Two-dimensional Brusselator Research Articles

A local radial basis function differential quadrature semi-discretisation technique for the simulation of time-dependent reaction-diffusion problems

PurposeThis paper aims to develop a meshfree algorithm based on local radial basis functions (RBFs) combined with the differential quadrature (DQ) method to provide numerical approximations of the solutions of time-dependent, nonlinear and spatially one-dimensional reaction-diffusion systems and to capture their evolving patterns. The combination of local RBFs and the DQ method is applied to discretize the system in space; implicit multistep methods are subsequently used to discretize in time.Design/methodology/approachIn a method of lines setting, a meshless method for their discretization in space is proposed. This discretization is based on a DQ approach, and RBFs are used as test functions. A local approach is followed where only selected RBFs feature in the computation of a particular DQ weight.FindingsThe proposed method is applied on four reaction-diffusion models: Huxley’s equation, a linear reaction-diffusion system, the Gray–Scott model and the two-dimensional Brusselator model. The method captured the various patterns of the models similar to available in literature. The method shows second order of convergence in space variables and works reliably and efficiently for the problems.Originality/valueThe originality lies in the following facts: A meshless method is proposed for reaction-diffusion models based on local RBFs; the proposed scheme is able to capture patterns of the models for big time T; the scheme has second order of convergence in both time and space variables and Nuemann boundary conditions are easy to implement in this scheme.

Simulation of activator–inhibitor dynamics based on cross-diffusion Brusselator reaction–diffusion system via a differential quadrature-radial point interpolation method (DQ-RPIM) technique

The current paper proposes an efficient numerical procedure for solving the two-dimensional Brusselator reaction–diffusion system. First, the time derivative is discretized by a semi-implicit finite difference scheme such that the nonlinear terms are approximated by using one term of the Taylor expansion. It is shown if the nonlinear terms satisfy the Lipshitz condition, then the proposed difference scheme is stable. In the next, the spatial derivative is discretized by the differential quadrature technique based upon the shape functions of radial point interpolation method. We study some practical problems to show the efficiency and acceptable results of the developed technique.

Parameter sensitivity analysis for biochemical reaction networks.

Biochemical reaction networks describe the chemical interactions occurring between molecular populations inside the living cell. These networks can be very noisy and complex and they often involve many variables and even more parameters. Parameter sensitivity analysis that studies the effects of parameter changes to the behaviour of biochemical networks can be a powerful tool in unravelling their key parameters and interactions. It can also be very useful in designing experiments that study these networks and in addressing parameter identifiability issues. This article develops a general methodology for analysing the sensitivity of probability distributions of stochastic processes describing the time-evolution of biochemical reaction networks to changes in their parameter values. We derive the coefficients that efficiently summarise the sensitivity of the probability distribution of the network to each parameter and discuss their properties. The methodology is scalable to large and complex stochastic reaction networks involving many parameters and can be applied to oscillatory networks. We use the two-dimensional Brusselator system as an illustrative example and apply our approach to the analysis of the Drosophila circadian clock. We investigate the impact of using stochastic over deterministic models and provide an analysis that can support key decisions for experimental design, such as the choice of variables and time-points to be observed.

An adaptive step size controller for iterative implicit methods

The automatic selection of an appropriate time step size has been considered extensively in the literature. However, most of the strategies developed operate under the assumption that the computational cost (per time step) is independent of the step size. This assumption is reasonable for non-stiff ordinary differential equations and for partial differential equations where the linear systems of equations resulting from an implicit integrator are solved by direct methods. It is, however, usually not satisfied if iterative (for example, Krylov) methods are used.In this paper, we propose a step size selection strategy that adaptively reduces the computational cost (per unit time step) as the simulation progresses, constraint by the tolerance specified. We show that the proposed approach yields significant improvements in performance for a range of problems (diffusion–advection equation, Burgers' equation with a reaction term, porous media equation, viscous Burgers' equation, Allen–Cahn equation, and the two-dimensional Brusselator system). While traditional step size controllers have emphasized a smooth sequence of time step sizes, we emphasize the exploration of different step sizes which necessitates relatively rapid changes in the step size.

Variational multiscale element free Galerkin (VMEFG) and local discontinuous Galerkin (LDG) methods for solving two-dimensional Brusselator reaction–diffusion system with and without cross-diffusion

The finite element method (FEM) is one of the basic methods for solving deterministic and stochastic partial differential equations. This method is proposed in the 19 decade and after years several modifications for this well-known technique such as mortal FEM, discontinuous Galerkin FEM, extended FEM, least squares FEM, spectral FEM, mixed FEM, immersed FEM, adaptive FEM, etc. have been proposed. Also, for improving the accuracy and for considering complex domain, shape functions of the moving least squares approximation have been replaced with the traditional shape function of the finite element technique. The name of this improved method is element free Galerkin (EFG) method which is classified in the category of meshless methods. The EFG method has been applied for solving many problems in engineering. In the current paper, we select two numerical procedures that are extracted from FEM. The discontinuous Galerkin approach is a useful technique for solving problems that their exact solutions have discontinuity. It should be noted that many enriched ideas have been explained for improving accuracy of EFG method. In the current paper, the local discontinuous Galerkin and variational multiscale EFG methods are applied for obtaining numerical solution of two-dimensional Brusselator system with and without cross-diffusion. The Brusselator system is a theoretical model for a type of autocatalytic reaction. Up to best of authors’ knowledge, the accuracy of the obtained numerical solutions using local discontinuous Galerkin method is very related to the used time-discrete scheme. Therefore, fourth-order exponential time differencing method has been employed for discretizing the time variable. Also, to achieve a full discretization scheme, the local discontinuous Galerkin finite element method is used. Moreover, several test problems are given that show the acceptable accuracy and efficiency of the proposed schemes.

Reflection and refraction of waves in oscillatory media

This paper uses the two-dimensional Brusselator model to study reflection and refraction of chemical waves. It presents some boundary conditions of chemical waves, with which occurence of observed phenomena at interface as refraction and reflection of chemical waves can be interpreted. Moreover, the angle of reflection may be calculated by using the boundary conditions. It finds that reflection and refraction of chemical waves can occur simultaneously even if plane wave goes from a medium with higher speed to a medium with lower speed, provided the incident angle is larger than the critical angle.

A Numerical Liapunov-Schmidt Method with Applications to Hopf Bifurcation on a Square

We discuss an iterative method for calculating the reduced bifurcation equation of the Liapunov-Schmidt method and its numerical approximation. Using appropriate genericity assumptions (with symmetry), we derive a Taylor series for the reduced equation, where the bifurcation behavior is determined by its numerical approximation at a finite order of truncation. This method is used to calculate reduced equations at Hopf bifurcation of the two-dimensional Brusselator equations on a square with Neumann and Dirichlet boundary conditions. We examine several Hopf bifurcations within the three-parameter space. There are regions where we observe direct bifurcation to branches of periodic solutions with submaximal symmetry.

A numerical Liapunov-Schmidt method with applications to Hopf bifurcation on a square

We discuss an iterative method for calculating the reduced bifurcation equation of the Liapunov-Schmidt method and its numerical approximation. Using appropriate genericity assumptions (with symmetry), we derive a Taylor series for the reduced equation, where the bifurcation behavior is determined by its numerical approximation at a finite order of truncation. This method is used to calculate reduced equations at Hopf bifurcation of the two-dimensional Brusselator equations on a square with Neumann and Dirichlet boundary conditions. We examine several Hopf bifurcations within the three-parameter space. There are regions where we observe direct bifurcation to branches of periodic solutions with submaximal symmetry.

Reentrant hexagonal Turing structures

A new structural transition from stripes to hexagons is reported for the two-dimensional Brusselator model. Its existence is explained by the properties of the quadratic nonlinear coupling.