Alya Red: A Computational heart

The human heart is still one of the biggest mysteries in medicine and anatomy. The main reason for our lack of understanding is the complexity of the heart’s structure and its phenotype. However, modern technology is helping us to understand this amazing organ. At the Barcelona Supercomputing Center, and in close collaboration with Medical Doctors and Bioengineers, we are developing a large scale simulator of the human heart called: Alya Red, the computational cardiac model. A computational description of the heart requires information at very different scales in time and space: from the ions inside the cells, or the muscular tissue that forms the organ, and up to the whole individual. Because it is not practical to compute all the scales to the same level of detail, our cardiac model is based on the organ scale. At this level, a heartbeat is driven by an electrical impulse that causes the muscular contraction, which in turn is responsible for the pumping action. For this reason, we say that the heart is a coupled physical system. In our simulator we can apply electric impulses directly to any zones of the heart, just like a pacemaker would do. These initial impulses unleash a generalized propagation of electricity through the whole cardiac structure in a coordinated way. Thanks to the optimized organization of muscular fibres, this electrical flash makes the ventricles contract, during what is known as the systole. To create the best possible cardiac simulator in terms of realism and detail, we rely on tools and data that have not been available until recently. The geometry and shape of the heart are measured using magnetic resonance imaging with a resolution of up to 36 micrometers, which allows us to construct a mesh with hundreds of thousands of computational elements. Electricity travels much faster along cardiac muscular fibres than across them, so a correct anatomical description of their arrangement is probably the most important element in obtaining a realistic electromechanical model of the heart. Cardiac fibres are specially organized to allow the contraction of the heart cavities in a coordinated, stable and efficient way. Until very recently, the only way to describe cardiac fiber arrangements was with simplified models based on histological sections of animal hearts. Today we can achieve a much better description of the fibres using a technique called Diffusion Tensor Imaging, using Magnetic Resonance to map the diffusion of water molecules along biological tissues. In our cardiac simulator we can use Diffusion Tensor Imaging information as well as mathematical models, allowing us to validate theory with experiments and improve our numerical methods. Alya, the software developed at the Barcelona Supercomputing Center, has been designed from scratch for an efficient use of large parallel clusters. Producing an accurate simulation of a heart requires considerable computing power. That´s why we perform our simulations on BSC’s supercomputer, Marenostrum, where calculations can be distributed among 10.000 processors working in a tightly coordinated way. These simulations will help medical doctors to better understand how our body works, to diagnose pathologies, to plan operations and treatments, and to test and design new drugs. Nowadays, large-scale simulations of the human body may seem like science fiction, but techniques like magnetic resonance were also science fiction only fifty years ago. With the help of information technology, the future of medicine is being built today.