Time-dependent localized patterns in a predator-prey model.

Numerical continuation is used to compute solution branches in a two-component reaction-diffusion model of Leslie-Gower type. Two regimes are studied in detail. In the first, the homogeneous state loses stability to supercritical spatially uniform oscillations, followed by a subcritical steady state bifurcation of Turing type. The latter leads to spatially localized states embedded in an oscillating background that bifurcate from snaking branches of localized steady states. Using two-parameter continuation, we uncover a novel mechanism whereby disconnected segments of oscillatory states zip up into a continuous snaking branch of time-periodic localized states, some of which are stable. In the second, the homogeneous state loses stability to supercritical Turing patterns, but steady spatially localized states embedded either in the homogeneous state or in a small amplitude Turing state are nevertheless present. We show that such behavior is possible when sideband Turing states are strongly subcritical and explain why this is so in the present model. In both cases, the observed behavior differs significantly from that expected on the basis of a supercritical primary bifurcation.

Localized and extended patterns in the cubic-quintic Swift-Hohenberg equation on a disk.

Axisymmetric and nonaxisymmetric patterns in the cubic-quintic Swift-Hohenberg equation posed on a disk with Neumann boundary conditions are studied via numerical continuation and bifurcation analysis. Axisymmetric localized solutions in the form of spots and rings known from earlier studies persist and snake in the usual fashion until they begin to interact with the boundary. Depending on parameters, including the disk radius, these states may or may not connect to the branch of domain-filling target states. Secondary instabilities of localized axisymmetric states may create multiarm localized structures that grow and interact with the boundary before broadening into domain-filling states. High azimuthal wave number wall states referred to as daisy states are also found. Secondary bifurcations from these states include localized daisies, i.e., wall states localized in both radius and angle. Depending on parameters, these states may snake much as in the one-dimensional Swift-Hohenberg equation, or invade the interior of the domain, yielding states referred to as worms, or domain-filling stripes.

Origin of jumping oscillons in an excitable reaction-diffusion system.

Oscillons, i.e., immobile spatially localized but temporally oscillating structures, are the subject of intense study since their discovery in Faraday wave experiments. However, oscillons can also disappear and reappear at a shifted spatial location, becoming jumping oscillons (JOs). We explain here the origin of this behavior in a three-variable reaction-diffusion system via numerical continuation and bifurcation theory, and show that JOs are created via a modulational instability of excitable traveling pulses (TPs). We also reveal the presence of bound states of JOs and TPs and patches of such states (including jumping periodic patterns) and determine their stability. This rich multiplicity of spatiotemporal states lends itself to information and storage handling.

Stripes on finite domains: Why the zigzag instability is only a partial story.

Stationary periodic patterns are widespread in natural sciences, ranging from nano-scale electrochemical and amphiphilic systems to mesoscale fluid, chemical, and biological media and to macro-scale vegetation and cloud patterns. Their formation is usually due to a primary symmetry breaking of a uniform state to stripes, often followed by secondary instabilities to form zigzag and labyrinthine patterns. These secondary instabilities are well studied under idealized conditions of an infinite domain; however, on finite domains, the situation is more subtle since the unstable modes depend also on boundary conditions. Using two prototypical models, the Swift-Hohenberg equation and the forced complex Ginzburg-Landau equation, we consider finite size domains with no flux boundary conditions transversal to the stripes and reveal a distinct mixed-mode instability that lies in between the classical zigzag and the Eckhaus lines. This explains the stability of stripes in the mildly zigzag unstable regime and, after crossing the mixed-mode line, the evolution of zigzag stripes in the bulk of the domain and the formation of defects near the boundaries. The results are of particular importance for problems with large timescale separation, such as bulk-heterojunction deformations in organic photovoltaic and vegetation in semi-arid regions, where early temporal transients may play an important role.

The role of spatial self-organization in the design of agroforestry systems.

The development of sustainable agricultural systems in drylands is currently a crucial issue in the context of mitigating the outcomes of population growth under the conditions of climatic changes. The need to meet the growing demand for food, fodder, and fuel, together with the hazards due to climate change, requires cross-disciplinary studies of ways to increase livelihood while minimizing the impact on the environment. Practices of agroforestry systems, in which herbaceous species are intercropped between rows of woody species plantations, have been shown to mitigate several of the predicaments of climatic changes. Focusing on agroforestry in drylands, we address the question of how we can improve the performance of agroforestry systems in those areas. As vegetation in drylands tends to self-organize in various patterns, it seems essential to explore the various patterns that agroforestry systems tend to form and their impact on the performance of these systems in terms of biomass production, resilience to droughts, and water use efficiency. We use a two-soil-layers vegetation model to study the relationship between deep-rooted woody vegetation and shallow herbaceous vegetation, and explore how self-organization in different spatial patterns influences the performance of agroforestry systems. We focus on three generic classes of patterns, spots, gaps, and stripes, assess these patterns using common metrics for agroforestry systems, and examine their resilience to droughts. We show that in contrast to the widespread practice of planting the woody and herbaceous species in alternating rows, that is, in a stripe pattern, planting the woody species in hexagonal spot patterns may increase the system's resilience to droughts. Furthermore, hexagonal spot patterns reduce the suppression of herbs growth by the woody vegetation, therefore maintaining higher crop yields. We conclude by discussing some limitations of this study and their significance.

Bending and pinching of three-phase stripes: From secondary instabilities to morphological deformations in organic photovoltaics.

Optimizing the properties of the mosaic nanoscale morphology of bulk heterojunction (BHJ) organic photovoltaics (OPV) is not only challenging technologically but also intriguing from the mechanistic point of view. Among the recent breakthroughs is the identification and utilization of a three-phase (donor-mixed-acceptor) BHJ, where the (intermediate) mixed phase can inhibit mesoscale morphological changes, such as phase separation. Using a mean-field approach, we reveal and distinguish between generic mechanisms that alter, through transverse instabilities, the evolution of stripes: the bending (zigzag mode) and the pinching (cross-roll mode) of the donor-acceptor domains. The results are summarized in a parameter plane spanned by the mixing energy and illumination, and show that donor-acceptor mixtures with higher mixing energy are more likely to develop pinching under charge-flux boundary conditions. The latter is notorious as it leads to the formation of disconnected domains and hence to loss of charge flux. We believe that these results provide a qualitative road map for BHJ optimization, using mixed-phase composition and, therefore, an essential step toward long-lasting OPV. More broadly, the results are also of relevance to study the coexistence of multiple-phase domains in material science, such as in ion-intercalated rechargeable batteries.

Defectlike structures and localized patterns in the cubic-quintic-septic Swift-Hohenberg equation.

We study numerically the cubic-quintic-septic Swift-Hohenberg (SH357) equation on bounded one-dimensional domains. Under appropriate conditions stripes with wave number k≈1 bifurcate supercritically from the zero state and form S-shaped branches resulting in bistability between small and large amplitude stripes. Within this bistability range we find stationary heteroclinic connections or fronts between small and large amplitude stripes, and demonstrate that the associated spatially localized defectlike structures either snake or fall on isolas. In other parameter regimes we also find heteroclinic connections to spatially homogeneous states and a multitude of dynamically stable steady states consisting of patches of small and large amplitude stripes with different wave numbers or of spatially homogeneous patches. The SH357 equation is thus extremely rich in the types of patterns it exhibits. Some of the features of the bifurcation diagrams obtained by numerical continuation can be understood using a conserved quantity, the spatial Hamiltonian of the system.

From bulk self-assembly to electrical diffuse layer in a continuum approach for ionic liquids: The impact of anion and cation size asymmetry.

Ionic liquids are solvent-free electrolytes, some of which possess an intriguing self-assembly at finite length scale due to Coulombic interactions. Using a continuum framework (based on Onsager's relations), it is shown that bulk nanostructures arise via linear (supercritical) and nonlinear (subcritical) bifurcations (morphological phase transitions), which also directly affect the electrical double layer structure. A Ginzburg-Landau amplitude equation is derived and the bifurcation type is related to model parameters, such as temperature, potential, and interactions. Specifically, the nonlinear bifurcation occurs for geometrically dissimilar ions and, surprisingly, is induced by perturbations on the order of thermal fluctuations. Finally, qualitative insights and comparisons to the experimentally decaying charge layers within the electrical double layer are discussed.

Desertification by front propagation?

Understanding how desertification takes place in different ecosystems is an important step in attempting to forecast and prevent such transitions. Dryland ecosystems often exhibit patchy vegetation, which has been shown to be an important factor on the possible regime shifts that occur in arid regions in several model studies. In particular, both gradual shifts that occur by front propagation, and abrupt shifts where patches of vegetation vanish at once, are a possibility in dryland ecosystems due to their emergent spatial heterogeneity. However, recent theoretical work has suggested that the final step of desertification - the transition from spotted vegetation to bare soil - occurs only as an abrupt shift, but the generality of this result, and its underlying origin, remain unclear. We investigate two models that detail the dynamics of dryland vegetation using a markedly different functional structure, and find that in both models the final step of desertification can only be abrupt. Using a careful numerical analysis, we show that this behavior is associated with the disappearance of confined spot-pattern domains as stationary states, and identify the mathematical origin of this behavior. Our findings show that a gradual desertification to bare soil due to a front propagation process can not occur in these and similar models, and opens the question of whether these dynamics can take place in nature.

Soliton transport in tubular networks: transmission at vertices in the shrinking limit.

Soliton transport in tubelike networks is studied by solving the nonlinear Schrödinger equation (NLSE) on finite thickness ("fat") graphs. The dependence of the solution and of the reflection at vertices on the graph thickness and on the angle between its bonds is studied and related to a special case considered in our previous work, in the limit when the thickness of the graph goes to zero. It is found that both the wave function and reflection coefficient reproduce the regime of reflectionless vertex transmission studied in our previous work.

Individual-based model for quorum sensing with background flow.

Quorum sensing is a wide-spread mode of cell-cell communication among bacteria in which cells release a signalling substance at a low rate. The concentration of this substance allows the bacteria to gain information about population size or spatial confinement. We consider a model for N cells which communicate with each other via a signalling substance in a diffusive medium with a background flow. The model consists of an initial boundary value problem for a parabolic PDE describing the exterior concentration u of the signalling substance, coupled with N ODEs for the masses ai of the substance within each cell. The cells are balls of radius R in R3, and under some scaling assumptions we formally derive an effective system of N ODEs describing the behaviour of the cells. The reduced system is then used to study the effect of flow on communication in general, and in particular for a number of geometric configurations.

Approximating the dynamics of communicating cells in a diffusive medium by ODEs-homogenization with localization.

Bacteria may change their behavior depending on the population density. Here we study a dynamical model in which cells of radius [R] within a diffusive medium communicate with each other via diffusion of a signalling substance produced by the cells. The model consists of an initial boundary value problem for a parabolic PDE describing the exterior concentration [u] of the signalling substance, coupled with [N] ODEs for the masses [ai] of the substance within each cell. We show that for small [R] the model can be approximated by a hierarchy of models, namely first a system of [N] coupled delay ODEs, and in a second step by [N] coupled ODEs. We give some illustrations of the dynamics of the approximate model.

Pattern formation for NO+NH3 on Pt(100): two-dimensional numerical results.

The Lombardo-Fink-Imbihl model of the NO+NH3 reaction on a Pt(100) surface consists of seven coupled ordinary differential equations (ODE) and shows stable relaxation oscillations with sharp transitions in the relevant temperature range. Here we study numerically the effect of coupling of these oscillators by surface diffusion in two dimensions. We find different types of patterns, in particular phase clusters and standing waves. In models of related surface reactions such clustered solutions are known to exist only under a global coupling through the gas phase. This global coupling is replaced here by relatively fast diffusion of two variables which are kinetically slaved in the ODE. We also compare our simulations with experimental results and discuss some shortcomings of the model.