Features | Partner Sites | Information | LinkXpress
Sign In
JIB
GLOBETECH PUBLISHING
BioConferenceLive

Supercomputer Simulates Beating Heart, Helping Drive Research

By BiotechDaily International staff writers
Posted on 04 Dec 2012
A new supercomputer had been built specifically to tackle weapon simulations, but before it goes into its intended work, it is generating cutting-edge cardiac simulations.

The Sequoia [IBM’s BlueGene/Q] holds the number two rank in the November 2012 TOP500 list of the world’s fastest computer systems [top ranked in the June 2012 TOP500 list].

Sequoia is bringing modeling and simulation and modeling to new peaks, timing in at 16.32 sustained petaflops (20 PF peak), enabling scientists to capture greater complexity in a shorter period. With this advanced capability, Lawrence Livermore US National Laboratory’s (LLNL; Livermore, CA, USA) scientists have been able to simulate the human heart down to the cellular level and use the resulting model to predict how the organ will respond to different drug compounds.

The simulations were made possible by an advanced modeling program, called Cardioid, which was designed by a group of scientists from LLNL and the IBM T. J. Watson Research Center (Yorktown Heights, NY, USA). The extremely scalable code simulates the electrophysiology of the heart. It functions by breaking down the heart into units: the smaller the unit, the more effective the model. Up to now, the optimal modeling programs could attain 0.2 mm in each direction. Cardioid can jump down to 0.1 mm. Where earlier, researchers could run the simulations for tens of heartbeats, Cardioid executing on Sequoia captures thousands of heartbeats.

Scientists are experiencing 300-fold speedups. It used to take 45 minutes to simulate just one beat, but now researchers can simulate an hour of heart activity--several thousand heartbeats--in seven hours. With the less sophisticated codes, it was impossible to model the heart’s response to a drug or perform an electrocardiogram trace for a particular heart disorder. That sort of testing entails longer run times, which was not possible before Cardioid.

The model could hypothetically evaluate a range of medications and devices such as pacemakers to examine their effect on the heart, creating an avenue for more effective and safer human testing. But it is particularly suited to examining arrhythmia, a disorder of the heart in which the organ does not pump blood efficiently. Arrhythmias can lead to congestive heart failure, an inability of the heart to supply sufficient blood flow to meet the needs of the body.

There are various types of medications that disrupt cardiac rhythms. Even those designed to prevent arrhythmias can be detrimental to some patients, and researchers do not yet completely understand precisely what causes these negative side effects. Cardioid will enable LLNL scientists to examine heart function as an antiarrhythmia drug enters the bloodstream. They will be able to identify when drug levels are highest and when they decline. “Observing the full range of effects produced by a particular drug takes many hours,” noted computational scientist Art Mirin of LLNL. “With Cardioid, heart simulations over this timeframe are now possible for the first time.”

The Livermore-IBM group is also working on a mechanical model that simulates the contraction of the heart and pumping of blood. The mechanical and electrical simulations will be allowed to interact with each other, adding more realism to the heart model.

The cardiac modeling research was performed during the system’s “shakedown period”--the set-up and assessment stage--and the scientists had to rush to complete in the allotted time span. Once Sequoia becomes classified, it is uncertain if it will still be available to run Cardioid and other unclassified programs, although access will certainly be more difficult since the computer’s key mission is running nuclear weapons codes.

Sequoia is an integral part of the US National Nuclear Security Administration’s (NNSA) Advanced Simulation and Computing (ASC) program, which is run by partner organizations LLNL, Los Alamos US National Laboratory, and Sandia National Laboratories. With 96 racks, 98,304 compute nodes, 1.6 million cores, and 1.6 petabytes of memory, Sequoia will help the NNSA fulfill its mission to “maintain and enhance the safety, security, reliability, and performance of the US nuclear weapons stockpile without nuclear testing.”

The Cardioid simulation has been chosen as a finalist in the 2012 Gordon Bell Prize competition, awarded each year to recognize supercomputing’s ultimate achievements. The scientists divulged their findings at the Supercomputing Conference in Salt Lake City (UT, USA), on November 13, 2012.

Related Links:

Lawrence Livermore U.S. National Laboratory
IBM T. J. Watson Research Center
US National Nuclear Security Administration




comments powered by Disqus

Channels

Genomics/Proteomics

view channel
Image: Microcomputed tomography images (top) and histology images (bottom) of the knees of mice fed a very high fat diet containing omega-3 fatty acid supplement (left) or only omega-6 fatty acids (right) after a knee injury. The omega-6 diet showed abnormal bone remodeling and calcified tissue formation in the joint (white arrow). The omega-6 diet also showed significant loss of cartilage (red staining, yellow arrowhead) and increased joint inflammation (Photo courtesy of Duke University).

Dietary Omega-3 Fatty Acids Moderate Severity of Osteoarthritis in a Mouse Model

Researchers working with an osteoarthritis (OA) obese mouse model found that the fat content of the animals' diet contributed more to the development or arrest of OA than did body weight.... Read more

Drug Discovery

view channel
Image: Molecular rendering of the crystal structure of parkin (Photo courtesy of Wikimedia Commons).

Cinnamon Feeding Blocks Development of Parkinson's Disease in Mouse Model

A team of neurological researchers has identified a molecular mechanism by which cinnamon acts to protect neurons from damage caused by Parkinson's disease (PD) in a mouse model of the syndrome.... Read more

Therapeutics

view channel

Vaccine Being Developed for Heart Disease Close to Reality

The world’s first vaccine for heart disease is becoming a possibility with researchers demonstrating significant arterial plaque reduction in concept testing in mice. Klaus Ley, MD, from the La Jolla Institute for Allergy and Immunology (LA Jolla, CA, USA), and a vascular immunology specialist, is leading the vaccine... Read more

Business

view channel

A Surge in IPOs Revitalize Investments for the Global Pharma and Biotech

Anti-infective drugs, oncology, and pharmaceutical contract laboratories attract the most investment up to now. The intensified private equity and venture capital (PEVC) deal activity in the global healthcare industry during the recession years, 2008–2010, witnessed a waning post-2010. However, the decline in deals... Read more
 
Copyright © 2000-2014 Globetech Media. All rights reserved.