NCSA NEWS

On the SGI Power Challenge Array, Wheeler and former graduate students Kurt Grafton and Scott Boesch first perform quantum chemical calculations to determine the positions of the electrons orbiting the quinone, a computationally intensive task in itself. Each run ties up eight processors and 256 megabytes of memory for several days.

"Our quantum mechanical calculations of only the quinones currently use 27 functions to approximate the electron distribution around each atom," Wheeler says. "Adding more functions -- by adding more atoms or adding more functions per atom -- would increase computer time by the fourth power of the number of functions. Computer time quickly becomes prohibitive for anything more than about a dozen atoms."

The next step is to figure out how the forces from the electric fields of the quinone electrons push around the atoms in the protein. For this they use the same F=ma formula learned in high school physics to figure out how the forces from the electrons' electric fields move the atoms around. But even these Newtonian dynamics are not simple. The protein consists of hundreds of amino acids. Even with some approximations, Wheeler's simulation tracks the movement of 4,500 atoms. That takes weeks on the Power Challenge Array.

"We couldn't do these calculations without the resources of NCSA," Wheeler says. "We could use gigabytes of memory and weeks of time, even on multiple processors."

And it is the high degree of detail that is producing results. They've already seen that the extra electron changes the quinone's chemistry. The second quinone normally binds to the protein in one particular place. Add the electron and the quinone binds in a slightly different spot, 12 billionths of a centimeter away.

How much of a difference that shift causes is unknown. Wheeler says that's the next step in the calculation: "seeing how it affects the energy."

Turning that idea around a bit, Wheeler's simulations are now "shaking" the molecules in certain ways to induce electron transfer reactions. By making a molecule vibrate a certain way, perhaps by shining an infrared laser on it, "You might be able to put the electrons exactly where you want them," he says.

If that idea -- manipulating reactions electron by electron -- ever makes it out of the computer and into the laboratory, it could prove chemistry's equivalent of genetic engineering: not only understanding how Nature works, but creating things that would never have existed.

This research is supported by the U.S. Department of Energy, the Oklahoma Center for the Advancement of Science & Technology, and the National Science Foundation. Previous support came from the National Institutes of Health.