As supercomputing hardware and software have evolved over the last few years, Brooks has begun using MD to simulate processes involved in how proteins unfold, which is believed to mirror the rules of folding. Because some of these events occur on such short time scales, laboratory methods have been unable to study them, and Brooks' computations exploring early stages of unfolding are in many ways like experiments. Using the supercomputer as a laboratory, he gathers data about a fundamental process that isn't well understood.
"We're exploring phenomena that haven't been explored before," says Brooks. "There's not a well defined model in which we provide input and get the answer. We don't know in detail what we're looking for, so we're coming as close to doing experiments as you can without being in the laboratory." Brooks was able to conduct a number of these experiments during the "friendly user" period of testing on Pittsburgh's CRAY C90. He focused on apomyoglobin, a partially unfolded form of myoglobin, an oxygen-carrying protein that occurs widely in muscle tissue.
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