A research team at the University of Illinois simulated a plant virus with as many as 1 million moving atoms.

The team was led by Professor Klaus Schulten. Their achievement is historic due to the sheer complexity of the problem: had the researchers relied on today’s desktop computer systems, they wouldn’t have finished until 2041.

Using a SGI Altix 3700 Bx2 system located at the National Center for Supercomputing Applications (NCSA), the team calculated how all the atoms interact every femtosecond, or one-millionth-of-a-billionth of second.

The project is the first successful case of biological reverse-engineering of a complete virus. While the virus attacks plants, the researchers predict that someday, drugs for animals or even humans may be designed and refined with the help of computer-based simulations like the one developed with SGI Altix.

Although the virus is small the ability to simulate the organism as it functions holds tremendous promise for medical research. “It allows us to see how the virus assembles and disassembles,” notes Peter Freddolino, a member of the Illinois research team. “Because assembly and disassembly are two of the key steps in the viral life cycle, understanding these events could lead to the development of drugs designed to attack them at these vulnerable points.”

For the researchers, NCSA’s Altix system proved a powerful, efficient resource. Despite the complexity of the project, the researchers needed just 50 days and a fraction of the NCSA’s 1,024-processor Altix system: most simulations used 256 processors and 128GB of total memory, leaving the rest of the NCSA system available for other projects. The team’s scalable molecular dynamics code, known as NAMD, segments tasks across processors and memory, enabling simulations to make the most of as many processors and as much memory as they require.

The smallest natural organisms known, viruses contain intricate mechanisms for infecting host cells. The Illinois researchers simulated one of the tiniest and most primitive viruses in an attempt to recreate the process of infection and propagation. The satellite tobacco mosaic virus attacks tomato plants, and relies on a host cell and a host virus to reproduce.

While they simulated the activity of the viral organism over just 50 nanoseconds of time, the researchers were able to determine that the virus, which appears symmetrical, actually pulses in and out in an asymmetrical pattern. “We observed that each part of the viral structure moves a little bit on its own,” noted Arkhipov, who has worked with Freddolino and Dr. Schulten since the project’s inception a little more than a year ago. The team’s simulated findings support observations made by others in traditional laboratory work. Those earlier observations, however, left researchers wondering what caused the behavior - something that remained a mystery until today.

The Altix family leverages the built-in SGI NUMAlink interconnect fabric, which allows global addressing of all memory in the system and delivers data up to 200 times faster than conventional interconnects. For the first time, more complex data sets and complete workflows can be driven entirely out of memory, enabling productivity breakthroughs that traditional Linux clusters or repurposed UNIX servers can’t achieve. Altix systems offer breakthrough flexibility and configurability, scaling to up to 512 processors per node. Based on a 64-bit Linux operating environment, the Altix family is uniquely capable of independently scaling processors, shared memory and/or I/O on a single, standard chassis with different expansion modules, providing optimal resource usage for demanding technical applications.

Image courtesy of the University of Illinois.