A comprehensive review of spatiotemporal pattern formation in systems driven away from equilibrium is presented, with emphasis on comparisons between theory and quantitative experiments. Examples include patterns in hydrodynamic systems such as thermal convection in pure fluids and binary mixtures, Taylor-Couette flow, parametric-wave instabilities, as well as patterns in solidification fronts, nonlinear optics, oscillatory chemical reactions and excitable biological media. The theoretical starting point is usually a set of deterministic equations of motion, typically in the form of nonlinear partial differential equations. These are sometimes supplemented by stochastic terms representing thermal or instrumental noise, but for macroscopic systems and carefully designed experiments the stochastic forces are often negligible. An aim of theory is to describe solutions of the deterministic equations that are likely to be reached starting from typical initial conditions and to persist at long times. A unified description is developed, based on the linear instabilities of a homogeneous state, which leads naturally to a classification of patterns in terms of the characteristic wave vector q0 and frequency ω0 of the instability. Type Is systems (ω0=0, q0≠0) are stationary in time and periodic in space; type IIIo systems (ω0≠0, q0=0) are periodic in time and uniform in space; and type Io systems (ω0≠0, q0≠0) are periodic in both space and time. Near a continuous (or supercritical) instability, the dynamics may be accurately described via "amplitude equations," whose form is universal for each type of instability. The specifics of each system enter only through the nonuniversal coefficients. Far from the instability threshold a different universal description known as the "phase equation" may be derived, but it is restricted to slow distortions of an ideal pattern. For many systems appropriate starting equations are either not known or too complicated to analyze conveniently. It is thus useful to introduce phenomenological order-parameter models, which lead to the correct amplitude equations near threshold, and which may be solved analytically or numerically in the nonlinear regime away from the instability. The above theoretical methods are useful in analyzing "real pattern effects" such as the influence of external boundaries, or the formation and dynamics of defects in ideal structures. An important element in nonequilibrium systems is the appearance of deterministic chaos. A greal deal is known about systems with a small number of degrees of freedom displaying "temporal chaos," where the structure of the phase space can be analyzed in detail. For spatially extended systems with many degrees of freedom, on the other hand, one is dealing with spatiotemporal chaos and appropriate methods of analysis need to be developed. In addition to the general features of nonequilibrium pattern formation discussed above, detailed reviews of theoretical and experimental work on many specific systems are presented. These include Rayleigh-Benard convection in a pure fluid, convection in binary-fluid mixtures, electrohydrodynamic convection in nematic liquid crystals, Taylor-Couette flow between rotating cylinders, parametric surface waves, patterns in certain open flow systems, oscillatory chemical reactions, static and dynamic patterns in biological media, crystallization fronts, and patterns in nonlinear optics. A concluding section summarizes what has and has not been accomplished, and attempts to assess the prospects for the future.

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Pattern formation outside of equilibrium

1980 Preface * 1999 Preface * 1999 Acknowledgements * Introduction * 1 Circular Logic * 2 Phase Singularities (Screwy Results of Circular Logic) * 3 The Rules of the Ring * 4 Ring Populations * 5 Getting Off the Ring * 6 Attracting Cycles and Isochrons * 7 Measuring the Trajectories of a Circadian Clock * 8 Populations of Attractor Cycle Oscillators * 9 Excitable Kinetics and Excitable Media * 10 The Varieties of Phaseless Experience: In Which the Geometrical Orderliness of Rhythmic Organization Breaks Down in Diverse Ways * 11 The Firefly Machine 12 Energy Metabolism in Cells * 13 The Malonic Acid Reagent ('Sodium Geometrate') * 14 Electrical Rhythmicity and Excitability in Cell Membranes * 15 The Aggregation of Slime Mold Amoebae * 16 Numerical Organizing Centers * 17 Electrical Singular Filaments in the Heart Wall * 18 Pattern Formation in the Fungi * 19 Circadian Rhythms in General * 20 The Circadian Clocks of Insect Eclosion * 21 The Flower of Kalanchoe * 22 The Cell Mitotic Cycle * 23 The Female Cycle * References * Index of Names * Index of Subjects

https://www.cambridge.org/core/services/aop-cambridge-core/content/view/596B270197FE27DE5FABB598B6210622/S0025557200150892a.pdf/div-class-title-span-class-italic-the-geometry-of-biological-time-span-by-a-t-winfree-pp-544-dm68-corrected-second-printing-1990-isbn-3-540-52528-9-springer-div.pdf

The geometry of biological time , by A. T. Winfree. Pp 544. DM68. Corrected Second Printing 1990. ISBN 3-540-52528-9 (Springer)

We propose a new multiphase level set framework for image segmentation using the Mumford and Shah model, for piecewise constant and piecewise smooth optimal approximations. The proposed method is also a generalization of an active contour model without edges based 2-phase segmentation, developed by the authors earlier in T. Chan and L. Vese (1999. In Scale-Space'99, M. Nilsen et al. (Eds.), LNCS, vol. 1682, pp. 141–151) and T. Chan and L. Vese (2001. IEEE-IP, 10(2):266–277). The multiphase level set formulation is new and of interest on its own: by construction, it automatically avoids the problems of vacuum and overlaps it needs only log n level set functions for n phases in the piecewise constant cases it can represent boundaries with complex topologies, including triple junctionss in the piecewise smooth case, only two level set functions formally suffice to represent any partition, based on The Four-Color Theorem. Finally, we validate the proposed models by numerical results for signal and image denoising and segmentation, implemented using the Osher and Sethian level set method.

/pdf/a-multiphase-level-set-framework-for-image-segmentation-1mvyq2we6z.pdf

A Multiphase Level Set Framework for Image Segmentation Using the Mumford and Shah Model

Monotone dynamical systems Stability and convergence Competitive and cooperative differential equations Irreducible cooperative systems Cooperative systems of delay differential equations Nonquasimonotone delay differential equations Quasimonotone systems of parabolic equations A competition model Appendix Bibliography.

Monotone Dynamical Systems: An Introduction to the Theory of Competitive and Cooperative Systems

Differential-Difference Equations. By Richard Bellman and Kenneth L. Cooke. Pp. xvi, 465. 1963. (Academic Press)

Exponential attractor for a chemotaxis-growth system of equations

It is well known from experiments that bacterial species Bacillus subtilis exhibit various colony patterns. These are essentially classified into five types in the morphological diagram, depending on the substrate softness and nutrient concentration. (A) diffusion-limited aggregation-like; (B) Eden-like; (C) concentric ring-like; (D) disk-like; and (E) dense branching morphology-like. There arises the naive question of whether the diversity of colony patterns observed in experiments is caused by different effects or governed by the same underlying principles. Our research has led us to propose reaction–diffusion models to describe the morphological diversity of colony patterns except for Eden-like ones.

Reaction-diffusion modelling of bacterial colony patterns

The effect of cross-population pressure on the Volterra type dynamics for two competing species is investigated. On the basis of cross-diffusion induced instability, spatial segregation is studied. Spatially discrete models are also discussed. It is shown that this effect has a tendency to enhance the stability assuring coexistence of species. In continuous and discrete cases, time-dependent segregation processes are studied numerically.

Spatial segregation in competitive interaction-diffusion equations

On a diffusive prey-predator model which exhibits patchiness

A population model including diffusion, chemotaxis and growth is studied. Assuming that the diffusion rate and the chemotactic rate are both very small compared with the growth rate, we derive a new equation to describe the time-evolution of the aggregating region of biological individuals and show the conditions for the existence and stability of radially symmetric equilibrium solutions of the equation, which indicate the aggregation of individuals.

Masayasu Mimura

Papers

Exponential attractor for a chemotaxis-growth system of equations

Reaction-diffusion modelling of bacterial colony patterns

Spatial segregation in competitive interaction-diffusion equations

On a diffusive prey-predator model which exhibits patchiness

Aggregating pattern dynamics in a chemotaxis model including growth