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Putting it all together
The system that Krueger and Zwier have put together involves four separate parts. Two are standard applications, including AMBER 7, a standard molecular dynamics code, and Gaussian 98, which does the quantum mechanics. What's unique about the code, however, is the "glue" that holds the two methods together--dozens of scripts written by Zwier that automate the collection of the molecular dynamics snapshots, convert them into a Gaussian-compatible format, parse out essential information, and send it to an output file for processing later. Performed once or a few times, these are simple procedures. However, Krueger and Zwier need to perform these tasks millions of times--which, as Krueger says, changes everything. "A lot of people write scripts to make their lives easier, but in this case, these scripts are absolutely necessary to doing the calculation." The fourth component of the code has also been developed by Zwier. Deceptively simple, it seems merely to plot the excitation energy of the oxazine molecules over time. However, this information is the key to the whole experiment: It describes the fluctuations in both the oxazine-4 molecules and the methanol molecules. "It turns out that after you've done both the molecular dynamics and the quantum mechanics, that energy versus time is really the only information you need in order to simulate the results from any kind of optical experiment," says Krueger. He anticipates that the code that Zwier has put together, with some modification, will be able to simulate a broad variety of spectroscopic experiments. Science on a shoestring The work of pulling together a complex framework for a scientific application is often done by advanced graduate students as part of a large research group. However, most of the work on this project has been done by Zwier, who doesn't actually begin his graduate work until Fall of 2004, when he will be entering the doctoral program in the Department of Chemistry at the University of Illinois at Urbana-Champaign. "I always was about 70 or 80 percent sure that I wanted to be in research as a career," says Zwier, "but this project has really solidified that. Furthermore, it indicated what I want to do in research--I've got it narrowed down to computational theoretical work or spectroscopy, as opposed to a broader area like physical chemistry or biochemistry." Krueger says that the development of the code has been a critical component both of his research and of Zwier's undergraduate education. "Many people probably have clusters of 100 CPUs or more, but at a liberal arts college, where our budgets aren't huge, we don't have a lot of local computing resources. NCSA has made it possible for us to do this." This research is supported by Research Corporation, Hope College, and the National Science Foundation's Research Experiences for Undergraduates program. Team members Brent Krueger
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