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HPC aPPliCations: BiomediCal
➤ muscles grow rapidly, and ultimately million grid points.’ time step we have to update the velocity
Accelerating the pace of engineering and science
occlude the vein somewhere downstream of The team looked at varying the and the pressure, and we have to update a
the anastomosis, or point at which the graft diameters of the graft. The grafts are set of equations to achieve that. Typically it
joins the vein. This occlusion eventually tapered, from 4mm at one end to 6mm turns out that we’re solving a large system
leads to failure of the graft. at the other end, in order to match the of equations, for three million grid points,
Fischer’s simulations focus on the join diameter change between the artery and with roughly 10 or 11 million unknown
between the graft and the vein. At this the vein. ‘We have found that this is one of values.’
point, high pressure blood from the artery the key ways in which to avoid turbulence; Using its simulations, the team has found
is introduced into the slower, low pressure we want to avoid having any sudden that if blood faces an adverse pressure
blood of the vein, and this is where transitions [in tube diameter].’ gradient because of a change in velocity, a
turbulence is known to have a detrimental For a single graft study, or simulation, transition to turbulence will occur at the
effect. In the simulations, the vein is 6mm a computational domain is created in the anastomosis. In order to reduce the effects
in diameter, and the simulation extends form of a mesh. The meshes do not only of this transition, the graft is angled at the
around 35mm up the graft, 25-30mm cover the surfaces of the graft and blood joint: ‘Where the graft joins into the vein,
upstream of the anastomosis, 35-40mm vessels, but also fill their interior. That set it is pointed towards the proximal segment
[the downstream side],’ says Fisher. ‘Even
so, the pressure can be sufficient to reverse
For a single graft study, or simulation, a computational domain is the flow of blood, even to the extent that
created in the form of a mesh. The meshes do not only cover the
blood from the graft can end up moving
in both directions within the vein. In our
surfaces of the graft and blood vessels, but also fill their interior.
study, this effect [of a split flow] was found
to be the most sensitive parameter.’
Over one million people around
The team found, based on simulations
the world speak MATLAB.
downstream of it, where failures are of three million points is partitioned over and on statistical research, that the cross-
Engineers and scientists in every field
most likely to occur. Fisher explains that 256 processors of the IBM Blue Gene. sectional area of the join between the graft
from aerospace and semiconductors
turbulence occurs on a much smaller scale Each processor is treated as an entire and the vein is a key parameter in reducing
to biotech, financial services,
than these dimensions, typically in the computational domain, and boundary data turbulence. ‘That gave us a fair amount of and earth and ocean sciences
order of 0.25-0.5mm: ‘There are a lot of is exchanged at the beginning of each confidence that we had discovered one of
use it to express their ideas.
small scale structures generated by this time-step in order to keep each component the mechanisms for turbulence in these AV
Do you speak MATLAB?
turbulence, and the simulation mesh we use accurate to its neighbours. ‘We partition grafts,’ says Fisher. Lessons learnt through
has to be smaller than the smallest length the domain, or the grid points, onto this study are already being implemented
scale,’ he says. ‘Typically, for the geometry separate processors, and then we time- in the AV grafts inserted into patients,
Electrons gain 42 billion
described, we’re looking at two or three march the unsteady blood flow. At every making a difference not only in the virtual,
electron volts in a plasma
wakefield accelerator.
but also in the real world.
Provided by Stanford Linear
Accelerator Center.
Storing one’s genome
Fischer’s simulations display how the
number-crunching characteristics
of HPC can make a difference in
contemporary medicine. But the abilities
of supercomputing systems to store and
process data are just as important in the
application of today’s research biology
to medical practice of the future. The
first sequence of the human genome was
rightly lauded as a landmark in biology
and medicine when it was completed.
However, no single individual’s genome

was sequenced – it was rather a generic,

‘reference’ genome. Now, the interest is
in sequencing individuals and correlating
variations in their DNA with their

individual health outcomes (and also their
individual reactions to pharmaceutical
drugs). In this way, genomics may lead to
personalised medicines. But first, all that ➤ The language of technical computing
SCIENTIFIC COMPUTING WORLD october/november 2009
SCWOct09 pp32-37 Bio.indd 34 10/2/09 4:38:28 PM
Client Name: The Mathworks
Job# MAT_FALAS Cosmos Communications 718.482.1800
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