Numerical simulation of a stroke: numerical problems and methodology

The numerical simulation of an ischemic stroke is a challenging problem: a complicated geometry, and a very stiff large system of reaction-diffusion equations. This paper, intended for mathematicians as well as for biologist, gives a survey and an introduction to the numerical methods used and some results

Task-based adaptive multiresolution for time-space multi-scale reaction-diffusion systems on multi-core architectures

A new solver featuring time-space adaptation and error control has been recently introduced to tackle the numerical solution of stiff reaction-diffusion systems. Based on operator splitting, finite volume adaptive multiresolution and high order time integrators with specific stability properties for each operator, this strategy yields high computational efficiency for large multidimensional computations on standard architectures such as powerful workstations. However, the data structure of the original implementation, based on trees of pointers, provides limited opportunities for efficiency enhancements, while posing serious challenges in terms of parallel programming and load balancing. The present contribution proposes a new implementation of the whole set of numerical methods including Radau5 and ROCK4, relying on a fully different data structure together with the use of a specific library, TBB, for shared-memory, task-based parallelism with work-stealing. The performance of our implementation is assessed in a series of test-cases of increasing difficulty in two and three dimensions on multi-core and many-core architectures, demonstrating high scalability

Temporal convergence analysis of a locally implicit discontinuous galerkin time domain method for electromagnetic wave propagation in dispersive media

International audienceThis paper is concerned with the approximation of the time domain Maxwell's equations in a dispersive propagation media by a Discontinuous Galerkin Time Domain (DGTD) method. The Debye model is used to describe the dispersive behaviour of the media. We adapt the locally implicit time integration method from [1] and derive a convergence analysis to prove that the locally implicit DGTD method for Maxwell's equations in dispersive media retains its second-order convergence

An implicit hybridized discontinuous Galerkin method for the 3D time-domain Maxwell equations

International audienceWe present a time-implicit hybridizable discontinuous Galerkin (HDG) method for numerically solving the system of three-dimensional (3D) time-domain Maxwell equations. This method can be seen as a fully implicit variant of classical so-called DGTD (Discontinuous Galerkin Time-Domain) methods that have been extensively studied during the last 10 years for the simulation of time-domain electromagnetic wave propagation. The proposed method has been implemented for dealing with general 3D problems discretized using unstructured tetrahedral meshes. We provide numerical results aiming at assessing its numerical convergence properties by considering a model problem on one hand, and its performance when applied to more realistic problems. We also include some performance comparisons with a centered flux time-implicit DGTD method

Locally implicit discontinuous Galerkin time domain method for electromagnetic wave propagation in dispersive media applied to numerical dosimetry in biological tissues

International audienceWe are concerned here with the numerical simulation of electromagnetic wave propagation in biological media. Because of their water content, these media are dispersive i.e. their electromagnetic material characteristics depend of the frequency. In the time-domain, this translates in a time dependency of these parameters that can be taken into account through and additional (auxiliary) differential equation for, e.g, the electric polarization, which is coupled to the system of Maxwell's equations. From the application point of view, the problems at hand most often involve irregularly shaped structures corresponding to biological tissues. Modeling realistically the interfaces between tissues is particularly important if one is interested in evaluating accurately the impact of field discontinuities at these interfaces. In this paper, we propose and study a locally implicit discon-tinuous Galerkin time-domain method formulated on an unstructured tetrahedral mesh for solving the resulting system of differential equations in the case of Debye-type media. Three-dimensional numerical simulations are presented concerning the exposure of head tissues to a localized source radiation. 1. Introduction. This article is concerned with the numerical simulation of electromagnetic wave propagation in dispersive media. These are materials in which either or both of the electromagnetic material parameters ε and µ are functions of frequency. Note that the conductivity σ may also be a function of frequency, but its effect can be rolled into the complex permittivity. In reality, all materials have frequency-dependent ε and µ, but many materials can be approximated as frequency-independent over a frequency band of interest, simplifying their analysis and simulation. Here, we will focus on the much more common case of frequency-dependent permittivity. A lot of practical electromagnetic wave propagation problems involve such propagation media, such as those involving the interaction of an electromagnetic wave with biological tissues. The numerical modeling of the propagation of electromagnetic waves through human tissues is at the heart of many biomedical applications such as the microwave imaging of cancer tumors or the treatment of the latter by hy-perthermia. For example, microwave imaging for breast cancer detection is expected to be safe for the patient and has the potential to detect very small cancerous tumors in the breast [3, 14, 24]. Beside, the definition of microwave-based hyperthermia as an immunotherapy strategy for cancer can also be cited [2, 11]. The electroporation technique can also be an application, which consists of applying nanopulses to the tissues, enabling only intracellular membranes to be affected, and then opening the route to therapeutic strategies such as electrochemotherapy or gene transfer [21, 30, 25, 26, 28]. Because for all these biomedical applications experimental modeling is almost impossible , computer simulation is the approach of choice for understanding the underlyin

Locally implicit time integration strategies in a discontinuous Galerkin method for Maxwell's equations

International audienceAn attractive feature of discontinuous Galerkin (DG) spatial discretization is the possibility of using locally refined space grids to handle geometrical details. However, locally refined meshes lead to severe stability constraints on explicit integration methods to numerically solve a time-dependent partial differential equation. If the region of refinement is small relative to the computational domain, the time step size restriction can be overcome by blending an implicit and an explicit scheme where only the solution variables living at fine elements are treated implicitly. The downside of this approach is having to solve a linear system per time step. But due to the assumed small region of refinement relative to the computational domain, the overhead will also be small while the solution can be advanced in time with step sizes determined by the coarse elements. In this paper, we present two locally implicit time integration methods for solving the time-domain Maxwell equations spatially discretized with a DG method. Numerical experiments for two-dimensional problems illustrate the theory and the usefulness of the implicit-explicit approaches in presence of local refinements

Adaptive time splitting method for multi-scale evolutionary partial differential equations

Accepted to publication in Confluentes Mathematici. Dedication : Cet article est dédié à la mémoire de Michelle Schatzman. Spécialiste des méthodes de décomposition d'opérateur, sa grande clairvoyance scientifique lui a permis d'orienter plusieurs chercheurs débutants sur ce sujet à un moment où il pouvait sembler achevé. Michelle aimait dire qu'il n'y a pas de frontière entre les branches des mathématiques et que seule une grande culture permet de naviguer dans cette forêt et d'y trouver les bonnes techniques pour résoudre un problème. Ce travail est un hommage; à la croisée des mathématiques et de leurs applications effectives, il tente d'illustrer cette assertion. Michelle, ton dynamisme, ton humour et ton plaisir à parler mathématiques nous manquent.International audienceThis paper introduces an adaptive time splitting technique for the solution of stiff evolutionary PDEs that guarantees an effective error control of the simulation, independent of the fastest physical time scale for highly unsteady problems. The strategy considers a second order Strang method and another lower order embedded splitting scheme that takes into account potential loss of order due to the stiffness featured by time-space multi-scale phenomena. The scheme is then built upon a precise numerical analysis of the method and a complementary numerical procedure, conceived to overcome classical restrictions of adaptive time stepping schemes based on lower order embedded methods, whenever asymptotic estimates fail to predict the dynamics of the problem. The performance of the method in terms of control of integration errors is evaluated by numerical simulations of stiff propagating waves coming from nonlinear chemical dynamics models as well as highly multi-scale nanosecond repetitively pulsed gas discharges, which allow to illustrate the method capabilities to consistently describe a broad spectrum of time scales and different physical scenarios for consecutive discharge/post-discharge phases

An implicit hybridized discontinuous Galerkin method for the 3D time-domain Maxwell equations

We present a time-implicit hybridizable discontinuous Galerkin (HDG) method for numerically solving the system of three-dimensional (3D) time-domain Maxwell equations. This method can be seen as a fully implicit variant of classical so-called DGTD (Discontinuous Galerkin Time-Domain) methods that have been extensively studied during the last 10 years for the simulation of time-domain electromagnetic wave propagation. The proposed method has been implemented for dealing with general 3D problems discretized using unstructured tetrahedral meshes. We provide numerical results aiming at assessing its numerical convergence properties by considering a model problem on one hand, and its performance when applied to more realistic problems. We also include some performance comparisons with a centered flux time-implicit DGTD method

An explicit hybridizable discontinuous Galerkin method for the 3D time-domain Maxwell equations

International audienceWe present an explicit hybridizable discontinuous Galerkin (HDG) method for numerically solving the system of three-dimensional (3D) time-domain Maxwell equations. The method is fully explicit similarly to classical so-called DGTD (Dis-continuous Galerkin Time-Domain) methods, is also high-order accurate in both space and time and can be seen as a generalization of the classical DGTD scheme based on upwind fluxes. We provide numerical results aiming at assessing its numerical convergence properties by considering a model problem and we present preliminary results of the superconvergence property on the H curl norm

An explicit hybridizable discontinuous Galerkin method for the 3D time-domain Maxwell equations

We present an explicit hybridizable discontinuous Galerkin (HDG) method for numerically solving the system of three-dimensional (3D) time-domain Maxwell equations. The method is fully explicit similarly to classical so-called DGTD (Discontinuous Galerkin Time-Domain) methods that have been extensively studied during the last 15 years for the simulation of time-domain electromagnetic wave propagation. This HDGTD (Hybridizable Discontinuous Galerkin Time-Domain) method is also high-order accurate in both space and time and can be seen as a generalization of the classical DGTD scheme based on upwind fluxes. In particular, it coincides with the latter scheme for a particular choice of the stabilization parameter introduced in the definition of numerical traces in the HDG framework. It posseses a superconvergence property that allows, by means of local postprocessing, to obtain new improved approximations of the variables at any time levels. In particular, the new approximation converge with order k + 1 instead of k in the H curl-norm for k ≥ 1 .The proposed method has been implemented for dealing with general 3D problems. We provide numerical results aiming at assessing its numerical convergence properties by considering first a model problem. Then, this HDGTD method is applied to a classical scattering problem