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Density Functional Theory
Density Functional Theory
Scientists from the University at Buffalo are using the Center for Computational Research's (CCR) high-performance computers to model the methylation reaction between DNA and the protein M.Hhal. Uncontrolled DNA methylation is responsible for the development of some types of cancer. Density Functional Theory calculations, performed in aqueous solution, show that the reaction occurs only when a cytosine base from the DNA is bonded to an amino acid of the protein, after the cytosine is flipped out of the DNA helix. Calculation results have been confirmed by experimental x-ray and NMR data.
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While the individual faculty members who carried out this research have grants with a diverse set of agencies such as the National Science Foundation (NSF), the National Institutes of Health, and the Department of Energy, the computing gresources utilized for this research were provided by the University at Buffalo's (UB) CCR, which was started in 1998 with a funding from a NSF Major Research Infrastructure (MRI) grant. From its relatively humble beginnings in 1998, CCR has become a substantial academic supercomputing facility, with a technical staff of 13 and a computing capacity of about 13 Tflops.
The five faculty members at UB that were principal investigators on the NSF MRI grant, which was titled "Structural Studies and Methodologies in Chemistry and Molecular Biology," were Philip Coppens, Thomas Furlani, Jiali Gao, Harry King, and Russ Miller. For more information about CCR, visit the CCR Web site at http://www.ccr.buffalo.edu/. (Date of Image: April 2007)
Credit: M. Freindorf and T. Furlani, Center for Computational Research; T. Szyperski, Dept. of Chemistry, University at Buffalo; J. Kong, Q-Chem Inc.; visualization by Adam Koniak, Center for Computational Research, University at Buffalo
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