A Broader View of Life's Instants


Anton 2 Will Increase Speed and Size of Melecular Simulations

When it comes to simulating the motions of large biomolecules, the D. E. Shaw Research (DESRES) Anton supercomputer hosted at PSC has been in a class by itself. It’s allowed researchers to identify unexpected but crucial molecular contortions that underlie previously puzzling properties of medically and biologically important molecules. Anton has powered 277 simulation projects by 127 different principal investigators across the U.S., resulting in more than 120 peerreviewed research papers. Three of these studies appeared in the scientific journal Nature, one of the international scientific community’s premier publications.

Now DESRES will provide a next-generation Anton 2 supercomputer to PSC without cost for use by the biomedical research community. In addition, a $1.8-million National Institutes of Health grant to PSC will provide operational funding for the new system, as well as extend the operation of the Anton 1 supercomputer currently at PSC until the new Anton 2 is deployed, expected in the Fall of 2016.

A specialized system for modeling the function and dynamics of biomolecules, the Anton 2 machine at PSC will be the only one of its kind publicly available to U.S. scientists. “Many life processes important to understanding the molecular basis of cellular events occur over timescales exceeding a millisecond in duration,” says PSC’s Phil Blood, principal investigator of the new grant. “Anton 2’s performance for molecular simulation will exceed that of current generalpurpose supercomputing systems by orders of magnitude, enabling the study of biological processes not otherwise possible and offering new possibilities in drug discovery and development.”

Molecular dynamics simulations can provide insights into the behavior of proteins, cell membranes, nucleic acids, and other molecules at the atomic scale.

But even the most advanced generalpurpose supercomputers struggle to simulate beyond the microsecond level—a thousand times shorter than the millisecond level—without taking months of computational time. Anton has changed this, giving researchers practical access to simulations at far longer timescales. The new, 128-node Anton 2 will expand on the power and capabilities of the Anton 1, increasing simulation speed approximately fourfold and enabling the simulation of biomolecular systems with around five times as many atoms.


In molecular biology circles, the EcoR1 protein is a superstar. A humble DNAcutting enzyme from the human gut bacterium E. coli, its unique ability to mix and match DNA sequences at will spurred the genetic engineering industry. EcoR1 provided John Rosenberg and colleagues at the University of Pittsburgh with a window into how proteins interact with DNA, either to cut it as EcoR1 does or to affect the activity of genes as the critical DNA regulatory proteins do. EcoR1 proved a fruitful exemplar of protein-DNA interaction; in first-of-itskind work with PSC’s Cray Y-MP in the early 1990s, Rosenberg’s team showed how merely binding to EcoR1 created a “kink” in the DNA helix, demonstrating that proteins could make surprisingly large changes in DNA’s shape.

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