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)

다중물리 해석 프로그램 : COMSOL Multiphysics

Nonlinear eigenvalue problems arise in a variety of science and engineering applications and in the past ten years there have been numerous breakthroughs in the development of numerical methods. This article surveys nonlinear eigenvalue problems associated with matrix-valued functions which depend nonlinearly on a single scalar parameter, with a particular emphasis on their mathematical properties and available numerical solution techniques. Solvers based on Newton's method, contour integration, and sampling via rational interpolation are reviewed. Problems of selecting the appropriate parameters for each of the solver classes are discussed and illustrated with numerical examples. This survey also contains numerous MATLAB code snippets that can be used for interactive exploration of the discussed methods.

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The nonlinear eigenvalue problem

Transport-dominated phenomena provide a challenge for common mode-based model reduction approaches. We present a model reduction method, which is suited for these kinds of systems. It extends the proper orthogonal decomposition (POD) by introducing time-dependent shifts of the snapshot matrix. The approach, called shifted proper orthogonal decomposition (sPOD), features a determination of the multiple transport velocities and a separation of these. One- and two-dimensional test examples reveal the good performance of the sPOD for transport-dominated phenomena and its superiority in comparison to the POD.

The Shifted Proper Orthogonal Decomposition: A Mode Decomposition for Multiple Transport Phenomena

pde2path is a free and easy to use Matlab continuation/bifurcation package for elliptic systems of PDEs with arbitrary many components, on general two dimensional domains, and with rather general boundary conditions. The package is based on the FEM of the Matlab pdetoolbox, and is explained by a number of examples, including Bratu’s problem, the Schnakenberg model, Rayleigh-Benard convection, and von Karman plate equations. These serve as templates to study new problems, for which the user has to provide, via Matlab function files, a description of the geometry, the boundary conditions, the coefficients of the PDE, and a rough initial guess of a solution. The basic algorithm is a one parameter arclength-continuation with optional bifurcation detection and branch-switching. Stability calculations, error control and mesh-handling, and some elementary time-integration for the associated parabolic problem are also supported. The continuation, branch-switching, plotting etc are performed via Matlab command-line function calls guided by the AUTO style. The software can be downloaded from www.staff.uni-oldenburg.de/hannes.uecker/pde2path, where also an online documentation of the software is provided such that in this paper we focus more on the mathematics and the example systems.

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pde2path - A Matlab Package for Continuation and Bifurcation in 2D Elliptic Systems

In this paper we develop numerical methods for integrating general evolution equations u t = F(u), $u(0)=u 0, where F is defined on a dense subspace of some Banach space (generally infinite-dimensional) and is equivariant with respect to the action of a finite-dimensional (not necessarily compact) Lie group. Such equations typically arise from autonomous PDEs on unbounded domains that are invariant under the action of the Euclidean group or one of its subgroups. In our approach we write the solution u(t) as a composition of the action of a time-dependent group element with a "frozen solution" in the given Banach space. We keep the frozen solution as constant as possible by introducing a set of algebraic constraints (phase conditions), the number of which is given by the dimension of the Lie group. The resulting PDAE (partial differential algebraic equation) is then solved by combining classical numerical methods, such as restriction to a bounded domain with asymptotic boundary conditions, half-explicit Eu...

https://epubs.siam.org/doi/pdf/10.1137/030600515

Freezing Solutions of Equivariant Evolution Equations

We present a continuation method for low-dimensional invariant subspaces of a parameterized family of large and sparse real matrices. Such matrices typically occur when linearizing about branches of steady states in dynamical systems that are obtained by spatial discretization of time-dependent PDE’s. The main interest is in subspaces that belong to spectral sets close the imaginary axis. Our continuation procedure provides bases of the invariant subspaces that depend smoothly on the parameter as long as the continued spectral subset does not collide with another eigenvalue. Generalizing results from [32] we show that this collision generically occurs when a real eigenvalue from the continued spectral set meets another eigenvalue from outside to form a complex conjugate pair. Such a situation relates to a turning point of the subspace problem and and we develop a method to inflate the subspace at such points.

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Continuation of Low-Dimensional Invariant Subspaces in Dynamical Systems of Large Dimension

We present a new numerical method for computing the pure-point spectrum associated with the linear stability of coherent structures. In the context of the Evans function shooting and matching approach, all the relevant information is carried by the flow projected onto the underlying Grassmann
manifold. We show how to numerically construct this projected flow in a stable and robust manner. In particular, the method avoids representation singularities by, in practice, choosing the best coordinate patch representation for the flow as it evolves. The method is analytic in the spectral parameter and of complexity bounded by the order of the spectral problem cubed. For large systems it represents a competitive method to those recently developed that are based on continuous orthogonalization. We demonstrate this by comparing the two methods in three applications: Boussinesq solitary waves, autocatalytic travelling waves and the Ekman boundary layer.

/pdf/grassmannian-spectral-shooting-4ni3psqqkz.pdf

Grassmannian spectral shooting

We present a numerical method for computing the pure-point spectrum associated with the linear stability of multi-dimensional travelling fronts to parabolic nonlinear systems. Our method is based on the Evans function shooting approach. Transverse to the direction of propagation we project the spectral equations onto a finite Fourier basis. This generates a large, linear, one-dimensional system of equations for the longitudinal Fourier coefficients. We construct the stable and unstable solution subspaces associated with the longitudinal far-field zero boundary conditions, retaining only the information required for matching, by integrating the Riccati equations associated with the underlying Grassmannian manifolds. The Evans function is then the matching condition measuring the linear dependence of the stable and unstable subspaces and thus determines eigenvalues. As a model application, we study the stability of two-dimensional wrinkled front solutions to a cubic autocatalysis model system. We compare our shooting approach with the continuous orthogonalization method of Humpherys and Zumbrun. We then also compare these with standard projection methods that directly project the spectral problem onto a finite multi-dimensional basis satisfying the boundary conditions.

Computing stability of multi-dimensional travelling waves

Integral phase conditions were first suggested by E.J. Doedel as an efficient tool for computing periodic orbits in dynamical systems. In general, phase conditions help in eliminating continuous symmetries as well as in reducing the effort for adaptive meshes during continuation. In this paper we discuss the usefulness of phase conditions for the numerical analysis of finiteand infinite-dimensional dynamical systems that have continuous symmetries. The general approach (called the freezing method) will be presented in an abstract framework for evolution equations that are equivariant with respect to the action of a (not necessarily compact) Lie group. We show particular applications of phase conditions to periodic, heteroclinic and homoclinic orbits in ODEs, to relative equilibria and relative periodic orbits in PDEs as well as to time integration of equivariant PDEs.

Vera Thümmler

Papers

Freezing Solutions of Equivariant Evolution Equations

Continuation of Low-Dimensional Invariant Subspaces in Dynamical Systems of Large Dimension

Grassmannian spectral shooting

Computing stability of multi-dimensional travelling waves

Phase Conditions, Symmetries and PDE Continuation