An analytical solution for diffusion and nonlinear uptake of oxygen in a spherical cell

We develop a new analytical solution for a reactive transport model that describes the steady-state distribution of oxygen subject to diffusive transport and nonlinear uptake in a sphere. This model was originally reported by Lin (Journal of Theoretical Biology, 1976 v60, pp449–457) to represent the distribution of oxygen inside a cell and has since been studied extensively by both the numerical analysis and formal analysis communities. Here we extend these previous studies by deriving an analytical solution to a generalized reaction-diffusion equation that encompasses Lin’s model as a particular case. We evaluate the solution for the parameter combinations presented by Lin and show that the new solutions are identical to a grid-independent numerical approximation.

Pulse dynamics in a three-component system : stability and bifurcations

In this article, we analyze the stability and the associated bifurcations of several types of pulse solutions in a singularly perturbed three-component reaction-diffusion equation that has its origin as a model for gas discharge dynamics. Due to the richness and complexity of the dynamics generated by this model, it has in recent years become a paradigm model for the study of pulse interactions. A mathematical analysis of pulse interactions is based on detailed information on the existence and stability of isolated pulse solutions. The existence of these isolated pulse solutions is established in previous work. Here, the pulse solutions are studied by an Evans function associated to the linearized stability problem. Evans functions for stability problems in singularly perturbed reaction-diffusion models can be decomposed into a fast and a slow component, and their zeroes can be determined explicitly by the NLEP method. In the context of the present model, we have extended the NLEP method so that it can be applied to multi-pulse and multi-front solutions of singularly perturbed reaction-diffusion equations with more than one slow component. The brunt of this article is devoted to the analysis of the stability characteristics and the bifurcations of the pulse solutions. Our methods enable us to obtain explicit, analytical information on the various types of bifurcations, such as saddle-node bifurcations, Hopf bifurcations in which breathing pulse solutions are created, and bifurcations into travelling pulse solutions, which can be both subcritical and supercritical.

Two novel numerical methods for solving the two-dimensional fractional Fitzhugh-Nagumo-monodomain model

Fractional mathematical models represent a new approach to modelling complex spatial problems in which there is heterogeneity at many spatial and temporal scales. In this paper, a two-dimensional fractional Fitzhugh-Nagumo-monodomain model with zero Dirichlet boundary conditions is considered. The model consists of a coupled space fractional diffusion equation (SFDE) and an ordinary differential equation. For the SFDE, we first consider the numerical solution of the Riesz fractional nonlinear reaction-diffusion model and compare it to the solution of a fractional in space nonlinear reaction-diffusion model. We present two novel numerical methods for the two-dimensional fractional Fitzhugh-Nagumo-monodomain model using the shifted Grunwald-Letnikov method and the matrix transform method, respectively. Finally, some numerical examples are given to exhibit the consistency of our computational solution methodologies. The numerical results demonstrate the effectiveness of the methods.

Deformation with coupled chemical diffusion

The deformation of rocks is commonly intimately associated with metamorphic reactions. This paper is a step towards understanding the behaviour of fully coupled, deforming, chemically reacting systems by considering a simple example of the problem comprising a single layer system with elastic-power law viscous constitutive behaviour where the deformation is controlled by the diffusion of a single chemical component that is produced during a metamorphic reaction. Analysis of the problem using the principles of non-equilibrium thermodynamics allows the energy dissipated by the chemical reaction-diffusion processes to be coupled with the energy dissipated during deformation of the layers. This leads to strain-rate softening behaviour and the resultant development of localised deformation which in turn nucleates buckles in the layer. All such diffusion processes, in leading to Herring-Nabarro, Coble or “pressure solution” behaviour, are capable of producing mechanical weakening through the development of a “chemical viscosity”, with the potential for instability in the deformation. For geologically realistic strain rates these chemical feed-back instabilities occur at the centimetre to micron scales, and so produce structures at these scales, as opposed to thermal feed-back instabilities that become important at the 100–1000 m scales.

Survival probability for a diffusive process on a growing domain

We consider the motion of a diffusive population on a growing domain, 0 < x < L(t ), which is motivated by various applications in developmental biology. Individuals in the diffusing population, which could represent molecules or cells in a developmental scenario, undergo two different kinds of motion: (i) undirected movement, characterized by a diffusion coefficient, D, and (ii) directed movement, associated with the underlying domain growth. For a general class of problems with a reflecting boundary at x = 0, and an absorbing boundary at x = L(t ), we provide an exact solution to the partial differential equation describing the evolution of the population density function, C(x,t ). Using this solution, we derive an exact expression for the survival probability, S(t ), and an accurate approximation for the long-time limit, S = limt→∞ S(t ). Unlike traditional analyses on a nongrowing domain, where S ≡ 0, we show that domain growth leads to a very different situation where S can be positive. The theoretical tools developed and validated in this study allow us to distinguish between situations where the diffusive population reaches the moving boundary at x = L(t ) from other situations where the diffusive population never reaches the moving boundary at x = L(t ). Making this distinction is relevant to certain applications in developmental biology, such as the development of the enteric nervous system (ENS). All theoretical predictions are verified by implementing a discrete stochastic model.

Robust solver based on modified particle swarm optimization for improved solution of diffusion transport through containment facilities

Accurate estimation of mass transport parameters is necessary for overall design and evaluation processes of the waste disposal facilities. The mass transport parameters, such as effective diffusion coefficient, retardation factor and diffusion accessible porosity, are estimated from observed diffusion data by inverse analysis. Recently, particle swarm optimization (PSO) algorithm has been used to develop inverse model for estimating these parameters that alleviated existing limitations in the inverse analysis. However, PSO solver yields different solutions in successive runs because of the stochastic nature of the algorithm and also because of the presence of multiple optimum solutions. Thus the estimated mean solution from independent runs is significantly different from the best solution. In this paper, two variants of the PSO algorithms are proposed to improve the performance of the inverse analysis. The proposed algorithms use perturbation equation for the gbest particle to gain information around gbest region on the search space and catfish particles in alternative iterations to improve exploration capabilities. Performance comparison of developed solvers on synthetic test data for two different diffusion problems reveals that one of the proposed solvers, CPPSO, significantly improves overall performance with improved best, worst and mean fitness values. The developed solver is further used to estimate transport parameters from 12 sets of experimentally observed diffusion data obtained from three diffusion problems and compared with published values from the literature. The proposed solver is quick, simple and robust on different diffusion problems. (C) 2012 Elsevier Ltd. All rights reserved.

Uniformly convergent finite element and finite difference methods for singularly perturbed ordinary differential equations

This thesis is concerned with uniformly convergent finite element and finite difference methods for numerically solving singularly perturbed two-point boundary value problems. We examine the following four problems: (i) high order problem of reaction-diffusion type; (ii) high order problem of convection-diffusion type; (iii) second order interior turning point problem; (iv) semilinear reaction-diffusion problem. Firstly, we consider high order problems of reaction-diffusion type and convection-diffusion type. Under suitable hypotheses, the coercivity of the associated bilinear forms is proved and representation results for the solutions of such problems are given. It is shown that, on an equidistant mesh, polynomial schemes cannot achieve a high order of convergence which is uniform in the perturbation parameter. Piecewise polynomial Galerkin finite element methods are then constructed on a Shishkin mesh. High order convergence results, which are uniform in the perturbation parameter, are obtained in various norms. Secondly, we investigate linear second order problems with interior turning points. Piecewise linear Galerkin finite element methods are generated on various piecewise equidistant meshes designed for such problems. These methods are shown to be convergent, uniformly in the singular perturbation parameter, in a weighted energy norm and the usual L2 norm. Finally, we deal with a semilinear reaction-diffusion problem. Asymptotic properties of solutions to this problem are discussed and analysed. Two simple finite difference schemes on Shishkin meshes are applied to the problem. They are proved to be uniformly convergent of second order and fourth order respectively. Existence and uniqueness of a solution to both schemes are investigated. Numerical results for the above methods are presented.

Lower semicontinuity of attractors for non-autonomous dynamical systems

This paper is concerned with the lower semicontinuity of attractors for semilinear non-autonomous differential equations in Banach spaces. We require the unperturbed attractor to be given as the union of unstable manifolds of time-dependent hyperbolic solutions, generalizing previous results valid only for gradient-like systems in which the hyperbolic solutions are equilibria. The tools employed are a study of the continuity of the local unstable manifolds of the hyperbolic solutions and results on the continuity of the exponential dichotomy of the linearization around each of these solutions.

Dynamics in dumbbell domains III. Continuity of attractors

In this paper we conclude the analysis started in [J.M. Arrieta, AN Carvalho, G. Lozada-Cruz, Dynamics in dumbbell domains I. Continuity of the set of equilibria, J. Differential Equations 231 (2006) 551-597] and continued in [J.M. Arrieta, AN Carvalho, G. Lozada-Cruz, Dynamics in dumbbell domains II. The limiting problem, J. Differential Equations 247 (1) (2009) 174-202 (this issue)] concerning the behavior of the asymptotic dynamics of a dissipative reaction-diffusion equation in a dumbbell domain as the channel shrinks to a line segment. In [J.M. Arrieta, AN Carvalho. G. Lozada-Cruz, Dynamics in dumbbell domains I. Continuity of the set of equilibria, J. Differential Equations 231 (2006) 551-597], we have established an appropriate functional analytic framework to address this problem and we have shown the continuity of the set of equilibria. In [J.M. Arrieta, AN Carvalho, G. Lozada-Cruz. Dynamics in dumbbell domains II. The limiting problem, J. Differential Equations 247 (1) (2009) 174-202 (this issue)], we have analyzed the behavior of the limiting problem. In this paper we show that the attractors are Upper semicontinuous and, moreover, if all equilibria of the limiting problem are hyperbolic, then they are lower semicontinuous and therefore, continuous. The continuity is obtained in L(p) and H(1) norms. (C) 2008 Elsevier Inc. All rights reserved.

Cascades of Hopf bifurcations from boundary delay

We consider a 1-dimensional reaction-diffusion equation with nonlinear boundary conditions of logistic type with delay. We deal with non-negative solutions and analyze the stability behavior of its unique positive equilibrium solution, which is given by the constant function u equivalent to 1. We show that if the delay is small, this equilibrium solution is asymptotically stable, similar as in the case without delay. We also show that, as the delay goes to infinity, this equilibrium becomes unstable and undergoes a cascade of Hopf bifurcations. The structure of this cascade will depend on the parameters appearing in the equation. This equation shows some dynamical behavior that differs from the case where the nonlinearity with delay is in the interior of the domain. (C) 2009 Elsevier Inc. All rights reserved.

Application of a bounded upwinding scheme to complex fluid dynamics problems

This paper is concerned with an overview of upwinding schemes, and further nonlinear applications of a recently introduced high resolution upwind differencing scheme, namely the ADBQUICKEST [V.G. Ferreira, F.A. Kurokawa, R.A.B. Queiroz, M.K. Kaibara, C.M. Oishi, J.A.Cuminato, A.F. Castelo, M.F. Tomé, S. McKee, assessment of a high-order finite difference upwind scheme for the simulation of convection-diffusion problems, International Journal for Numerical Methods in Fluids 60 (2009) 1-26]. The ADBQUICKEST scheme is a new TVD version of the QUICKEST [B.P. Leonard, A stable and accurate convective modeling procedure based on quadratic upstream interpolation, Computer Methods in Applied Mechanics and Engineering 19 (1979) 59-98] for solving nonlinear balance laws. The scheme is based on the concept of NV and TVD formalisms and satisfies a convective boundedness criterion. The accuracy of the scheme is compared with other popularly used convective upwinding schemes (see, for example, Roe (1985) [19], Van Leer (1974) [18] and Arora & Roe (1997) [17]) for solving nonlinear conservation laws (for example, Buckley-Leverett, shallow water and Euler equations). The ADBQUICKEST scheme is then used to solve six types of fluid flow problems of increasing complexity: namely, 2D aerosol filtration by fibrous filters; axisymmetric flow in a tubular membrane; 2D two-phase flow in a fluidized bed; 2D compressible Orszag-Tang MHD vortex; axisymmetric jet onto a flat surface at low Reynolds number and full 3D incompressible flows involving moving free surfaces. The numerical simulations indicate that this convective upwinding scheme is a good generic alternative for solving complex fluid dynamics problems. © 2012.

Spatial dynamics of a population with stage-dependent diffusion

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Continuity of Dynamical Structures for Nonautonomous Evolution Equations Under Singular Perturbations

In this paper we study the continuity of invariant sets for nonautonomous infinite-dimensional dynamical systems under singular perturbations. We extend the existing results on lower-semicontinuity of attractors of autonomous and nonautonomous dynamical systems. This is accomplished through a detailed analysis of the structure of the invariant sets and its behavior under perturbation. We prove that a bounded hyperbolic global solutions persists under singular perturbations and that their nonlinear unstable manifold behave continuously. To accomplish this, we need to establish results on roughness of exponential dichotomies under these singular perturbations. Our results imply that, if the limiting pullback attractor of a nonautonomous dynamical system is the closure of a countable union of unstable manifolds of global bounded hyperbolic solutions, then it behaves continuously (upper and lower) under singular perturbations.

Turing patterns in the chlorine dioxide-iodine-malonic acid reaction with square spatial periodic forcing

We use the photosensitive chlorine dioxide-iodine-malonic acid reaction-diffusion system to study wavenumber locking of Turing patterns to two-dimensional "square" spatial forcing, implemented as orthogonal sets of bright bands projected onto the reaction medium. Various resonant structures emerge in a broad range of forcing wavelengths and amplitudes, including square lattices and superlattices, one-dimensional stripe patterns and oblique rectangular patterns. Numerical simulations using a model that incorporates additive two-dimensional spatially periodic forcing reproduce well the experimental observations.

A nonlinear elliptic problem with terms concentrating in the boundary

In this paper, we investigate the behavior of a family of steady-state solutions of a nonlinear reaction diffusion equation when some reaction and potential terms are concentrated in a e-neighborhood of a portion G of the boundary. We assume that this e-neighborhood shrinks to G as the small parameter e goes to zero. Also, we suppose the upper boundary of this e-strip presents a highly oscillatory behavior. Our main goal here was to show that this family of solutions converges to the solutions of a limit problem, a nonlinear elliptic equation that captures the oscillatory behavior. Indeed, the reaction term and concentrating potential are transformed into a flux condition and a potential on G, which depends on the oscillating neighborhood. Copyright (C) 2012 John Wiley & Sons, Ltd.