Highlights of our Work

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Many proteins store gases like oxygen, carbon dioxide, and nitric oxide, or react with them. The gases are conducted into the protein through access routes that exist only in passing and as a result of a protein's fluctuations. Accordingly, access routes are difficult to establish, but researchers are now able to image gas access pathways inside proteins computationally. The new method has many implications for biotechnology and science (see our hydrogenase page and Sep 2005 highlight, "Hydrogen Fuel from Protein"). Imaging gas access systematically over whole protein families, e.g., the family of myoglobins, requires a large number of calculations that need to be run and monitored. The traditional means of doing so is very wasteful of the researchers' time. To solve this problem, NAMD-G, a grid-based automation engine for biomolecular simulations running the NAMD software, has been developed in a collaboration with the National Center for Supercomputing Applications (see recent paper). From the researchers' workstations, NAMD-G "farms out" a large number of calculations, in parallel, to supercomputers on the TeraGrid. NAMD-G monitors and manages multiple sequences of calculations at distant sites, and performs the necessary data transfers and backups on an as-needed basis. While the gas transport simulations provide a clear scientific driver for the development, NAMD-G is quite general and will aid any NAMD user with access to the TeraGrid. The result? Less time spent baby-sitting runs and more time for science.