## Pattern formation

*24 Jul 2023 21:50*

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
- Nonequilibrium Statistical Mechanics
- Nonlinear Dynamics
- Random Fields
- Self-Organization
- Slime Molds
- Spatial Statistics
- Spatio-Temporal Statistics
- Winding Number

- Recommended, big picture:
- Philip Ball, The Self-Made Tapestry: Pattern Formation in Nature [Review: The Blind Snowflake-Maker]
- M. C. Cross and P. C. Hohenberg, "Pattern Formation out of
Equilibrium", Reviews of Modern Physics
**65**(1993) 851--1112 [Review] - 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

- Recommended, close-ups:
- 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
- Janko Gravner and David Griffeath, Snowfakes [Models of snow-crystal formation]
- 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 - 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
- John A. Adam, Mathematics in Nature: Modeling Patterns in the Natural World
- 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
- Kenneth A. Brakke, The Motion of a Surface by Its Mean Curvature [1978]
- 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 - Pierre Collet and Jean-Pierre Eckmann, Instabilities and Fronts in Extended Systems
- 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
- 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
- Jonathan H. McCoy, Will Brunner, Werner Pesch and Eberhard Bodenschatz, "Self-Organization of Topological Defects due to Applied Constraints",
Physical Review Letters
**101**(2008): 254102 - 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) - David R. Nelson, Defects and Geometry in Condensed Matter Physics
- 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