This page contains an brief overview of some of the faculty based research that is carried out using CCR resources. For additional details or to add your research to this page, please contact us. We are always interested in featuring new research.

Slide show of faculty based research supported by CCR (pdf 13mb)

Contents

Anthropology

• Social and Behavior Sciences: Development and deployment of infrastructure in support of worldwide monitoring of human rights abuses for peoples with disabilities. Large-scale collaboration including York University and the DRPI (Disability Rights Promotion International) . This work is led by Ezra Zubrow (Anthropology).

Bioinformatics

• Microarray Data Analysis: The choice of probe set algorithms for expression summary in a GeneChip study has a great impact on subsequent gene expression data analysis. We developed three novel approaches for assessing data variance and result bias using two sample t-test statistics from redundant probe sets, by which researchers are able to assess the relative performance of different probe set algorithms on their experimental data, without using exogenous controls. Paper entitled "Utilization of two sample t-test statistics from redundant probe sets to evaluate different probe set algorithms in GeneChip studies" was published in BMC Bioinformatics. This group is led by Dr. Zihua Hu (CCR).

• REDfly is a curated collection of known Drosophila transcriptional cis-regulatory modules (CRMs). Despite more than 20 years of experimental determination of these elements, the data have never been collected into a single searchable database. REDfly seeks to include all experimentally verified fly CRMs along with their DNA sequence, their associated genes, and the expression patterns they direct. Expression patterns are annotated using a defined anatomy ontology to enable high interoperability with FlyBase, the BDGP in situ hybridization database, and other model organism resources. Paper entitled "REDfly: A Regulatory Element Database for Drosophila" published in Bioinformatics. This group is led by Dr. Marc Halfon (The Center of Excellence in Bioinformatics, Dept of Biochemistry) and supported by Steve Gallo (CCR).

• Development of Bio-NMR methods for structural genomics: CCR supports the Northeast Structural Genomics Consortium (NESC), an NIH funded consortium in structural genomics. High-throughput NMR structure determination. This group is led by Thomas Szyperski (Chemistry).

• Shake-and-Bake Research Group: Direct-Methods crystal structure determination targeted at SeMet and atomic resolution data. The group is led by Nobel Laureate Herbert A. Hauptman (HWI), Russ Miller (CSE), and Charles M. Weeks (HWI).

• X-Ray Diffraction of Solids: The development of new experimental and theoretical methods for the study of solids by X-ray diffraction. This group is led by Philip Coppens (Chemistry).

• Gene Regulatory Networks: Genomic Approaches to Elucidating Developmental Regulatory Networks. This group is led by Marc Halfon (The Center of Excellence in Bioinformatics, Dept of Biochemistry).

• Metabolic Engineering and Transcription Profiling: Modification of genes endogenous to the host organism to alter metabolic flux. Introduction of novel pathways by the introduction of new genes into the organism. Identification of targets for the development of antibacterial agents, and biotechnological processes optimization by identifying targets for metabolic pathway modification and eventually biocatalyst improvement. This group is led by Mattheos Koffas (CE).

• Vaccine Development: Genomic approaches to the development of vaccines against mucosal pathogens. This group is led by Timothy Murphy (School of Medicine) and carried out in collaboration with Dr. Zihua Hu (CCR).

• Cellular Metabolism of Vanadium: The role of oxovanadium compounds in cellular metabolism and use of vanadium to alleviate the symptoms of diabetes in mammalian systems. This group is led by Gail Willsky (Biochemistry) and Dr. Zihua Hu (CCR).

• Molecular Physiology, Endocrinology and Pharmacology: Mechanical regulation of the sensitivity of muscles to glucocorticoids, insulin and recombinant growth hormone. This research is led by Richard Almon (Biology).

Collaborative Technologies

• Upstate New York Practice Based Research Network (UNYNET): UNYNET's mission is to rapidly improve patient care by translating research into practice and by involving practices in research. UNYNET is part of NIH roadmap initiative to create Electronic Primary Care Research Network (EPCRN) under the leadership of Dr. Kevin Peterson (University of Minnesota) and utilizes the Access Grid at CCR with plans to implement a high-speed video conferencing capability in locations throughout the eight counties of Western New York. This research is led by Chet Fox and supported by Steve Gallo (CCR).

Computational Chemistry

• Chemistry in the Condensed Phase: Development and application of computational techniques to treat the condensed phase chemistry. This research is led by Eli Ruckenstein (CE) and David Kofke (CE).

• Catalytic Reaction Pathways: Ab-initio calculations that complement experimental studies of heterogeneous catalytic reaction pathways. Structures, energetics, and spectroscopic predictions from the calculations are compared to experimental data to help deepen the understanding of the reaction intermediates and pathways. This research group is led by Carl Lund (CE).

• Enzymatic reaction pathways: Study of enzymatic reaction pathways in biological systems such as proteins using combined QM/MM methodologies. This research is carried out by Dr. Marek Freindorf (CCR) and Dr. Tom Furlani (CCR).

• Molecular Electronic Structure Theory: Development of computational methods in theoretical chemistry. Development of parallel algorithms for distributed- and shared-memory parallel computers, which can be used to solve Grand Challenge class problems. Study of the role of electron spin in chemical reactions involving biradicals. Quantum mechanical study of the reactions. This research is led by Harry F. King (Chemistry) and Dr. Tom Furlani (CCR).

• Commercial Software Development: Joint research with Q-Chem Inc. to develop commercial quantum chemistry software. This research is supported by Dr. Tom Furlani (CCR) and Dr. Marek Freindorf (CCR).

• Binding in a drug receptor complex: Thrombin is a human protein which reacts with fibrinogen to create blood clots. The activity of Thrombin can be regulated by small molecules which bind to the active site of the protein. Combined QM/MM calculations of the interaction between small ligands and the Thrombin active site are being carried out in order to discover molecular ligands with strong affinities for the protein active site. The project is carried out by Dr. Marek Freindorf (CCR) in collaboration with Professor David Hangauer (Chemistry).

• Molecular modeling of Integrin active site: Integrins are human membrane proteins, which are responsible for signals from the cell interior to the extracellular matrix. The signal transduction is related to cell growth and cell division, and defects in transduction pathways may arise in diseases such as diabetes or cancer. Combined QM/MM calculations are being performed in order to elucidate the mechanism of the ligand - active site interaction in these proteins. The project is carried out by Dr. Marek Freindorf (CCR) and Dr. Vivian Cody (Hauptman-Woodward Medical Research Institute).

• Hydrogen bonding in clusters: The intermolecular interactions in small cationic clusters give insight into the nature of hydrogen bonding interactions, which is one of the most fundamental interactions in biological systems. In the project we calculate stabilization energies of small clusters, and reaction profiles of chemical reactions in clusters, using Density Functional Theory. The results of the calculations are compared with experimental data based on mass spectroscopy. The project is carried out by Dr. Marek Freindorf (CCR) and Dr. Tom Furlani (CCR) in collaboration with Dr. James Garvey (Chemistry).

• Calculations of active site of cytochrome P450: Cytochrome P450 is a heme enzyme which is responsible for drug metabolism. Combined QM/MM theory is being employed by CCR computational scientist Dr. Marek Freindorf (CCR) to model the interactions between various ligands and the enzyme active site. The calculations are performed in order to clarify the mechanism of ligand binding to the enzyme active site, and to improve our understanding of the biological activity of this protein.

• Materials Processing: Ab-initio electronic structure calculations to investigate chemical species and reactions important in high temperature vapor-phase materials processing, particularly for silicon and aluminum containing compounds. Kinetic Monte Carlo simulation methods to investigate the gas phase nucleation of nanoparticles of silicon by chemical reaction. This research is led by Mark Swihart (CE).

• Magnetic Properties Modeling: Research in theoretical and computational chemistry, magnetic properties of molecules (NMR etc.), theory and computation of optical activity, and transition metal systems. This research is led by Jochen Autschbach (Chemistry).

• Chemical Engineering: Research in statistical thermodynamics, structure of complex fluids, molecular simulation, biopreservation. This research is led by Jeffrey R. Errington (CE).

• Computing the Nonlinear Properties of Organic Chromophores: Density Functional Theory (DFT) Quadratic Response (QR) method implemented in the Dalton program is applied to calculations of two-photon absorption transition matrix elements of a series of large donor-acceptor substituted conjugated molecules. This approach, also known as time-dependent DFT theory (TDDFT), is a numerically efficient method for accurate quantitative calculations of resonant nonlinear properties of large organic chromophores. The Cubic Response function is also implemented allowing for calculations of higher order properties such as three-photon absorption transition matrix elements. Mixed magneto-electrical properties of chiral media are the subject to the future investigations. This research is led by Professor Paras Prasad (Chemistry, Institute for Lasers, Photonics, and Biophotonics) and Dr. Alexander Baev (Chemistry).

Computational Fluid Dynamics

• Turbulent and Multiphase Flow Analysis: Holographic measurement of particle-turbulence interaction in isotropic turbulence, Dynamics of Aerosol particles in Isotropic Turbulence, Microgravity, and New Approaches of Holographic Particle Image Velocimetry for Studying Turbulence. This group is led by Prof. Hui Meng (MAE).

• Chemically Reacting Flows: Thermal-fluid science, turbulence, combustion, and multiphase transport. This research is led by Cyrus Madnia (MAE).

• BioMechanical Systems: The development of efficient new schemes with higher order accuracy (using solution adaptive schemes) for simulations of complex biomechanical systems. The ACM2E (Applied Computational Mathematics and Mechanics Research Group) research group is led by Dr. Abani Patra (MAE).

• Turbulent Flows: Research in numerical simulation of fire phenomena, large eddy simulation of two-phase metalized combustion, systems, modeling transport processes in cluttered environments. This research is led by Dr. Paul DesJardin (MAE).

Data Mining and Database Development

• REDfly is a curated collection of known Drosophila transcriptional cis-regulatory modules (CRMs). More information can be found under the Bioinformatics section of this page. This group is led by Dr. Marc Halfon (The Center of Excellence in Bioinformatics, Dept of Biochemistry) and supported by Steve Gallo (CCR).

• Tops Markets Purchasing Research: Professor Arun Jain of the School of Management is carrying out leading edge research on the buying habits of customers at Tops Markets by using data mining techniques to analyze extremely large Oracle database of customer purchases over several years. Research led by Professor Arun Jain (School of Management) and supported by Steve Gallo (CCR).

• Computational Approaches to Disease Causes and Treatment: This research is aimed at using advanced data mining techniques to analyze medical data. Research led by Aidong Zhang (CSE) and Zihua Hu (CCR).

• Shared Healthcare Database: Providers, payers, and healthcare resource managers throughout Western New York need better information about the individual and aggregate healthcare needs of patients and communities throughout the region. A shared regional database with this kind of information will have significant potential for improving both economic and health benefits to vastly improve the quality of life in our region. Such a resource will also prove to be extremely important as part of a bio-terrorism surveillance system for this region. Carried out in collaboration with: Julian L. Ambrus, Jr., MD (Buffalo General Hospital), David Penniman (Dean, School of Bioinformatics), Anthony J. Billittier IV, MD (Commissioner of Health, Erie County), David G. Ellis, MD, (Assoc. Director of Emergency Services, ECMC), Gregory Young, MD (Medical Director Western Region, NYS Department of Health), Maurizio Trevisan, MD (Interim Dean, School of Public Health and Health Professions), and Steve Gallo (CCR).

• Association of Academic Health Science Libraries (AAHSL): AAHSL comprises the libraries serving the accredited U.S. and Canadian medical schools belonging to or affiliated with the Association of American Medical Colleges. The organization promotes the advancement of knowledge management and furthers the effectiveness and value of educational and other library services. CCR has worked with AAHSL to develop a portal that allows the AAHSL membership to collect, analyze, and present annual statistical information for libraries in the United States and Canada. This work is led by Dr. Gary Byrd (Health Sciences Library) and Steve Gallo (CCR).

Earthquake Engineering

• CSEE, MCEER, NEES, and CCR Collaborative Platform: The installation of a powerful server in the Center for Computational Research to serve as a collaborative platform for the Multidisciplinary Center for Earthquake Engineering (MCEER), the Network for Earthquake Engineering Simulation (NEES) and the Civil, Structural, and Environmental Engineering department (CSEE) researchers and collaborators delivers high-performance computational and visualization capabilities. This research is led by a team that includes Andrei M. Reinhorn (CSEE/SEESL), Gary F. Dargush (MAE), and Mark L. Green (CSEE).

• Passively-damped Structural Systems: Research focused on the development of an evolutionary framework for computational aseismic design of passively-damped structural systems. This research is led by Gary F. Dargush (MAE) and Mark L. Green (CSEE).

• Earthquake Resistant Design: Research focused on seismic evaluation and retrofit of existing steel bridges, steel buildings, and unreinforced masonry buildings, behavior of steel, metal and advanced composite structures, and the behavior of guyed-towers, cable structures, log-span and tall structures. This research is led by Michel Bruneau (CSEE/MCEER).

• Performance of Structural and Geotechnical Systems: Research using Open System for Earthquake Engineering Simulation (OpenSees) to evaluate and improve modeling and computational simulation in earthquake engineering. This research is led by Andrew S. Whittaker (CSEE).

• Damage Mechanics: Application of fiber reinforced composite materials in the infrastructure, composite materials damage mechanics, and computational mechanics. This research is led by Amjad J. Aref (CSEE).

Environmental Modeling and Simulation

• Ground Water Modeling: High performance analytic element methods for modeling ground-water flow at either regional or local scales. This research is led by a team that includes Alan J. Rabideau (CSEE), Matthew W. Becker (Geology), Igor Janckovic (CSEE), and Doug Flewelling (Geography).

• Geophysical Mass Flows: Computational techniques to study volcanic plume motion and sedimentation. This work has implications for volcanic hazards and short-term climate change. This multi-disciplinary research is led by Abani Patra (MAE), Marcus Bursik (Geology), Michael Sheridan (Geology), Bruce Pitman (Math), and Dr. Matt Jones (CCR).

• Harmful Algal Blooms: Research focused on the goal of predicting bloom movement in the Great Lakes, the main objectives of the transport modeling system are to maintain a near real-time database for water velocity fields in the lakes and to provide relatively short-term predictions (over several days to several weeks, and possibly longer) of lake circulations. This research is led by Joseph F. Atkinson (CSEE) and Mark L. Green (CSEE) including the Great Lakes Program (GLP).

Grid Computing

• Open Science Grid Collaboration (OSG): The Open Science Grid is a distributed computing infrastructure for scientific resarch. Comprised of an alliance of universities, national laboratories, scientific collaborations and software developers, the OSG brings petascale computing and storage resources into a uniform shared cyberinfrastructure. CCR is an active participant in the OSG and provides opportunistic access to over 2100 processors as well as maintaining the support center for the GRASE Virtual Organization. This collaboration is led by Steve Gallo (CCR) and Jon Bednasz (CCR).

• New York State Grid (NYSGrid): The New York State Grid aims to create an advanced collaborative technological infrastructure that supports and enhances the research and educational missions of institutions in New York State. CCR provides technical grid computing expertise as well as outreach and training to the NYSGrid. Jon Bednasz (CCR) chairs the technical working group and is supported by Steve Gallo (CCR).

• Cyberinfrastructure Laboratory at UB:* The Cyberinfrastructure Laboratory performs state-of-the-art grid computing research by focusing on the development of the underlying technologies (grid middleware) to enable grid computing. The CI laboratory is led by Dr. Russ Miller (CSE) and is supported by Steve Gallo (CCR) and Jon Bednasz (CCR).

• Grid Computing Support: CCR focus on enabling faculty led research groups to take full advantage of the resources available on the grid. In addition to maintaining the underlying grid infrastructure at CCR, this typically involves educating users on using the grid and assisting them with the modification of their applications to make use of the grid. Grid computing projects are often performed in collaboration with the Cyberinfrastructure Laboratory. This work is supported by Steve Gallo (CCR), Jon Bednasz (CCR), and Dr. Matt Jones (CCR).

Homeland Security

• Capabilities and Research in Homeland Security: Visualization of border crossings and the supercomputing resources at CCR play a large part in homeland security research being done at UB.

Medical and Scientific Imaging

• MRI Imaging: Research in clincal and neuroimaging correlation in neurologic disease states, especially multiple sclerosis. Carried out in collaboration with the Buffalo Neuroimaging Analysis Center and Martins Innus (CCR).

• CT Imaging: 3D imaging of CT and MRI data, development of a PC based application, complete with GUI. Carried out in collaboration with Dr. Philip Glick of The Women & Children's Hospital of Buffalo and Martins Innus (CCR). Exploring commercial development of software.

• Single Photon Emission Computerized Tomography: Computer Assisted SPECT Diagnosis of Vascular Dementia - looking at SPECT images to come up with a way to diagnose small vessel disease. Carried out in collaboration with Dr. John Baker (Nuclear Medicine), Dr. Robert Miletich (Nuclear Medicine / Dent Neurology), and Martins Innus (CCR).

• PET Applications for Biomedical Research: Investigating techniques of data correction and processing, image reconstruction, and image quality evaluation for human and animal Positron Emission Tomography (PET). This group is led by Rutao Yao (Nuclear Medicine) and supported by Dr. Matt Jones (CCR).

• Analysis of Mouse Jaw Micro-CT: Using 3D volume rendering to analyze and measure bone loss in diseased mice. Collaboration with Ken Hoffmann (Toshiba Stroke Center), Richard Evans (Oral Biology), Sarah Gaffen (Oral Biology), and Martins Innus (CCR).

National Technology Alliance

• Rosettex: CCR is a partner with Rosettex Inc on a contract from the National Technology Alliance to develop and exploit dual use technologies that meet the needs of the federal government (including the Department of Defense) but that can also be used for commercial applications. Currently working with UB's Center for Multisource Information Fusion (Tarun Singh (MAE), Rekesh Nagi (IE), Bharat Jayaraman (CSE), Thenkurssi Kesavadas (MAE), Ann Bisantz (IE), Jim Llinas (IE), Dr. Matt Jones (CCR), and Dr. Tom Furlani (CCR)) to develop Innovative Data Fusion Capabilities for use in a command and control military environment.

Physics

• Spectroscopy: Techniques of pulsed terahertz spectroscopy (PTS) to study carrier and phonon dynamics in solid-state materials and energy transfer to conformational vibrational modes in biomolecules. This research is led by Prof. Andrea Markelz (Physics).

• Quantum Monte Carlo: Quantum Monte Carlo methods in condensed matter physics, Hartree-Fock methods for magnetized systems, atoms and the behavior of molecules in strong magnetic fields. Total energy techniques in condensed matter (density functional and tight-binding LCAO techniques). This research is led by Dr. Matt Jones (CCR).

• Many Body Theory: Research in computational many body theories, microscopic theory for spin-triplet pairing, dynamical mean field theory, magnetic nanostructure, superconducting nanostructures, computational algorithm for electronic transport in nanoscale. This research is led by Jong Han (Physics).

• Nonlinear and Dynamical Systems: Mechanical energy propagation in nonlinear systems: discrete solitary waves, boundary effects, quasi-equilibrium phase, detection of buried objects (mine detection/imaging), chock absorption, and nanoprinting. This research is led by Surajit Sen (Physics).

• Cosmology: Research in inflationary cosmology, cosmic microwave background physics, accelerating universe, and dark matter. This research is led by William H. Kinney (Physics).

• Electronic Packaging: Several computational and experimental studies including material nonlinear analysis of surface mount packaging (thermal and dynamic), damage mechanics of Pb/Sn solder alloys based on thermodynamics and statistical mechanics, and damage mechanics of solder interconnects under high electrical current density. This research is led by Cemal Basaran (CSEE) including the Electronic Packaging Laboratory.

• CMS: U.S. CMS is a collaboration of US scientists participating in the Compact Muon Solenoid (CMS) experiment at the Large Hadron Collider (LHC) at CERN in Geneva, Switzerland. Researchers Dr. Karl Ecklund (Physics) and Dr. Avto Kharchilava (Physics) are utilizing CCR facilities for their CMS research work. This work is supported by Dr. Matt Jones (CCR) and Steve Gallo (CCR).

Visualization and Urban Planning

• Peace Bridge Plaza Design and Visualization: Joint project to develop 3D models of 4 proposed plaza options on the American side of the Peace Bridge. Carried out with Professor Robert Shibley (School of Architecture), CCR, and Bergmann Associates.

• Peace Bridge Project: Joint project, funded by the Peace Bridge Authority to develop a detailed 3D visualization of the current Peace Bridge and all the proposed bridges and toll plaza's. Collaboration between CCR, Bergmann Associates, IBC Digital, eMedia, and Niagara College of Canada.

• Williamsville Toll Barrier Improvement Project: Joint project between Bergmann Associates, TVGA Engineering, and CCR to develop a detailed 3D visualization of a new proposed high speed toll barrier to be located on the NYS Thruway. Funded by NYS Thruway Authority.

• Traffic Accident Reconstruction Visualization: Development of 3D real-time visualizations of traffic accidents for use in civil proceedings. Carried out in conjunction with TVGA Engineering and CCR.

• Buffalo Niagara Medical Campus: 3D Immersive visualization of an 8 block region in downtown Buffalo for use in urban planning for the construction of 3 new life sciences buildings. Carried out in collaboration with CCR and IBC Digital.

• StreetScenes: Henrique Bucher (formerly with CCR) developed a stand-alone program that allows users to import the output of traffic simulation studies into 3D models.

Virtual Reality Simulations and Performances

• Virtual Site Museum: 3D Immersive visualization of the Northwest Palace of King Ashur-nasir-pal II. Work featured on several television documentaries, including PBS. This work is led by Profs. Samuel Paley (Classics) and Thenkurussi Kesavadas (MAE).

• The Thing Growing: Interactive, immersive, virtual reality experiences. Most recently, "The Thing Growing" was presented as a show at the ICC museum in Tokyo in June. This is the work of Josephine Anstey (Media Studies).

• ELV: Alive on the Grid: This project is a collection of virtual art worlds where participants from different geographic locations can interact in shared virtual spaces. Josephine Anstey (Media Studies) is leading this work.

• The Active-Stimulation Feedback Platform: The Active-Stimulation Feedback Platform is a highly interactive electronic artwork about networks and flows, consent and resistance, desire and aversion. It is a global simulation, extruded from the computer onto a physical interactive platform, a circle 16 feet in diameter, densely covered with arcade-style push buttons. Viewer / participants will interact with the simulation by walking, crawling and rolling across these buttons. Their movement's trigger and bias playback of audio samples ("yes" or "no") recorded from 2000 people worldwide. This research is led by Paul Vanouse (Art) and Dr. Tom Furlani (CCR).