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March 17, 2006

Computer Simulation of an Entire Life Form

It's a simple little virus -- so simple that biologists often refer to it as a "particle" rather than organism, so small and primitive that it can only proliferate in a cell that's already been hijacked by another virus. But a recent simulation of the satellite tobacco mosaic virus is also a striking first. There's never been a computer simulation of an entire life form at atomic detail. Until now.

A report on the work by Klaus Schulten and his collaborators at the University of Illinois at Urbana-Champaign and the University of California at Irvine appears in the March edition of Structure. It relied on computing systems at the National Center for Supercomputing Applications (NCSA), home to the largest open academic computing environment in the country.

"The ideal situation is to work with a powerful computing platform that provides output quickly and with minimal disturbance. In this way, the underlying science is the focus of the effort. NCSA provided exactly that. NCSA has always provided that," says Schulten, a long-time user.

"The federal government is renewing its commitment to high-performance computing through a series of major upcoming awards for systems substantially larger than those we support today. It's incumbent upon centers like NCSA to make the most of these investments by working closely with scientists like Prof. Schulten as well as entire communities of scientists. We have developed new ways to allocate supercomputing resources to give scientists what they need in order to make incredible breakthroughs like the simulation of an entire living thing," says Thom Dunning, NCSA's director.

Previously, all-atom molecular dynamics simulations on such a large structure have been infeasible. As a result, researchers often look at only part of a symmetric virus and use symmetric boundary conditions. Or they might simulate smaller portions of the virus or simulate the entire virus at a much coarser resolution.

Computer-simulated visualization of the satellite tobacco mosaic virus. Credit: University of Illinois/NCSA. The simulations of the satellite tobacco mosaic virus involved as many as one million atoms and simulation times of more than 50 nanoseconds. This required massive amounts of computing time -- 35 processor years. And it required a modern, scalable molecular dynamics code -- NAMD, which Schulten and his team have been developing for years. The computer simulations provided an unprecedented view into the dynamics of the virus.

"This is on the highest end of what is feasible today," says Schulten. "The approach is something that we learned from engineers: Reverse engineer the subjects you're interested in and test fly them in the computer to see if they work in silico the way they do in vivo. Naturally, deeper understanding of the mechanistic properties of other, more complicated viruses will eventually contribute to public health and medicine."

The simulations allow the research team to compare the behavior of the full virus and will help scientists determine what factors are important to the virus' structural integrity and how those factors might influence assembly of the virus inside host cells.

Deeper understanding of the mechanistic properties of viruses, the researchers say, could not only contribute to improvements in public health, but also in the creation of artificial nanomachines made of capsids -- a small protein shell that contains a viral building plan, a genome, in the form of DNA or RNA.

It may take still a long time to simulate a dog wagging its tail in the computer, says Schulten. "But a big first step has been taken to 'test fly' living organisms," he said. "Naturally, this step will assist modern medicine as we continue to learn more about how viruses live."

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Sources: National Center for Supercomputing Applications; University of Illinois at Urbana-Champaign

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