The Center for Computational Research will be providing tours as part of a field trip to the Buffalo Niagara Medical Campus by students in the Excelsior Scholars Program. The program runs August 4-14 and is offered to students from the Buffalo Public School system who have excelled in math and/or science and will be entering the 8th grade this year. The students must receive an invitation to participate from the Superintendent of Schools so it is quite an honor for those 50 attending. The base of the program will be held at the Buffalo Museum of Science with field trips to Tifft Nature Preserve, Roswell Park Cancer Institute, the Center of Excellence in Bioinformatics & Life Sciences, and Hauptman-Woodward Institute. The program ends with a poster session and celebration for the students and their parents. [More information…]

Steve Gallo, CCR Software Engineer, has published a paper featured in the journal Informatics in Primary Care. Entitled “Improving collaboration between primary care research networks using Access Grid technology”, the paper discusses the use of the Access Grid to enhance communication and coordination among Practice Based Research Networks in North America.

Dr. Marek Freindorf, CCR Computational Chemist, is teaching a semester long course entitled “Computer Modeling of Biological Systems.” The course, which is divided into 3 parts (Part I, II and III), is designed to serve as an introduction to computational methods for molecular modeling of biological systems such as proteins and nucleic acids. The course is for seniors and graduate students who are interested in studying biological systems at the molecular level. The goal is to provide a general overview of computational quantum chemistry (Part I), molecular mechanics (Part II), and a combined QM/MM method (Part III) as applied to molecules of biological interest. Prerequisites for Part III are Part I and Part II.

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CCR will again be hosting The Eric Pitman Annual Summer Workshop in Computational Science
for high school students this summer. The workshop runs from June 30 - July 11, 2008. For details and application information, please visit our website.

OSG News reports on the first NYSGrid Cyberinfrastructure Days held recently in Albany, NY.

UB faculty research inspires an episode of the History Channel’s “Mega Disasters” series called “The Next Pompeii?” Professor Michael F. Sheridan, director of UB’s Center for Geohazards Studies, recently coauthored a paper in the Proceedings of the National Academy of Sciences suggesting that the next eruption of Vesuvius might pose a serious threat to Naples, home to more than 3 million people. It wasn’t exactly welcome news in Naples, where hazard mitigation plans did not include the possibility that the next eruption of Vesuvius might pose a serious threat to Naples. Dr. Chris S. Renschler, UB associate professor of geography, also is featured in the Mega Disasters episode, which was filmed in part at the Center for Computational Research, along with Dr. Maurizio Trevisan, former dean of UB’s School of Public Health and Health Professions. More details can be found on UB’s News website

Dr. Zihua Hu, CCR Bioinformatics Computational Scientist, has published a paper that is featured in BMC Journals. Entitled “Prediction of synergistic transcription factors by function conservation” the paper explains a new strategy proposed for identifying synergistic transcription factors by function conservation, leading to the identification of 51 homotypic transcription-factor combinations.

CCR’s visualization work is featured at UB’s Master Plan meeting held at the M. Wile Building at the downtown campus Tuesday, December 4th. The first of four public forums sought to gain the public’s insight on future expansion plans by the University and the Buffalo-Niagara Medical Campus. The meeting was highlighted in the Buffalo News article “UB gears up for campuses’ makeover”.

Due to CCR’s widely recognized work on local high-profile community projects such as the Bridge Visualization Project, CCR was contracted to develop an interactive 3D model of the Buffalo-Niagara Medical Campus. Working with IBC Digital (a Buffalo based production/modeling/animation company), CCR developed a real-time simulation of the campus, which spans eight city blocks of the downtown Buffalo area. It is currently being utilized by UB’s Urban Design Project (led by Professor Robert Shibley) on the 2020 Campus Master Plan. This work was carried out by CCR staff members Martins Innus and Adrian Levesque as well as former staff member Adam Koniak.

CCR visualization work is, for the second year, featured in the yearly calendar distributed by Presagis, Inc. Modeling done for the University at Buffalo’s Campus Master Plan and the Casselberry Interchange in Florida is pictured to display the various features used in the 3D modeling software Creator. The work was carried out by CCR staff members Adrian Levesque and Martins Innus, and former staff member Adam Koniak. Additional detail on these projects and similar work can be found on the visualization page of the CCR website.

Research carried out at the University at Buffalo, using supercomputers housed in UB’s Center for Computational Research, is featured on the cover of the 2007 Coalition for Academic Scientific Computing (CASC) Brochure, which is widely distributed, including to all members of congress.

Pictured on the cover of the 2007 CASC Brochure is the active site of the enzyme (protein) Cytochrome P450, which plays a crucial role in the metabolism of drugs and toxins in our body. Cytochrome P450 was modeled on the 13 Teraflop Linux cluster at the University at Buffalo’s Center for Computational Research (CCR) using Density Functional Theory. The calculations predict changes in the active site geometry upon binding of the protein Putidaredoxin, key to the function of Cytochrome P450. Insight such as this, which is in many cases available only through high-performance computing, is critical to the development of new therapeutic measures to treat disease and improve the quality of life.

The calculations were carried out by UB researchers Doctors Marek Freindorf and Thomas R. Furlani of CCR, and by Doctors Jing Kong and Yihan Shao of Q-Chem, Inc., Pittsburgh, Pennsylvania. The resulting image was created using VMD [Visual Molecular Dynamics] and then rendered on a visualization cluster using POV-Ray [Persistence of Vision Raytracer] by Adam Koniak of the CCR.

Founded in 1989, the Coalition for Academic Scientific Computation (CASC) is an educational nonprofit organization with 50 member institutions representing many of the nation’s most forward thinking universities and computing centers. CASC advocates the use of the most advanced computing technology to accelerate scientific discovery critical to national competitiveness, global security, and economic success. CASC also promotes advanced technology as an essential tool in the development of a skilled and diverse 21st century workforce to fuel the nation’s technological leadership.

The mission of CASC is to:

• disseminate information about the value of high performance computing and advanced communications technologies;

• provide an expert resource for the Executive Office of the President, the Congress, and federal agencies, as well as state and local government bodies; and

• facilitate information exchange within the academic scientific computation and communication community.

Computational science has become the third pillar of scientific enterprise, a peer with traditional methods of physical experiments and theoretical investigations.

Coalition members provide high performance computing (HPC) resources, massive data storage facilities, visualization environments, and software. Connected via high-capacity optical networks, cyberinfrastructure enables large-scale, long-term, multi-disciplinary networking and information technology R&D, and innovative research at the frontiers of science. By applying advanced technology, CASC members extend the state of the art to achieve scientific, technical and information management breakthroughs beyond imagination, positioning the U.S. at the forefront of the 21st century knowledge economy.

The CASC brochure provides a snapshot of the research contributions of CASC members – from simulating new pharmaceuticals to modeling climate change, and from detecting brain aneurisms to developing new energy technologies. More detailed descriptions of each CASC members’ contributions to discovery, innovation, and learning are available at: www.casc.org/members.html