- The Washington Times - Thursday, June 21, 2007

Video games might lead the way to the cure for Alzheimer’s disease. Go figure. Gamers who own a PlayStation 3 can take part in an amazing experiment in which their console’s powerful processor is tapped into and used by researchers at Stanford University to simulate protein-folding experiments that eventually could conquer some diseases.

Vijay Pande, director of the [email protected] project and associate professor of chemistry at Stanford University, took some time to reveal the mysteries of proteins and magic behind the computer initiative.

Q: What are proteins and why do they need to fold?

A: They are nature’s nanomachines. Proteins are the molecules the body uses to get everything done. They act as catalysts to speed up chemical bonds that might take a billion years through other types of biological machinery. Whenever something needs to get done in biology, odds are, proteins are at work.

Q: What happens when the process does not work?

A: When proteins do not fold correctly, trouble occurs. There are lots of ways this can occur. A human can be missing the protein, as is the case in cystic fibrosis. What is more prevalent is that there are a whole class of diseases that were thought not to be related to one another, such as mad cow, Alzheimer’s, Parkinson’s, types of cancer and amyotrophic lateral sclerosis (ALS), that are related to protein misfolding.

Q: What are the latest breakthroughs in the field of biochemistry?

A: The connection between biology and nanotechnology is very exciting, and for decades it has been a dream to be able to rationally design drugs. … The dream is to design molecules the way we design macroscopic objects. Sounds easy, but being so small, you must be really, really accurate, and it is very computationally demanding.

Q: Where did you get the Folding@Home idea?

A: It started to take shape in 1999. I had been working in the protein-folding field since 1992, and I really wanted to develop something that would push the envelope in the field.

We needed to bridge the gap between simulations and experiments, and it became clear that one of the biggest bottlenecks was the computational limits involved in the simulations. It took us about a year to really figure out how to do it, and we began using distributed computing.

Q: What is distributed computing?

A: Even back then, the calculations we wanted to do would take about a million days on a fast processor. So it seemed natural that we might be able to get it done in 10 days if we had access to 100,000 processors. So, in using distributed computing, we could run pieces of the simulation through networked computers to speed up the results.

Q: Why don’t you just use a supercomputer?

A: One typically holds 5,000 processors, but each often is surprisingly slower than a fast processor in a PC these days. Also, you never get the supercomputer to use for yourself; you share the processors. So the power in terms of raw performance in comparison to what we can do in [email protected], is about 100 times slower.

Q: How did the PlayStation 3 get involved?

A: Even with our [email protected] program for PCs, there are certain calculations, even with the amount of computers we have, that still take 18 months to run.

When I saw the specs of the PS3 come out, I knew it could have a lot of potential power for the type of simulations. We worked with Sony, and the early tests showed better than a 20 time speedup.

Q: What are your goals with the program?

A: We can handle about 2 million PS3s right now, but only about 30,000 are folding. We hope to be able to get more PS3 owners involved and make some exciting experimental predictions that bear out. It’s hard to know how long it will take to come up with therapeutics for diseases. We could be close or a hundred years away, but distributing computing will help speed up the process.

To join Folding@Home, PS3 owners with system version 1.6 or later simply click on the Folding@Home icon within the Network menu of the console’s Xross Media Bar. When the PS3 goes into idle mode, it automatically will begin simulations.

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