Dr. Schulten's team leveraged part of an SGI Altix 3700 Bx2 system located at the National Center for Supercomputing Applications (NCSA). The Altix system allowed them to calculate how all the atoms interact every femtosecond, or one-millionth-of-a-billionth of second.
Although the virus is small - so small, in fact, that biologists refer to it as a particle - 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", noted Peter Freddolino, a member of the Illinois research team, which also includes physicist Anton Arkhipov. "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."
The project, reported in the March issue of the scientific journal Structure, is the first successful case of biological reverse-engineering of a complete virus. "This is on the highest end of what is feasible today", stated Dr. 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 - or simulated on a computer - the way they do in vivo - in the body. Naturally, deeper understanding of the mechanistic properties of other, more complicated viruses will eventually contribute to public health and medicine."
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.
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 1024-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 Altix platform has excellent single node performance and a very efficient MPI implementation", stated Peter Freddolino, "and both of these factors made the system very useful in performing our work efficiently." "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", added Dr. Schulten, a long-time NCSA 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", stated Thom Dunning, director, NCSA. "It's incumbent upon centres like NCSA to make the most of these investments by working closely with scientists like Professor Schulten as well as entire communities of scientists. We have developed new ways to allocate supercomputing resources, such as our large-scale SGI Altix deployment, to give scientists what they need in order to make incredible breakthroughs like the simulation of an entire living thing."
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 throughout the United States, 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 Anton Arkhipov, who has worked with Peter 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 behaviour - 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 work flows 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.
More SGI news is available in the VMW March 2006 article Robarts Research Institute chooses SGI technology to enable advanced medical simulation for minimally invasive surgery.