Bifurcation software is an essential tool in the study of dynamical systems. From the beginning (the first packages were written in the 1970's) it was also used in the modelling process, in particular to determine the values of critical parameters. More recently, it is used in a systematic way in the design of dynamical models and to determine which parameters are relevant. MatCont and Cl_MatCont are freely available matlab numerical continuation packages for the interactive study of dynamical systems and bifurcations. MatCont is the GUI-version, Cl_MatCont is the command-line version. The work started in 2000 and the first publications appeared in 2003. Since that time many new functionalities were added. Some of these are fairly simple but were never before implemented in continuation codes, e.g. Poincaré maps. Others were only available as toolboxes that can be used by experts, e.g. continuation of homoclinic orbits. Several others were never implemented at all, such as periodic normal forms for codimension 1 bifurcations of limit cycles, normal forms for codimension 2 bifurcations of equilibria, detection of codimension 2 bifurcations of limit cycles, automatic computation of phase response curves and their derivatives, continuation of branch points of equilibria and limit cycles. New numerical algorithms for these computations have been published or will appear elsewhere; here we restrict to their software implementation. We further discuss software issues that are in practice important for many users, e.g. how to define a new system starting from an existing one, how to import and export data, system descriptions, and computed results.

We discuss new and improved algorithms for the bifurcation analysis of fixed points and periodic orbits (cycles) of maps and their implementation in matcont, a MATLAB toolbox for continuation and bifurcation analysis of dynamical systems. This includes the numerical continuation of fixed points of iterates of the map with one control parameter, detecting and locating their bifurcation points (i.e., limit point, period-doubling, and Neimark–Sacker) and their continuation in two control parameters, as well as detection and location of all codimension 2 bifurcation points on the corresponding curves. For all bifurcations of codim 1 and 2, the critical normal form coefficients are computed, both numerically with finite directional differences and using symbolic derivatives of the original map. Using a parameter-dependent center manifold reduction, explicit asymptotics are derived for bifurcation curves of double and quadruple period cycles rooted at codim 2 points of cycles with arbitrary period. These asymptotics are implemented into the software and allow one to switch at codim 2 points to the continuation of the double and quadruple period bifurcations. We provide two examples illustrating the developed techniques: a generalized Hénon map and a juvenile/adult competition model from mathematical biology.

In this paper we derive explicit formulas for the normal form coefficients to verify the nondegeneracy of eight codimension two bifurcations of fixed points with one or two critical eigenvalues. These include all strong resonances, as well as the degenerate flip and Neimark--Sacker bifurcations. Applying our results to n-dimensional maps, one avoids the computation of the center manifold, but one can directly evaluate the critical normal form coefficients in the original basis. The formulas remain valid also for n=2 and allow one to avoid the transformation of the linear part of the map into Jordan form. The developed techniques are tested on two examples: (1) a three-dimensional map appearing in adaptive control; (2) a periodically forced epidemic model. We compute numerically the critical normal form coefficients for several codim 2 bifurcations occurring in these models. To compute the required derivatives of the Poincaré map for the epidemic model, the automatic differentiation package ADOL-C is used.

The fold-flip bifurcation occurs if a map has a fixed point with multipliers +1 and -1 simultaneously. In this paper the normal form of this singularity is calculated explicitly. Both local and global bifurcations of the unfolding are analyzed by exploring a close relationship between the derived normal form and the truncated amplitude system for the fold-Hopf bifurcation of ODEs. Two examples are presented, the generalized Hénon map and an extension of the Lorenz-84 model. In the latter example the first-, second- and third-order derivatives of the Poincaré map are computed using variational equations to find the normal form coefficients.

Measurements of neuronal signals during human seizure activity and evoked epileptic activity in experimental models suggest that, in these pathological states, the individual nerve cells experience an activity driven depolarization block, i.e. they saturate. We examined the effect of such a saturation in the Wilson–Cowan formalism by adapting the nonlinear activation function; we substituted the commonly applied sigmoid for a Gaussian function. We discuss experimental recordings during a seizure that support this substitution. Next we perform a bifurcation analysis on the Wilson–Cowan model with a Gaussian activation function. The main effect is an additional stable equilibrium with high excitatory and low inhibitory activity. Analysis of coupled local networks then shows that such high activity can stay localized or spread. Specifically, in a spatial continuum we show a wavefront with inhibition leading followed by excitatory activity. We relate our model simulations to observations of spreading activity during seizures.

We study two-parameter bifurcation diagrams of a generalized Hénon map (GHM) that is known to describe dynamics of iterated maps near homoclinic and heteroclinic tangencies. We prove the nondegeneracy of codimension (codim) 2 bifurcations of fixed points of the GHM analytically and compute its various global and local bifurcation curves numerically. Special attention is given to the interpretation of the results and their application to the analysis of bifurcations of the homoclinic tangency of a neutral saddle in two-parameter families of planar diffeomorphisms. In particular, an infinite cascade of homoclinic tangencies of neutral saddle cycles is shown to exist near the homoclinic tangency of the primary neutral saddle.