Natural Computation and Self-Organization—Physics 256AB

Here are several lists—one for articles, others for
books—that
complement the assigned readings. Some might be helpful for thinking
of projects or for technical detail for projects. Some give an
historical view and put a human face on the history of the topics
we're covering. And some describe applications of information theory,
dynamics, and computational mechanics.

**Articles**:

*TDCS*: J. P. Crutchfield and C. R. Shalizi, "Thermodynamic Depth of Causal States: Objective Complexity via Minimal Representations", Physical Review E**59**(1999) 275-283.

[Abstract] [ps.gz] [ps] [pdf]

*TBCA*: J. P. Crutchfield and J. E. Hanson, "Turbulent Pattern Bases for Cellular Automata", Physica D**69**(1993) 279-301.

[Abstract] [ps.gz] [pdf]

*DNCO*: D. P. Feldman and J. P. Crutchfield, "Discovering Noncritical Organization: Statistical Mechanical, Information Theoretic, and Computational Views of Patterns in One-Dimensional Spin Systems".

[Abstract] [ps.gz]*2DNNN*: D. P. Feldman and J. P. Crutchfield, "Structural Information in Two-Dimensional Patterns: Entropy Convergence and Excess Entropy", Physical Review E**67**(2003) 051104.

[Abstract] [ps.gz] [ps] [pdf]

*BTFM*: D. P. Varn, G. S. Canright, and J. P. Crutchfield, "Discovering Planar Disorder in Close-Packed Structures from X-Ray Diffraction: Beyond the Fault Model", Physical Review B**66**:17 (2002) 156-159.

[Abstract] [ps.gz] [ps] [pdf]

- These days we use Python. If you know some programming, a quick way to get started is to work through the Python Labs.
- Easy introduction to Python: Non-Programmer's Tutorial for Python.
- From Python's creator: Tutorial by Guido van Rossum.
- Dive Into Python.
- If you are already a decent programmer: Building Skills in Python.
*Numerical Recipes in Fortran/C/C++/Pascal/...*, William Press et al., Cambridge University Press, WWW.*Algorithms in C/C++: Fundamentals, Data Structures, Sorting, Searching*, Robert Sedgewick (1999).*The Art of Computer Programming (Vols 1, 2, & 3), 2nd edition*, Donald Knuth (1998).

*Henri Poincare: A Scientific Biography*, Jeremy Gray, Princeton University Press (2012).*Alan Turing: The Enigma*, Andrew Hodges, Walker and Company (2000).*Dark Hero Of The Information Age: In Search of Norbert Wiener The Father of Cybernetics*, Flo Conway and Jim Siegelman, Basic Books (2004).*John Von Neumann: The Scientific Genius Who Pioneered the Modern Computer, Game Theory, Nuclear Deterrence, and Much More*, Norman MacRae, American Mathematical Society (2000).*Incompleteness: The Proof and Paradox of Kurt Gödel*, Rebecca Goldstein, W. W. Norton & Company (2005).

*The Most Powerful Idea in the World: A Story of Steam, Industry, and Invention*, William Rosen, Random House (New York, 2010).*Einstein's Clocks, Poincaré's Maps: Empires of Time*, Peter Gallison, W. W. Norton & Company (2005).*New Methods of Celestial Mechanics*, Henri Poincaré, Daniel L. Goroff (editor), AIP Press (1992).- E. N. Lorenz,
*Deterministic Aperiodic Flow*, J. Atmos. Sci.**20**(1963) 130-141.

*The Self-Made Tapestry: Pattern Formation in Nature*, Philip Ball, Oxford University Press (1998).*The Computational Beauty of Nature: Computer Explorations of Fractals, Chaos, Complex Systems, and Adaptation*, Gary W. Flake, MIT Press (2000).*Cellular Automata Machines: A New Environment for Modeling*, Tommaso Toffoli and Norman Margolus, MIT Press (1987).*The Geometry of Biological Time*, Arthur Winfree, Springer-Verlag (1980).

*Chaos in Dynamical Systems*, Edward Ott, Cambridge University Press (1993).*Introduction to Applied Nonlinear Dynamical Systems and Chaos*, S. Wiggins, Springer-Verlag (1990).*Global Bifurcations and Chaos: Analytical Methods*, S. Wiggins, Springer-Verlag (1988).*Order within chaos: Towards a deterministic approach to turbulence*, P. Berge, Y. Pomeau, and C. Vidal, Wiley (1986).*Nonlinear Oscillations, Dynamical Systems, and Bifurcations of Vector Fields*, J. Guckenheimer and P. Holmes, Springer-Verlag (1983).*Dynamics, the Geometry of Behavior*, Ralph Abraham and Christopher Shaw, Aerial Press (1984).*Chaos and Time-Series Analysis*, Clint Sprott, Oxford University Press (2003).*Does God Play Dice? The New Mathematics of Chaos*, Ian Stewart, Blackwell Publishers (1990).*Understanding Nonlinear Dynamics*, Daniel Kaplan and Leon Glass, Springer (1995).- Bob Devaney's books.

*The Mathematical Theory of Communication*, Claude Shannon and Warren Weaver, University of Illinois Press (1962).*Science from Fisher information: A unification*, B. Roy Frieden, Cambridge University Press (2004).

*Quantum Computation and Quantum Information*, M. A. Nielsen and I. L. Chuang, Cambridge University Press (2011).

*Introduction to Automata Theory, Languages, and Computation*, J. E. Hopcroft and J. D. Ullman, Addison-Wesley (1979).*Elements of the Theory of Computation*, H. R. Lewis and C. H. Papadimitriou, Prentice-Hall (1998).

- Here's a quick review (6 pages) from Barber's
*Bayesian Reasoning*: First half of chapter 1. - This is the one I used as an undergrad. It's good:
Paul G. Hoel, Sidney C. Port, Charles J. Stone,
*Introduction to Probability Theory*. **The**reference is: William Feller, An Introduction to Probability Theory and Its Applications, Volume 1 and Volume 2. The current price will make you gasp. Good, though.- Free and good: Grinstead and Snell, Introduction to Probability (2006). Free downloadable book there. Here's a local copy.
- Finally, a slightly more in-depth introduction to probability theory,
lecture notes on measure theory: Christel Geiss and Stefan Geiss,
*An Introduction to Probability Theory*and also a local copy.