Fw: [evol-psych] Success for distributed computing

From: Philip Jonkers (ephilution@attbi.com)
Date: Wed 23 Oct 2002 - 06:02:36 GMT

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          Folding@home scientists report first distributed computing success
          As you read this sentence, millions of personal computers around the world are
          working overtime - performing complex computations on their screensavers in the
          name of science. This growing Internet phenomenon, known as "distributed
          computing," is being used for everything from the search for extraterrestrial
          intelligence (SETI) to the design of new therapeutic drugs.

          Now, for the first time, a distributed computing experiment has produced
          significant results that have been published in a scientific journal. Writing
          in the advanced online edition of Nature magazine, Stanford University
          scientists Christopher D. Snow and Vijay S. Pande describe how they - with the
          help of 30,000 personal computers - successfully simulated part of the complex
          folding process that a typical protein molecule undergoes to achieve its
          unique, three-dimensional shape. Their findings were confirmed in the
          laboratory of Houbi Nguyen and Martin Gruebele - scientists from the University
          of Illinois at Urbana-Champaign who co-authored the Nature study.

          Understanding disease

          Every protein molecule consists of a chain of amino acids that must assume a
          specific three-dimensional shape to function normally.

          "The process of protein folding remains a mystery," said Pande, assistant
          professor of chemistry and of structural biology at Stanford. "When proteins
          misfold, they sometimes clump together, forming aggregates in the brain that
          have been observed in patients with Alzheimer's, Parkinson's and other

          How proteins fold into their ideal conformation is a question that has
          tantalized scientists for decades. To solve the problem, researchers have
          turned to computer simulation - a process that requires an enormous amount of
          computing power.

          "One reason that protein folding is so difficult to simulate is that it occurs
          amazingly fast," Pande explained. "Small proteins have been shown to fold in a
          timescale of microseconds [millionths of a second], but it takes the average
          computer one day just to do a one-nanosecond [billionth-of-a-second] folding

          Simulating protein folding is often considered a "holy grail" of computational
          biology, he added. "This is an area of hot competition that includes a number
          of heavy weights, such as IBM's $100-million, million-processor Blue Gene
          supercomputer project."


          Two years ago, Pande launched Folding@home - a distributed computing project
          that so far has enlisted the aid of more than 200,000 PC owners, whose
          screensavers are dedicated to simulating the protein-folding process.

          The Stanford project operates on principles similar to earlier projects, such
          as SETI@home, which allows anyone with an Internet connection to search for
          intelligent life in the universe by downloading special data-analysis software.
          When a SETI@home screensaver is activated, the PC begins processing packets of
          radio telescope data. Completed packets are sent back to a central computer,
          and new ones are assigned automatically.

          For the Nature study, Pande and Snow - a biophysics graduate student - asked
          volunteer PCs to resolve the folding dynamics of two mutant forms of a tiny
          protein called BBA5. Each computer was assigned a specific simulation pattern
          based on its speed.

          With 30,000 computers at their disposal, Pande and Snow were able to perform
          32,500 folding simulations and accumulate 700 microseconds of folding data.
          These simulations tested the folding rate of the protein on a 5-, 10- and
          20-nanosecond timescale under different temperatures. Using these data, the
          scientists were able to predict the folding rate and trajectory of the
          "average" molecule.

          Experimental verification

          To confirm their predictions, the Stanford team asked Gruebele and Nguyen to
          conduct "laser temperature-jump experiments" at their Illinois lab. In this
          technique, an unfolded protein is pulsed with a laser, which heats the molecule
          just enough to cause it to bend into its native state. A fluorescent amino acid
          imbedded inside the molecule grows dimmer as the protein folds. Researchers use
          the changing fluorescence to measure folding events as they occur.

          The results of the laser experiments were in "excellent agreement" with the
          Folding@home predictions, Pande and his colleagues concluded.

          Specifically, the computers predicted that one experimental protein would fold
          in 6 microseconds, while laboratory observations revealed an actual folding
          time of 7.5 microseconds.

          "These experiments represent a great success for distributed computing," Pande
          said. "Understanding how proteins fold will likely have a great impact on
          understanding a wide range of diseases."

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