Unlike typical parallel processors, the 10,000 processors in this supercomputer (called Quantum Chromodynamics on a Chip, or QCDOC, for its original application in physics) each contain their own memory and the equivalent of a 24-lane superhighway for communicating with one another in six dimensions. This configuration allows the supercomputer to break the task of deciphering the three-dimensional arrangement of a protein's atoms -- 100,000 in a typical protein -- into smaller chunks of 10 atoms per processor. Working together, the chips effectively cut the computing time needed to solve a protein's structure by a factor of 1000, says James Davenport, a physicist at Brookhaven. This would reduce the time for a simulation from approximately 20 years to 1 week.
"The computer analyzes the forces of attraction and repulsion between atoms, depending on their positions, distances, and angles. It shuffles through all the possible arrangements to arrive at the most stable three-dimensional configuration," Davenport says.
The technique is complementary to other methods of protein-structure determination, such as x-ray crystallography -- where the pattern of x-rays scattering off atoms in crystallized proteins is used to determine structure. It will be particularly useful for proteins that are impossible or difficult to crystallize, such as those that control the movement of molecules across the cellular membrane. The high-speed analysis will al
Contact: Karen McNulty Walsh
DOE/Brookhaven National Laboratory