pde2path - A Matlab package for continuation and bifurcation in 2D elliptic systems

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

On the dynamics of a non-local parabolic equation arising from the Gierer-Meinhardt system

This is an author-created, un-copyedited version of an article accepted for publication in Nonlinearity. The publisher is not responsible for any errors or omissions in this version of the manuscript or any version derived from it. The Version of Record is available online at http://iopscience.iop.org/article/10.1088/1361-6544/aa64b2/metaThe purpose of the current paper is to contribute to the comprehension of the dynamics of the shadow system of an activator-inhibitor system known as a Gierer-Meinhardt model. Shadow systems are intended to work as an intermediate step between single equations and reaction-diffusion systems. In the case where the inhibitor's response to the activator's growth is rather weak, then the shadow system of the Gierer-Meinhardt model is reduced to a single though non-local equation whose dynamics will be investigated. We mainly focus on the derivation of blow-up results for this non-local equation which can be seen as instability patterns of the shadow system. In particular, a {\it diffusion driven instability (DDI)}, or {\it Turing instability}, in the neighbourhood of a constant stationary solution, which it is destabilised via diffusion-driven blow-up, is obtained. The latter actually indicates the formation of some unstable patterns, whilst some stability results of global-in-time solutions towards non-constant steady states guarantee the occurrence of some stable patterns

Delayed Reaction Kinetics and the Stability of Spikes in the Gierer--Meinhardt Model

A linear stability analysis of localized spike solutions to the singularly perturbed two-component Gierer--Meinhardt (GM) reaction-diffusion (RD) system with a fixed time delay $T$ in the nonlinear reaction kinetics is performed. Our analysis of this model is motivated by the computational study of Lee, Gaffney, and Monk [Bull. Math. Bio., 72 (2010), pp. 2139--2160] on the effect of gene expression time delays on spatial patterning for both the GM model and some related RD models. It is shown that the linear stability properties of such localized spike solutions are characterized by the discrete spectra of certain nonlocal eigenvalue problems (NLEP). Phase diagrams consisting of regions in parameter space where the steady-state spike solution is linearly stable are determined for various limiting forms of the GM model in both 1-dimensional and 2-dimensional domains. On the boundary of the region of stability, the spike solution is found to undergo a Hopf bifurcation. For a special range of exponents in the nonlinearities for the 1-dimensional GM model, and assuming that the time delay only occurs in the inhibitor kinetics, this Hopf bifurcation boundary is readily determined analytically. For this special range of exponents, the challenging problem of locating the discrete spectrum of the NLEP is reduced to the much simpler problem of locating the roots to a simple transcendental equation in the eigenvalue parameter. By using a hybrid analytical-numerical method, based on a parametrization of the NLEP, it is shown that qualitatively similar phase diagrams occur for general GM exponent sets and for the more biologically relevant case where the time delay occurs in both the activator and inhibitor kinetics. Overall, our results show that there is a critical value $T_{\star}$ of the delay for which the spike solution is unconditionally unstable for $T>T_{*}$, and that the parameter region where linear stability is assured is, in general, rather limited. A comparison of the theory with full numerical results computed from the RD system with delayed reaction kinetics for a particular parameter set suggests that the Hopf bifurcation can be subcritical, leading to a global breakdown of a robust spatial patterning mechanism