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2004
WELCOME
FROM VICE PRESIDENT DAN DWYER
QUICK
LOOKS
A ROUNDUP OF UM SCIENCE NEWS
PHARMACY
SCHOOL
ON THE GROW
SCHOOL
OF THE MIND
BRAIN STUDIES MAY COMBAT CENTRAL NERVOUS SYSTEM DISEASES
PATHWAYS
OF LIFE
NEW LAB TACKLES VASCULAR DISEASE
GENETIC
HEALING
BIOLOGIST SEEKS DNA-LEVEL CURES FOR HEARING LOSS, CANCER PAIN
HIGH
TECH INSTRUMENT CENTER
SUPER COMPUTING AIDS UM RESEARCH
RETURN
TO BLACK MOUNTAIN
LESS THAN A YEAR AFTER FIRE, NATURE THRIVES
EXTREME
LIVING
HOT POOL CREATURES MAY OFFER GLIMPSE OF LIFE BEYOND EARTH
TUNNELS
TO SAFETY
ANIMALS USE CULVERTS TO CROSS HIGHWAYS
VIENNA
EXPERIENCE
STUDY-ABROAD PROGRAM LEAVES A LASTING IMPRESSION
PROTEINS
MAY UNLOCK MAD COW DISEASE
UM RESEARCHER MICHELE MCGUIRL WORKS TO PROTECT FOOD SUPPLIES
WHEN
SPEECH WASN'T FREE
PROFESSORS DELVE INTO MONTANA'S TROUBLED PAST
FAMILY
ALCHEMY
RESEARCHERS BALANCE SCIENCE, MARRIAGE AND KIDS
CULTURE
CLASH
DIFFERENCES IMPACT ACADEMIC SUCCESS
INVISIBLE
SPACE RAIN
RESEARCHER STUDIES MYSTERIOUS COSMIC RAYS
BRAIN
PAIN
RESEARCHER OFFERS TIPS FOR MIGRAINE SUFFERERS
CAMAS
MAGAZINE
VOICES RISING IN THE WEST
HIGH
TECH INSTRUMENT CENTER
Super
computing aids UM research
By CARY SHIMEK
Photography by TODD GOODRICH
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| John Gerdes, director of UM's Computational Core Facility. |
A view of a crystallized protein — resembling a vast, multicolored Erector set — rotates in three dimensions on a computer screen. To David Holley, the graduate student creating the image, the protein seems to emerge from the screen. You see, Holley is wearing 3-D glasses to help him better visualize the detailed structure of the protein.
As he works, Holley uses deft mouse strokes to dock drug molecules into the protein, in order to understand how the structures fit together.
Such stunning scientific imagery is made possible by UM's Molecular Computational Core Facility, a scientific computing environment. Started in 2001 and located in the basement of the Davidson Honors College building, MCCF is a resource for computational and visual experimentation used by UM chemistry, pharmacy and biology researchers, among others.
"I think this facility is very unique for a university the size of UM," says MCCF director John Gerdes. "We serve as a locus for useful, contemporary digital scientific technology to generate models and as a resource for diverse expertise to help our researchers — particularly those dealing with molecular computational issues."
Gerdes says about 25 investigators now use the computing facility. Their projects range from modeling how drugs bind to proteins to studying the HIV envelope protein to visualizing surfaces of tiny ligated organometallic clusters, which someday may assist in the reclamation of polluted mining sites.
Gerdes and his indispensable system administrator Rohn Wood say researchers may access the MCCF from the comfort of their own offices or labs. Up to 40 people could use the system at once, if they all needed equal amounts of computing power. But projects often require a great deal of system resources, so usually they are set up in a queue for the supercomputer to tackle individually or a few at a time.
Gerdes says having a high-tech infrastructure available for UM researchers is a cost-effective way to drive a portion of UM's biomedical research. The facility also brings together scientists from different units, encouraging interdisciplinary collaborations and investigations.
Gerdes says, "It's my view that this facility offers an opportunity to change our campus culture a bit — to use computational studies to drive different scientific experiments and hypotheses."
MCCF imaging capabilities for viewing molecular models have the ability to make the abstract real, Gerdes says. University researchers often work at the atomic level with proteins and smaller molecules, but the ability to create 3-D models of their work and to actually move through these constructs via computer — to see how the proteins and other drugs work in a more concrete way — may lead to a better understanding of protein structure as related to its function.
UM's investment in the facility already is paying dividends. Gerdes says the computational power and custom software diversity his facility provides already has led to several funded proposals to various investigators. In other words: Build the facility, perform initial computational analyses and the grants will come.
MCCF is one of 10 facilities in UM's Center for Structural and Functional Neuroscience, which is funded by the National Institutes of Health as a Center for Biomedical and Research Excellence. Initial funding for MCCF came from a variety of sources, including the NIH COBRE award for the CSFN and the National Science Foundation's Experimental Program to Stimulate Competitive Research.
In 2002, CSFN Director Rich Bridges was the principal investigator for a supplemental grant that enhanced the facility with items such as additional hardware, software, and a new supercomputer and a server room.
"We've really had the opportunity to grow our technology and expertise here," Gerdes says, "and I think the investigators using the MCCF are making the most of it."