Second African Conference on Computational Mechanics - An International Conference - AfriCOMP11

January 5 - 8, 2011, Cape Town, South Africa

A.G. Malan, P. Nithiarasu and B.D. Reddy (Eds.)
HIGH PERFORMANCE COMPUTATIONAL
ELECTROMECHANICAL MODEL OF THE HEART
Mariano V azquez

, Pierre Lafortune

, Ruth Ars

, Guillaume Houzeaux

, and Antoine
J erusalem

Barcelona Supercomputing Center BSC-CNS, Campus Nord UPC, Spain,

mariano.vazquez@bsc.es

IMDEA Materials Institute, Madrid, Spain, antoine.jerusalem@imdea.org

SUMMARY
In this paper, we present a high performance computational electromechanical model of the heart
that includes coupling between electrical activation and mechanical deformation, capable of run-
ning efciently in up to thousands of processors. The electrical activation propagation is modelled
by different strategies, such as FitzHugh-Nagumos or Fenton-Karmas, including ber orienta-
tion with a special treatment for regions with large gradients in the ber elds. The mechanical
deformation is treated using anisotropic hyper-elastic materials in a total Lagrangian formulation.
We tested several material models, such as models based on biaxial tests on excised myocardium
or orthotropic formulations. Coupling is treated using the Cross-Bridges model of Peterson. The
scheme is implemented in Alya, which run simulations in parallel with almost linear scalability
properties in large-scale computers. The computational model is assessed through several tests,
including those to evaluate its parallel performance.
Key Words: Computational Electrophysiology, Computational Solid Biomechanics, Cardiac Me-
chanics, Parallelization
1 INTRODUCTION
This paper continues previous works in Cardiac Computational Mechanics [1,2,3,4,5,6] where we
progressively go from Electrophysiology models in simple geometries up to coupled Electrome-
chanical models for subject-specic geometries running in large scale parallel computers. Due
to our background as computational mechanics researchers, it is not our intention to make direct
contributions in Physiology or Medical research but to develop tools to be used decisively by those
who can do those contributions. Of course, in the process of development, Physiologists and Med-
ical doctors play a central role because they pose the problems to be solved. However, the nal
objective is to develop exible simulation tools for complex biomechanical problems capable of
running efciently in supercomputers and made them available to researchers in the medical eld.
This concept is thoroughly dened and explored in [7].
2 THE COMPUTATIONAL MODEL
The computational model presented simulates two different Physical problems and a coupling
strategy between them.
2.1 Electrophysiology
The basic form of the electrical activation potentials

propagation equation is
1
:

t
=

x
i

D
ij

x
j

+L(

). (1)
Latin subindices counts the space dimension of the problem. Greek subindices counts the number
of activation potentials involved, being = 1 for monodomain models and = 1, 2 for bido-
main ones, extracellular and intracellular. The equations right hand side represents the transient
macroscopical model, based in the well known continuum cable equation. The diffusion term is
governed by the diffusion tensor D
ij
. The equation is set in a xed reference frame and D
ij
must
describe the cable (i.e. cardiac tissue bers) orientation in the xed reference frame. Then, D
ij
can be written as
D
ij
= C
1
ik
D
loc
lk
C
lj
, (2)
where C
lk
is the base change matrix from the local ber-aligned reference frame (a
i
, c
1
i
, c
2
i
) (i.e.
one axial vector and two crosswise ones) to the global reference frame. D
loc
lk
is the local diagonal
diffusion matrix, whose diagonal components are the axial and crosswise ber diffusions. L(

)
is a reaction non-linear local term. We present results for FitzHugh-Nagumo and Fenton-Karma
models.
2.2 Mechanical Deformation
The local form of the linear momentum balance, to be solved using a Lagrangian (solid mechanics)
FEM formulation, is written as

2
u
i
t
2
=
P
iJ
X
J
+
o
B
i
, (3)
which in its weak form is

2
u
i
t
2
=

x
J
P
iJ
+

o
N
J
P
iJ
+

o
B
i
(4)
for each space dimension i. P
iJ
, the nominal stress or rst Piola-Kirchoff stress tensor, depends
on the second Piola-Kirchoff stress tensor S
IJ
. Depending on the model, it includes active and
passive stresses and a volumetric correction. We present results for a transversally isotropic law,
based on Lin-Yin [8] and an orthotropic law based on Holzapfel and Ogden [9].
2.3 Coupling
The excitation-contraction (E-C) coupling use by Watanabe et al. [10] is based on the four-state
model of Peterson. The excitation model dictates, for a specic location, the instant the concen-
tration of Ca
2+
ion concentration starts changing. The active force is proportional to the concen-
tration of attached cross-bridges, created by the binding of Ca
2+
with the protein TnC. This is
obtained by solving a set of four ordinary differential equations at each Gauss point.
1
Einstein convention on repeated indexes is used.
Figure 1: Activation potential evolution in the two ventricles (left) on a 12M tetrahedra mesh
and scalability plot up to 1000 CPUs.
2.4 Parallelization
The simulation models presented here are implemented in the Alya System, conceived for simu-
lating complex computational mechanics problems in parallel. Alya is designed from scratch to
take prot of parallel architectures with two premises: programming exibility and parallel ef-
ciency. In order to have an efcient algorithm to run on thousands of processors, some important
aspects of the parallelization must be carefully treated: mesh partitioning, node numbering and
communication scheduling. These issues will be discussed at the conference presentation.
3 CONCLUSIONS
We present a high performance computational electromechanical model of the heart that includes
coupling between electrical activation and mechanical deformation, capable of running efciently
in up to thousands of processors meshes of millions of elements. The computational model is
assessed through several numerical tests for different electrophysiology, mechanical and coupling
models.
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