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Reducto ad absurdum on the LANL ASCI Q?

A research team at Los Alamos National Laboratory has topped a world record for biological simulations, and given us a taste of reducto ad absurdum. As reported in the Nov. 1 issue of PNAS the LANL team, led by Kevin Sanbonmatsu, used 768 of the 8,192 CPUs in LANL's ASCI Q supercomputer to model the motion of 2.64 million atoms in a ribosome complex -- 250,000 in the ribosome itself, and most of the rest from water molecules. The processors chugged away for some 260 days, completing 20 milli

By | October 25, 2005

A research team at Los Alamos National Laboratory has topped a world record for biological simulations, and given us a taste of reducto ad absurdum. As reported in the Nov. 1 issue of PNAS the LANL team, led by Kevin Sanbonmatsu, used 768 of the 8,192 CPUs in LANL's ASCI Q supercomputer to model the motion of 2.64 million atoms in a ribosome complex -- 250,000 in the ribosome itself, and most of the rest from water molecules. The processors chugged away for some 260 days, completing 20 million frames of motion. Sounds impressive, right? It is: it's six times larger than any biological simulation ever done. LANL has made a Quicktime movie of the simulation available on its Web site. The sim is a bit jerky, but it shows in atomic detail how the A-site tRNA binds to the ribosome and swings the new amino acid into position during translation, looking much like a nucleic acid crane. According to the LANL press release, the research identified a "corridor inside the ribosome that the transfer RNA must pass through for the decoding to occur" -- a potential site for new antibiotics development. Further, the study demonstrates the active role tRNA plays in the ribosome's motion, and "sets the stage for further biochemical research". But let's for one minute consider the numbers. The simulation's 20 million frames represent just 2 nanoseconds of real time -- or 1e-16 seconds per frame. Put another way, the computer worked at a rate of about 8 picoseconds per day. Claymation animator Nick Park's team, by contrast, produced about three usable seconds of film per day when shooting the 85-minute Wallace & Gromit: The Curse of the Were-Rabbit. Now I'm a huge fan of tech, gadgets, and the like, and I love this study for its scale and beauty. But is this the best way to spend nine months of time on what is currently the 12th fastest supercomputer in the world? If new antibiotics really come out of this, then I suppose it was. So it's wait and see time -- just like the simulation itself. [Via CNET News]
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