March 10, 2010
Jeremy Craig, 404-413-1357
ATLANTA - A Georgia State University chemist and his colleagues are among a just a few teams in the country who have been given access to powerful supercomputers by the U.S. Department of Energy to model the mechanisms surrounding the replication and repair of DNA. This research may lead to further understanding about basic processes underlying cancer and degenerative diseases.
Assistant professor Ivaylo Ivanov and his colleagues are part of the Department of Energy's Innovative and Novel Computational Impact on Theory and Experiment (INCITE) program, which provides powerful supercomputing resources to allow scientists to conduct cutting-edge research in fields such as biology, astrophysics, climate change, new materials and energy production in order to increase U.S. competitiveness.
Ivanov's team, one of 69 teams nationwide named to the program, has been allocated 4 million processor hours on a Cray XT supercomputer at the Department of Energy's Leadership Computing Facility at the Oak Ridge National Laboratory in Oak Ridge, Tenn.
"With our methods, we can address different aspects of the mechanisms involved in these processes," Ivanov said. "The supercomputer at Oak Ridge National Laboratory is one of the largest in the world. With the size of the project, we hope to make a significant impact."
The processor-hour allocation means that Ivanov's team can accomplish what a single computer, with a single central processing unit, can accomplish in 4 million hours - taking decades off of the required calculation time to model biological processes, said Ivanov, a computational chemist.
"The problems are of intrinsic interest, but they are also very relevant to human diseases, such as cancer," Ivanov said.
One part of the project investigates the enzymes involved in the duplication and repair of DNA, as well as the cellular responses to DNA damage.
In a single day, about 7 billion cells divide, requiring massive amounts of base pairs - carriers of the genetic code - to be replicated. While the mechanisms of replication produce only one error per 10,000,000 base pairs, that's still too many damage-causing errors.
Cells have evolved ways to repair DNA, such as basic excision repair, where a variety of enzymes act like scissors - cutting the DNA backbone and removing the incorrect base. The DNA is then resealed after repair. When this and other repair functions do not work properly, they are linked to cancer and degenerative diseases.
Ivanov and his associates' research seeks to examine the principles governing cells' responses to DNA damage and the protein/DNA complexes involved in repair pathways. To do this, they rely on tools like molecular simulation, statistical mechanics, classical and quantum mechanics, and other experimental work.
Another project of his team's research examines what is called a sliding clamp - a ring-shaped protein that encircles DNA at sites of replication and repair. Sliding clamps serve as mobile platforms for the attachment of many important parts of the cell's replication machinery.
Ivanov's colleagues include John Tainer with the Scripps Research Institute and Lawrence Berkeley National Laboratory; Xiaolin Chang with the Oak Ridge National Laboratory; and J. Andrew McCammon, with the University of California San Diego and the Howard Hughes Medical Institute.