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. 2011 Apr 9:2:14.
doi: 10.3389/fphys.2011.00014. eCollection 2011.

Simulating human cardiac electrophysiology on clinical time-scales

Steven Niederer  1 , Lawrence Mitchell, Nicolas Smith, Gernot Plank
Affiliations

Simulating human cardiac electrophysiology on clinical time-scales

Steven Niederer et al. Front Physiol. .

Abstract

In this study, the feasibility of conducting in silico experiments in near-realtime with anatomically realistic, biophysically detailed models of human cardiac electrophysiology is demonstrated using a current national high-performance computing facility. The required performance is achieved by integrating and optimizing load balancing and parallel I/O, which lead to strongly scalable simulations up to 16,384 compute cores. This degree of parallelization enables computer simulations of human cardiac electrophysiology at 240 times slower than real time and activation times can be simulated in approximately 1 min. This unprecedented speed suffices requirements for introducing in silico experimentation into a clinical workflow.

Keywords: monodomain model; personalized health care; strong scalability.

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Figures

Figure 1
Figure 1
(A) Human heart mesh derived from CRT patient MRI. (B) Shows the high resolution unstructured tetrahedral mesh required to solve the monodomain equations.
Figure 2
Figure 2
Activation sequence. The red isosurfaces show the points in the heart where the transmembrane potential is 0 mV. The heart is stimulated in the right ventricular freewall at 0 ms and then at the left ventricular septal endocardium at 33 ms.
Figure 3
Figure 3
Benchmark results of strong scalability experiments. Shown are the effects of nodal-based (NBP) versus ParMeTis-based (PaBP) domain decomposition, implicit (IM) versus explicit (EX) solver strategy, and inline versus asynchronous (async) I/O strategy on strong scalability for a range of cores Nc between 128 and 16,384. The top panel shows parallel speedup and realtime lag factor ξr whereas the bottom panel shows parallel efficiency.
See this image and copyright information in PMC

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