Simulation of human ischemic stroke in realistic 3D geometry

Thierry Dumont 1, * Max Duarte 2 Stéphane Descombes 3, 4 Marie-Aimée Dronne 5 Marc Massot 2 Violaine Louvet 1, 6
* Corresponding author
4 NACHOS - Numerical modeling and high performance computing for evolution problems in complex domains and heterogeneous media
CRISAM - Inria Sophia Antipolis - Méditerranée , JAD - Laboratoire Jean Alexandre Dieudonné : UMR6621
5 Evaluation et modélisation des effets thérapeutiques
Département biostatistiques et modélisation pour la santé et l'environnement [LBBE]
6 NUMED - Numerical Medicine
UMPA-ENSL - Unité de Mathématiques Pures et Appliquées, Inria Grenoble - Rhône-Alpes
Abstract : In silico research in medicine is thought to reduce the need for expensive clinical trials under the condition of reliable mathematical models and accurate and efficient numerical methods. In the present work, we tackle the numerical simulation of reaction-diffusion equations modeling human ischemic stroke. This problem induces peculiar difficulties like potentially large stiffness which stems from the broad spectrum of temporal scales in the nonlinear chemical source term as well as from the presence of steep spatial gradients in the reaction fronts, spatially very localized. Furthermore, simulations on realistic 3D geometries are mandatory in order to describe correctly this type of phenomenon. The main goal of this article is to obtain, for the first time, 3D simulations on realistic geometries and to show that the simulation results are consistent with those obtain in experimental studies or observed on MRI images in stroke patients. For this purpose, we introduce a new resolution strategy based mainly on time operator splitting that takes into account complex geometry coupled with a well-conceived parallelization strategy for shared memory architectures. We consider then a high order implicit time integration for the reaction and an explicit one for the diffusion term in order to build a time operator splitting scheme that exploits efficiently the special features of each problem. Thus, we aim at solving complete and realistic models including all time and space scales with conventional computing resources, that is on a reasonably powerful workstation. Consequently and as expected, 2D and also fully 3D numerical simulations of ischemic strokes for a realistic brain geometry, are conducted for the first time and shown to reproduce the dynamics observed on MRI images in stroke patients. Beyond this major step, in order to improve accuracy and computational efficiency of the simulations, we indicate how the present numerical strategy can be coupled with spatial adaptive multiresolution schemes. Preliminary results in the framework of simple geometries allow to assess the proposed strategy for further developments.
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Thierry Dumont, Max Duarte, Stéphane Descombes, Marie-Aimée Dronne, Marc Massot, et al.. Simulation of human ischemic stroke in realistic 3D geometry. Communications in Nonlinear Science and Numerical Simulation, Elsevier, 2013, 18 (6), pp.1539-1557. ⟨10.1016/j.cnsns.2012.10.002⟩. ⟨hal-00546223v3⟩

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