Canada's biggest calculator supplies computational power for protein folding and biological membranes

St. John's 17 September 2004The Atlantic Computational Excellence Network (ACEnet), the NRC's Canadian Bioinformatics Resource, the University of Alberta, C3.ca, and partners have performed the Third Canadian Internetworked Scientific Supercomputer (CISS-3) experiment. The experiment completed 20 years of computation in 48 hours. Two chemo-biological problems, both requiring high-performance computational power, were tackled: protein folding and biological membranes.

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Modern science and engineering rely on computers as fundamental tools. Computers are able to simulate problems that span the scale from galaxies to the molecules in our bodies. For example, atoms and the interactions of proteins are mathematically modelled to understand their fundamental properties. Computers can also help answer "what if" questions that would be difficult or impossible to control in a physical experiment. However, these simulations require tens of thousands of hours of computation to complete.

The Atlantic Computational Excellence Network (ACEnet), one of six High Performance Computing Consortia in Canada, is putting Atlantic Canada on the map in terms of computing power. The current members of ACEnet - Memorial University of Newfoundland lead institution, Saint Mary's University, St. Francis Xavier University, the University of New Brunswick, Dalhousie University, Mount Allison University, and the University of Prince Edward Island - have been working hard to support the CISS-3 experiment and the Trellis Project in a national computer initiative.

The Trellis Project, a team led by Dr. Paul Lu, Assistant Professor, Department of Computing Science, University of Alberta, has developed the technical infrastructure to create virtual supercomputers that span many different universities. The aggregated power of the virtual supercomputer can tackle problems that would otherwise be too large for one research group or one institution. In November 2002, the Trellis Project set a Canadian milestone when it completed 3,5 years worth of computation in a single day, studying the fundamental properties of chiral molecules, using the first Canadian Internetworked Scientific Supercomputer (CISS-1) with 1376 computers at 16 different partner universities.

Today, with the help of the Atlantic Computational Excellence Network (ACEnet) and the Canadian Bioinformatics Resource (CBR/NRC) the CISS-3 experiment is being completed. This experiment is setting a new Canadian milestone through the partnership of the University of Alberta, C3.ca, 19 different universities, 6 high-performance computing (HPC) consortia including Atlantic Canada's ACEnet, 3 research institutions, and several networking partners across Canada.

Using newer techniques and more sophisticated software than in 2002, CISS-3 is combining the computational power of approximately 4000 computers across Canada, from Victoria to St. John's, to solve two different computational chemistry problems, in protein folding and biological membranes, led by researchers at the Universities of Calgary and Toronto, and the Hospital for Sick Children in Toronto.

In the first case, the Trellis Project helped a University of Calgary research project headed by Dr. Peter Tieleman. He and his research team are trying to understand the way a protein folds on itself. Proper folding is essential for a protein's function. Misfolding can lead to disorders such as Alzheimer's and "mad cow" diseases. Dr. Tieleman's team is studying an important step in the folding process, in which parts of the protein form the final structure of the entire protein. To study this process, they use detailed mathematical models that describe how the atoms in the protein interact. Computer simulations trace the motions of tens of thousands of atoms according to these models, showing in "real time" how a protein might fold.

The Trellis Project also aided a second study at Toronto's Hospital for Sick Children, which is examining the way protons are transported across biological membranes. The phenomenon is considered one of the most important chemical reactions in life. The physical basis for this reaction is difficult to characterize. A high level of molecular detail is required to understand how proton transport arises, and how it is coupled to other reactions.

In a 48 hour period, between September 15 to September 17, approximately 20 years worth of computation were completed. The technical infrastructure provided by Trellis, and the social infrastructure built by the generous co-operation of the many CISS-3 partners, help provide Canadian computational scientists with the raw computing power to tackle the most difficult problems in science and engineering. Researchers in Atlantic Canada are thrilled by the regional show of support toward this initiative. From 8 different sites throughout Atlantic Canada, ACEnet has been able to contribute in excess of 750 computer processors towards the CISS-3 and Trellis initiative.


Leslie Versweyveld

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