First Atom-by-Atom Simulation of a Life Form


The computing horsepower of one of the world’s most powerful supercomputers has been harnessed by Swanlund Professor of Physics Klaus Schulten and his research group to visualize the behavior of a complete life form, the satellite tobacco mosaic virus. "This is just a first glimpse of a moving virus,” Schulten said, “but it looks gorgeous.”

According to the researchers, their simulation is the first to capture an entire biological organism in atom-by-atom detail. The simulation was done at the National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign.

A better understanding of viral structures and mechanisms is an essential step in allowing scientists to develop improved methods of combatting viral infections in plants, animals, and eventually, humans.

Schulten’s group, which includes Peter Freddolino, a graduate student in biophysics and computational biology, and Anton Arkhipov, a graduate student in physics, collaborated with crystallographers at the University of California, Irvine—Alexander McPherson, a professor of molecular biology and biochemistry, and research specialist Steven Larson. The group’s results were published in the March issue of Structure (P.L. Freddolino, et al., Structure 14, 1767–1777 [2006]).

The researchers visualized the dynamic atomic structure of the virus in a saline solution by calculating, in femtosecond time steps, how each of its »1 million atoms moved.

The simulation utilized the latest version of NAMD, a software program developed by Schulten and his colleagues over the last decade to model the molecular dynamics of biological molecules. The program allowed the supercomputer’s five hundred processors to work in parallel on the same problem. Even so, the simulation took about 50 days to generate 50 ns of virus activity.

“Such a task would take a desktop computer around 35 years," according to Schulten.

“The simulations followed the life of the satellite tobacco mosaic virus, but only for a very brief time,” added Freddolino and Arkhipov. “Nevertheless, they allowed us to discover key physical properties of the viral particle, as well as providing crucial information on its assembly.”

In the brief simulation, the virus looks spherical but expands and contracts asymmetrically, as if it were “breathing.” The model also shows that the virus coat collapses without its genetic material, suggesting that when reproducing, the virus builds its coat around the genetic material, rather than inserting it into a pre-existing coat as was commonly assumed. “We saw something that is truly revolutionary,” Schulten said.

Ultimately, computational biophysicists will generate longer simulations of larger biological macromolecules, but that development will wait on the next generation of supercomputers, the so-called “petascale high-performance computing systems.”

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

This work was supported by the National Institutes of Health and by allotments of computing time from the National Center for Supercomputing Applications through its National Science Foundation funding. The conclusions presented are those of the authors and not necessarily those of the funding agencies.

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