| dc.description.abstract |
Cardiac arrhythmias and fibrillation are potentially life threatening diseases that
can result from the improper conduction of electrical impulses in the heart. Experimental
study of such cardiac abnormalities are dangerous at best, often requiring the subject
to be placed in fibrillation for some time before attempting a large ``rescue'' shock.
Thus, most all studies are done in animals and not humans. Furthermore, there is some
indication that heart size may have considerable implications for fibrillation and
other conduction abnormalities. Thus animal models for defibrillation studies must
be chosen with great care. As an alternative, researchers are now using computer simulation
to study the factors that generate and sustain arrhythmias, hoping to obtain at least
preliminary data to guide fewer, more targeted experimental studies. Computer simulations
of the Bidomain Equations have become very complex as they have been applied to many
problems in cardiac electrophysiology. More complex membrane dynamics, irregular grids,
and 3-D data sets are all being investigated. Software engineering principles will
need to be applied to manage this continuing growth in complexity. We propose a modular
framework for development of a Simulation System whereby a researcher may mix and
match program elements to generate a simulator tailored to their particular problem.
The modular approach will simplify the generation and maintenance of the different
program elements and it will enable the end-researcher to determine the proper mix
of complexity versus speed for their particular problem of interest. The contrary
approach, one monolithic program which can run all simulations of all complexities,
is simply unrealistic. It would impose too great a burden on maintenance and upgradability,
and it would be difficult to provide good performance for a wide range of applications.
The modular approach also allows for the incremental inclusion of various complexities
in the bidomain model. From a simple 2-D homogeneous, isotropic regular grid, monodomain
simulation, we can progress, step by step, to a bidomain simulation with a fully implicit
time-integration scheme on irregular, 3-D grids with arbitrary anisotropy and inhomogeneity,
with a non-trivial membrane model. Simulations with such a wealth of complexity have
not been performed to date. As microprocessors have become cheaper and more powerful,
parallel computing has become more widespread. Machines with hundreds of high-performance
CPUs connected by fast networks are commonplace and are now capable of surpassing
traditional vector-based supercomputers in terms of overall performance. The Simulation
System presented here incorporates data-parallelism to allow large scale Bidomain
problems to be run on these newest parallel supercomputers. The large amount of distributed
memory in such machines can be harnessed to allow extremely large scale simulations
to be run. The large number of CPUs provide a tremendous amount of computational power
which can be used to run such simulations more quickly. Finally, the results presented
here show that a modular Simulation System is feasible for a wide range of pplications,
and that it can obtain very good performance over this range of applications. The
parallel speed-up seen was very good, regularly achieving a factor of 13 speed-up
on 16 processors. The results presented here also show that we can simulate bidomain
problems using an implicit time-integrator with an irregular, anisotropic and inhomogeneous,
grid and a non-trivial membrane model. We are able to run such simulations on parallel
computers, thereby harnessing a tremendous amount of memory and computational resources.
Such simulations have not been run to date.
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