Cells build proteins by linking amino acids into a chain, which spontaneously folds into a three-dimensional shape that lets the protein do its various jobs. Researchers suspect that diseases such as Mad Cow, Parkinson's and Alzheimer's result from proteins that fold improperly and get tangled together, thereby gumming up the brain. But simulating that process—to understand it and come up with drugs that interfere with it—is difficult even for the fastest computers.
The PS3 will let gamers join a project called Folding@Home (FAH), which breaks up complex simulations of proteins into manageable pieces and sends them to home computers that crunch the numbers in their spare time—similar to a screen saver. As the home machines finish their individual simulations, FAH computers assemble them into a complete picture of how a protein morphs from one shape into another.
Right now FAH includes about 2,000,000 computers and has slashed simulation times from 30 years for a mid-size protein to two or three years, says biophysicist Vijay Pande of Stanford University, who began the project in 2000. But "there's a certain point where adding more computers doesn't help anymore," he says, because some parts of the simulation cannot be broken down any further.
That's where the PS3 comes in: its highly touted Cell Broadband Engine Architecture (Cell) microprocessor can solve crucial parts of the simulation 20 times faster than standard computers, Pande says. "We can do a lot even with 10,000 processors," he says—out of two million PS3s sold so far. "It's really dramatic. It turns two years into two months."
Pande says that he will concentrate on simulating amyloid-beta, deposits of which are found in the brains of people with Alzheimer's. His goal, he adds, is to identify a drug candidate for Alzheimer's disease that pharmaceutical companies will want to evaluate. "I would really love to say a year or two from now [that] we've made a fundamental advance in Alzheimer's," he says.
He notes that he expects PS3 owners to get involved for the same reasons that others have: "people are interested in the science, in the competition, in the possibilities that we can make an impact on disease," he says.
Users will be able to run the FAH software whenever they like, or set it to switch on when the system is idle and in-between games, says Richard Marks, a senior researcher at Sony. He says Sony designers tried to make the simulation resemble other online games: The protein folds on the screen in real time, and users can zoom in or out, or rotate their view as well as monitor the number of simulations they have completed and see where around the world other PS3s are running simulations. "I think they will feel compelled to do it," he says, "just because it resonates with what they know."
The speedup that Pande envisions would allow computers to simulate many proteins at once, or much more rapidly study the effects of different chemicals or mutations on proteins, says biological physicist José Onuchic of the University of California, San Diego, who was not involved in the project. Faster computers will not answer every question, "but I think it's an important ingredient," he says. "It opens a new frontier."