Difference between revisions of "CSSS 2008 Argentina-Readings"
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An important part of the school has to do with interacting with Faculty and your class mates. To foster this interaction interdisciplinary working groups will be formed. Each group will work on a project that will be presented by the end of the school. Projects are expected to elaborate on questions emerging from the working group internal brainstorming. Use the help and advise of the faculty around. They are open to interact and provide advise for the development of working group projects. And remember, the best way of tackling complexity is to aim for simplicity! | An important part of the school has to do with interacting with Faculty and your class mates. To foster this interaction interdisciplinary working groups will be formed. Each group will work on a project that will be presented by the end of the school. Projects are expected to elaborate on questions emerging from the working group internal brainstorming. Use the help and advise of the faculty around. They are open to interact and provide advise for the development of working group projects. And remember, the best way of tackling complexity is to aim for simplicity! | ||
==Week 1 | ==Week 1== | ||
* [http://www. | * [http://www.santafe.edu/profiles/?pid=64 Geoffrey West] | ||
''Supporting Material:'' | |||
[[Media: Dubai_talk2.pdf| The Biology of Business; Size Matters - G. West]] | |||
[[Media: Bettencourt_et_al_2007.pdf| Bettencourt et al. 2007]] | |||
[[Media: Bettencourt_et_al_2007_Supporting_Material.pdf| Bettencourt et al. 2007 -- supporting material]] | |||
[[Media: West_&_Brown_2005_Scaling_Review.pdf| West & Brown 2005 Scaling Review]] | |||
[[Media: WestEtal2001.pdf| West et al. 2001]] | |||
* [http://www.cs.colorado.edu/~lizb/ Elizabeth Bradley] | |||
''Supporting Material:'' | |||
[[Media: ida-chapter.pdf| Time Series Analysis - E. Bradley]]<br /> | |||
[[Media: error.pdf| Error in Numerical Methods - E. Bradley]]<br /> | |||
[[Media: ode-notes.pdf| Numerical Solution for Differential Equations - E. Bradley]] | |||
* [http://www.ifca.unican.es/~wio/ Horacio S. Wio] | |||
''Supporting Material:'' | ''Supporting Material:'' | ||
[[Media: | [[Media: Book_.pdf| Nonequilibrium Potential in Reaction-Diffusion Systems - Horacio S. Wio]]<br /> | ||
[[Media: | [[Media: Cross-Hohem2.pdf| Pattern formation outside of equilibrium - M.C. Cross, P.C. Hohenberg]]<br /> | ||
[[Media: | |||
* [http://www.santafe.edu/~jdf/SFI%20Template/About%20Me.html J. Doyne Farmer] | |||
''Talks:''<br /> | |||
[[Media: bariloche1.pdf| Are there quantitative mathematical laws underlying financial markets? - J. D. Farmer]]<br /> | |||
[[Media: bariloche2.pdf| Patterns of technological evolution - J. D. Farmer]]<br /> | |||
''Supporting Material:'' | |||
[[Media: critique19.pdf| The virtues and vices of equilibrium and the future of financial economics - J. D. Farmer, J. Geanakoplos]]<br /> | |||
[[Media: londonAccord8.pdf| Dynamics of technological development in the energy sector - J. D. Farmer, J. Trancik]]<br /> | |||
[[Media: handbook19.pdf| How markets slowly digest changes in supply and demand - J. Bouchaud, J. D. Farmer, F. Lillo]] | |||
* [http://www.brain.riken.jp/labs/mns/ysato/ Yuzuru Sato] | |||
''Supporting Material:'' | |||
[[Media: cls2pg02.pdf| Chaos in learning a simple two-person game]]<br /> | |||
[[Media: credlmas03.pdf| Coupled replicator equations for the dynamics of learning in multiagent systems]]<br /> | |||
[[Media: sdca05.pdf| Stability and diversity in collective adaption]]<br /> | |||
[[Media: adimp.pdf| Adaptive Dynamics for Interacting Markovian Processes]]<br /> | |||
Line 51: | Line 72: | ||
[http://users.cse.ucdavis.edu/~cmg/compmech/pubs/oic.htm - The Organization of Intrinsic Computation: Complexity-Entropy Diagrams and the Diversity of Natural Information Processing] <br /> | [http://users.cse.ucdavis.edu/~cmg/compmech/pubs/oic.htm - The Organization of Intrinsic Computation: Complexity-Entropy Diagrams and the Diversity of Natural Information Processing] <br /> | ||
[http://users.cse.ucdavis.edu/~cmg/compmech/pubs/son.htm - Structure or Noise?] <br /> | [http://users.cse.ucdavis.edu/~cmg/compmech/pubs/son.htm - Structure or Noise?] <br /> | ||
* [http://www.df.uba.ar/~paz/ Juan Pablo Paz] | |||
[[Media: sfi-paz.pdf| Quantum Computation]] | |||
* [http://fontana.med.harvard.edu/www/index.htm Walter Fontana] | |||
''Supporting Material:'' | |||
[[Media: kappa.language.pdf| Programs as models: Kappa language basics - J. Kirvine, V. Danos, J. Feret, R. Harmer, W. Fontana]]<br /> | |||
[[Media: kappa.execution.pdf| Programs as models: Execution - J. Kirvine, V. Danos, J. Feret, R. Harmer, W. Fontana]]<br /> | |||
* [http://www.santafe.edu/~krakauer/Site/Welcome.html David Krakauer] | |||
[[Media: Krakauer_Fundamentals.pdf| Evolutionary Theory Foundations - D. Krakauer]]<br /> | |||
[[Media: Krakauer_Frontiers.pdf| Evolutionary Theory Frontiers? - D. Krakauer]] | |||
Line 82: | Line 122: | ||
<br /> | <br /> | ||
==Week 2== | |||
* [http:// | * [http://cabfst28.cnea.gov.ar/~abramson/ Guillermo Abramson] | ||
''Supporting Material:'' | ''Supporting Material:'' | ||
[[Media: | [[Media: Collective behavior in complex networks-144.pdf| Collective behavior in complex networks - G. Abramson]] | ||
* [http://cabfst28.cnea.gov.ar/ Marcelo Kuperman] | |||
''Supporting Material:'' | |||
[[Media: introduction to complex networks.pdf| Introduction to Complex Networks - M. Kuperman]] | |||
[ | * [http://www.foodwebs.org/cv/cvjenn/jennset.html Jennifer A. Dunne] | ||
''Supporting Material:'' | |||
[[Media: WilliamsMartinez2000.pdf| Simple rules yield complex food webs - R. Williams & N. Martinez]]<br /> | |||
[[Media: dunne.pdf| Network Structure and biodiversity loss in food webs: robustness increases with connectance - J. Dunne, R. Williams & N. Martinez]]<br /> | |||
* [http://www.santafe.edu/~jflack/ Jessica Flack] | |||
''Supporting Material:'' | ''Supporting Material:'' | ||
[[Media: FlackLogicNetRobust11_30_08.pdf| The Experimental Logic of Network Approaches to Robustness in Complex Systems - J. Flack]] | |||
[[Media: | |||
* [http://www. | * [http://www.arteuna.com/ManuelCaceres/MOC.htm Manuel O. Cáceres] | ||
''Supporting Material:'' | ''Supporting Material:'' | ||
[[Media: | [[Media: Caceres-Reverte.pdf| Elementos de estadistica de no equilbrio y sus aplicaciones al transporte en medios desordenados - M. Caceres]]<br /> | ||
[[Media: | [[Media: caceres3.pdf| First Passage Time Statistics in the Logistic Model - M. Caceres]] | ||
* [http://www.santafe.edu/profiles/?pid=75 D. Eric Smith] | * [http://www.santafe.edu/profiles/?pid=75 D. Eric Smith] | ||
Line 143: | Line 171: | ||
* [http://www.df.uba.ar/~silvina/ Silvina Ponce Dawson] | * [http://www.df.uba.ar/~silvina/ Silvina Ponce Dawson]<br /> | ||
''Supporting Material:''<br /> | |||
[[Media: berridge.pdf| Calcium - a life and death signal]]<br /> | [[Media: berridge.pdf| Calcium - a life and death signal]]<br /> | ||
[[Media: calcium_and_LTP.pdf| Calcium stores regulate the polarity and input specificity of synaptic modification]]<br /> | [[Media: calcium_and_LTP.pdf| Calcium stores regulate the polarity and input specificity of synaptic modification]]<br /> | ||
Line 152: | Line 181: | ||
[[Media: phasic_characteristic_3608.pdf| Phasic characteristic of elementary Ca2 release sites underlies quantal responses to IP3]]<br /> | [[Media: phasic_characteristic_3608.pdf| Phasic characteristic of elementary Ca2 release sites underlies quantal responses to IP3]]<br /> | ||
[[Media: puffs_and_repetitive_oscillations65.pdf| Role of elementary Ca2 puffs in generating repetitive Ca2+ oscillations]]<br /> | [[Media: puffs_and_repetitive_oscillations65.pdf| Role of elementary Ca2 puffs in generating repetitive Ca2+ oscillations]]<br /> | ||
* [http://www.ulb.ac.be/cenoliw3/PERSO-PAGES/gnicolis.html Grégoire Nicolis] | |||
''References:'' | |||
-G. Nicolis and C. Nicolis, Foundations of Complex Systems, World Scientific, Singapore (2007).<br /> | |||
-W. Ebeling and G. Nicolis, Word frequency and entropy of symbolic sequences: a dynamical perspective, Chaos Solitons and Fractals 2, 635 (1992).<br /> | |||
-G. Nicolis and P. Gaspard, Toward a probabilistic approach to complex systems, Chaos Solitons and Fractals 4, 41 (1994).<br /> | |||
-G. Nicolis, Thermodynamics today, Physica A213, 1 (1995).<br /> | |||
-G. Nicolis and D. Daems, Probabilistic and thermodynamic aspects of dynamical systems, Chaos 8, 311 (1998).<br /> | |||
-G. Nicolis, Nonequilibrium Statistical Mechanics, in Encyclopedia of Nonlinear Science, A. Scott ed., Routledge, New York (2005).<br /> | |||
-P. Gaspard, Chaos, Scattering and Statistical Mechanics, Cambridge University Press, Cambridge (1998).<br /> | |||
-P. Gaspard, Time-reversed dynamical entropy and irreversibility in Markovian random processes, J. Stat. Phys. 117, 599 (2004).<br /> | |||
''Supporting Material:'' | |||
[http://www.scholarpedia.org/article/Complex_systems Complex Systems - Scholarpedia]<br /> | |||
[[Media: G_Nicolis.pdf| Interdisciplinary Center for Nonlinear Phenomena and Complex Systems - G. Nicolis]]<br /> | |||
[[Media: ERWnicolis1.pdf| Foundations of Complex Systems - G. Nicolis, C. Nicolis]]<br /> | |||
[[Media: ERWnicolisfig1.pdf| Figure 1]]<br /> | |||
[[Media: ERWnicolisfig2.pdf| Figure 2]]<br /> | |||
[[Media: ERWnicolisfig3.pdf| Figure 3]]<br /> | |||
[[Media: A_VIEW_FROM_THE_FOUNDATIONS.pdf| Frontiers of Complex Systems Research: A View From the Foundations]]<br /> | |||
<br /> |
Latest revision as of 03:36, 19 December 2008
CSSS Argentina 2008 |
Forming project group teams
An important part of the school has to do with interacting with Faculty and your class mates. To foster this interaction interdisciplinary working groups will be formed. Each group will work on a project that will be presented by the end of the school. Projects are expected to elaborate on questions emerging from the working group internal brainstorming. Use the help and advise of the faculty around. They are open to interact and provide advise for the development of working group projects. And remember, the best way of tackling complexity is to aim for simplicity!
Week 1
Supporting Material:
The Biology of Business; Size Matters - G. West
Bettencourt et al. 2007 -- supporting material
West & Brown 2005 Scaling Review
Supporting Material:
Time Series Analysis - E. Bradley
Error in Numerical Methods - E. Bradley
Numerical Solution for Differential Equations - E. Bradley
Supporting Material:
Nonequilibrium Potential in Reaction-Diffusion Systems - Horacio S. Wio
Pattern formation outside of equilibrium - M.C. Cross, P.C. Hohenberg
Talks:
Are there quantitative mathematical laws underlying financial markets? - J. D. Farmer
Patterns of technological evolution - J. D. Farmer
Supporting Material:
The virtues and vices of equilibrium and the future of financial economics - J. D. Farmer, J. Geanakoplos
Dynamics of technological development in the energy sector - J. D. Farmer, J. Trancik
How markets slowly digest changes in supply and demand - J. Bouchaud, J. D. Farmer, F. Lillo
Supporting Material:
Chaos in learning a simple two-person game
Coupled replicator equations for the dynamics of learning in multiagent systems
Stability and diversity in collective adaption
Adaptive Dynamics for Interacting Markovian Processes
Supporting Material:
- Is Anything Ever New? Considering Emergence
- Regularities Unseen, Randomness Observed: Levels of Entropy Convergence
- The Calculi of Emergence: Computation, Dynamics, and Induction
- Computational Mechanics: Pattern and Prediction, Structure and Simplicity
- The Organization of Intrinsic Computation: Complexity-Entropy Diagrams and the Diversity of Natural Information Processing
- Structure or Noise?
Supporting Material:
Programs as models: Kappa language basics - J. Kirvine, V. Danos, J. Feret, R. Harmer, W. Fontana
Programs as models: Execution - J. Kirvine, V. Danos, J. Feret, R. Harmer, W. Fontana
Evolutionary Theory Foundations - D. Krakauer
Evolutionary Theory Frontiers? - D. Krakauer
- Kunihiko Kaneko (Complex Systems Biology)
References: (Book)
K. Kaneko, Life: An Introduction to Complex Systems Biology, Springer, 2006
K. Kaneko and I.Tsuda, Complex Systems: Chaos and Beyond, Springer 2000
(Papers) available at: [1] (including some other related materials)
C. Furusawa and K. Kaneko, ``A generic mechanism for adaptive gowth
rate regulation", PLoS Computationa Biology, 4(2008) e3
K. Kaneko, Evolution of Robustness to Noise and Mutation in Gene
Expression Dynamics, PLoS One(2007) 2 e434
K. Kaneko and C. Furusawa, "An Evolutionary Relationship between
Genetic Variation and Phenotypic Fluctuation", J. Theo. Biol. 240
(2006) 78-86
K. Kaneko" On Recursive Production and Evolvabilty of Cells: Catalytic
Reaction Network Approach " Adv. Chem. Phys. , 130 (2005) 543-598
K. Sato, Y. Ito, T. Yomo, and K. Kaneko " On the Relation between
Fluctuation and Response in Biological Systems " Proc. Nat. Acad. Sci.
USA 100 (2003) 14086-14090
C. Furusawa and K. Kaneko " Zipf's law in Gene Expression " Phys. Rev.
Lett., 90 (2003) 088102
C. Furusawa and K. Kaneko"Theory of Robustness of Irreversible
Differentiation in a Stem Cell System: Chaos Hypothesis" J. Theor.
Biol. (2001) 209 (2001) 395-416
K. Kaneko and T. Yomo," ``Isologous Diversification for Robust
Development of Cell Society", J.theor.Biol. 199 (1999) 243-256
Week 2
Supporting Material:
Collective behavior in complex networks - G. Abramson
Supporting Material:
Introduction to Complex Networks - M. Kuperman
Supporting Material:
Simple rules yield complex food webs - R. Williams & N. Martinez
Network Structure and biodiversity loss in food webs: robustness increases with connectance - J. Dunne, R. Williams & N. Martinez
Supporting Material:
The Experimental Logic of Network Approaches to Robustness in Complex Systems - J. Flack
Supporting Material:
Elementos de estadistica de no equilbrio y sus aplicaciones al transporte en medios desordenados - M. Caceres
First Passage Time Statistics in the Logistic Model - M. Caceres
Supporting Material:
Classical thermodynamics and economic general equilibrium theory - E. Smith & D. Foley
Thermodynamics of natural selection I: Energy flow and the limits of organization - E. Smith
Thermodynamics of natural selection II: Chemical Carnot cycles - E. Smith
Thermodynamics of natural selection III: Landauer's principle in computation and chemistry - E. Smith
Supporting Material:
Calcium - a life and death signal
Calcium stores regulate the polarity and input specificity of synaptic modification
Noise Propagation in Gene Networks
The organization and functions of local Ca2+ signals
Phasic characteristic of elementary Ca2 release sites underlies quantal responses to IP3
Role of elementary Ca2 puffs in generating repetitive Ca2+ oscillations
References:
-G. Nicolis and C. Nicolis, Foundations of Complex Systems, World Scientific, Singapore (2007).
-W. Ebeling and G. Nicolis, Word frequency and entropy of symbolic sequences: a dynamical perspective, Chaos Solitons and Fractals 2, 635 (1992).
-G. Nicolis and P. Gaspard, Toward a probabilistic approach to complex systems, Chaos Solitons and Fractals 4, 41 (1994).
-G. Nicolis, Thermodynamics today, Physica A213, 1 (1995).
-G. Nicolis and D. Daems, Probabilistic and thermodynamic aspects of dynamical systems, Chaos 8, 311 (1998).
-G. Nicolis, Nonequilibrium Statistical Mechanics, in Encyclopedia of Nonlinear Science, A. Scott ed., Routledge, New York (2005).
-P. Gaspard, Chaos, Scattering and Statistical Mechanics, Cambridge University Press, Cambridge (1998).
-P. Gaspard, Time-reversed dynamical entropy and irreversibility in Markovian random processes, J. Stat. Phys. 117, 599 (2004).
Supporting Material:
Complex Systems - Scholarpedia
Interdisciplinary Center for Nonlinear Phenomena and Complex Systems - G. Nicolis
Foundations of Complex Systems - G. Nicolis, C. Nicolis
Figure 1
Figure 2
Figure 3
Frontiers of Complex Systems Research: A View From the Foundations