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World's fastest supercomputer tasked with dark matter, DNA sequencing

World's fastest supercomputer tasked with dark matter, DNA sequencing

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The world's fastest supercomputer may have been built to model nuclear explosions, but it's now being tasked with simulating the Big Bang and managing more than 10,000 DNA sequences infected with HIV.

The world's fastest supercomputer may have been built to model nuclear explosions, but it's now being tasked with simulating the Big Bang and managing more than 10,000 DNA sequences infected with HIV.

Originally built by IBM and the U.S. Department of Energy, the Roadrunner supercomputer was turned on last November. Now, two new experiments used its number-crunching power for more peaceful means.

In one experiment, Roadrunner created the largest family tree of HIV-infected DNA sequences ever produced, incorporating more than 10,000 sequences culled from more than 400 subjects.

Since viruses can mutate rapidly, this allowed scientists to compare results across an array of patients and learn how mutations relate back to the initial infecting agent. That could expose a weak link in the virus that scientists could exploit to develop a vaccine, said physicist Tanmoy Bhattacharya and HIV researcher Bette Korber.

"The petascale supercomputer gives us the capacity to look for similarities across whole populations of acute patients," Bhattacharya said in a statement. "At this scale we can begin to figure out the relationships between chronic and acute infections using statistics to determine the interconnecting branches—and it is these interconnections where a specially-designed vaccine might be most effective."

In another experiment, Roadrunner simulated the Big Bang in an attempt to understand the existence of dark matter in the universe. The supercomputer created an early model of the universe by calculating the physics behind more than 64 billion protogalaxies, each with a mass of approximately one billion suns.

Roadrunner's computing power is necessary to handle the scope of something as large as a section of the universe, said Salman Habib of the Laboratory's Nuclear and Particle Physics, Astrophysics and Cosmology group.

"There is five times more of an unknown 'dark matter' than there is ordinary matter in the universe, and we now it's there from many different observations, most spectacularly, we've seen it bend light in pictures from the Hubble Space Telescope, but its origin is also not understood," said in a statement, adding that the simulation will help scientists better survey the universe.

What's the sustained speed it takes to qualify as the world's fastest supercomputer, by the way? Precisely 1 petaflop, or 1 million billion calculations, per second.

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Andrew Nusca

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Andrew Nusca is editor of SmartPlanet and an associate editor for ZDNet. Previously, he worked at Money, Men's Vogue and Popular Mechanics magazines. He holds degrees from the Columbia University Graduate School of Journalism and New York University. He is based in New York but resides in Philadelphia. Follow him on Twitter. Disclosure