A strand of DNA being pulled through the pore of hemolysim. Image Courtesy Peter Coveney, University College, London

Last month, SPICE also won the Life Sciences Award of the International Supercomputer Conference for the paper that reports on the SC|05 project. Project leader Peter Coveney will present the paper at ISC in Dresden, Germany, June 27-30. It outlines the scientific motivation and why grid resources are critical for such projects, and also documents lessons learned in carrying out such a large-scale, multi-site project.

"Our work at SC|05, in which we collaborated with groups at Tufts and Brown Universities, established that there are applications sufficiently mature to make effective use of resources that span computational grids," says Coveney, who directs the Centre for Computational Science at University College, London. "Furthermore, it also underscored the need to run at even larger scales, with grids-of-grids."

The ability to use systems at multiple TeraGrid and UK sites simultaneously, which SPICE demonstrated, made possible many interactive simulations. First, the team dynamically explored the parameter space of the DNA-protein system, and then, having reduced the search space, distributing approximately 100 large-scale non-equilibrium simulations across the interconnected transatlantic grid. The project relied on the RealityGrid Steering Library and associated middleware. The five participating sites were the National Center for Supercomputing Applications, the San Diego Supercomputer Center, the Pittsburgh Supercomputing Center, Daresbury Laboratory and Computer Services for Academic Research at the University of Manchester.

Using novel algorithms based on a mathematical relation known as Jarzynsky's identity, SPICE applied steered molecular dynamics to pull a strand of DNA through the pore of hemolysim, a channel protein, embedded in a bilayer membrane. With a total size exceeding 250,000 atoms, the problem would require 25 years to simulate with standard molecular dynamics. The problem became tractable, says Coveney, only with grid-enabled resources.

Such biomolecule translocation, a process not well understood, occurs with messenger-RNA and DNA. Detailed knowledge of translocation is critical to many problems, from genetic information transfer to design of high-throughput DNA screening. The SPICE simulations identified a constriction in the pore structure that may have physical consequences, with analysis still underway.

More information about the International Supercomputer Conference and the SPICE paper can be found at http://www.isc2006.org/newsletter. Also visit this TeraGrid press release and the SPICE Web site.