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{{CSSS 2008 Argentina}}
{{CSSS 2008 Argentina}}
==Week 1 (tentative)==


Forming project group teams
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==
* [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]]


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!
[[Media: WestEtal2001.pdf| West et al. 2001]]




* [http://www.cs.colorado.edu/~lizb/  Elizabeth Bradley]


* [http://www.cs.colorado.edu/~lizb/  Elizabeth Bradley] (Nonlinear dynamics)
''Supporting Material:''


Definition of chaos; examples in various fields
[[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]]


An extended example: the logistic map. Introduce:
bifurcations; bifurcation diagram and its structure, incl. Feigenbaum number; fractals and their connection to chaos


Continuous-time dynamics: definition
* [http://www.ifca.unican.es/~wio/ Horacio S. Wio]


Introduce concepts: state variables, state space, trajectory, initial condition, transient, attractor, basin of attraction, fixed point, stability, bifurcation, parameter
''Supporting Material:''


An extended example: the Lorenz system: history, physical meaning, trajectories, attractors, bifurcations (examples & definitions), types of attractors, stability: definition & mathematics, eigen. , un/stable manifolds, Lyapunov exponent and the connection to chaos
[[Media: Book_.pdf| Nonequilibrium Potential in Reaction-Diffusion Systems - Horacio S. Wio]]<br />
[[Media: Cross-Hohem2.pdf| Pattern formation outside of equilibrium - M.C. Cross, P.C. Hohenberg]]<br />


Numerical solvers: roles and issues


Shadowing
* [http://www.santafe.edu/~jdf/SFI%20Template/About%20Me.html J. Doyne Farmer]


Projection vs section
''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 />


Poincare sections in space & time
''Supporting Material:''


Delay-coordinate embedding
[[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]]


Examples: roulette, the SFI competition


Applications: filtering, control of chaos, synchronization & communication, spacecraft orbits, chaos in the solar system, harnessing the butterfly effect in fluids
* [http://www.brain.riken.jp/labs/mns/ysato/ Yuzuru Sato]


''Supporting Material:''
''Supporting Material:''


[[Media: ida-chapter.pdf| Time Series Analysis - E. Bradley]]<br />
[[Media: cls2pg02.pdf| Chaos in learning a simple two-person game]]<br />
[[Media: error.pdf| Error in Numerical Methods - E. Bradley]]<br />
[[Media: credlmas03.pdf| Coupled replicator equations for the dynamics of learning in multiagent systems]]<br />
[[Media: ode-notes.pdf| Numerical Solution for Differential Equations - E. Bradley]]
[[Media: sdca05.pdf| Stability and diversity in collective adaption]]<br />
[[Media: adimp.pdf| Adaptive Dynamics for Interacting Markovian Processes]]<br />




Line 46: Line 65:


''Supporting Material:''
''Supporting Material:''
[http://users.cse.ucdavis.edu/~cmg/compmech/pubs/EverNewTitlePage.htm - Is Anything Ever New? Considering Emergence] <br />
[http://users.cse.ucdavis.edu/~cmg/compmech/pubs/ruro.htm - Regularities Unseen, Randomness Observed: Levels of Entropy Convergence] <br />
[http://users.cse.ucdavis.edu/~cmg/compmech/pubs/CalcEmergTitlePage.htm - The Calculi of Emergence: Computation, Dynamics, and Induction] <br />
[http://users.cse.ucdavis.edu/~cmg/compmech/pubs/cmppss.htm - Computational Mechanics: Pattern and Prediction, Structure and Simplicity] <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://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]]
* [http://chaos.c.u-tokyo.ac.jp/ Kunihiko Kaneko] (Complex Systems Biology)
References: (Book)
K. Kaneko,  Life: An Introduction to Complex Systems Biology, Springer, 2006<br />
K. Kaneko and I.Tsuda, Complex Systems: Chaos and Beyond, Springer 2000<br />
(Papers) available at:  [http://chaos.c.u-tokyo.ac.jp/study.html]
(including some other related materials)
C. Furusawa and K. Kaneko, ``A generic mechanism for adaptive gowth
rate regulation", PLoS Computationa Biology, 4(2008) e3<br />
K. Kaneko, Evolution of Robustness to Noise and Mutation in Gene
Expression Dynamics, PLoS One(2007) 2 e434<br />
K. Kaneko and C. Furusawa, "An Evolutionary Relationship between
Genetic Variation and Phenotypic Fluctuation", J. Theo. Biol. 240
(2006) 78-86<br />
K. Kaneko" On Recursive Production and Evolvabilty of Cells: Catalytic
Reaction Network Approach " Adv. Chem. Phys. , 130 (2005) 543-598<br />
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<br />
C. Furusawa and K. Kaneko " Zipf's law in Gene Expression " Phys. Rev.
Lett., 90 (2003) 088102<br />
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<br />
K. Kaneko and T. Yomo," ``Isologous Diversification for Robust
Development of Cell Society", J.theor.Biol. 199 (1999) 243-256
<br />


==Week 2==
==Week 2==
* [http://cabfst28.cnea.gov.ar/~abramson/  Guillermo Abramson]
''Supporting Material:''
[[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:''
[[Media: FlackLogicNetRobust11_30_08.pdf| The Experimental Logic of Network Approaches to Robustness in Complex Systems - J. Flack]]
* [http://www.arteuna.com/ManuelCaceres/MOC.htm  Manuel O. Cáceres]
''Supporting Material:''
[[Media: Caceres-Reverte.pdf| Elementos de estadistica de no equilbrio y sus aplicaciones al transporte en medios desordenados - M. Caceres]]<br />
[[Media: caceres3.pdf| First Passage Time Statistics in the Logistic Model - M. Caceres]]
* [http://www.santafe.edu/profiles/?pid=75 D. Eric Smith]
''Supporting Material:''
[[Media: Smith_&_Foley_2008.pdf| Classical thermodynamics and economic general equilibrium theory - E. Smith & D. Foley]]<br />
[[Media: Smith_2008_JTB1.pdf| Thermodynamics of natural selection I: Energy flow and the limits of organization - E. Smith]]<br />
[[Media: Smith_2008_JTB2.pdf| Thermodynamics of natural selection II: Chemical Carnot cycles - E. Smith]]<br />
[[Media: Smith_2008_JTB3.pdf| Thermodynamics of natural selection III: Landauer's principle in computation and chemistry - E. Smith]]
* [http://www.df.uba.ar/~silvina/ Silvina Ponce Dawson]<br />
''Supporting Material:''<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: noise_propagation_gene_networks_science_1965.pdf| Noise Propagation in Gene Networks]]<br />
[[Media: organization_function_local-ca_signals_bootman.pdf| The organization and functions of local Ca2+ signals]]<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 />


* [http://www.ulb.ac.be/cenoliw3/PERSO-PAGES/gnicolis.html Grégoire Nicolis]
* [http://www.ulb.ac.be/cenoliw3/PERSO-PAGES/gnicolis.html Grégoire Nicolis]
Line 70: Line 204:
[[Media: ERWnicolisfig2.pdf| Figure 2]]<br />
[[Media: ERWnicolisfig2.pdf| Figure 2]]<br />
[[Media: ERWnicolisfig3.pdf| Figure 3]]<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 />
<br />
* [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 />
<br />
* [http://www.santafe.edu/profiles/?pid=75 D. Eric Smith]
''Supporting Material:''
[[Media: Smith_&_Foley_2008.pdf| Classical thermodynamics and economic general equilibrium theory - E. Smith & D. Foley]]<br />
[[Media: Smith_2008_JTB1.pdf| Thermodynamics of natural selection I: Energy flow and the limits of organization - E. Smith]]<br />
[[Media: Smith_2008_JTB2.pdf| Thermodynamics of natural selection II: Chemical Carnot cycles - E. Smith]]<br />
[[Media: Smith_2008_JTB3.pdf| Thermodynamics of natural selection III: Landauer's principle in computation and chemistry - E. Smith]]

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

Bettencourt et al. 2007 -- supporting material

West & Brown 2005 Scaling Review

West et al. 2001


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?


Quantum Computation


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


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

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