Working Fast to Slow Things Down

By Robert Gelber

February 13, 2012

Hideaki Fujitani is a professor at Tokyo University’s Laboratory for Systems Biology and Medicine (LSBM). He has a supercomputer and aims to cure cancer with it — that according to a recent article in The Japan Times, in which Fujitani’s work is described.

According to the article, Fujitani spends most of his time running simulations of antibodies bonding, or attempting to bond, to antigens. For those of you who slept during biology class, antibodies are proteins the immune system uses to attach to antigens (foreign molecules); in this case Fujitani is studying antigens specific to cancer cells.  The LSBM, led by Tatsuhiko Kodoma, is focused developing drugs for patients with recurring and advanced stages of cancer.

The simulations are aimed at making an antibody bond to and neutralize an antigen. There is one catch though, the simulation is of 30,000 to 40,000 atoms, made up of antigen, antibody and surrounding water. Also, the molecules move extremely fast, “A molecule moves in about 1 femtosecond, gradually changing the shape of proteins over microseconds,” says Fujitani, “To see the dynamics, you need to solve about one billion equations. If one CPU were able to solve one equation per second, it would still take 32 years to solve all the problems. That’s why we need the fastest supercomputer with lots of CPUs.”

Luckily for Fujitani the LSBM acquired a 612-core supercomputer in 2010 that can crack 34 teraflops. Just months after the super’s arrival, he was verifying his simulation results with an X-Ray of an actual antibody. As amazing as his work may seem, gaining support for computer-aided drug development was not so simple. He struggled to receive support from Fujitsu, his former employer, and the Japanese pharmaceutical industry, before taking his talents to the University of Tokyo.

Because of the nature of his practice, Fujitani can always use more computational power. Fortunately he will soon be getting that with a project that will tap into what is currently the fastest computer in the world, the 10-petaflop K computer. “The K will be 240 times faster than the machine here, so we can do the calculations much more quickly, and run different programs simultaneously,” he continued, “What takes a month to simulate here will be done in three or four days.”

Fujitani seems confident that the work he and the rest of Kodoma’s team will be able to find a cure for cancer.  He says that in the future even people with advanced stages of cancer will be able to be cured.
 

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