic etiology of HRV to complex feedbacks and nonlinear dynamics have similarly lacked mechanistic explanation. We leverage concepts from physiology, evolution, and control theory to analyze data from exercising athletes and develop mechanistic models explaining correlations between health, stress, and HRV.
*[http://cds-web1.cds.caltech.edu/~doyle2/wiki/index.php?title=Networking Internet and Networking] ([http://www.cds.caltech.edu/~chenlj/ Lijun Chen], [http://www.cds.caltech.edu/~lavaei/ Javad Lavaei], [http://www.cds.caltech.edu/~sojoudi/ Somayeh Sojoudi])
**Collaborators: [http://netlab.caltech.edu/slow/ Steven Low]
*Economics (Jerry Cruz)
** Market Bubbles and Crashes: We use tools from mathematical finance and stochastic control theory to investigate asset price bubbles and crashes in financial markets. We wish to gain insight using models that account for financial intermediation and associated frictions. Moreover, recent local-martingale characterizations of bubbles may provide avenues into developing new methods of empirical testing for bubbles.
*Distributed Control ([http://www.cds.caltech.edu/~lavaei/ Javad Lavaei], [http://www.cds.caltech.edu/~motee Nader Motee], Li Na)
**Designing Games for Distributed Opitmization (Li Na) The central goal in multiagent systems is to design local control laws for the individual agents to ensure that the emergent global behavior is desirable with respect to a given system level objective. Ideally, a system designer seeks to satisfy this goal while conditioning each agent's control law on the least amount of information possible. Unfortunately, there are no existing methodologies for addressing this design challenge. The goal of this research is to address this challenge using the field of game theory. We develop a systematic methodology for distributed optimization using the framework of state based potential games.

==Research Grants==
*[http://www.nsf.gov/index.jsp NSF] award: [http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=0326635 ITR COLLAB: Theory and Software Infrastructure for a Scalable Systems Biology], 2003-present

*Some joint projects with [http://www.cds.caltech.edu/~murray/wiki/Main_Page#Research Prof. Richard Murray] (with links to his wiki below)
**[http://www.cds.caltech.edu/~murray/VaVmuri/index.php?title=Main_Page Specification, Design and Verification of Distributed Embedded Systems] (MURI/AFOSR)
**Networked Feedback Systems in Biology (ARO ICB)
**[http://www.cds.caltech.edu/~murray/wiki/Model-Based_Design_and_Qualification_of_Complex_Systems Model-Based Design and Qualification of Complex Systems] (Boeing)

*Some joint grants with [http://netlab.caltech.edu/~slow/ Prof. Steven Low]:
**MURI Analysis and modeling of networks with long range dependence (LRD) characteristics (PI - Jean Walrand, UC Berkeley; Co-PIs - John Doyle, Steven Low, R. Srikanth (UIUC), V. Anantharam & A. Zakhor (UC Berkeley), D. Towsley & W. Gong (U. Mass. Amherst)2008
**NSF RI WAN in Lab (Newman, Psaltis, Yip) 2003-08
**NSF NeTS Collaborative Research: Optimization and Games in Interdomain Routing 2006
**NSF STI Multi-Gbps TCP: Data Intensive Networks for Science & Engineering (Bunn, Newman) 2002-05
**NSF ITR Optimal and Robust TCP Congestion Control 2001-04
**ARO DURIP Hybrid WAN in Lab (Newman, Psaltis, Yip) 2004-05
**ARO Network Research Analytical Theory of Protocols 2002-05
**ARO Network Science Networked control systems (Murray, Parrilo (MIT)) 2005-2006
(Note that other Co-PI are noted in brackets on these joint grants with Prof. Low and Prof. Doyle)

== Past Projects ==
Caltech
*[http://www.cds.caltech.edu/~doyle/hot/ HOT : Highly Optimized/Organized Tradeoffs/Tolerance, A unified theory of complex networks ]
*[http://www.cds.caltech.edu/sostools/ SOSTOOLS : Software for analysis of complex systems]
*[http://www.cds.caltech.edu/~doyle/MURI.html "Mathematical Infrastructure for Robust Virtual Engineering"] MURI award 1996
*Past projects with Prof Murray (links to his wiki)
**[http://www.cds.caltech.edu/~murray/projects/afosr95-vehicles/ Robust Nonlinear Control Theory with Application to Aerospace Vehicles] (AFOSR)
**[http://www.cds.caltech.edu/~murray/cdspanel/ Panel on Future Directions in Control, Dynamics, and Systems]
**[http://www.cds.caltech.edu/~murray/projects/nsf93-crcd/index.html Curriculum in Control and Dynamical Systems] (NSF)

Other

==Collaborative groups==
*[http://www.cimms.caltech.edu/whatiscimms.html CIMMS: Center for Integrative Multiscale Modeling and Simulation]
*[http://www.cds.caltech.edu/~murray/wiki/Main_Page Prof. Richard Murray]
* [http://biochemistry.ucsf.edu/labs/elsamad/home/index.html Prof. Hana El-Samad (UCSF)]
* [http://leecenter.caltech.edu/theory.html Lee Center for Networking]
*[http://netlab.caltech.edu/ Netlab]
**[http://netlab.caltech.edu/FAST/FAST: Fast AQM Scalable TCP, new internet protocol design.]

*[http://www.sisl.caltech.edu/ SISL]

* and more...

==See also==
*[[Papers]]
*[[Special:Allpages|All articles]]
*[[Special:Categories|Pages listed by Categories]]

===More research links===
Caltech
*[http://www.cds.caltech.edu/~murray/wiki/Main_Page#Research Prof. Murray's projects]
*[http://netlab.caltech.edu/projects.php Prof. Low's projects]
*[http://www.cds.caltech.edu/research/ CDS]
*[http://leecenter.caltech.edu/doyle-res.html HOT at Lee Center]
*[http://www.sisl.caltech.edu/people/index.html SISL]

UCSB
*[http://www.physics.ucsb.edu/~complex/ Jean Carlson’s HOT website]
[[Category:Research]]

Research

2011-07-11T03:18:44Z

Fiona: /* Current Projects */

"Professor Doyle's current '''research''' interests are in theoretical foundations for complex networks, primarily in network engineering and biology." He is also "interested in multiscale physics and financial markets, and the interplay between robustness, feedback, control, dynamical systems, computation, communications, and statistical physics." <http://www.cds.caltech.edu/people/> Aug 2008

Prof. Doyle has "applied complex ideas of robust design and control to many fields and is working on a unified theory of control in engineering, physics and biology." <http://www.ieee.org/portal/pages/about/awards/bios/2004controlsystems.html> Aug 2008

==Current Projects==
*[http://cds-web1.cds.caltech.edu/~doyle2/wiki/index.php?title=Systems_biology Systems Biology] ([http://www.its.caltech.edu/~fiona Fiona Chandra], Genti Buzi)
**Fundamental constraints and trade-offs of autocatalytic networks.
**Collaborators: [http://biochemistry.ucsf.edu/labs/elsamad/home/index.html Hana El-Samad], [http://sysos.eng.ox.ac.uk/control/sysos/index.php/User:Antonis Antonis Papachristodoulou]
*Fluids: [http://cds-web1.cds.caltech.edu/~doyle2/wiki/index.php?title=Turbulence Turbulence Modeling] ([https://www.cds.caltech.edu/~dennice/ Dennice Gayme])
**Collaborators: [http://engineering.ucsb.edu/~bamieh/ Bassam Bamieh], [http://www.mckeon.caltech.edu/ Beverly McKeon]
*[http://openwetware.org/wiki/Doyle Physiology]: Dynamic Modeling of Heart Rate Variability (Li Na, Jerry Cruz)
**Heart rate (HR) in healthy humans has high variability, and loss of this HR variability (HRV) is a signature of stress, fatigue, aging, or disease1-9. Correlating health and high HRV using time series analyses is popular in clinical and athletic training10 research, but its practical impact has been limited by lack of specific physiological mechanisms explaining HRV patterns. Conjectures attributing the cryptic etiology of HRV to complex feedbacks and nonlinear dynamics have similarly lacked mechanistic explanation. We leverage concepts from physiology, evolution, and control theory to analyze data from exercising athletes and develop mechanistic models explaining correlations between health, stress, and HRV.
*[http://cds-web1.cds.caltech.edu/~doyle2/wiki/index.php?title=Networking Internet and Networking] ([http://www.cds.caltech.edu/~chenlj/ Lijun Chen], [http://www.cds.caltech.edu/~lavaei/ Javad Lavaei], [http://www.cds.caltech.edu/~sojoudi/ Somayeh Sojoudi])
**Collaborators: [http://netlab.caltech.edu/slow/ Steven Low]
*Economics (Jerry Cruz)
** Market Bubbles and Crashes: We use tools from mathematical finance and stochastic control theory to investigate asset price bubbles and crashes in financial markets. We wish to gain insight using models that account for financial intermediation and associated frictions. Moreover, recent local-martingale characterizations of bubbles may provide avenues into developing new methods of empirical testing for bubbles.
*Distributed Control ([http://www.cds.caltech.edu/~lavaei/ Javad Lavaei], [http://www.cds.caltech.edu/~motee Nader Motee], Li Na)
**Designing Games for Distributed Opitmization (Li Na) The central goal in multiagent systems is to design local control laws for the individual agents to ensure that the emergent global behavior is desirable with respect to a given system level objective. Ideally, a system designer seeks to satisfy this goal while conditioning each agent's control law on the least amount of information possible. Unfortunately, there are no existing methodologies for addressing this design challenge. The goal of this research is to address this challenge using the field of game theory. We develop a systematic methodology for distributed optimization using the framework of state based potential games.

==Research Grants==
*[http://www.nsf.gov/index.jsp NSF] award: [http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=0326635 ITR COLLAB: Theory and Software Infrastructure for a Scalable Systems Biology], 2003-present

*Some joint projects with [http://www.cds.caltech.edu/~murray/wiki/Main_Page#Research Prof. Richard Murray] (with links to his wiki below)
**[http://www.cds.caltech.edu/~murray/VaVmuri/index.php?title=Main_Page Specification, Design and Verification of Distributed Embedded Systems] (MURI/AFOSR)
**Networked Feedback Systems in Biology (ARO ICB)
**[http://www.cds.caltech.edu/~murray/wiki/Model-Based_Design_and_Qualification_of_Complex_Systems Model-Based Design and Qualification of Complex Systems] (Boeing)

*Some joint grants with [http://netlab.caltech.edu/~slow/ Prof. Steven Low]:
**MURI Analysis and modeling of networks with long range dependence (LRD) characteristics (PI - Jean Walrand, UC Berkeley; Co-PIs - John Doyle, Steven Low, R. Srikanth (UIUC), V. Anantharam & A. Zakhor (UC Berkeley), D. Towsley & W. Gong (U. Mass. Amherst)2008
**NSF RI WAN in Lab (Newman, Psaltis, Yip) 2003-08
**NSF NeTS Collaborative Research: Optimization and Games in Interdomain Routing 2006
**NSF STI Multi-Gbps TCP: Data Intensive Networks for Science & Engineering (Bunn, Newman) 2002-05
**NSF ITR Optimal and Robust TCP Congestion Control 2001-04
**ARO DURIP Hybrid WAN in Lab (Newman, Psaltis, Yip) 2004-05
**ARO Network Research Analytical Theory of Protocols 2002-05
**ARO Network Science Networked control systems (Murray, Parrilo (MIT)) 2005-2006
(Note that other Co-PI are noted in brackets on these joint grants with Prof. Low and Prof. Doyle)

== Past Projects ==
Caltech
*[http://www.hot.caltech.edu/ HOT : Highly Optimized/Organized Tradeoffs/Tolerance, A unified theory of complex networks ]
*[http://www.cds.caltech.edu/sostools/ SOSTOOLS : Software for analysis of complex systems]
*[http://www.cds.caltech.edu/~doyle/MURI.html "Mathematical Infrastructure for Robust Virtual Engineering"] MURI award 1996
*Past projects with Prof Murray (links to his wiki)
**[http://www.cds.caltech.edu/~murray/projects/afosr95-vehicles/ Robust Nonlinear Control Theory with Application to Aerospace Vehicles] (AFOSR)
**[http://www.cds.caltech.edu/~murray/cdspanel/ Panel on Future Directions in Control, Dynamics, and Systems]
**[http://www.cds.caltech.edu/~murray/projects/nsf93-crcd/index.html Curriculum in Control and Dynamical Systems] (NSF)

Other

==Collaborative groups==
*[http://www.cimms.caltech.edu/whatiscimms.html CIMMS: Center for Integrative Multiscale Modeling and Simulation]
*[http://www.cds.caltech.edu/~murray/wiki/Main_Page Prof. Richard Murray]
* [http://biochemistry.ucsf.edu/labs/elsamad/home/index.html Prof. Hana El-Samad (UCSF)]
* [http://leecenter.caltech.edu/theory.html Lee Center for Networking]
*[http://netlab.caltech.edu/ Netlab]
**[http://netlab.caltech.edu/FAST/FAST: Fast AQM Scalable TCP, new internet protocol design.]

*[http://www.sisl.caltech.edu/ SISL]

* and more...

==See also==
*[[Papers]]
*[[Special:Allpages|All articles]]
*[[Special:Categories|Pages listed by Categories]]

===More research links===
Caltech
*[http://www.cds.caltech.edu/~murray/wiki/Main_Page#Research Prof. Murray's projects]
*[http://netlab.caltech.edu/projects.php Prof. Low's projects]
*[http://www.cds.caltech.edu/research/ CDS]
*[http://leecenter.caltech.edu/doyle-res.html HOT at Lee Center]
*[http://www.sisl.caltech.edu/people/index.html SISL]

UCSB
*[http://www.physics.ucsb.edu/~complex/ Jean Carlson’s HOT website]
[[Category:Research]]

Research

2011-07-11T03:10:21Z

Fiona: /* Current Projects */

"Professor Doyle's current '''research''' interests are in theoretical foundations for complex networks, primarily in network engineering and biology." He is also "interested in multiscale physics and financial markets, and the interplay between robustness, feedback, control, dynamical systems, computation, communications, and statistical physics." <http://www.cds.caltech.edu/people/> Aug 2008

Prof. Doyle has "applied complex ideas of robust design and control to many fields and is working on a unified theory of control in engineering, physics and biology." <http://www.ieee.org/portal/pages/about/awards/bios/2004controlsystems.html> Aug 2008

==Current Projects==
*[http://cds-web1.cds.caltech.edu/~doyle2/wiki/index.php?title=Systems_biology Systems Biology] ([http://www.its.caltech.edu/~fiona Fiona Chandra], Genti Buzi)
**Fundamental constraints and trade-offs of autocatalytic networks.
**Collaborators: [http://biochemistry.ucsf.edu/labs/elsamad/home/index.html Hana El-Samad], [http://sysos.eng.ox.ac.uk/control/sysos/index.php/User:Antonis Antonis Papachristodoulou]
*Fluids: [http://cds-web1.cds.caltech.edu/~doyle2/wiki/index.php?title=Turbulence Turbulence Modeling] ([https://www.cds.caltech.edu/~dennice/ Dennice Gayme])
**Collaborators: [http://engineering.ucsb.edu/~bamieh/ Bassam Bamieh], [http://www.mckeon.caltech.edu/ Beverly McKeon]
*[http://openwetware.org/wiki/Doyle Physiology]: Dynamic Modeling of Heart Rate Variability (Li Na, Jerry Cruz)
**Heart rate (HR) in healthy humans has high variability, and loss of this HR variability (HRV) is a signature of stress, fatigue, aging, or disease1-9. Correlating health and high HRV using time series analyses is popular in clinical and athletic training10 research, but its practical impact has been limited by lack of specific physiological mechanisms explaining HRV patterns. Conjectures attributing the cryptic etiology of HRV to complex feedbacks and nonlinear dynamics have similarly lacked mechanistic explanation. We leverage concepts from physiology, evolution, and control theory to analyze data from exercising athletes and develop mechanistic models explaining correlations between health, stress, and HRV.
*[http://cds-web1.cds.caltech.edu/~doyle2/wiki/index.php?title=Networking Internet and Networking] ([http://www.cds.caltech.edu/~chenlj/ Lijun Chen], [http://www.cds.caltech.edu/~lavaei/ Javad Lavaei], [http://www.cds.caltech.edu/~sojoudi/ Somayeh Sojoudi])
**Collaborators: [http://netlab.caltech.edu/slow/ Steven Low]
*Economics (Jerry Cruz)
** Market Bubbles and Crashes: We use tools from mathematical finance and stochastic control theory to investigate asset price bubbles and crashes in financial markets. We wish to gain insight using models that account for financial intermediation and associated frictions. Moreover, recent local-martingale characterizations of bubbles may provide avenues into developing new methods of empirical testing for bubbles.
*Distributed Control ([http://www.cds.caltech.edu/~lavaei/ Javad Lavaei], [http://www.cds.caltech.edu/~motee Nader Motee])

==Research Grants==
*[http://www.nsf.gov/index.jsp NSF] award: [http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=0326635 ITR COLLAB: Theory and Software Infrastructure for a Scalable Systems Biology], 2003-present

*Some joint projects with [http://www.cds.caltech.edu/~murray/wiki/Main_Page#Research Prof. Richard Murray] (with links to his wiki below)
**[http://www.cds.caltech.edu/~murray/VaVmuri/index.php?title=Main_Page Specification, Design and Verification of Distributed Embedded Systems] (MURI/AFOSR)
**Networked Feedback Systems in Biology (ARO ICB)
**[http://www.cds.caltech.edu/~murray/wiki/Model-Based_Design_and_Qualification_of_Complex_Systems Model-Based Design and Qualification of Complex Systems] (Boeing)

*Some joint grants with [http://netlab.caltech.edu/~slow/ Prof. Steven Low]:
**MURI Analysis and modeling of networks with long range dependence (LRD) characteristics (PI - Jean Walrand, UC Berkeley; Co-PIs - John Doyle, Steven Low, R. Srikanth (UIUC), V. Anantharam & A. Zakhor (UC Berkeley), D. Towsley & W. Gong (U. Mass. Amherst)2008
**NSF RI WAN in Lab (Newman, Psaltis, Yip) 2003-08
**NSF NeTS Collaborative Research: Optimization and Games in Interdomain Routing 2006
**NSF STI Multi-Gbps TCP: Data Intensive Networks for Science & Engineering (Bunn, Newman) 2002-05
**NSF ITR Optimal and Robust TCP Congestion Control 2001-04
**ARO DURIP Hybrid WAN in Lab (Newman, Psaltis, Yip) 2004-05
**ARO Network Research Analytical Theory of Protocols 2002-05
**ARO Network Science Networked control systems (Murray, Parrilo (MIT)) 2005-2006
(Note that other Co-PI are noted in brackets on these joint grants with Prof. Low and Prof. Doyle)

== Past Projects ==
Caltech
*[http://www.hot.caltech.edu/ HOT : Highly Optimized/Organized Tradeoffs/Tolerance, A unified theory of complex networks ]
*[http://www.cds.caltech.edu/sostools/ SOSTOOLS : Software for analysis of complex systems]
*[http://www.cds.caltech.edu/~doyle/MURI.html "Mathematical Infrastructure for Robust Virtual Engineering"] MURI award 1996
*Past projects with Prof Murray (links to his wiki)
**[http://www.cds.caltech.edu/~murray/projects/afosr95-vehicles/ Robust Nonlinear Control Theory with Application to Aerospace Vehicles] (AFOSR)
**[http://www.cds.caltech.edu/~murray/cdspanel/ Panel on Future Directions in Control, Dynamics, and Systems]
**[http://www.cds.caltech.edu/~murray/projects/nsf93-crcd/index.html Curriculum in Control and Dynamical Systems] (NSF)

Other

==Collaborative groups==
*[http://www.cimms.caltech.edu/whatiscimms.html CIMMS: Center for Integrative Multiscale Modeling and Simulation]
*[http://www.cds.caltech.edu/~murray/wiki/Main_Page Prof. Richard Murray]
* [http://biochemistry.ucsf.edu/labs/elsamad/home/index.html Prof. Hana El-Samad (UCSF)]
* [http://leecenter.caltech.edu/theory.html Lee Center for Networking]
*[http://netlab.caltech.edu/ Netlab]
**[http://netlab.caltech.edu/FAST/FAST: Fast AQM Scalable TCP, new internet protocol design.]

*[http://www.sisl.caltech.edu/ SISL]

* and more...

==See also==
*[[Papers]]
*[[Special:Allpages|All articles]]
*[[Special:Categories|Pages listed by Categories]]

===More research links===
Caltech
*[http://www.cds.caltech.edu/~murray/wiki/Main_Page#Research Prof. Murray's projects]
*[http://netlab.caltech.edu/projects.php Prof. Low's projects]
*[http://www.cds.caltech.edu/research/ CDS]
*[http://leecenter.caltech.edu/doyle-res.html HOT at Lee Center]
*[http://www.sisl.caltech.edu/people/index.html SISL]

UCSB
*[http://www.physics.ucsb.edu/~complex/ Jean Carlson’s HOT website]
[[Category:Research]]

Group

2011-07-08T07:18:49Z

Fiona: /* Graduate students */

John Doyle's research '''group''' is part of [http://www.cms.caltech.edu/people CDS department] at Caltech.

==Current Group==

===Faculty===
John Doyle 
John G Braun Professor of Control & Dynamical Systems, Electrical Engineering, and BioEngineering 
*Academic Summary: BS, MS EE MIT. Ph.D. Math, UC Berkeley. 
*Awards: IEEE Centennial, Hickernell, Eckman, Friedman, NSF PYI, ONR YI. 
*Prize papers: IEEE Transactions (2), ACC, IEEE Baker Prize, ``top 10 most influential papers in mathematics 1981-1993.''

===Postdocs===
{| class="wikitable" border="0" width="80%"
|-
|[http://www.cds.caltech.edu/~chen/ Lijun Chen]
[http://www.cds.caltech.edu/people/portal/?id=331 Dennice Maynard Gayme]
|[http://www.cs.caltech.edu/~krister/ Krister Jacobsson]
[http://www.cds.caltech.edu/~motee Nader Motee]
|[http://www.cds.caltech.edu/people/portal/?id=384 Gentian Buzi]
[http://www.cds.caltech.edu/~lavaei/ Javad Lavaei-Yanesi]
|}

===Graduate students===
{| class="wikitable" border="0" width="80%"
|-
|[http://www.cds.caltech.edu/people/portal/?id=4 Aristotelis Asimakopoulos]
| Simon Chien
|Hamed Hamze-Bajgiran
|-
|[http://www.its.caltech.edu/~fiona Fiona Chandra]
|[http://www.cds.caltech.edu/~andyl/ Andrew Lamperski]
|Matanya Horowitz
|-
|[http://www.cds.caltech.edu/people/portal/?id=753 Na Li]
|Zhaoqian (Steven) Xie
|Nikolai Matni
|-
|[http://www.cds.caltech.edu/~sojoudi/ Somayeh Sojoudi]
|Jerry Cruz

|}

===Undergraduate students===
{| class="wikitable" border="0" width="80%"
|-
|[http://www.cds.caltech.edu/people/portal/index.php?id=772 George Hines]||[http://www.cds.caltech.edu/people/portal/?id=803 Nicholas Fette]
|}
===Admin===
Anissa Scott

===Visitors===
[http://www.cds.caltech.edu/~lun/ Lun Li, also alumni]
====Students====
{| class="wikitable" border="1"
|-
|''SURF 2008''||''Other''
|-
|Jackson Wang Ji Young Lee||Paul Fang, student from Temple City High School
|}

==Past Group==
===Alumni===
{| class="wikitable" border="0" width="80%"
|-
|'''2007-2011'''||'''2000-2006'''||'''1990-1999'''
|-
| [http://www.cds.caltech.edu/people/portal/?id=522 Marcos Nahmad Bensusan]
[http://www.cds.caltech.edu/~chen/ Lijun Chen]

[http://www.cds.caltech.edu/~lun Lun Li]

[http://www.cds.caltech.edu/people/portal/?id=6 Xin Liu]

[http://www.cds.caltech.edu/~alfredo/ Alfredo Martinez]

[http://www.cds.caltech.edu/people/portal/?id=184 Oluwatosin Otitoju]
|
[http://faculty.nps.edu/dlalders/ David Alderson]

Nizar Batada

[http://www.cds.caltech.edu/~xlfeng/ Xiaolin Feng]

Irene Gregory

[http://www.seas.upenn.edu/~jadbabai/ Ali Jadbabaie]

[http://webfiles.uci.edu/yjing/www/ Yindi Jing]

Sven Khatri

[http://users.ox.ac.uk/~engs0587/ Antonis Papachristodoulou]

[http://www.mit.edu/~parrilo/ Pablo Parrilo]

[http://www.cds.caltech.edu/~prajna/ Stephen Prajna]

[http://www.cds.caltech.edu/~jiantao/ Jiantao Wang]

[http://www.cds.caltech.edu/~jyu/ Jie Yu]

[http://www.cds.caltech.edu/~xyzhu/ Xiaoyun Zhu]

|Carolyn Beck

Raff D'Andrea

Sonja Glavaski

Irene Gregory

Yun Huang

Michael Kantner

[http://www.ee.ucla.edu/~paganini/ Fernando Paganini]

[http://www.stanford.edu/dept/MSandE/people/faculty/primbs/index.html James Primbs]

Stefano Soatto

Jorge Tierno
|}

===Past Postdocs===
{| class="wikitable" border="0" width="80%"
|-
|'''2009-2011'''||'''2007-2008'''||'''2000-2006'''||'''1990-1999'''
|-
|
[http://www.ist.caltech.edu/~brecht/ Ben Recht]
|
[http://www.cds.caltech.edu/people/portal/?id=662 Aaron D. Ames]

[http://www.cds.caltech.edu/~dtarraf/ Danielle C.Tarraf]

[http://www.cds.caltech.edu/~maryam/ Maryam Fazel, Research scientist]
|
Masahiro Yanagisawa

[http://www-control.eng.cam.ac.uk/~jmg77/ Jorge Goncalves]

[http://devcell.bio.uci.edu/faculty/yi.htm Tau-Mu Yi]
|
[http://www.nps.navy.mil/orfacpag/resumePages/alderson.htm David Alderson]

[http://www.bmc.riken.jp/~reiko/index.htm Reiko Tanaka]
|}

===Past Admin===

?-2008 Gloria Bain

===Past Visitors===
{| class="wikitable" border="0" width="80%"
|-
|'''2007'''
|'''2000-2006
|'''1990-1999'''
|-
|Panagiota Stratou
|?
|?
|}

==MURF and SURF Students==
{| class="wikitable" border="0" width="80%"
|'''2008'''||'''2007''' ||'''2000-2006'''
|-
|Jackson Wang Ji Young Lee ||[http://www.cds.caltech.edu/people/portal/?id=722 Chinwendu Enyioha]||
|-
| ||
|}

==Other collaborators==
{| class="wikitable" border="0" width="80%"
|-
|[[Image:3profs07.jpg|200px]]||[[Image:John-and-marie.jpg]]
|-
|2007 Commencement: Prof.'s John Doyle, Richard Murray & Steven Low. ||John Doyle and Marie Csete
|}

[[Image:JCDgraph.jpg]]

Some collaborators at John Doyle's 50th birthday Connections Workshop, 2004:

*[http://userwww.service.emory.edu/~mcsete/ Marie Csete, Lab] at [http://www.emory.edu/change_mode.cfm?mode=text Emory University], Atlanta.
**[http://www.emory.edu/PROVOST/greatscholars/MarieCsete.htm About Marie Csete's work.]

==See also==
*[[Group Meetings]]
*[[Calendar]]
*<http://www.cds.caltech.edu/people/portal/?un=doyle>

Main Page

2011-07-08T06:28:45Z

Fiona: /* Teaching */

<table border=1 width=100% style="color:black; " cellpadding="20" cellspacing="0">
<tr>
<td align=center width=20%> [[Image:Smallpic.JPG]]</td>
<td width=60% align=center>
John C. Doyle 

John G Braun Professor 
of Control and Dynamical Systems 
Electrical Engineering 
and BioEngineering 
Division of Engineering and Applied Science 
California Institute of Technology 

</td>
<td align=center width=20%>


[[J. Doyle’s Bio]]

[[News]]

[[Calendar]]

[[#Contact|Contact]]

[https://www.cds.caltech.edu/squirrelmail/src/login.php CDS Webmail]
</td>
</tr></table>
{| align=center
|[[Image:Blossoms900strip.jpg]]||[[Image:Blossoms900strip.jpg]]||[[Image:Blossoms900strip.jpg]]||[[Image:Blossoms900strip.jpg]]
|}
<hr>

==News==
*Visiting this week: Ioannis Lestas
*[[Research|MURI 2008]]
*[http://discovermagazine.com/2007/nov/this-man-wants-to-control-the-internet Discover magazine] interviews Prof. Doyle.

"This man wants to control the internet" by Carl Zimmer, Discover magazine, 10/25/2007.

==Recent Papers==
*[http://cds-web1.cds.caltech.edu/~doyle2/wiki/images/4/4e/7.PNAS_InPress_June_2011.pdf Architecture, constraints, and behavior.] JC Doyle, MC Csete. PNAS, in press, July 2011
*[http://cds-web1.cds.caltech.edu/~doyle2/wiki/images/b/b6/Science-2011-Chandra-187-92.pdf Gycolytic oscillations and limits on robust efficiency.] FA Chandra, G Buzi, JC Doyle Science, in press, July 2011
*[http://cds-web1.cds.caltech.edu/~doyle2/wiki/images/c/c4/2.IEEE_TransAutoCtrl_Feb_2011_.pdf On Lossless Approximations, the Fluctuation-Dissipation Theorem, and Limitations of Measurements] H Sandberg, JC Delvenne, JC Doyle IEEE Trans Auto Control, v56:2, 293-308 (2011)
*[[Papers|'''More Papers''']]

== Research ==
John Doyle's '''[[research]]''' interests are in theoretical foundations for complex networks in engineering and biology, as well as multiscale physics, and include integrating modeling, ID, analysis and design of uncertain nonlinear systems, and computation in analysis and simulation, including complexity theory to guide algorithm development. Applications interests are motivated by the interplay between: control, dynamical systems, and design and analysis of large, complex systems.

*[[Research|Research projects and grants list]]

== Teaching ==

*[http://www.cds.caltech.edu/~murray/wiki/CDS_212_Fall_2010 CDS 212, Feedback Control Theory (Fall 2010)]
*[[CDS 213|The Architecture of Robust, Evolvable Networks (Wi10)]]

== Contact ==
{| width=100%
|- valign=top
| width=50% |

'''Mailing Address'''

John Doyle 
California Institute of Technology 
Control and Dynamical Systems, MC 107-81 
1200 E. California Blvd 
Pasadena, CA 91125 USA
| width=50% |

'''Contact information'''

E-mail: doyle AT cds dot caltech dot edu 
Office: 109 Steele, 
Phone: 626.395.4808 Fax: 626.395.6170 

'''Admin Assistant''': Anissa Scott 
Office: 107 Steele, 
Email: anissa AT caltech dot edu 
Phone: 626.395.4140 
Labs: 12 STL, 110 GUG (x2319)
|-
|

===Other Caltech links===

*[http://www.caltech.edu California Institute of Technology]
**[http://www.eas.caltech.edu Engineering and Applied Science Division]
***[http://www.be.caltech.edu/ Bioengineering Department]
***[http://www.cds.caltech.edu Control and Dynamical Systems Department]
***[http://www.ee2.caltech.edu/ Electrical Engineering Department]
|}

Research

2011-07-08T06:27:55Z

Fiona: /* Current Projects */

"Professor Doyle's current '''research''' interests are in theoretical foundations for complex networks, primarily in network engineering and biology." He is also "interested in multiscale physics and financial markets, and the interplay between robustness, feedback, control, dynamical systems, computation, communications, and statistical physics." <http://www.cds.caltech.edu/people/> Aug 2008

Prof. Doyle has "applied complex ideas of robust design and control to many fields and is working on a unified theory of control in engineering, physics and biology." <http://www.ieee.org/portal/pages/about/awards/bios/2004controlsystems.html> Aug 2008

==Current Projects==
*[http://cds-web1.cds.caltech.edu/~doyle2/wiki/index.php?title=Systems_biology Systems Biology] ([http://www.its.caltech.edu/~fiona Fiona Chandra], Genti Buzi)
**Fundamental constraints and trade-offs of autocatalytic networks.
**Collaborators: [http://biochemistry.ucsf.edu/labs/elsamad/home/index.html Hana El-Samad], [http://sysos.eng.ox.ac.uk/control/sysos/index.php/User:Antonis Antonis Papachristodoulou]
*Fluids: [http://cds-web1.cds.caltech.edu/~doyle2/wiki/index.php?title=Turbulence Turbulence Modeling] ([https://www.cds.caltech.edu/~dennice/ Dennice Gayme])
**Collaborators: [http://engineering.ucsb.edu/~bamieh/ Bassam Bamieh], [http://www.mckeon.caltech.edu/ Beverly McKeon]
*[http://openwetware.org/wiki/Doyle Physiology] (Li Na, Jerry Cruz)
*[http://cds-web1.cds.caltech.edu/~doyle2/wiki/index.php?title=Networking Internet and Networking] ([http://www.cds.caltech.edu/~chenlj/ Lijun Chen], [http://www.cds.caltech.edu/~lavaei/ Javad Lavaei], [http://www.cds.caltech.edu/~sojoudi/ Somayeh Sojoudi])
**Collaborators: [http://netlab.caltech.edu/slow/ Steven Low]
*Economics (Jerry Cruz)
** Market Bubbles and Crashes: We use tools from mathematical finance and stochastic control theory to investigate asset price bubbles and crashes in financial markets. We wish to gain insight using models that account for financial intermediation and associated frictions. Moreover, recent local-martingale characterizations of bubbles may provide avenues into developing new methods of empirical testing for bubbles.
*Distributed Control ([http://www.cds.caltech.edu/~lavaei/ Javad Lavaei], [http://www.cds.caltech.edu/~motee Nader Motee])

==Research Grants==
*[http://www.nsf.gov/index.jsp NSF] award: [http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=0326635 ITR COLLAB: Theory and Software Infrastructure for a Scalable Systems Biology], 2003-present

*Some joint projects with [http://www.cds.caltech.edu/~murray/wiki/Main_Page#Research Prof. Richard Murray] (with links to his wiki below)
**[http://www.cds.caltech.edu/~murray/VaVmuri/index.php?title=Main_Page Specification, Design and Verification of Distributed Embedded Systems] (MURI/AFOSR)
**Networked Feedback Systems in Biology (ARO ICB)
**[http://www.cds.caltech.edu/~murray/wiki/Model-Based_Design_and_Qualification_of_Complex_Systems Model-Based Design and Qualification of Complex Systems] (Boeing)

*Some joint grants with [http://netlab.caltech.edu/~slow/ Prof. Steven Low]:
**MURI Analysis and modeling of networks with long range dependence (LRD) characteristics (PI - Jean Walrand, UC Berkeley; Co-PIs - John Doyle, Steven Low, R. Srikanth (UIUC), V. Anantharam & A. Zakhor (UC Berkeley), D. Towsley & W. Gong (U. Mass. Amherst)2008
**NSF RI WAN in Lab (Newman, Psaltis, Yip) 2003-08
**NSF NeTS Collaborative Research: Optimization and Games in Interdomain Routing 2006
**NSF STI Multi-Gbps TCP: Data Intensive Networks for Science & Engineering (Bunn, Newman) 2002-05
**NSF ITR Optimal and Robust TCP Congestion Control 2001-04
**ARO DURIP Hybrid WAN in Lab (Newman, Psaltis, Yip) 2004-05
**ARO Network Research Analytical Theory of Protocols 2002-05
**ARO Network Science Networked control systems (Murray, Parrilo (MIT)) 2005-2006
(Note that other Co-PI are noted in brackets on these joint grants with Prof. Low and Prof. Doyle)

== Past Projects ==
Caltech
*[http://www.hot.caltech.edu/ HOT : Highly Optimized/Organized Tradeoffs/Tolerance, A unified theory of complex networks ]
*[http://www.cds.caltech.edu/sostools/ SOSTOOLS : Software for analysis of complex systems]
*[http://www.cds.caltech.edu/~doyle/MURI.html "Mathematical Infrastructure for Robust Virtual Engineering"] MURI award 1996
*Past projects with Prof Murray (links to his wiki)
**[http://www.cds.caltech.edu/~murray/projects/afosr95-vehicles/ Robust Nonlinear Control Theory with Application to Aerospace Vehicles] (AFOSR)
**[http://www.cds.caltech.edu/~murray/cdspanel/ Panel on Future Directions in Control, Dynamics, and Systems]
**[http://www.cds.caltech.edu/~murray/projects/nsf93-crcd/index.html Curriculum in Control and Dynamical Systems] (NSF)

Other

==Collaborative groups==
*[http://www.cimms.caltech.edu/whatiscimms.html CIMMS: Center for Integrative Multiscale Modeling and Simulation]
*[http://www.cds.caltech.edu/~murray/wiki/Main_Page Prof. Richard Murray]
* [http://biochemistry.ucsf.edu/labs/elsamad/home/index.html Prof. Hana El-Samad (UCSF)]
* [http://leecenter.caltech.edu/theory.html Lee Center for Networking]
*[http://netlab.caltech.edu/ Netlab]
**[http://netlab.caltech.edu/FAST/FAST: Fast AQM Scalable TCP, new internet protocol design.]

*[http://www.sisl.caltech.edu/ SISL]

* and more...

==See also==
*[[Papers]]
*[[Special:Allpages|All articles]]
*[[Special:Categories|Pages listed by Categories]]

===More research links===
Caltech
*[http://www.cds.caltech.edu/~murray/wiki/Main_Page#Research Prof. Murray's projects]
*[http://netlab.caltech.edu/projects.php Prof. Low's projects]
*[http://www.cds.caltech.edu/research/ CDS]
*[http://leecenter.caltech.edu/doyle-res.html HOT at Lee Center]
*[http://www.sisl.caltech.edu/people/index.html SISL]

UCSB
*[http://www.physics.ucsb.edu/~complex/ Jean Carlson’s HOT website]
[[Category:Research]]

2010-2011

2011-07-08T06:25:53Z

Fiona: /* 2011 */

==2011==
===Journals===
[http://cds-web1.cds.caltech.edu/~doyle2/wiki/images/4/4e/7.PNAS_InPress_June_2011.pdf Architecture, constraints, and behavior] 
JC Doyle, MC Csete 
PNAS, in press, July 2011

[http://cds-web1.cds.caltech.edu/~doyle2/wiki/images/b/b6/Science-2011-Chandra-187-92.pdf Gycolytic oscillations and limits on robust efficiency] 
FA Chandra, G Buzi, JC Doyle 
Science, in press, July 2011

[http://cds-web1.cds.caltech.edu/~doyle2/wiki/images/8/87/PhysFluids_23_065108.pdf Amplification and nonlinear mechanisms in plane Couette flow.] 
D Gayme, B McKeon, B Bamieh, A Papachristodolou, and J Doyle. 
Physics of Fluids v23:6:065108 (2011)

[http://cds-web1.cds.caltech.edu/~doyle2/wiki/images/a/a2/6.AutomaticaJune2011.pdf Analysis of autocatalytic networks in biology] 
G Buzi, U Topcu, J Doyle 
Automatica 47:1123-1130 (2011)

[http://cds-web1.cds.caltech.edu/~doyle2/wiki/images/c/c4/2.IEEE_TransAutoCtrl_Feb_2011_.pdf On Lossless Approximations, the Fluctuation-Dissipation Theorem, and Limitations of Measurements] 
H Sandberg, JC Delvenne, JC Doyle 
IEE Trans Auto Control, v56:2, 293-308 (2011)

[http://cds-web1.cds.caltech.edu/~doyle2/wiki/images/6/62/9.ComputerNetworksFeb2011.pdf Cross-layer design in multihop wireless networks] 
L Chen, SH Low, and JC Doyle 
Computer Networks 55:480–496 (2011)

Javad Lavaei, Aydin Babakhani, Ali Hajimiri and John C. Doyle, "Solving
Large-Scale Hybrid Circuit-Antenna Problems," IEEE Transactions on Circuits
and Systems I, vol. 58, no. 2, pp. 374-387, Feb. 2011.

===Conferences===

Effects of Buffers on Stability of Internet Congestion Controllers 
Somayeh Sojoudi, Steven Low and John Doyle 
IEEE International Conference on Computer Communications (INFOCOM), mini conference, China, 2011.

==2010==
===Journals===
[http://cds-web1.cds.caltech.edu/~doyle2/wiki/images/a/ab/8.IEEETransNetworkingAug2010.pdf Random access game and medium access control design] 
Lijun Chen, Steven Low, and John Doyle 
IEEE Trans Networking 18:4:1303-1316, AUG 2010.

[http://cds-web1.cds.caltech.edu/~doyle2/wiki/images/d/de/1.IEEE_TransSysMCyber_AldersonDoyle-July2010.pdf Contrasting views of complexity and their implications for network-centric infrastructures] 
David Alderson and John Doyle 
IEEE Trans Systems Man Cybernetics—Part A: Syst Humans 40:839-852, JUL 2010.

[http://www.cds.caltech.edu/~dennice/PublishedVersionJFM2010.pdf A streamwise constant model of turbulence in plane Couette flow] 
Gayme DF, McKeon BJ, Papachristodoulou A, Bamieh B, and Doyle JC 
Journal of Fluid Mechanics 665:99-119 (2010)

===Conferences===
Performance Limitations in Autocatalytic Networks in Biology 
Motee N, Chandra F, Bamieh B, Khammash M, and Doyle J 
In Proc 49th IEEE Conf Decision and Control, 4715-4720, Dec 2010.

Passively Controllable Smart Antennas 
Javad Lavaei, Aydin Babakhani, Ali Hajimiri and John C. Doyle 
IEEE Global Communications Conference (GLOBECOM), Miami, Florida, 2010.

Finding Globally Optimum Solutions in Antenna Optimization Problems 
Aydin Babakhani, Javad Lavaei, John C. Doyle and Ali Hajimiri 
IEEE International Symposium on Antennas and Propagation, Toronto, Canada, 2010.

Programmable Antenna Design Using Convex Optimization 
Javad Lavaei, Aydin Babakhani, Ali Hajimiri and John C. Doyle 
19th International Symposium on Mathematical Theory of Networks and Systems, Budapest, Hungary, 2010.

Javad Lavaei, Aydin Babakhani, Ali Hajimiri and John C. Doyle, "A Study of
Near-Field Direct Antenna Modulation Systems Using Convex Optimization," in
American Control Conference, Baltimore, 2010.

Javad Lavaei, John C. Doyle and Steven Low, "Utility Functionals Associated
With Available Congestion Control Algorithms," IEEE International
Conference on Computer Communications (INFOCOM), San Diego, California,
2010.

Networking

2011-07-08T06:24:20Z

Fiona: /* 2011 */

Intro: ...'''networking''' at Doyle's [[group]] covers...

Keywords: '''network(s)''',

'''internet''', architecture, infrastructure, graphs, game theory, congestion control, coding, ...

and biological, biochemical, metabolic...

Some papers from <http://www.cds.caltech.edu/~doyle/RecentPapers/>

==Networks==
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/f/f5/PRE06.pdf ''Diversity of graphs with highly variable connectivity''] 
David Alderson and Lun Li 
Phys. Rev. E 75, 046102, 2007. (3.9MB)

==Internet networks==
Keywords: '''internet''', '''networks''', architecture, coding, infrastructure, graphs, game theory, congestion control,...

===2011===
[http://cds-web1.cds.caltech.edu/~doyle2/wiki/images/6/62/9.ComputerNetworksFeb2011.pdf Cross-layer design in multihop wireless networks] 
L Chen, SH Low, and JC Doyle 
Computer Networks 55:480–496 (2011)

Effects of Buffers on Stability of Internet Congestion Controllers 
Somayeh Sojoudi, Steven Low and John Doyle 
IEEE International Conference on Computer Communications (INFOCOM), mini conference, China, 2011.

===2007===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/3/36/IEEEProc_NetsLayer.pdf'' Layering as optimization decomposition: A Mathematical Theory of Network Architectures''] (invited), 
Mung Chiang, Steven H. Low, A. Robert Calderbank, John C. Doyle 
in Proc. IEEE 95(1) Jan 2007. (3.2MB)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/9/96/Netcod-info07.pdf ''Optimization Based Rate Control for Multi-cast with Network Coding''] 
Lijun Chen, Tracey Ho, Steven H. Low, Mung Chiang and John C. Doyle. 
in Proc. IEEE Infocom, Anchorage, Alaska, May 2007. (191K)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/6/6b/Oscor_mass.pdf Opportunistic Source Coding for Data Gathering in Wireless Sensor Networks]
Tao Cui, Lijun Chen, Tracey Ho, Steven H. Low and Lachlan H. Andrew 
in Proc. IEEE MASS (Mobile Ad-hoc and Sensor Systems), Pisa, Italy, Oct 2007.

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/7/71/Rag07.pdf ''Game-Theoretic Model for Medium Access Control''] 
Lijun Chen, Tao Cui, Steven H. Low and John C. Doyle 
in Proc. WICON, Austin,Texas, Oct 2007.

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/9/96/Netcod-info07.pdf ''Optimization Based Rate Control for Multi-cast with Network Coding''] 
Lijun Chen, Tracey Ho, Steven H. Low, Mung Chiang and John C. Doyle. 
in Proc. IEEE Infocom, Anchorage, Alaska, May 2007.

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/6/6e/CSMC2007.pdf ''Can complexity science support the engineering of critical network infrastructures?''] 
Alderson, D.L. and Doyle, J.C.; 
IEEE International Conference on Systems, Man and Cybernetics, pp 44 - 51 , 7-10 Oct. 2007

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/3/38/Ragmac07.pdf Contention Control: A Game-Theoretic Approach] (invited) 
Lijun Chen, Steven H. Low and John C. Doyle 
in Proc. IEEE CDC pp3428 - 3434, New Orleans, LA, 12-14 Dec 2007.

[http://www.springerlink.com/content/qp4x0125v16p2g83/?p=cd9b949b2ef14cef910ce160b6ead5c2&pi=6 ''Dual scheduling algorithm in a generalized switch: asymptotic optimality and throughput optimality''], 
L. Chen and S. H. Low and J. C. Doyle, 
in [http://www.springer.com/west/home?SGWID=4-102-22-92732347-0&changeHeader=true ''High-Performance Packet Switching Architectures''], Itamar Elhanany and Mounir Hamdi (Eds), Springer, 2007.

===2006===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/1/1d/InternetMath06.pdf ''Towards a Theory of Scale-Free Graphs: Definition, Properties, and Implications''] 
L. Li, D. Alderson, J. C. Doyle and W. Willinger, 
Internet Mathematics, 2(4): 431-523, Mar 2006 (1.8MB)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/a/ae/Wireless-Chen-infocom06.pdf ''Cross-layer congestion control, routing and scheduling design in ad hoc wireless network''], 
L. Chen and S. H. Low and M. Chiang and J. C. Doyle, 
in Proc. IEEE Infocom, pp1-13; Barcelona, Spain, Apr 2006. (431K)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/f/fe/Hotnets06.pdf ''Discovering Dependencies for Network Management''], 
Victor Bahl, Paul Barham, Richard Black, Ranveer Chandra, Moises Goldszmidt, Rebecca Isaacs, Srikanth Kandula, Lun Li, John MacCormick, David A. Maltz, Richard Mortier, Mike Wawrzoniak, and Ming Zhang, 
In Proc. ACM/SIGCOMM HotNets, Irvine, CA, Sept 2006.

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/5/58/Informs-tc04-chap6.pdf ''The Optimization-based Approach to Modeling Internet Topology''] 
D. Alderson, W. Willinger, L. Li, and J. Doyle, 
[http://www.springer.com/west/home/engineering/electronics?SGWID=4-191-22-81597755-detailsPage=ppmmedia|aboutThisBook Telecommunications Planning: Innovations in Pricing, Network Design and Management.] S. Raghavan and G. Anandlingham, eds. Springer. 2006.

===2005===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/7/74/Ton_topology.pdf ''Understanding Internet Topology: Principles, Models, and Validation,''] 
D. Alderson, L. Li, W. Willinger, J. C. Doyle, 
IEEE/ACM Transaction on Networking, 13(6), Dec. 2005. (1.2MB)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/1/16/PNAS_Internet05.pdf ''The ‘‘robust yet fragile’’ nature of the Internet''] 
John C. Doyle, David L. Alderson, Lun Li, Steven Low, Matthew Roughan, Stanislav Shalunov, Reiko Tanaka, and Walter Willinger 
Proc. Natl. Acad. Sci. USA, 102(41):14497-14502, Oct 11 2005. (635K)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/6/64/Fast-network05.pdf ''FAST TCP: From Theory to Experiments''], 
C. Jin, D. X. Wei, S. H. Low, G. Buhrmaster, J. Bunn, D. H. Choe, R. L. A. Cottrell, J. C. Doyle, W. Feng, O. Martin, H. Newman, F. Paganini, S. Ravot and S. Singh, 
IEEE Network, 19(1):4-11, Jan/Feb 2005.(638k)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/0/02/Tcpip-ton2004-2005.pdf ''Cross-layer optimization in TCP/IP networks''] 
J. Wang, L. Li, S. H. Low and J. C. Doyle. 
IEEE/ACM Transactions on Networking, 13(3):582-568, Jun 2005 (409k)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/e/e5/Paganini-fast-jour-2005.pdf ''Congestion control for high performance, stability and fairness in general networks''] 
F. Paganini, Z. Wang, J. C. Doyle and S. H. Low. 
IEEE/ACM Transactions on Networking, 13(1):43-56, Feb 2005 (444k)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/1/1b/Tcpmac-infocom05.pdf ''Joint congestion control and media access control design for wireless ad hoc networks''] 
Lijun Chen, Steven H. Low and John C. Doyle. 
in Proc. IEEE Infocom, Miami, FL, Mar 2005 (193k).

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/d/dd/Sigmetrics05.pdf ''Optimization model of internet protocols''] 
Steven H. Low, John Doyle, Lun Li, Ao Tang and Jiantao Wang 
in Proceedings of SIGMETRICS, pp277 - 277, Banff, Alberta, Canada, June 6-10, 2005.

''[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/4/4e/Part1_vers4.pdf Robustness and the Internet: Design and evolution]'', 
W. Willinger, J Doyle, 
in Robust Design: A Repertoire of Biological, Ecological, and Engineering Case Studies 
(Santa Fe Institute Studies on the Sciences of Complexity), 
Erica Jen, Editor

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/f/f6/Li-SFGraph-IM-0508-2005.pdf ''Towards a theory of scale-free graphs: definitions, properties, and implications''] 
L. Li, D. Alderson, J. C. Doyle and W. Willinger 
Internet Mathematics, 2005 (909k).

===2004===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/2/28/Ccr-papachr04.pdf ''Methodological Frameworks for Large-scale Network Analysis and Design''] 
Antonis Papachristodoulou, Lun Li and John C. Doyle, 
CCR (Computer Communication Review), 34(3), Jul 2004 (828Kk)

==Biological networks==
Keywords: '''network''', biological, biochemical, metabolic...

===2006===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/7/74/IEEEProc_Bio.pdf ''Advanced Methods and Algorithms for Biological Networks Analysis''], 
H El-Samad , A Papachristodoulou, S Prajna, J Doyle, and M Khammash 
In Proc. IEEE, 94 (4): 832-853 APR 2006 (900K)

===2005===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/f/f2/IEESysBio05.pdf ''Highly optimised global organisation of metabolic networks''], 
R. Tanaka, M. Csete and J. Doyle, 
IEE Proc.-Syst. Biol. 152(4): 179, Dec 2005 (820K)
===2003===
*''The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models'', 
Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, 
Bioinformatics 19 (4): 524-531, Mar 1 2003.

===2002===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/1/12/JtheorBiol2002.pdf ''Robustness as a measure of plausibility in models of biochemical networks''], 
Morohashi M, Winn AE, Borisuk MT, Bolouri H, Doyle J, Kitano H, 
Journal Of Theoretical Biology 216 (1): 19-30 May 7, 2002 .

==Related reading==
[[Network architecture and protocols]]
[[Category:Papers]]

[[Category:Papers by topic]]

Group

2011-07-08T06:23:18Z

Fiona: /* Graduate students */

John Doyle's research '''group''' is part of [http://www.cms.caltech.edu/people CDS department] at Caltech.

==Current Group==

===Faculty===
John Doyle 
John G Braun Professor of Control & Dynamical Systems, Electrical Engineering, and BioEngineering 
*Academic Summary: BS, MS EE MIT. Ph.D. Math, UC Berkeley. 
*Awards: IEEE Centennial, Hickernell, Eckman, Friedman, NSF PYI, ONR YI. 
*Prize papers: IEEE Transactions (2), ACC, IEEE Baker Prize, ``top 10 most influential papers in mathematics 1981-1993.''

===Postdocs===
{| class="wikitable" border="0" width="80%"
|-
|[http://www.cds.caltech.edu/~chen/ Lijun Chen]
[http://www.cds.caltech.edu/people/portal/?id=331 Dennice Maynard Gayme]
|[http://www.cs.caltech.edu/~krister/ Krister Jacobsson]
[http://www.cds.caltech.edu/~motee Nader Motee]
|[http://www.cds.caltech.edu/people/portal/?id=384 Gentian Buzi]
[http://www.cds.caltech.edu/~lavaei/ Javad Lavaei-Yanesi]
|}

===Graduate students===
{| class="wikitable" border="0" width="80%"
|-
|[http://www.cds.caltech.edu/people/portal/?id=4 Aristotelis Asimakopoulos]
| Simon Chien
|Hamed Hamze-Bajgiran
|-
|[http://www.its.caltech.edu/~fiona Fiona Chandra]
|[http://www.cds.caltech.edu/~andyl/ Andrew Lamperski]
|Matanya Horowitz
|-
|[http://www.cds.caltech.edu/people/portal/?id=753 Na Li]
|Zhaoqian (Steven) Xie
|Nikolai Matni
|-
|[http://www.cds.caltech.edu/~murray/wiki/CDS_212_Fall_2010 Somayeh Sojoudi]
|Jerry Cruz

|}

===Undergraduate students===
{| class="wikitable" border="0" width="80%"
|-
|[http://www.cds.caltech.edu/people/portal/index.php?id=772 George Hines]||[http://www.cds.caltech.edu/people/portal/?id=803 Nicholas Fette]
|}
===Admin===
Anissa Scott

===Visitors===
[http://www.cds.caltech.edu/~lun/ Lun Li, also alumni]
====Students====
{| class="wikitable" border="1"
|-
|''SURF 2008''||''Other''
|-
|Jackson Wang Ji Young Lee||Paul Fang, student from Temple City High School
|}

==Past Group==
===Alumni===
{| class="wikitable" border="0" width="80%"
|-
|'''2007-2011'''||'''2000-2006'''||'''1990-1999'''
|-
| [http://www.cds.caltech.edu/people/portal/?id=522 Marcos Nahmad Bensusan]
[http://www.cds.caltech.edu/~chen/ Lijun Chen]

[http://www.cds.caltech.edu/~lun Lun Li]

[http://www.cds.caltech.edu/people/portal/?id=6 Xin Liu]

[http://www.cds.caltech.edu/~alfredo/ Alfredo Martinez]

[http://www.cds.caltech.edu/people/portal/?id=184 Oluwatosin Otitoju]
|
[http://faculty.nps.edu/dlalders/ David Alderson]

Nizar Batada

[http://www.cds.caltech.edu/~xlfeng/ Xiaolin Feng]

Irene Gregory

[http://www.seas.upenn.edu/~jadbabai/ Ali Jadbabaie]

[http://webfiles.uci.edu/yjing/www/ Yindi Jing]

Sven Khatri

[http://users.ox.ac.uk/~engs0587/ Antonis Papachristodoulou]

[http://www.mit.edu/~parrilo/ Pablo Parrilo]

[http://www.cds.caltech.edu/~prajna/ Stephen Prajna]

[http://www.cds.caltech.edu/~jiantao/ Jiantao Wang]

[http://www.cds.caltech.edu/~jyu/ Jie Yu]

[http://www.cds.caltech.edu/~xyzhu/ Xiaoyun Zhu]

|Carolyn Beck

Raff D'Andrea

Sonja Glavaski

Irene Gregory

Yun Huang

Michael Kantner

[http://www.ee.ucla.edu/~paganini/ Fernando Paganini]

[http://www.stanford.edu/dept/MSandE/people/faculty/primbs/index.html James Primbs]

Stefano Soatto

Jorge Tierno
|}

===Past Postdocs===
{| class="wikitable" border="0" width="80%"
|-
|'''2009-2011'''||'''2007-2008'''||'''2000-2006'''||'''1990-1999'''
|-
|
[http://www.ist.caltech.edu/~brecht/ Ben Recht]
|
[http://www.cds.caltech.edu/people/portal/?id=662 Aaron D. Ames]

[http://www.cds.caltech.edu/~dtarraf/ Danielle C.Tarraf]

[http://www.cds.caltech.edu/~maryam/ Maryam Fazel, Research scientist]
|
Masahiro Yanagisawa

[http://www-control.eng.cam.ac.uk/~jmg77/ Jorge Goncalves]

[http://devcell.bio.uci.edu/faculty/yi.htm Tau-Mu Yi]
|
[http://www.nps.navy.mil/orfacpag/resumePages/alderson.htm David Alderson]

[http://www.bmc.riken.jp/~reiko/index.htm Reiko Tanaka]
|}

===Past Admin===

?-2008 Gloria Bain

===Past Visitors===
{| class="wikitable" border="0" width="80%"
|-
|'''2007'''
|'''2000-2006
|'''1990-1999'''
|-
|Panagiota Stratou
|?
|?
|}

==MURF and SURF Students==
{| class="wikitable" border="0" width="80%"
|'''2008'''||'''2007''' ||'''2000-2006'''
|-
|Jackson Wang Ji Young Lee ||[http://www.cds.caltech.edu/people/portal/?id=722 Chinwendu Enyioha]||
|-
| ||
|}

==Other collaborators==
{| class="wikitable" border="0" width="80%"
|-
|[[Image:3profs07.jpg|200px]]||[[Image:John-and-marie.jpg]]
|-
|2007 Commencement: Prof.'s John Doyle, Richard Murray & Steven Low. ||John Doyle and Marie Csete
|}

[[Image:JCDgraph.jpg]]

Some collaborators at John Doyle's 50th birthday Connections Workshop, 2004:

*[http://userwww.service.emory.edu/~mcsete/ Marie Csete, Lab] at [http://www.emory.edu/change_mode.cfm?mode=text Emory University], Atlanta.
**[http://www.emory.edu/PROVOST/greatscholars/MarieCsete.htm About Marie Csete's work.]

==See also==
*[[Group Meetings]]
*[[Calendar]]
*<http://www.cds.caltech.edu/people/portal/?un=doyle>

Papers

2011-07-08T06:22:30Z

Fiona: /* Topic */

'''Papers''' span many years and cover a diverse range of topics, from understanding the internet to financial market analysis, control theory and also covering certain aspects of biology, physics and physiology. '''Papers''' have been sorted by topic and year (see below.) These pages list some of Doyle's papers and related reading in these areas!



==Year==
[[2010-2011]]

[[2005-2009]]

[[2000-2004]]

[[1995-1999]]

[[1990-1994]]

[[1985-1989]]

==Topic==
*[[Distributed Control]] ([http://www.cds.caltech.edu/~lavaei/ Javad Lavaei], [http://www.cds.caltech.edu/~motee Nader Motee])
*[[General complexity]]
*[[Networking]] ([http://www.cds.caltech.edu/~chenlj/ Lijun Chen], [http://www.cds.caltech.edu/~lavaei/ Javad Lavaei], [http://www.cds.caltech.edu/~sojoudi/ Somayeh Sojoudi])
*[[Network architecture and protocols]]
*[[Physiology]] (Li Na, Jerry Cruz)
*[[Statistical Mechanics]]
*[[Systems biology]] ([http://www.its.caltech.edu/~fiona Fiona Chandra], Genti Buzi)
*[[Turbulence]] ([https://www.cds.caltech.edu/~dennice/ Dennice Gayme])
*[[Wildfire ecology]]

==Older topics==
*[[Complex networks]]
*[[Complexity and robustness]]

==See also==
[[Tips: Research papers, Publishing and Other Trivia]]

[[Research]]

See [[DoyleWiki:Copyrights|Copyright statment]] before downloading or viewing papers.

[[Category:Papers]]
[[Category:Papers by year]]
[[Category:Papers by topic]]

Research

2011-07-08T00:09:46Z

Fiona: /* Current Projects */

"Professor Doyle's current '''research''' interests are in theoretical foundations for complex networks, primarily in network engineering and biology." He is also "interested in multiscale physics and financial markets, and the interplay between robustness, feedback, control, dynamical systems, computation, communications, and statistical physics." <http://www.cds.caltech.edu/people/> Aug 2008

Prof. Doyle has "applied complex ideas of robust design and control to many fields and is working on a unified theory of control in engineering, physics and biology." <http://www.ieee.org/portal/pages/about/awards/bios/2004controlsystems.html> Aug 2008

==Current Projects==
*[http://cds-web1.cds.caltech.edu/~doyle2/wiki/index.php?title=Systems_biology Systems Biology] ([http://www.its.caltech.edu/~fiona Fiona Chandra], Genti Buzi)
**Fundamental constraints and trade-offs of autocatalytic networks.
**Collaborators: [http://biochemistry.ucsf.edu/labs/elsamad/home/index.html Hana El-Samad], [http://sysos.eng.ox.ac.uk/control/sysos/index.php/User:Antonis Antonis Papachristodoulou]
*Fluids: [http://cds-web1.cds.caltech.edu/~doyle2/wiki/index.php?title=Turbulence Turbulence Modeling] ([https://www.cds.caltech.edu/~dennice/ Dennice Gayme])
**Collaborators: [http://engineering.ucsb.edu/~bamieh/ Bassam Bamieh], [http://www.mckeon.caltech.edu/ Beverly McKeon]
*[http://openwetware.org/wiki/Doyle Physiology] (Li Na, Jerry Cruz)
*[http://cds-web1.cds.caltech.edu/~doyle2/wiki/index.php?title=Networking Internet and Networking] ([http://www.cds.caltech.edu/~chenlj/ Lijun Chen], [http://www.cds.caltech.edu/~lavaei/ Javad Lavaei])
**Collaborators: [http://netlab.caltech.edu/slow/ Steven Low]
*Economics (Jerry Cruz)
** Market Bubbles and Crashes: We use tools from mathematical finance and stochastic control theory to investigate asset price bubbles and crashes in financial markets. We wish to gain insight using models that account for financial intermediation and associated frictions. Moreover, recent local-martingale characterizations of bubbles may provide avenues into developing new methods of empirical testing for bubbles.
*Distributed Control ([http://www.cds.caltech.edu/~lavaei/ Javad Lavaei], [http://www.cds.caltech.edu/~motee Nader Motee])

==Research Grants==
*[http://www.nsf.gov/index.jsp NSF] award: [http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=0326635 ITR COLLAB: Theory and Software Infrastructure for a Scalable Systems Biology], 2003-present

*Some joint projects with [http://www.cds.caltech.edu/~murray/wiki/Main_Page#Research Prof. Richard Murray] (with links to his wiki below)
**[http://www.cds.caltech.edu/~murray/VaVmuri/index.php?title=Main_Page Specification, Design and Verification of Distributed Embedded Systems] (MURI/AFOSR)
**Networked Feedback Systems in Biology (ARO ICB)
**[http://www.cds.caltech.edu/~murray/wiki/Model-Based_Design_and_Qualification_of_Complex_Systems Model-Based Design and Qualification of Complex Systems] (Boeing)

*Some joint grants with [http://netlab.caltech.edu/~slow/ Prof. Steven Low]:
**MURI Analysis and modeling of networks with long range dependence (LRD) characteristics (PI - Jean Walrand, UC Berkeley; Co-PIs - John Doyle, Steven Low, R. Srikanth (UIUC), V. Anantharam & A. Zakhor (UC Berkeley), D. Towsley & W. Gong (U. Mass. Amherst)2008
**NSF RI WAN in Lab (Newman, Psaltis, Yip) 2003-08
**NSF NeTS Collaborative Research: Optimization and Games in Interdomain Routing 2006
**NSF STI Multi-Gbps TCP: Data Intensive Networks for Science & Engineering (Bunn, Newman) 2002-05
**NSF ITR Optimal and Robust TCP Congestion Control 2001-04
**ARO DURIP Hybrid WAN in Lab (Newman, Psaltis, Yip) 2004-05
**ARO Network Research Analytical Theory of Protocols 2002-05
**ARO Network Science Networked control systems (Murray, Parrilo (MIT)) 2005-2006
(Note that other Co-PI are noted in brackets on these joint grants with Prof. Low and Prof. Doyle)

== Past Projects ==
Caltech
*[http://www.hot.caltech.edu/ HOT : Highly Optimized/Organized Tradeoffs/Tolerance, A unified theory of complex networks ]
*[http://www.cds.caltech.edu/sostools/ SOSTOOLS : Software for analysis of complex systems]
*[http://www.cds.caltech.edu/~doyle/MURI.html "Mathematical Infrastructure for Robust Virtual Engineering"] MURI award 1996
*Past projects with Prof Murray (links to his wiki)
**[http://www.cds.caltech.edu/~murray/projects/afosr95-vehicles/ Robust Nonlinear Control Theory with Application to Aerospace Vehicles] (AFOSR)
**[http://www.cds.caltech.edu/~murray/cdspanel/ Panel on Future Directions in Control, Dynamics, and Systems]
**[http://www.cds.caltech.edu/~murray/projects/nsf93-crcd/index.html Curriculum in Control and Dynamical Systems] (NSF)

Other

==Collaborative groups==
*[http://www.cimms.caltech.edu/whatiscimms.html CIMMS: Center for Integrative Multiscale Modeling and Simulation]
*[http://www.cds.caltech.edu/~murray/wiki/Main_Page Prof. Richard Murray]
* [http://biochemistry.ucsf.edu/labs/elsamad/home/index.html Prof. Hana El-Samad (UCSF)]
* [http://leecenter.caltech.edu/theory.html Lee Center for Networking]
*[http://netlab.caltech.edu/ Netlab]
**[http://netlab.caltech.edu/FAST/FAST: Fast AQM Scalable TCP, new internet protocol design.]

*[http://www.sisl.caltech.edu/ SISL]

* and more...

==See also==
*[[Papers]]
*[[Special:Allpages|All articles]]
*[[Special:Categories|Pages listed by Categories]]

===More research links===
Caltech
*[http://www.cds.caltech.edu/~murray/wiki/Main_Page#Research Prof. Murray's projects]
*[http://netlab.caltech.edu/projects.php Prof. Low's projects]
*[http://www.cds.caltech.edu/research/ CDS]
*[http://leecenter.caltech.edu/doyle-res.html HOT at Lee Center]
*[http://www.sisl.caltech.edu/people/index.html SISL]

UCSB
*[http://www.physics.ucsb.edu/~complex/ Jean Carlson’s HOT website]
[[Category:Research]]

Systems biology

2011-07-07T23:23:15Z

Fiona: /* 2011 */

Intro: We study fundamental constraints and trade-offs in biological systems using analytical tools from control theory, information theory, and graph theory. There are hard trade-offs between complexity and robustness in every system, which is worse in systems with particular architecture. We are interested in pinpointing these problems and analyzing how nature manages these trade-offs.

Keywords: '''systems biology''', SBML mark-up, robustness, complexity, networks, biology, proteins.

A few papers were copied from <http://www.cds.caltech.edu/~doyle/RecentPapers/ >

==Systems biology==
Keywords: '''systems biology''', biological networks, complexity, control, heat-shock, protein, robustness, metabolism.

===2011===
[http://cds-web1.cds.caltech.edu/~doyle2/wiki/images/4/4e/7.PNAS_InPress_June_2011.pdf Architecture, constraints, and behavior] 
JC Doyle, MC Csete 
PNAS, in press, July 2011

[http://cds-web1.cds.caltech.edu/~doyle2/wiki/images/b/b6/Science-2011-Chandra-187-92.pdf Glycolytic Oscillations and Limits on Robust Efficiency] 
Fiona Chandra, Gentian Buzi, and John Doyle 
Science (In Press)

[http://cds-web1.cds.caltech.edu/~doyle2/wiki/images/a/a2/6.AutomaticaJune2011.pdf Analysis of autocatalytic networks in biology] 
G Buzi, U Topcu, J Doyle 
Automatica 47:1123-1130 (2011)

===2009===
[http://www.nt.ntnu.no/users/skoge/prost/proceedings/acc09/data/papers/0207.pdf ''Linear control analysis of the autocatalytic glycolysis system''] 
Fiona Chandra, Gentian Buzi, John Doyle 
In Proc. American Control Conf, 319-324 JUN 2009

===2007===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/4/43/Nature_Connections07.pdf ''Rules of engagement''] 
John Doyle and Marie Csete 
Nature Vol 446:860 April 19 2007 (142K)

===2006===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/7/74/IEEEProc_Bio.pdf ''Advanced Methods and Algorithms for Biological Networks Analysis''], 
H El-Samad , A Papachristodoulou, S Prajna, J Doyle, and M Khammash 
In Proc. IEEE, 94 (4): 832-853 APR 2006 (900K)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/1/1f/PlosCompBio_HS06.pdf ''Module-Based Analysis of Robustness Tradeoffs in the Heat Shock Response System ''] 
Hiroyuki Kurata, Hana El-Samad, Rei Iwasaki, Hisao Ohtake, John C Doyle, Irina Grigorova, Carol A. Gross, Mustafa Khammash, 
[http://compbiol.plosjournals.org/ PLoS Comput Biol] 2(7): July 2006 (1.1MB)

===2005===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/9/98/FEBS_PPI05.pdf ''Some protein interaction data do not exhibit power law statistics''], 
R. Tanaka, T-M Yi, and J. Doyle 
FEBS letters, 579 (23): 5140-5144 Sept 26 2005 (221K)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/f/f2/IEESysBio05.pdf ''Highly optimised global organisation of metabolic networks''], 
R. Tanaka, M. Csete and J. Doyle, 
IEE Proc.-Syst. Biol. 152(4): 179, Dec 2005 (820K)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/a/a7/PLOS_Primer05.pdf ''Motifs, control, and stability''] (including ''Supplementary Notes: Elementary Feedback Concepts'') 
Doyle J and Csete M 
[http://www.plosbiology.org PLoS Biol] 3(11): e392; 2005. (387K)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/b/b4/PNAS_HeatShock05.pdf ''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)

===2004===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/1/13/Cell04.pdf ''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)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/8/82/Trends04.pdf ''Bow ties, metabolism, and disease''], 
Csete M.E. and J.C. Doyle, 
Trends in Biotechnology 22(9):446-50 Sept 2004. (121K)

===2002===
[http://www.cds.caltech.edu/~doyle2/wiki/skins/common/images/icons/fileicon-pdf.png ''Reverse Engineering of Biological Complexity''] 
Csete M and Doyle J, 
Science 295 (5560): 1664-1669 Mar 1, 2002. (1.2MB)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/1/12/JtheorBiol2002.pdf ''Robustness as a measure of plausibility in models of biochemical networks''], 
Morohashi M, Winn AE, Borisuk MT, Bolouri H, Doyle J, Kitano H, 
Journal Of Theoretical Biology 216 (1): 19-30 May 7, 2002.

===2000===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/f/f0/PNAS4649-2000.full.pdf ''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.

==SBML==
Keywords: '''SBML''', systems biology mark-up language, computer software, biochemical reaction networks

===2004===
[http://scitation.aip.org/dbt/dbt.jsp?KEY=IPSBDJ&Volume=1 '' Evolving a lingua franca and associated software infrastructure for computational systems biology: theSystemsBiologyMarkupLanguage(SBML) project''], 
M. Hucka; A. Finney; B.J. Bornstein; S.M. Keating; B.E. Shapiro; J. Matthews; B.L. Kovitz; M.J. Schilstra; A. Funahashi; J.C. Doyle; and H. Kitano 
IEE Systems Biology. 1:41-53, 2004

*''MathSBML: a package for manipulating SBML-based biological models'', 
Shapiro BE, Hucka M, Finney A, Doyle J. 
Bioinformatics, Nov 1, 2004

===2002===
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11928498&dopt=Abstract ''The ERATO Systems Biology Workbench: enabling interaction and exchange between software tools for computational biology'' (Abstract)] 
Hucka, M., Finney, A., Sauro, H. M., Bolouri, H., Doyle, J., and Kitano,H. 
in Proc. Pac Symp Biocomput. 450-61, 2002.

===2001===
*''The Systems Biology Markup Language'' 
Finney AM, Hucka M, Sauro HM, Doyle J, Kitano H, Bolouri H, 
Molecular Biology of the Cell 12: 708 Suppl. S NOV 2001.

==More Biology==
Keywords: '''biology''', cell, HOT (highly optimized tolerance), SOSTOOLS (sums of squares optimization), robustness
===2005===
''Evolutionary dynamics and highly optimized tolerance,''
Zhou T, Carlson JM, Doyle J 
Journal of Theoretical Biology 236 (4): 438-447 Oct 21 2005

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/0/01/PNAS_HOTFire05.pdf ''Wildfires, complexity, and highly optimized tolerance''], 
MA Moritz, ME Morais, LA Summerell, JM Carlson, J Doyle 
Proc. Natl. Acad. Sci. USA, December 13, 2005; 102 (50):17912–17917 (403K)

===2003===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/f/f8/CDC2003.pdf ''Model validation and robust stability analysis of the bacterial heat shock response using SOSTOOLS.''] 
H. El-Samad, S. Prajna, A. Papachristodoulou, M. Khammash and J. C. Doyle 
in Proc. IEEE CDC, vol. 4:3766 - 3771; Maui, Hawaii, 9-12 Dec. 2003.

===2002===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/7/72/PNAS2538-2002.full.pdf ''Complexity and robustness''], 
Carlson JM, Doyle J, 
Proc. Natl. Acad. Sci. USA 99: 2538-2545 Suppl. 1 Feb 19, 2002.

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/8/85/PNAS2049-2002.full.pdf ''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.

===2001===
*''Oxygen-mediated regulation of skeletal muscle satellite cell proliferation and adipogenesis in culture'' 
Csete M, Walikonis J, Slawny N, Wei Y, Korsnes S , Doyle JC, Wold B, 
Journal of Cellular Physiology, Volume 189, Issue 2, Nov. 2001. 189-196

==Related reading==
[[Papers]]

[[Research]]

[[Tips: Research papers, Publishing and Other Trivia]]

===Other===

===External links===
*[http://sbml.org/Main_Page SBML Definition and homepage]
*[http://sbml.org/Documents SBML documents]
*[http://www.systems-biology.org/ Systems Biology Portal]
*[http://www.hot.caltech.edu/ HOT : Highly Optimized/Organized Tradeoffs/Tolerance, A unified theory of complex networks ]
*[http://www.cds.caltech.edu/sostools/ SOSTOOLS : Software for analysis of complex systems]

[[Category:Research]]
[[Category:Papers by topic]]
[[Category:Papers]]

2010-2011

2011-07-07T23:22:55Z

Fiona: /* Journals */

==2011==
===Journals===
[http://cds-web1.cds.caltech.edu/~doyle2/wiki/images/4/4e/7.PNAS_InPress_June_2011.pdf Architecture, constraints, and behavior] 
JC Doyle, MC Csete 
PNAS, in press, July 2011

[http://cds-web1.cds.caltech.edu/~doyle2/wiki/images/b/b6/Science-2011-Chandra-187-92.pdf Gycolytic oscillations and limits on robust efficiency] 
FA Chandra, G Buzi, JC Doyle 
Science, in press, July 2011

[http://cds-web1.cds.caltech.edu/~doyle2/wiki/images/8/87/PhysFluids_23_065108.pdf Amplification and nonlinear mechanisms in plane Couette flow.] 
D Gayme, B McKeon, B Bamieh, A Papachristodolou, and J Doyle. 
Physics of Fluids v23:6:065108 (2011)

[http://cds-web1.cds.caltech.edu/~doyle2/wiki/images/a/a2/6.AutomaticaJune2011.pdf Analysis of autocatalytic networks in biology] 
G Buzi, U Topcu, J Doyle 
Automatica 47:1123-1130 (2011)

[http://cds-web1.cds.caltech.edu/~doyle2/wiki/images/c/c4/2.IEEE_TransAutoCtrl_Feb_2011_.pdf On Lossless Approximations, the Fluctuation-Dissipation Theorem, and Limitations of Measurements] 
H Sandberg, JC Delvenne, JC Doyle 
IEE Trans Auto Control, v56:2, 293-308 (2011)

[http://cds-web1.cds.caltech.edu/~doyle2/wiki/images/6/62/9.ComputerNetworksFeb2011.pdf Cross-layer design in multihop wireless networks] 
L Chen, SH Low, and JC Doyle 
Computer Networks 55:480–496 (2011)

Javad Lavaei, Aydin Babakhani, Ali Hajimiri and John C. Doyle, "Solving
Large-Scale Hybrid Circuit-Antenna Problems," IEEE Transactions on Circuits
and Systems I, vol. 58, no. 2, pp. 374-387, Feb. 2011.

==2010==
===Journals===
[http://cds-web1.cds.caltech.edu/~doyle2/wiki/images/a/ab/8.IEEETransNetworkingAug2010.pdf Random access game and medium access control design] 
Lijun Chen, Steven Low, and John Doyle 
IEEE Trans Networking 18:4:1303-1316, AUG 2010.

[http://cds-web1.cds.caltech.edu/~doyle2/wiki/images/d/de/1.IEEE_TransSysMCyber_AldersonDoyle-July2010.pdf Contrasting views of complexity and their implications for network-centric infrastructures] 
David Alderson and John Doyle 
IEEE Trans Systems Man Cybernetics—Part A: Syst Humans 40:839-852, JUL 2010.

[http://www.cds.caltech.edu/~dennice/PublishedVersionJFM2010.pdf A streamwise constant model of turbulence in plane Couette flow] 
Gayme DF, McKeon BJ, Papachristodoulou A, Bamieh B, and Doyle JC 
Journal of Fluid Mechanics 665:99-119 (2010)

===Conferences===
Performance Limitations in Autocatalytic Networks in Biology 
Motee N, Chandra F, Bamieh B, Khammash M, and Doyle J 
In Proc 49th IEEE Conf Decision and Control, 4715-4720, Dec 2010.

Passively Controllable Smart Antennas 
Javad Lavaei, Aydin Babakhani, Ali Hajimiri and John C. Doyle 
IEEE Global Communications Conference (GLOBECOM), Miami, Florida, 2010.

Finding Globally Optimum Solutions in Antenna Optimization Problems 
Aydin Babakhani, Javad Lavaei, John C. Doyle and Ali Hajimiri 
IEEE International Symposium on Antennas and Propagation, Toronto, Canada, 2010.

Programmable Antenna Design Using Convex Optimization 
Javad Lavaei, Aydin Babakhani, Ali Hajimiri and John C. Doyle 
19th International Symposium on Mathematical Theory of Networks and Systems, Budapest, Hungary, 2010.

Javad Lavaei, Aydin Babakhani, Ali Hajimiri and John C. Doyle, "A Study of
Near-Field Direct Antenna Modulation Systems Using Convex Optimization," in
American Control Conference, Baltimore, 2010.

Javad Lavaei, John C. Doyle and Steven Low, "Utility Functionals Associated
With Available Congestion Control Algorithms," IEEE International
Conference on Computer Communications (INFOCOM), San Diego, California,
2010.

Main Page

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John C. Doyle 

John G Braun Professor 
of Control and Dynamical Systems 
Electrical Engineering 
and BioEngineering 
Division of Engineering and Applied Science 
California Institute of Technology 

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[[J. Doyle’s Bio]]

[[News]]

[[Calendar]]

[[#Contact|Contact]]

[https://www.cds.caltech.edu/squirrelmail/src/login.php CDS Webmail]
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==News==
*Visiting this week: Ioannis Lestas
*[[Research|MURI 2008]]
*[http://discovermagazine.com/2007/nov/this-man-wants-to-control-the-internet Discover magazine] interviews Prof. Doyle.

"This man wants to control the internet" by Carl Zimmer, Discover magazine, 10/25/2007.

==Recent Papers==
*[http://cds-web1.cds.caltech.edu/~doyle2/wiki/images/4/4e/7.PNAS_InPress_June_2011.pdf Architecture, constraints, and behavior.] JC Doyle, MC Csete. PNAS, in press, July 2011
*[http://cds-web1.cds.caltech.edu/~doyle2/wiki/images/b/b6/Science-2011-Chandra-187-92.pdf Gycolytic oscillations and limits on robust efficiency.] FA Chandra, G Buzi, JC Doyle Science, in press, July 2011
*[http://cds-web1.cds.caltech.edu/~doyle2/wiki/images/c/c4/2.IEEE_TransAutoCtrl_Feb_2011_.pdf On Lossless Approximations, the Fluctuation-Dissipation Theorem, and Limitations of Measurements] H Sandberg, JC Delvenne, JC Doyle IEEE Trans Auto Control, v56:2, 293-308 (2011)
*[[Papers|'''More Papers''']]

== Research ==
John Doyle's '''[[research]]''' interests are in theoretical foundations for complex networks in engineering and biology, as well as multiscale physics, and include integrating modeling, ID, analysis and design of uncertain nonlinear systems, and computation in analysis and simulation, including complexity theory to guide algorithm development. Applications interests are motivated by the interplay between: control, dynamical systems, and design and analysis of large, complex systems.

*[[Research|Research projects and grants list]]

== Teaching ==

*[[CDS 213|The Architecture of Robust, Evolvable Networks (Wi10)]]

== Contact ==
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'''Mailing Address'''

John Doyle 
California Institute of Technology 
Control and Dynamical Systems, MC 107-81 
1200 E. California Blvd 
Pasadena, CA 91125 USA
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'''Contact information'''

E-mail: doyle AT cds dot caltech dot edu 
Office: 109 Steele, 
Phone: 626.395.4808 Fax: 626.395.6170 

'''Admin Assistant''': Anissa Scott 
Office: 107 Steele, 
Email: anissa AT caltech dot edu 
Phone: 626.395.4140 
Labs: 12 STL, 110 GUG (x2319)
|-
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===Other Caltech links===

*[http://www.caltech.edu California Institute of Technology]
**[http://www.eas.caltech.edu Engineering and Applied Science Division]
***[http://www.be.caltech.edu/ Bioengineering Department]
***[http://www.cds.caltech.edu Control and Dynamical Systems Department]
***[http://www.ee2.caltech.edu/ Electrical Engineering Department]
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File:7.PNAS InPress June 2011.pdf

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