October 25, 2001-Vol33n8: CCR is key resource for researchers

CCR is key resource for researchers
Super computing center has helped attract $40 million in external funding

By ELLEN GOLDBAUM
Contributing Editor

After completing his post-doctoral work at Princeton University, Jeffrey Errington considered returning to his native Western New York, but he figured the odds were pretty much against him.

"My family was telling me I should try and get a job in Buffalo," said Errington, "but I told them the odds were pretty slim."

"The Thing Growing" is a virtual reality narrative in which the user creates an interactive story and engages with the "Thing" at an emotional level.

Like any newly minted Ph.D. in the sciences, Errington viewed his job search in purely national terms.

A graduate of UB's School of Engineering and Applied Sciences who earned his doctorate at Cornell University, Errington was seeking an institution with the appropriate facilities for pursuing his research on the properties of materials and chemical systems from a microscopic perspective. He writes computer codes that model interactions between molecules in complex fluids and biological systems to better understand their behavior. To enact those simulations, he needs the power of supercomputers.

Coincidentally, UB's Department of Chemical Engineering and the easy access to the university's supercomputing facility—the Center for Computational Research, one of the world's leading academic high-performance computing sites—offered just what his research requires.

"VR-Fact!" is an interactive virtual factory development software that explores the application of virtual environments in the area of manufacturing automation.

"I was very impressed with the facilities of CCR," he said. "I guess I was surprised at the sheer magnitude of the complex."

Errington also was impressed with the accessibility that faculty have to CCR, regardless of their rank.

At Princeton, he recalled, faculty and students have to pay what he called "a fairly steep charge" to use its supercomputing facility.

"That's not the case with CCR," said Errington. "One of the very nice things about CCR, especially for new assistant professors who have very few funds when they are starting out, is that there is this resource right on campus that's completely available to faculty and completely free."

Errington noted that supercom-puting facilities at some other schools also require that faculty undergo an elaborate application process in order to use the facility, and even if granted that privilege, use can be restricted; CCR, on the other hand, is open to all faculty members who can prove that their research requires supercomputers.

CCR, IBC Digital and UB's Virtual Reality Laboratory have developed an interactive, 3-D computer animation of the leading Peace Bridge proposals.

For more and more new and existing faculty researchers at UB, having CCR on campus is more than a perk; it is an increasingly critical resource that is helping to propel major projects.

Supercomputing has made major inroads in a broad range of projects at UB, helping to garner about $40 million in external funding for UB faculty members. As Errington's case proves, quite a few UB department heads have found it's also playing a role in faculty recruitment.

Maurizio Trevisan, professor and chair of the Department of Social and Preventive Medicine and interim dean of the School of Health Related Professions, discovered that this summer while recruiting for a biostatistician.

"The fact that CCR is here was very important to me," he said. "Being able to send candidates over there and have them talk with the center's staff scientists really helped. Any institution that wants to be in the forefront of research has to have something like CCR."

John Cowell, chair of the cancer genetics department at Roswell Park Cancer Institute, agrees. CCR, he noted, is becoming increasingly important as the bioinformatics center in Western New York gains momentum. "It's definitely a plus," he said. "The disadvantage of having to go off-site is that supercomputing centers in other regions can always bump you off their site because on-site people have priority. Here, no one can log in over me."

Since opening its doors in May 1999, CCR has been the source of an ever-expanding group of enthusiastic supporters among faculty members, allowing them to pursue new avenues in their work and making it possible to apply for new grants that require easy access to supercomputing facilities even to be considered.

The fact that getting supercom-puting time at CCR is just that—relatively easy in comparison with other, more established centers—as well as free, also is a draw for new and current faculty members.

"Supercomputing time is very accessible at CCR," explained Carl Lund, professor and chair of the Department of Chemical Engineering.

At some other institutions, he said, scientists may obtain an account, but then have to wait weeks or even months before they actually can use the machines.

For Lund, who conducts research on making more efficient use of catalysts used by the chemical industry, having CCR available has meant being able to develop new skills to advance his research.

"CCR has provided me with the motivation to learn to do quantum chemistry," said Lund. Calculations performed at CCR have helped Lund develop "virtual catalysts" that guide the development of real catalysts once he is back in the lab.

Some of the most established users of CCR are in the area of bioinformatics, including X-ray crystallography projects at UB and its affiliated institutions, such as Hauptman Woodward Medical Research Institute, where senior research scientist Charles Weeks uses CCR's massive computing power to solve ever more complex molecular structures that are targets for new pharmaceuticals.

Yaoqi Zhou, assistant professor in the Department of Physiology and Biophysics, is uncovering the complexities of protein folding, using CCR to do theoretical and simulation studies of protein folding, protein binding and protein-protein interactions. The research covers the area of bioinformatics, structure-based drug design, biophysics and computational biology.

Paras Prasad, SUNY Distinguished Professor in the departments of Chemistry and Physics, and executive director of the Institute for Lasers, Photonics and Biophotonics, has used CCR's visualization resources to create a fully immersive, three-dimensional image of a human cell based on two-dimensional slices obtained using confocal microscopy.

While researchers studying atoms and molecules have been some of the earliest users of supercomputers, CCR's base of users is growing broader all the time.

Researchers studying computational fluid dynamics also rely heavily on CCR's computing resources. Cyrus Madnia and Peyman Givi, professors of mechanical and aerospace engineering, use state-of the-art computer models developed in their labs to study turbulent flow and combustion processes. The goal of this research is to be able to design more efficient devices, such as turbine engines and home furnaces.

Faculty from disciplines not traditionally associated with supercomputing also have begun to tap into CCR's facilities.

For example, Josephine Anstey, visiting assistant professor in the Department of Media Study, is an avid CCR user who relies on the center's visualization capabilities to explore interactive, community-based virtual reality. Anstey is working on a Japanese translation of her interactive, virtual reality fiction, "The Thing Growing," for a show at a museum in Tokyo. She also is using CCR's Internet 2 connectivity and high-end visualization facilities to collaborate with the Electronic Visualization Laboratory at the University of lllinois at Chicago on a networked virtual reality art project. The project recently was shown at the Ars Electronica Festival in Linz, Austria.

Another non-traditional user is Samuel Paley, professor of classics, who is collaborating with Thenkurussi Kesavadas, professor of mechanical and aerospace engineering, and others to use CCR visualization facilities to develop virtual tours of sites of archaeological interest, including the palace of an ancient Assyrian king.

Scientists from the Department of Civil, Structural and Environmental Engineering, including Alan Rabideau, associate professor, and Igor Janckovic, assistant professor, working with Matt Becker, assistant professor of geology, and Doug Flewelling, assistant professor of geography, are developing a computer model that can be used to predict the flow of contaminants in groundwater. The project is funded by the Environmental Protection Agency.

Local businesses also have taken advantage of CCR, using super-computers in sectors ranging from studying industrial gases to improving banking services to facility planning and layout.

Community outreach projects have included the visualization of models of various options for a new or expanded Peace Bridge and plaza, and a virtual reality walk-through of the 1901 Pan-American Exposition.

Most recently, CCR has begun a collaboration with Philip Glick, professor of surgery and obstetrics and gynecology and executive director of the Miniature Access Surgery, Teaching, Training and Research Center, on a project designed to bring virtual reality technology into the operating room to assist in preoperative planning of complicated operations and in training the next generation of surgeons in a safe and controlled environment.