Thursday, May 01, 2003

The Fastest Computer in the World?

In 1998, two researchers published a report in Science (Y. Duan and P. A. Kollman, “Pathways to a Protein Folding Intermediate Observed in a 1-Microsecond Simulation in Aqueous Solution,” Science 282, No. 5389, 740–744 (1998)) that reported their efforts to simulate the folding of a protein. Briefly, one of the central questions in molecular biology is determining why (or how) a protein, made up of a given sequence of amino acids, folds into a specific three-dimensional shape. Right now, we're almost completely unable to predict that 3D shape, making it very difficult to do things like rational drug discovery or proteomics.

So these researchers borrowed a 256-node Cray T3E, one of the fastest computers in the world. They ran it for three months. And at the end of three months, they had simulated only a microsecond of the protein folding.

Now we can think of this problem in two ways. One, as IBM did, is to think about the opportunity for research in computer architecture to build a really, really fast computer, optimized for the message-passing characteristics of simulating protein folding.

Or, think about it this way: the protein, a single molecule, "figures out" how to fold in a little more than a microsecond!. One little molecule! It just does it! That's something like a trillion-fold difference in performance, if you buy that a protein folding is something like computation.

What's going on? How can a simple little molecule accomplish a task in an instant that one of the fastest machines in the world struggles to do over a course of many months? It may have something to do with the inherent massive parallelism of nature: each atom in the protein molecule acts independently. It may have something to do with the "bus" of nature: every pair of atoms can affect each other (by electromagnetic forces, for example) at the same time. And it may have something to do with the fact that nature has infinite precision, while digital computers are by their nature quantized. [It's true that time and space may be quantized, but they may not be, and in any case if they are, it is at an incredibly tiny scale.]

In any case, we must recognize the potential that every protein in our bodies may in some way represent a computer a trillion times faster than one of the most powerful human-built computers in the world.