Spatial instabilities in reaction random walks with direction-independent kinetics

We study spatial instabilities in reacting and diffusing systems, where diffusion is modeled by a persistent random walk instead of the usual Brownian motion. Perturbations in these reaction walk systems propagate with finite speed, whereas in reaction-diffusion systems localized disturbances affect every part instantly, albeit with heavy damping. We present evolution equations for reaction random walks whose kinetics do not depend on the particles' direction of motion. The homogeneous steady state of such systems can undergo two types of transport-driven instabilities. One type of bifurcation gives rise to stationary spatial patterns and corresponds to the Turing instability in reaction-diffusion systems. The other type occurs in the ballistic regime and leads to oscillatory spatial patterns; it has no analog in reaction-diffusion systems. The conditions for these bifurcations are derived and applied to two model systems. We also analyze the stability properties of one-variable systems and find that small wavelength perturbations decay in an oscillatory manner.     

Stochastic Simulation of Turing Patterns

We investigate the effects of intrinsic noise on Turing pattern formation near the onset of bifurcation from the homogeneous state to Turing pattern in the reaction-diffusion Brusselator. By performing stochastic simulations of the master equation and using Gillespie＇s algorithm, we check the spatiotemporal behaviour influenced by internal noises. We demonstrate that the patterns of occurrence frequency for the reaction and diffusion pro- cesses are also spatially ordered and temporally stable. Turing patterns are found to be robust against intrinsic fluctuations. Sfochastic simulations also reveal that under the influence of intrinsic noises, the onset of Turing instability is advanced in comparison to that predicted deterministically.     

Pattern formation in an N+Q component reaction-diffusion system

A general N+Q component reaction-diffusion system is analyzed with regard to pattern forming instabilities (Turing bifurcations). The system consists of N mobile species and Q immobile species. The Q immobile species form in response to reactions between the N mobile species and an immobile substrate and allow the Turing instability to occur. These results are valid both for bifurcations from a spatially uniform state and for systems with an externally imposed gradient as in the experimental systems in which Turing patterns have been observed. It is shown that the critical wave number and the location of the instability in parameter space are independent of the substrate concentration. It is also found that the system necessarily undergoes a Hopf bifurcation as the total substrate concentration is decreased. Further, in the case that all the mobile species diffuse at identical rates we show that if the full system is at a point of Turing bifurcation then the N component mobile subsystem is at transition from an unstable focus to an unstable node, and the critical wave number is simply related to the degenerate positive eigenvalue of the mobile subsystem. A sequence of bifurcations that occur in the eigenspectra as the total substrate concentration is decreased to zero is also discussed.     

双层耦合非对称反应扩散系统中的超点阵斑图

通过线性耦合Brusselator模型和Lengyel-Epstein模型,数值研究了双层耦合非对称反应扩散系统中图灵模之间的相互作用以及斑图的形成机理.模拟结果表明,合适的波数比以及相同的对称性是两个图灵模之间达到空间共振的必要条件,而耦合强度则直接影响了图灵斑图的振幅大小.为了保证对称性相同,两个图灵模的本征值高度要位于一定的范围内.只有失稳模为长波模时,才能对另一个图灵模产生调制作用,并形成多尺度时空斑图.随着波数比的增加,短波模子系统依次经历黑眼斑图、白眼斑图以及时序振荡六边形斑图的转变.研究表明失稳图灵模与处于短波不稳定区域的高阶谐波模之间的共振是产生时序振荡六边形的主要原因.     

Selkov模型不同扩散和流速下非Turing不稳定化学反应机制

建立了Selkov模型中间反应物具有不同扩散和不同流速条件下的反应 扩散 流动方程 ,理论分析了非Turing不稳定形成的条件 ,求得其参数区间 ,对Andresen的结论作了拓展 .研究还发现 ,在振荡Hopf区域之外 ,静止波动 (空间周期结构FDS)仍然可以存在 .因而 ,此结构存在的参数空间大于Andresen的结果 .同时 ,还将此种不稳定参数区间与Turing不稳定和差速流动引起不稳定 (DIFI)的结果进行了比较 ,结果发现静态FDS值总是处于DIFI临界曲线相应的最小值之上 ,这表明动力学机制是由DIFI不稳定造成的 ,DIFI不稳定区是产生静止波FDS不稳定结构的必要条件     

Numerical simulation and analysis of complex patterns in a two-layer coupled reaction diffusion system

The resonance interaction between two modes is investigated using a two-layer coupled Brusselator model. When two different wavelength modes satisfy resonance conditions, new modes will appear, and a variety of superlattice patterns can be obtained in a short wavelength mode subsystem. We find that even though the wavenumbers of two Turing modes are fixed, the parameter changes have influences on wave intensity and pattern selection. When a hexagon pattern occurs in the short wavelength mode layer and a stripe pattern appears in the long wavelength mode layer, the Hopf instability may happen in a nonlinearly coupled model, and twinkling-eye hexagon and travelling hexagon patterns will be obtained. The symmetries of patterns resulting from the coupled modes may be different from those of their parents, such as the cluster hexagon pattern and square pattern. With the increase of perturbation and coupling intensity, the nonlinear system will convert between a static pattern and a dynamic pattern when the Turing instability and Hopf instability happen in the nonlinear system. Besides the wavenumber ratio and intensity ratio of the two different wavelength Turing modes, perturbation and coupling intensity play an important role in the pattern formation and selection. According to the simulation results, we find that two modes with different symmetries can also be in the spatial resonance under certain conditions, and complex patterns appear in the two-layer coupled reaction diffusion systems.     

An efficient and robust numerical algorithm for estimating parameters in Turing systems

We present a new algorithm for estimating parameters in reaction–diffusion systems that display pattern formation via the mechanism of diffusion-driven instability. A Modified Discrete Optimal Control Algorithm (MDOCA) is illustrated with the Schnakenberg and Gierer–Meinhardt reaction–diffusion systems using PDE constrained optimization techniques. The MDOCA algorithm is a modification of a standard variable step gradient algorithm that yields a huge saving in computational cost. The results of numerical experiments demonstrate that the algorithm accurately estimated key parameters associated with stationary target functions generated from the models themselves. Furthermore, the robustness of the algorithm was verified by performing experiments with target functions perturbed with various levels of additive noise. The MDOCA algorithm could have important applications in the mathematical modeling of realistic Turing systems when experimental data are available.     

局域浓度调控扩散系数的次氯酸-碘离子-丙二酸系统图灵斑图形成中的反常扩散

通过数值模拟及振幅方程解析解方法,从实空间和倒空间分析了受局域浓度扩散系数调控下次氯酸-碘离子-丙二酸反应扩散系统图灵斑图形成的扩散机理.在零扩散系数调节下,斑图形成为典型的菲克扩散;而在负向正向扩散系数调节下,斑图的形成依赖欠扩散和超扩散.图灵系统的浓度稳态振幅对随机初始条件敏感性随局域浓度扩散调控系数k的增大而增加.     

Turing instability in reaction-diffusion systems with nonlinear diffusion

The Turing instability is studied in two-component reaction-diffusion systems with nonlinear diffusion terms, and the regions in parametric space where Turing patterns can form are determined. The boundaries between super- and subcritical bifurcations are found. Calculations are performed for one-dimensional brusselator and oregonator models.     

Pattern formation in forced reaction diffusion systems with nearly degenerate bifurcations

The existence and stability of stable standing-wave patterns in an assembly of spatially distributed generic oscillators governed by a couple of complex Ginzburg-Landau equations, subjected to parametric forcing, are reported. The mechanism of a dispersion-induced pattern in dissipative oscillators parametrically forced near the degenerate Turing-Hopf bifurcation is also illustrated. We show that, when excitation occurs just after the Turing bifurcation and before the Hopf instability, the system exhibits a new type of stable standing-wave structures, namely the mixed-mode solutions. The Brussellator-model, parametrically forced below the threshold of oscillations, is analyzed as an example of calculation.     

Non-linear systems

We review the general properties of non-linear systems and show the basic techniques, used universally, to study the symmetry breaking and bifurcation properties. We exemplify these characteristics by using a Turing system that is general enough as to present many of the universal features of non-linear systems. We then show some interesting applications to various problems that we have treated in the past.     

反应扩散模型在图灵斑图中的应用及数值模拟

反应扩散方程模型常被用于描述生物学中斑图的形成.从反应扩散模型出发,理论推导得到GiererMeinhardt模型的斑图形成机理,解释了非线性常微分方程系统的稳定常数平衡态在加入扩散项后会发生失稳并产生图灵斑图的过程.通过计算该模型,得到图灵斑图产生的参数条件.数值方法中采用一类有效的高精度数值格式,即在空间离散条件下采用Chebyshev谱配置方法,在时间离散条件下采用紧致隐积分因子方法.该方法结合了谱方法和紧致隐积分因子方法的优点,具有精度高、稳定性好、存储量小等优点.数值模拟表明,在其他条件一定的情况下,系统控制参数κ取不同值对于斑图的产生具有重要的影响,数值结果验证了理论结果.     

Pattern dynamics of network-organized system with cross-diffusion

Cross-diffusion is a ubiquitous phenomenon in complex networks, but it is often neglected in the study of reaction–diffusion networks. In fact, network connections are often random. In this paper, we investigate pattern dynamics of random networks with cross-diffusion by using the method of network analysis and obtain a condition under which the network loses stability and Turing bifurcation occurs. In addition, we also derive the amplitude equation for the network and prove the stability of the amplitude equation which is also an effective tool to investigate pattern dynamics of the random network with cross diffusion. In the meantime, the pattern formation consistently matches the stability of the system and the amplitude equation is verified by simulations. A novel approach to the investigation of specific real systems was presented in this paper. Finally, the example and simulation used in this paper validate our theoretical results.     

Segmented waves from a spatiotemporal transverse wave instability

We observe traveling waves emitted from Turing spots in the chlorine dioxide-iodine-malonic acid reaction. The newborn waves are continuous, but they break into segments as they propagate, and the propagation of these segments ultimately gives rise to spatiotemporal chaos. We model the wave-breaking process and the motion of the chaotic segments. We find stable segmented spirals as well. We attribute the segmentation to an interaction between front rippling via a transverse instability and front symmetry breaking by a fast-diffusing inhibitor far from the codimension-2 Hopf-Turing bifurcation, and the chaos to a secondary instability of the periodic segmentation.     

Turing patterns beyond hexagons and stripes

The best known Turing patterns are composed of stripes or simple hexagonal arrangements of spots. Until recently, Turing patterns with other geometries have been observed only rarely. Here we present experimental studies and mathematical modeling of the formation and stability of hexagonal and square Turing superlattice patterns in a photosensitive reaction-diffusion system. The superlattices develop from initial conditions created by illuminating the system through a mask consisting of a simple hexagonal or square lattice with a wavelength close to a multiple of the intrinsic Turing pattern's wavelength. We show that interaction of the photochemical periodic forcing with the Turing instability generates multiple spatial harmonics of the forcing patterns. The harmonics situated within the Turing instability band survive after the illumination is switched off and form superlattices. The square superlattices are the first examples of time-independent square Turing patterns. We also demonstrate that in a system where the Turing band is slightly below criticality, spatially uniform internal or external oscillations can create oscillating square patterns.     

Pattern formation in a predator–prey model with spatial effect

In this paper, spatial dynamics in the Beddington–DeAngelis predator–prey model with self-diffusion and cross-diffusion is investigated. We analyze the linear stability and obtain the condition of Turing instability of this model. Moreover, we deduce the amplitude equations and determine the stability of different patterns. Numerical simulations show that this system exhibits complex dynamical behaviors. In the Turing space, we find three types of typical patterns. One is the coexistence of hexagon patterns and stripe patterns. The other two are hexagon patterns of different types. The obtained results well enrich the finding in predator–prey models with Beddington–DeAngelis functional response.     

Spontaneous symmetry breaking turing-type pattern formation in a confined Dictyostelium cell mass

We have discovered a new type of patterning which occurs in a two-dimensionally confined cell mass of the cellular slime mold Dictyostelium discoideum. Besides the longitudinal structure reported earlier, we observed a spontaneous symmetry breaking spot pattern whose wavelength shows similar strain dependency to that of the longitudinal pattern. We propose that these structures are due to a reaction-diffusion Turing instability similar to the one which has been exemplified by CIMA (chlorite-iodide-malonic acid) reaction. The present finding may exhibit the first biochemical Turing structure in a developmental system with a controllable boundary condition.     

Additive global noise delays Turing bifurcations

We apply a stochastic center manifold method to the calculation of noise-induced phase transitions in the stochastic Swift-Hohenberg equation. This analysis is applied to the reduced mode equations that result from Fourier decomposition of the field variable and of the temporal noise. The method shows a pitchfork bifurcation at lower perturbation order, but reveals a novel additive-noise-induced postponement of the Turing bifurcation at higher order. Good agreement is found between the theory and the numerics for both the reduced and the full system. The results are generalizable to a broad class of nonlinear spatial systems.     

Turing pattern selection in a reactionben diffusion epidemic modelast

We present Turing pattern selection in a reaction—diffusion epidemic model under zero-flux boundary conditions. The value of this study is twofold. First, it establishes the amplitude equations for the excited modes, which determines the stability of amplitudes towards uniform and inhomogeneous perturbations. Second, it illustrates all five categories of Turing patterns close to the onset of Turing bifurcation via numerical simulations which indicates that the model dynamics exhibits complex pattern replication: on increasing the control parameter v, the sequence “H₀ hexagons → H₀-hexagon-stripe mixtures → stripes → H_π-hexagon-stripe mixtures → H_π hexagons” is observed. This may enrich the pattern dynamics in a diffusive epidemic model.     

Spontaneous motion of cavity solitons in vertical-cavity lasers subject to optical injection and to delayed feedback

We consider a rate equation model describing broad area vertical-cavity surface-emitting lasers subject to injection and to time-delayed optical feedback. We show that the inclusion of an external cavity affects dramatically the space-time behavior of this system by modifying the instability threshold as well as the wavelength of the Turing instability. We show also that the delayed feedback is responsible for the appearance of traveling wave instability. Finally, we demonstrate that a single cavity soliton exhibits a spontaneous motion with a constant velocity. Without delayed feedback transition to the moving cavity soliton does not exist.