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Peck explained that through the Folding@Home project, which is a large-scale
distributed computing system, a new way to simulate protein folding
was developed that breaks the microsecond barrier by dividing the work
between multiple processors. A near linear speed up is achieved as
processors are added. Thus, with thousands of processors, researchers
can break the microsecond barrier and better explore the mysteries
of protein folding.
Molecular dynamics is one way to
simulate the folding of amino acids into proteins. The group’s
poster examined the performance of GROMACS, a popular open
source molecular dynamics package, running on Beowulf clusters--parallel
computing platforms assembled from commodity-off-the-shelf
(COTS) components. Beowulf clusters enable relatively small
research groups to cost-effectively pursue computationally
based research.
“I think this award highlights
the quality of research that can be achieved in a small, intensive
environment such as Earlham,” Hursey said. “The
close relationship between faculty and students and the interdisciplinary
nature of Earlham support a research environment where computer
scientists, chemists, mathematicians, and others can easily
collaborate on interesting research projects.”
McCoy agreed: “The simple
fact that the faculty are willing to spend their time working
so closely with undergraduates says a lot for their dedication
to education. Being a part of the Cluster Computing Group,
doing research, and going to conferences has helped me to develop
the skills needed to perform well at the next level of education.”
Mic Jackson, professor of mathematics,
said SIAM membership rolls include many of the best and brightest
mathematicians in the world.
“The work on protein folding
done at Earlham was impressive to the other mathematicians
and computer scientists at the meeting,” Jackson said. “Their
award was a surprise and a significant honor earned in a highly
competitive and intellectually rich setting.”
“It was a very close atmosphere,” Hursey
said, “and at times a bit intimidating discussing our
research goals and future plans with major researchers from
national laboratories and research universities around the
world.”
Along with the poster award, the
group brought back another project to work on, Folding@Clusters.
As exciting as the initial protein folding work has been, the
group is even more excited with this new project.
“Instead of being run on
many individual computers, the protein folding simulation will
be setup to run on a variety of parallel computing platforms,” Peck
said. “This will enable researchers to consider different
molecular forms and return results more quickly.”
Hursey said in many ways the efforts
thus far have been in preparation for the cluster project.
The work of Earlham’s Cluster
Computing Group has been funded by various grants and donations
including contributions from the Howard Hughes Medical Institute,
the Arthur Vining Davis Foundation, Apple Computers, Safe Passage
Communications and Ray Ontko ‘84.
Contact:
Charlie Peck,
assistant professor of computer science
765/983-1667
Josh
Hursey, adjunct instructor of computer science
765/983-2132
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