Stanford Cluster to Bridge Sciences

Stanford University is using supercomputer clusters as a way to bridge the once-isolated disciplines of physics, biology and engineering.

Vijay Pande, an assistant professor of chemistry at Stanford who spearheaded the project, said 20 to 40 research groups across several disciplines will be using the cluster. The groups will be housed in the new Bio-X lab scheduled for completion this summer.

Bioinformatics will be among the first applications to leverage the cluster, according to Pande, in Stanford, Calif. Specifically, researchers will use the cluster technology to study and model protein structures and dynamics (also known as “protein folding”).

Protein folding—a fairly new science—models the process in which proteins assemble themselves from their initial, unfolded (or “random coil”) state of amino acids. In the mid-1990s, scientists theorized that protein misfolding leads to several diseases, including muscle degeneration, Mad Cow disease, and Alzheimers and other age-related diseases.

The problem facing scientists is that proteins fold naturally in fractions of seconds. Modeling the data points, therefore, requires massive amounts of data, and thats where supercomputer clusters come in.

One user of the new cluster is Tanya Raschke, a postdoctoral fellow studying structural biology at Stanford. Raschke is studying the chemical interactions in proteins and small molecules, as well as the interactions between proteins and surrounding water molecules.

Raschke said simulations that took as long as three days to run on an older computing cluster made up of Advanced Micro Devices Inc. Athlon-based systems will take a half-day to run on the new cluster.