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Numerical modeling of cardiac electrophysiology at the cellular scale

Project description

Modelling heart electrophysiology

Cardiac arrhythmia, irregular beating of the heart, is a frequent cause of death and disability. To study the complex electrical system that is behind these arrhythmia, mathematical models are widely used. Scientists of the EU-funded MICROCARD project want to build a successor to these cardiac electrophysiology models that represents individual cells and their interconnections. However, this greatly increases the size and complexity of the simulations and requires exascale computing. MICROCARD will develop a sophisticated simulation platform that is suitable for exascale computers and provides reliable insight into the electrophysiology of the heart and similar biological systems such as nerves, muscles, the eye, and the brain.


Cardiovascular diseases are the most frequent cause of death worldwide and half of these deaths are due to cardiac arrhythmia, a disorder of the heart's electrical synchronization system. Numerical models of this complex system are highly sophisticated and widely used, but to match observations in aging and diseased hearts they need to move from a continuum approach to a representation of individual cells and their interconnections. This implies a different, harder numerical problem and a 10,000-fold increase in problem size. Exascale computers will be needed to run such models.

We propose to develop an exascale application platform for cardiac electrophysiology simulations that is usable for cell-by-cell simulations. The platform will be co-designed by HPC experts, numerical scientists, biomedical engineers, and biomedical scientists, from academia and industry. We will develop, in concert, numerical schemes suitable for exascale parallelism, problem-tailored linear-system solvers and preconditioners, and a compiler to translate high-level model descriptions into optimized, energy-efficient system code for heterogeneous computing systems. The code will be parallelized with a recently developed runtime system that is resilient to hardware failures and will use an energy-aware task placement strategy.

The platform will be applied in real-life use cases with high impact in the biomedical domain and will showcase HPC in this area where it is painfully underused. It will be made accessible for a wide range of users both as code and through a web interface.

We will further employ our HPC and biomedical expertise to accelerate the development of parallel segmentation and (re)meshing software, necessary to create the extremely large and complex meshes needed from available large volumes of microscopy data.

The platform will be adaptable to similar biological systems such as nerves, and components of the platform will be reusable in a wide range of applications.


Net EU contribution
€ 756 250,00
33000 Bordeaux

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Nouvelle-Aquitaine Aquitaine Gironde
Activity type
Higher or Secondary Education Establishments
Total cost
€ 1 610 000,00

Participants (12)