General theory of instabilities for patterns with sharp interfaces in reaction-diffusion systems

Spherical Caps in Cell Polarization

Intracellular symmetry breaking plays a key role in wide range of biological processes, both in single cells and in multicellular organisms. An important class of symmetry-breaking mechanisms relies on the cytoplasm/membrane redistribution of proteins that can autocatalytically promote their own recruitment to the plasma membrane. We present an analytical construction and a comprehensive parametric analysis of stable localized patterns in a reaction-diffusion model of such a mechanism in a spherical cell. The constructed patterns take the form of high-concentration patches localized into spherical caps, similar to the patterns observed in the studies of symmetry breaking in single cells and early embryos.

Observation of Mode-Locked Spatial Laser Solitons

A stable nonlinear wave packet, self-localized in all three dimensions, is an intriguing and much sought after object in nonlinear science in general and in nonlinear photonics in particular. We report on the experimental observation of mode-locked spatial laser solitons in a vertical-cavity surface-emitting laser with frequency-selective feedback from an external cavity. These spontaneously emerging and long-term stable spatiotemporal structures have a pulse length shorter than the cavity round-trip time and may pave the way to completely independent cavity light bullets.

Self-Replication of Localized Vegetation Patches in Scarce Environments

Desertification due to climate change and increasing drought periods is a worldwide problem for both ecology and economy. Our ability to understand how vegetation manages to survive and propagate through arid and semiarid ecosystems may be useful in the development of future strategies to prevent desertification, preserve flora-and fauna within-or even make use of scarce resources soils. In this paper, we study a robust phenomena observed in semi-arid ecosystems, by which localized vegetation patches split in a process called self-replication. Localized patches of vegetation are visible in nature at various spatial scales. Even though they have been described in literature, their growth mechanisms remain largely unexplored. Here, we develop an innovative statistical analysis based on real field observations to show that patches may exhibit deformation and splitting. This growth mechanism is opposite to the desertification since it allows to repopulate territories devoid of vegetation. We investigate these aspects by characterizing quantitatively, with a simple mathematical model, a new class of instabilities that lead to the self-replication phenomenon observed.

Predicted formation of localized superlattices in spatially distributed reaction-diffusion solutions

We study numerically the formation of localized superlattices in spatially distributed systems. We predict that in wide regions of the parameter space, stable localized, either bright or dark, superlattices may form in reaction-diffusion systems. Localized superlattices are patterns which consist of a piece of superlattice. Each single ring is surrounded by spots. The number of rings and their spatial distribution are determined by the initial conditions. The peak concentration remains unaltered for fixed values of the parameters.

Chemical morphogenesis: recent experimental advances in reaction-diffusion system design and control

In his seminal 1952 paper, Alan Turing predicted that diffusion could spontaneously drive an initially uniform solution of reacting chemicals to develop stable spatially periodic concentration patterns. It took nearly 40 years before the first two unquestionable experimental demonstrations of such reaction-diffusion patterns could be made in isothermal single phase reaction systems. The number of these examples stagnated for nearly 20 years. We recently proposed a design method that made their number increase to six in less than 3 years. In this report, we formally justify our original semi-empirical method and support the approach with numerical simulations based on a simple but realistic kinetic model. To retain a number of basic properties of real spatial reactors but keep calculations to a minimal complexity, we introduce a new way to collapse the confined spatial direction of these reactors. Contrary to similar reduced descriptions, we take into account the effect of the geometric size in the confinement direction and the influence of the differences in the diffusion coefficient on exchange rates of species with their feed environment. We experimentally support the method by the observation of stationary patterns in red-ox reactions not based on oxihalogen chemistry. Emphasis is also brought on how one of these new systems can process different initial conditions and memorize them in the form of localized patterns of different geometries.

Oscillons localized inside breathing periodical structures in a two-variable model of a one-dimensional infinite excitable reaction-diffusion system

A two-variable model of a one-dimensional (1D), infinite, excitable, reaction-diffusion system describing oscillons localized inside an expanding breathing periodical structure emitting traveling impulses is presented. The model is based on two coupled catalytic (enzymatic) reactions.

Instabilities of a three-dimensional localized spot

We investigate the behavior of localized spots in three spatial dimensions in a model two-variable system describing the Belousov-Zhabotinsky reaction in water-in-oil microemulsion. We find three types of instabilities: splitting of a single spot (i) into two spots, (ii) into a torus, and (iii) into an unstable shell that splits almost immediately to six or eight new spots.

Excitable population dynamics, biological control failure, and spatiotemporal pattern formation in a model ecosystem

Biological control has been attracting an increasing attention over the last two decades as an environmentally friendly alternative to the more traditional chemical-based control. In this paper, we address robustness of the biological control strategy with respect to fluctuations in the controlling species density. Specifically, we consider a pest being kept under control by its predator. The predator response is assumed to be of Holling type III, which makes the system's kinetics "excitable." The system is studied by means of mathematical modeling and extensive numerical simulations. We show that the system response to perturbations in the predator density can be completely different in spatial and non-spatial systems. In the nonspatial system, an overcritical perturbation of the population density results in a pest outbreak that will eventually decay with time, which can be regarded as a success of the biological control strategy. However, in the spatial system, a similar perturbation can drive the system into a self-sustained regime of spatiotemporal pattern formation with a high pest density, which is clearly a biological control failure. We then identify the parameter range where the biological control can still be successful and describe the corresponding regime of the system dynamics. Finally, we identify the main scenarios of the system response to the population density perturbations and reveal the corresponding structure of the parameter space of the system.

Localized patterns in reaction-diffusion systems

We discuss a variety of experimental and theoretical studies of localized stationary spots, oscillons, and localized oscillatory clusters, moving and breathing spots, and localized waves in reaction-diffusion systems. We also suggest some promising directions for future research in this area.

Stability of asymmetric spike solutions to the Gierer-Meinhardt system

In this paper, we study the spectra of asymmetric spike solutions to the Gierer-Meinhardt system. It has previously been shown that the spectra of such solutions may be determined by finding the generalized eigenvalues of matrices, which are determined by the positions of the spikes and various parameters from the system. We will examine the spectra of asymmetric solutions near the point at which they bifurcate off of a symmetric branch. We will confirm that all such solutions are unstable in a neighborhood of the bifurcation point and we derive an explicit expression for the leading order terms of the critical eigenvalues.

Spot deformation and replication in the two-dimensional Belousov-Zhabotinski reaction in a water-in-oil microemulsion

In the limit of a large duffusivity ratio, spotlike solutions in the two-dimensional Belousov-Zhabotinski reaction in water-in-oil microemulsion are studied. It is shown analytically that such spots undergo an instability as the diffusivity ratio is decreased. An instability threshold is derived. For spots of small radius, it is shown that this instability leads to a spot splitting into precisely two spots. For larger spots, it leads to deformation, fingering patterns, and space-filling curves. Numerical simulations are shown to be in close agreement with the analytical predictions.

Hydrodynamics of bacterial colonies: a model

We propose a hydrodynamic model for the evolution of bacterial colonies growing on soft agar plates. This model consists of reaction-diffusion equations for the concentrations of nutrients, water, and bacteria, coupled to a single hydrodynamic equation for the velocity field of the bacteria-water mixture. It captures the dynamics inside the colony as well as on its boundary and allows us to identify a mechanism for collective motion towards fresh nutrients, which, in its modeling aspects, is similar to classical chemotaxis. As shown in numerical simulations, our model reproduces both usual colony shapes and typical hydrodynamic motions, such as the whirls and jets recently observed in wet colonies of Bacillus subtilis. The approach presented here could be extended to different experimental situations and provides a general framework for the use of advection-reaction-diffusion equations in modeling bacterial colonies.

Theory of domain patterns in systems with long-range interactions of Coulomb type

We develop a theory of the domain patterns in systems with competing short-range attractive interactions and long-range repulsive Coulomb interactions. We take an energetic approach, in which patterns are considered as critical points of a mean-field free energy functional. Close to the microphase separation transition, this functional takes on a universal form, allowing us to treat a number of diverse physical situations within a unified framework. We use asymptotic analysis to study domain patterns with sharp interfaces. We derive an interfacial representation of the pattern's free energy which remains valid in the fluctuating system, with a suitable renormalization of the Coulomb interaction's coupling constant. We also derive integro-differential equations describing stationary domain patterns of arbitrary shapes and their thermodynamic stability, coming from the first and second variations of the interfacial free energy. We show that the length scale of a stable domain pattern must obey a certain scaling law with the strength of the Coulomb interaction. We analyzed the existence and stability of localized (spots, stripes, annuli) and periodic (lamellar, hexagonal) patterns in two dimensions. We show that these patterns are metastable in certain ranges of the parameters and that they can undergo morphological instabilities leading to the formation of more complex patterns. We discuss nucleation of the domain patterns by thermal fluctuations and pattern formation scenarios for various thermal quenches. We argue that self-induced disorder is an intrinsic property of the domain patterns in the systems under consideration.

Modeling and computational analysis of EGF receptor-mediated cell communication in Drosophila oogenesis

Autocrine signaling through the Epidermal Growth Factor Receptor (EGFR) operates at various stages of development across species. A recent hypothesis suggested that a distributed network of EGFR autocrine loops was capable of spatially modulating a simple single-peaked input into a more complex two-peaked signaling pattern, specifying the formation of a pair organ in Drosophila oogenesis (two respiratory appendages on the eggshell). To test this hypothesis, we have integrated genetic and biochemical information about the EGFR network into a mechanistic model of transport and signaling. The model allows us to estimate the relative spatial ranges and time scales of the relevant feedback loops, to interpret the phenotypic transitions in eggshell morphology and to predict the effects of new genetic manipulations. We have found that the proposed mechanism with a single diffusing inhibitor is sufficient to convert a single-peaked extracellular input into a two-peaked pattern of intracellular signaling. Based on extensive computational analysis, we predict that the same mechanism is capable of generating more complex patterns. At least indirectly, this can be used to account for more complex eggshell morphologies observed in related fly species. We propose that versatility in signaling mediated by autocrine loops can be systematically explored using experiment-based mechanistic models and their analysis.

Growth pulsations in symmetric dendritic crystallization in thin polymer blend films

The crystallization of polymeric and metallic materials normally occurs under conditions far from equilibrium, leading to patterns that grow as propagating waves into the surrounding unstable fluid medium. The Mullins-Sekerka instability causes these wave fronts to break up into dendritic arms, and we anticipate that the normal modes of the dendrite tips have a significant influence on pattern growth. To check this possibility, we focus on the dendritic growth of polyethylene oxide in a thin-film geometry. This crystalline polymer is mixed with an amorphous polymer (polymethyl-methacrylate) to "tune" the morphology and clay was added to nucleate the crystallization. The tips of the main dendrite trunks pulsate during growth and the sidebranches, which grow orthogonally to the trunk, pulsate out of phase so that the tip dynamics is governed by a limit cycle. The pulsation period P increases sharply with decreasing film thickness L and then vanishes below a critical value L(c) approximately 80 nm. A change of dendrite morphology accompanies this transition.

Two-dimensional model of a reaction-diffusion system as a typewriter

Pattern formation is a common phenomenon, which appears in biological systems, especially in cell differentiation processes. The proper level for understanding the creation of patterns seems to be a physicochemical description. The most fundamental models should be based on systems, in which only chemical reactions and diffusion transport occur (reaction-diffusion systems). In order to present a richness of patterns, we show here the asymptotic patterns in the form of capital letters obtained in two-dimensional reaction-diffusion systems with zero-flux boundary conditions. All capital letters are obtained in the same model, but initial conditions and sizes of the systems are different for each letter. The chemical model consists of elementary reactions and is realistic. It can be realized experimentally in continuous-flow unstirred reactor with an enzymatic reaction allosterically inhibited by an excess of its reactant and product.

Coexistence of large amplitude stationary structures in a model of reaction-diffusion system

The two-variable reaction-diffusion model of a chemical system describing the spatiotemporal evolution to large amplitude stationary periodical structures in a one-dimensional open, continuous-flow, unstirred reactor is investigated. Numerical solutions show that the structures are generated by divisions of the traveling impulse and its stopping at the boundary of the system. Analyses of projections of numerical solutions on the phase plane of two variables elaborated in the present paper allow qualitative explanation of the results. The coexistence of the large amplitude stationary periodical structures is shown. A number of coexisting structures grows strongly with increasing length of the reactor and may be as large as one wishes. The relationship of these results to biological systems is stressed.

Nonlocal boundary dynamics of traveling spots in a reaction-diffusion system

The boundary integral method is extended to derive a closed integro-differential equation applicable to computation of the shape and propagation speed of a steadily moving spot and to the analysis of dynamic instabilities in the sharp boundary limit. Expansion of the boundary integral near the locus of traveling instability in a standard reaction-diffusion model proves that the bifurcation is supercritical whenever the spot is stable to splitting. Thus, stable propagating spots do already exist in the basic activator-inhibitor model, without additional long-range variables.

Phase dynamics of nearly stationary patterns in activator-inhibitor systems

The slow dynamics of nearly stationary patterns in a FitzHugh-Nagumo model are studied using a phase dynamics approach. A Cross-Newell phase equation describing slow and weak modulations of periodic stationary solutions is derived. The derivation applies to the bistable, excitable, and Turing unstable regimes. In the bistable case stability thresholds are obtained for the Eckhaus and zigzag instabilities and for the transition to traveling waves. Neutral stability curves demonstrate the destabilization of stationary planar patterns at low wave numbers to zigzag and traveling modes. Numerical solutions of the model system support the theoretical findings.