Researchers at Rice University use Cray supercomputer to unlock biomedical mysteries and aid future diagnostics

Seattle 26 June 2007Research teams using a Cray supercomputer at Rice University's Computer and Information Technology Institute (CITI) have developed computational techniques that will eventually assist medical workers in diagnosing and treating some of the most devastating diseases afflicting humans - ranging from cerebral aneurysms to illnesses such as bacterial/viral infections and cancer.


"The large-scale processing provided by our Cray supercomputer enables researchers to develop highly detailed models and sophisticated algorithms that more closely match actual conditions in the body", stated Jan Odegard, the executive director of CITI. "One research team is conducting blood-flow simulations at a level of accuracy that was not feasible before we had this degree of computational power. And new computer algorithms developed by another team reduce the time it takes to analyse biomolecular processes from days and months to mere minutes."

Members of the Team for Advanced Flow Simulation and Modelling at Rice are collaborating with colleagues from other institutions to create computational fluid dynamics models that mimic how blood courses through the brain's arteries and interacts with an aneurysm on a vessel wall. An aneurysm is a balloon-like protrusion of an artery that could be fatal if it bursts. The team uses the Cray system to simulate numerically how the blood, artery and aneurysm interact with each other. The data is then loaded into a programme from Computational Engineering International called EnSight, which provides visualization and analytical capabilities.

"Accurate blood-flow simulations are extremely complex because an artery wall isn't rigid and blood pressure fluctuates with the beating of the heart", stated Tayfun Tezduyar, professor of mechanical engineering at Rice. "We want to understand how much a cerebral artery wall deforms, how blood flow is affected and what stresses are created that could affect the aneurysm. A precise understanding of this dynamic will be of great benefit to brain surgeons when they have to make a decision about whether or not to operate."

Another team of researchers at CITI has partnered with colleagues at the University of Texas Health Science Center at Houston to develop new algorithms for studying the biomolecular interactions that occur when a disease-causing bit of protein, referred to as a "ligand", attaches itself to another molecule known as a "receptor". A traditional Singular Value Decomposition algorithm running on a conventional computer does not preserve the symmetry of the molecule, making it difficult to isolate and study a protein's characteristics. The team developed more accurate algorithms that they "parallelized" to run quickly on the supercomputer. The new techniques promise to help medical researchers invent new drugs that work by keeping the ligand from docking to the receptor, preventing the disease mechanism from operating.

"The algorithms we developed significantly compress the search we have to perform by focusing on the controlling behaviour and retaining the symmetry of the protein, while giving us the flexibility to gain deeper knowledge of the biomolecular mechanisms involved", stated Danny Sorensen, professor and department chair of Computational and Applied Mathematics at Rice, who leads the research team. "We're dealing with sizable data sets. Running even the simplest computations for these molecular complexes would be nearly impossible on a less-powerful computer."

"Scalable computation is crucial to modern medical research", stated Jan Silverman, senior vice president, corporate strategy and business development for Cray. "Cray supercomputers are playing a prominent role in the important advances achieved by research teams such as those affiliated with Rice University's CITI. This is the type of science that can ultimately result in people living longer and healthier lives, and Cray is proud to be a part of it."

CITI is a research-centric institute dedicated to the advancement of applied interdisciplinary research in the areas of computation and information technology by bringing together scholars with complementary expertise to solve complex problems. Research areas include parallel computation, robotics, telecommunications, data modelling and analysis, bioinformatics, advanced computation, computational neuroscience, sensor networks and computational fluid dynamics. Rice acquired the Cray system with funding from the National Science Foundation (CNS-0421109 & CNS 0454333).

As a global expert in supercomputing, Cray provides highly advanced supercomputers and world-class services and support to government, industry and academia. Cray technology enables scientists and engineers to achieve remarkable breakthroughs by accelerating performance, improving efficiency and extending the capabilities of their most demanding applications. Cray's Adaptive Supercomputing vision will result in innovative next-generation products that integrate diverse processing technologies into a unified architecture, allowing customers to surpass today's limitations and meeting the market's continued demand for realized performance. More company news can be found in the VMW May 2007 article Researchers use Cray XT3 supercomputer at PSC to break through drug-resistant bacteria's defenses.

Leslie Versweyveld

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