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Journal North: Home | Sports | Opinion | Obits | Entertainment
Saturday, November 07, 2009
Computer Scores Against HIV
By John Fleck
Journal Staff Writer
In the deadly game of cat and mouse between HIV and the human immune system, the immune system has acquired an unusual ally.
A New Mexico supercomputer built for nuclear weapons research, using computer chips originally designed for video games, has been used to build a sort of family tree of the remarkably diverse and dangerous virus that causes AIDS.
More than idle genetic curiosity, the work is part of en effort to develop an effective vaccine against the deadly disease, said Bette Korber, a Los Alamos National Laboratory biologist and one of the world's leading AIDS geneticists.
For the human immune system, and the scientists trying to help it, HIV is a shape-shifter with the maddening ability to rapidly evolve away from the countermeasures the body and science try to deploy against it.
To help gain ammunition for the battle, Korber and her colleagues have been using Roadrunner, the world's fastest supercomputer. Completed in 2008 for nuclear weapons research and development, Roadrunner was first handed over to nonweapons scientists like Korber for a shakedown phase, testing the computer's capabilities on nonclassified problems like cosmology and AIDS research.
Korber and her colleagues took genetic material in HIV taken from 400 different infected people and studied it, looking for patterns.
The problem, Korber explained, is that once HIV enters the human body, its rapid rate of reproduction and mutation means it is a constantly changing target for the immune system.
Just as the immune system recognizes the virus and learns how to fight it, a new mutation gives it a different appearance. The immune system has to start the fight all over again, against what looks like a new opponent.
"HIV is just massively variable," Korber said. "It's like this ongoing battle."
For a vaccine to work, it has to teach the immune system to recognize the virus when it first arrives. To get a better handle on the problem, Korber and her colleagues used Roadrunner to study the huge variety of genetic patterns in the virus from 400 different patients, using the family tree to try to better understand what they have in common, and what the differences are.
Roadrunner was ideal for the job because of the clever way it concentrates the ability to do many simultaneous calculations on each computer chip, said Marcus Daniels, another Los Alamos scientist who did the computer programming on the project.
Roadrunner is made of thousands of Cell computer chips, which were originally developed for the Sony Playstation 3 video game console. Last year, the $120-million machine, built by IBM, became the first computer to perform a million billion calculations per second, and it is still the world's fastest.
The genetics of HIV is a longstanding area of expertise at Los Alamos, dating to the 1980s when lab scientist Gerry Myers realized the importance of collecting genetic data on the virus in one place for scientists around the world to use. The lab remains the home of the global HIV genetic database.
After the shakedown period working on HIV genetics and other nonweapons work, Roadrunner is being moved "behind the fence" to do classified nuclear weapons work. But Daniels noted that a smaller supercomputer cluster based on the same technology known as Cerrillos is still available to continue the HIV research.
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