We fold our own

Thanks to Mark and Michelle, the Cohens are now part of the largest distributed computing project in history! Among the many marvels of our new Playstation 3: the ease with which we are suddenly folding@home. Wikipedia will tell you that means we’re letting Stanford University use our playstation’s “downtime” to “perform computationally intensive simulations of protein folding and other molecular dynamics.”

Why simulate protein folding? Here’s what f@h says:

Proteins are biology’s workhorses — its “nanomachines.” Before proteins can carry out their biochemical function, they remarkably assemble themselves, or “fold.” The process of protein folding, while critical and fundamental to virtually all of biology, remains a mystery. Moreover, perhaps not surprisingly, when proteins do not fold correctly (i.e. “misfold”), there can be serious effects, including many well known diseases, such as Alzheimer’s, Mad Cow (BSE), CJD, ALS, and Parkinson’s disease…

With simulations, one can study aspects of folding and misfolding (and related disease) that one could never see with just experiment alone. Simulations won’t replace experiment, but can be a critically useful tool to go beyond what one could solely do in the lab. We are combining our simulation predictions with laboratory tests (either done in my lab or in collaborators). Working together, we can greatly push the boundary of what used to be considered to be impossible, even just a year or two ago.

Wee. And, it looks pretty. And, it has cool sound effects. The f@h client shows you your molecule (yes, look honey that’s our molecule!) as it calculates its myriad possible folding combinations. It is alive with calculations, pulsating with math. And it is rendered beautifully, you can zoom in and turn it around and change its style and treat it like your own little Tamagotchi for the seven hours it takes to complete its permutations. When it is complete, Stanford gets your data and sends you another job. Then you get another little molecule to call your own. We’ve folded 5 already. Also cool is the big globe that is in the background of your molecule simulation screen that shows all the computing nodes currently chewing on folding simulations. You can spin the globe and see the reach of the giant computing system. Hey, L.A., the East Coast, Britain and the Netherlands look pretty busy; the Sudan, Iran, North Korea, China not so much.

Here’s a nice — if blurry — little video that will give you the idea (2:33):

Want a molecule to call your own? There’s a client for every computer, even ones with far less computing muscle that our shiny new, perfectly wonderful, graciously gifted, Playstation 3.

You will note the new playstation category at the nitenote. It deserves one of its own.