Pattern formation

29 Apr 2008 13:17

---

Spiral leads me to sleep

I should probably spin off reaction-diffusion models as a separate notebook.

See also: Cellular Automata; Complexity; Developmental Biology; Dissipative Structures; Nonlinear Dynamics; Self-Organization; Spatial Statistics and Spatial Stochastic Processes; Winding Number

Recommended:
• Philip Ball, The Self-Made Tapestry: Pattern Formation in Nature [Review: The Blind Snowflake-Maker]
• Eric Bonabeau, "From Classical Models of Morphogenesis to Agent-Based Models of Pattern Formation," Artifical Life 3 (1997): 191--211
• John Tyler Bonner, On Development
• M. C. Cross and P. C. Hohenberg, Pattern Formation out of Equilibrium (a.k.a. Reviews of Modern Physics 65 (1993) 851-1112 [Review]
• David Griffeath, Primordial Soup Kitchen
• Gemunu H. Gunaratne, David K. Hoffman and Donald J. Kouri, "Characterization of Natural Patterns," Physical Review E 57 (1998): 5146--5149
• Gemunu H. Gunaratne, Anuradha Ratnaweera and K. Tennekone, "Emergence of Order in Textured Patterns," patt-sol/9809001
• Lionel Harrison, Kinetic Theory of Living Form
• Paul Manneville, Dissipative Structures and Weak Turbulence
• Przemyslaw Prusinkiewicz and Mark Hammel, Visual Models of Morphogenesis: A Guided Tour
• Thimo Rohlf and Stefan Bornholdt
  • "Self-organized pattern formation and noise-induced control from particle computation", cond-mat/0312366 [Short version]
  • "Morphogenesis by coupled regulatory networks", q-bio.MN/0401024 [Long version]
• Satoshi Sawai, Peter A. Thomason and Edward C. Cox, "An autoregulatory circuit for long-range self-organization in Dictyostelium cell populations", Nature 433 (2005): 323--326
• Peter S. Stevens, Patterns in Nature
• Ian Stewart and Golubitsky, Fearful Symmetry [Groups, symmetries, broken symmetries and pattern-formation for the non-mathematical]
• D'Arcy Wentworth Thompson, On Growth and Form
• Vladimir K. Vanang and Irving R. Epstein, "Stationary and Oscillatory Localized Patterns, and Subcritical Bifurcations", Physical Review Letters 92 (2004): 128301
• Arthur Winfree
  • When Time Breaks Down
  • The Geometry of Biological Time

To read:
• Edward R. Abraham, "Sea urchin feeding fronts", q-bio.PE/0610004
• Mark S. Alber, Yi Jiang and Maria A. Kiskowski, "Lattice gas cellular automata model for rippling and aggregation in myxobacteria", q-bio/0401014
• Aris, Aronson + Swinney, Patterns and Dynamics in Reactive Media
• J. Buceta, Katja Lindenberg, and J. M. R. Parrondo, "Stationary and Oscillatory Spatial Patterns Induced by Global Periodic Switching," cond-mat/0110542
• A. Carpio, "Wave trains, self-oscillations and synchronization in discrete media", cond-mat/0506119
• Pierre-Henri Chavanis, "A stochastic Keller-Segel model of chemotaxis", arxiv:0804.4425
• Elisheva Cohen, David A. Kessler and Herbert Levine, "Fluctuation-Regularized Front Propagation Dynamics in Reaction-Diffusion Systems", Physical Review Letters 94 (2005): 158302
• Catherine Crawford and Hermann Riecke, "Oscillon-Type Structures and Their Interaction in a Swift-Hohenberg Model," patt-sol/9804005
• Karen E. Daniels, Christian Beck and Eberhard Bodenschatz, "Defect turbulence and generalized statistical mechanics," cond-mat/0302623
• Jörn Davidsen, Ronaldo Erichsen, Raymond Kapral and Hughes Chaté, "From ballistic to Brownian vortex motion in complex oscillatory media", Physical Review Letters 93 (2004): 018305 = nlin.PS/0410033
• Epstein and Pojman, An Introduction to Nonlinear Chemical Dynamics
• Amatzia Genin, Jules S. Jaffe, Ruth Reef, Claudio Richter, Peter J. S. Franks, "Swimming Against the Flow: A Mechanism of Zooplankton Aggregation", Science 308 (2005): 860--862
• Solomon W. Golomb, Polyominoes illus. Waren Lushbaugh
• Nigel Goldenfeld, Pak Yuen Chan and john Veysey, "Dynamics of Precipitation Pattern Formation at Geothermal Hot Springs", Physical Revieew Letters 96 (2006): 254501 = nlin.PS/0601028
• Roman O. Grigoriev and Andreas Handel, "Nonnormality and the localized control of extended systems," nlin.PS/0207023
• Ramon Grima, "Strong-coupling dynamics of a multi-cellular chemotactic system", q-bio.CB/0505004
• Peter Grindrod, Theory and Application of Reaction Diffusion Equations: Patterns and Waves
• Kevin Hall and Leon Glass, "How to Tell a Target from a Spiral: The Two Probe Problem," Physical Review Letters 82 (1999): 5164--5167
• Rebecca Hoyle, Pattern Formation: An Introduction to Methods [Blurb]
• Lukas Jahnke and Jan W. Kantelhardt, "Comparison of models and lattice-gas simulations for Liesegang patterns", arxiv:0803.3634
• Y. Kuramoto, Chemical Oscillations, Waves, and Turbulence [Now re-issued as a cheap Dover paperback]
• Julio Largo, Piero Tartaglia, Francesco Sciortino, "Effective non-additive pair potential for lock-and-key interacting particles: the role of the limited valence", cond-mat/0703383
• Men Li, Heimo Schnablegger and Stephen Mann, "Coupled Synthesis and Self-Assembly of Nanoparticles to Give Structures with Controlled Organization," Nature 402 (1999): 393--395
• Markus Loecher, Noise Sustained Patterns: Fluctuations and Nonlinearities
• Juan M. Lopez and Henrik J. Jensen, "Generic model of morphological changes in growing colonies of fungi," cond-mat/0110509
• Paul Manneville, Instabilities, Chaos and Turbulence
• K. R. Mecke and D. stoyan (eds.), Statistical Physics and Spatial Statistics: The Art of Analyzing and Modeling Spatial Structures and Pattern Formation
• Girish Nathan and Gemunu Gunaratne, "Set of measures to analyze the dynamics of nonequilibrium structures", Physical Review E 71 (2005): 035101(R)
• Wouter-Jan Rappel, Alastair Nicol, Armand Sarkissian, Herbert Levine and William F. Loomis, "Self-Organized Vortex State in Two-Dimensional Dictyostelium Dynamics," patt-sol/9811001
• D. Reguera (ed.), Coherent Structures in Complex Systems
• Hermann Riecke, "Localized Structures in Pattern-Forming Systems," patt-sol/9810002
• Jori E. Ruppert-Felsot, Olivier Praud, Eran Sharon, Harry L. Swinney, "Extraction of coherent structures in a rotating turbulent flow experiment", physics/0410161
• J. M. Sancho and Jordi Garcia-Ojalvo, "Noise-Induced Order in Extended Systems: A Tutorial", cond-mat/0608511
• Sumithra Sankararaman, Gautam I. Menon and P. B. Sunil Kumar, "Self-organized pattern formation in motor-microtubule mixtures", Physical Review E 70 (2004): 031905
• Smoller, Shock Waves and Reaction-Diffusion Equations
• Swinney and Krinsky (eds). Waves and Patterns (a.k.a. Phyisca D 49)
• Uwe C. Tauber, Martin Howard and Benjamin P. Vollmayr-Lee, "Applications of field-theoretic renormalization group methods to reaction-diffusion problems", Journal of Physics A 38 (2005): 79--131 = cond-mat/0501678
• Steffen Trimper and Knud Zabrocki, "Memory Driven Pattern Formation", cond-mat/0406269
• 25 Years of Non-Equilibrium Statistical Mechanics: Proceedings, Sitges, Barcelona, 1994
• Paul Umbanhowar, Pattern Formation in Granular Materials
• Daniel Walgraef, Spatio-temporal Pattern Formation: with Examples from Physics, Chemistry and Materials Science
• Stephen Whitelam and Phillip L. Geissler, "Cluster algorithm for pairwise-interacting particles", cond-mat/0508100 [with special application to self-assembling particle systems]
• Lancelot Whyte (ed.). Aspects of Form
• H. S. Wio, S. Bouzat and B. von Haeften, "Stochastic Resonance in Spatially Extended Systems: The Role of Far from Equilibrium Potentials," cond-mat/0109452