Dynamics Of Reaction-diffusion System Research Articles

Phase-Space Geometry of Mass-Conserving Reaction-Diffusion Dynamics

Experimental studies of protein-pattern formation have stimulated new interest in the dynamics of reaction-diffusion systems. However, a comprehensive theoretical understanding of the dynamics of such highly nonlinear, spatially extended systems is still missing. Here we show how a description in phase space, which has proven invaluable in shaping our intuition about the dynamics of nonlinear ordinary differential equations, can be generalized to mass-conserving reaction-diffusion (McRD) systems. We present a comprehensive analysis of two-component McRD systems, which serve as paradigmatic minimal systems that encapsulate the core principles and concepts of the local equilibria theory introduced in the paper. The key insight underlying this theory is that shifting local (reactive) equilibria -- controlled by the local total density -- give rise to concentration gradients that drive diffusive redistribution of total density. We show how this dynamic interplay can be embedded in the phase plane of the reaction kinetics in terms of simple geometric objects: the reactive nullcline and the diffusive flux-balance subspace. On this phase-space level, physical insight can be gained from geometric criteria and graphical constructions. The effects of nonlinearities on the global dynamics are simply encoded in the curved shape of the reactive nullcline. In particular, we show that the pattern-forming `Turing instability' in McRD systems is a mass-redistribution instability, and that the features and bifurcations of patterns can be characterized based on regional dispersion relations, associated to distinct spatial regions (plateaus and interfaces) of the patterns. In an extensive outlook section, we detail concrete approaches to generalize local equilibria theory in several directions, including systems with more than two-components, weakly-broken mass conservation, and active matter systems.

Computational analysis of the roles of biochemical reactions in anomalous diffusion dynamics**Project supported by the Thailand Research Fund and Mahidol University (Grant No. TRG5880157), the Thailand Center of Excellence in Physics (ThEP), CHE, Thailand, and the Development Promotion of Science and Technology.

Most biochemical processes in cells are usually modeled by reaction–diffusion (RD) equations. In these RD models, the diffusive process is assumed to be Gaussian. However, a growing number of studies have noted that intracellular diffusion is anomalous at some or all times, which may result from a crowded environment and chemical kinetics. This work aims to computationally study the effects of chemical reactions on the diffusive dynamics of RD systems by using both stochastic and deterministic algorithms. Numerical method to estimate the mean-square displacement (MSD) from a deterministic algorithm is also investigated. Our computational results show that anomalous diffusion can be solely due to chemical reactions. The chemical reactions alone can cause anomalous sub-diffusion in the RD system at some or all times. The time-dependent anomalous diffusion exponent is found to depend on many parameters, including chemical reaction rates, reaction orders, and chemical concentrations.

Perturbations and dynamics of reaction-diffusion systems with mass conservation.

In some reaction-diffusion systems where the total mass of their components is conserved, solutions with initial values near a homogeneous equilibrium converge to a simple localized pattern (spike) after exhibiting Turing-like patterns near the equilibrium for appropriate diffusion coefficients. In this study, we investigate the perturbed reaction-diffusion systems of such conserved systems. We show that a reaction-diffusion model with a globally stable homogeneous equilibrium can exhibit large amplitude Turing-like patterns in the transient dynamics. Moreover, we propose a three-component model, which exhibits an alternating repetition of spatially (almost) homogeneous oscillations and large amplitude Turing-like patterns.

Dynamics of reaction-diffusion systems and applications

The dynamics of a system of arbitrary number of nonlinear parabolic equations in terms of the quasisolutions of the corresponding system of elliptic equations is discussed. The conclusions for the general system are used to study the coexistence and permanence of a three-species predator-prey model and a food-chain model arising from ecology.

Cellular automata approach to pattern formation in reaction-diffusion systems

The dynamics of reaction-diffusion systems in low dimensions is often driven by fluctuations and a simple-minded description in terms of rate equations is not sufficient. Moreover, the emergence of complex patterns in such systems can involve simultaneously several new mechanisms as, for example, aggregation and precipitation. We shall show that the properties of these complex systems can be well understood in the framework of a mesoscopic description based on cellular automata models.

Nonlinear Dynamics of Reaction-Diffusion Systems: Analysis and Computations

In this paper, equilibria and dynamics of reaction-diffusion systems are studied by means of analysis and computations based on a central expansion method for radially symmetric as well as angularly asymmetric distributions. Effects of boundary conditions are included. The interplay between the different processes in the evolution of the system is considered. The investigation provides a unified description in one, two, and three dimensions. A particular application concerns the time evolution of temperature profiles in a fusion reactor plasma.