Supercomputer Builds a Virus
One of the world's most powerful supercomputers has conjured a fleeting moment in the life of a virus. The researchers say the simulation is the first to capture a whole biological organism in such intricate molecular detail. The simulation pushes today's computing power to the limit. But it is only a first step. In future researchers hope that bigger, longer simulations will reveal details about how viruses invade cells and cause disease. Klaus Schulten at the University of Illinois, Urbana, and his colleagues built a computer model of the satellite tobacco mosaic virus, a tiny spherical package of RNA. Their success depended on the latest version of a computer program called NAMD, which Schulten and his colleagues have built over the past decade to simulate biological molecules. The program allows the several hundred different processors within a supercomputer to work in parallel on the same problem. Running on a machine at the National Center for Supercomputing Applications, Urbana, the program calculated how each of the million or so atoms in the virus and a surrounding drop of salt water was interacting with almost every other atom every femtosecond, or millionth of a billionth of a second. The team managed to model the entire virus in action for 50 billionths of a second. Such a task would take a desktop computer around 35 years, says Schulten. "This is just a first glimpse," he says. "But it looks gorgeous." Read more... This was seized 4 u at Nature |
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