Large-scale integrative modeling of the human heart: purpose, solutions, and new challenges
Mark Potse
Invited lecture, SGI User Group Conference,
Los Angeles, June 2008.


The contraction of the heart is triggered by an electrical impulse that propagates from one muscle cell to another. This organized activity generates a potential field that can be measured as an electrocardiogram (ECG) on the skin, or with a catheter inside the heart. The measured signals provide a wealth of diagnostic information. On the other hand, the electrical activation process itself is susceptible to a variety of diseases that are potentially lethal. The purpose of computer heart models is to give insight in the disorders of the electrical activation process, and the way heart diseases affect measurable signals.

The possibilities of computer heart modeling depend crucially on the availability of computing resources. While many questions have been resolved long ago with very simple models, the increasing power of today's supercomputers allows much more realistic models, which can simulate a wider range of diseases and inspire more confidence in the reliability of their predictions. Previously, models were highly simplified and abstract representations of reality. Today, we can construct a whole-heart model from its most basic components: the ionic channels in the cell membrane. This leads to very complex models.

The challenge that such models are facing is the necessity to solve very large linear systems, for several thousands of time steps in a single heart beat. Due to an SGI Altix system and algorithmic developments we have been able to create the first such model for a human heart. Systems of 60 million equation had to be solved to achieve this. More recently we have shown that the same methods can be used to solve systems of upto 2 billion equations. This was possible on an Altix-4700 with 768 cores and 1.5 TB memory.

When such equipment becomes available for routine work, it will become possible to study “cardiomyopathies,” degenerative heart muscle diseases. Cardiomyopathy is frequently encountered as a complication of a previous heart attack. But it is also present in a congenital form, and as such is the most important cause of sudden cardiac death in young, apparently healthy people. It leads to structural changes on a very small scale, while its acute effects happen on the scale of an entire heart. Extremely large models are therefore needed to help understand this disease. With the algorithms already proven to work, we think that models of the myopathic heart will become feasible in a very near future.


Computational resources for this work were provided by the Réseau québécois de calcul de haute performance (RQCHP). The author gratefully acknowledges financial support from the Research Center of Sacré-Coeur Hospital, Montréal, Québec, Canada; the Interuniversity Cardiology Institute of the Netherlands (ICIN); and The Netherlands Heart Foundation (NHS) grant 2005B092.