Faculty (A-G)
A-G | H-N | O-Z
The Center for Simulation and Modeling has assembled a group of more than 50 faculty members from across the University who are engaged in computational research. These include faculty in Chemistry, Biology, Computational Biology, Physics and Astronomy, Mathematics, Computer Science, Economics and several of the departments in the Swanson School of Engineering, as well as faculty from the Schools of Public Health, and Medicine, and the Graduate School of Public and International Affairs for the purpose of leveraging both their work and expertise.
Civil and Environmental Engineering
Dr. Abad leads the Earth Processes & Environmental Flows (EPEF) research group which performs experimental and numerical research. His research interests related to computational areas are: development of Computational Fluid Dynamics (CFD) models for earth processes and environmental flows (especially those related to subaerial and submarine environments), prediction of short- (engineering time scale) and long-term (geological time scales) evolution of river systems. Sediment transport and multiphase flow modeling.
Figure 1: Flow over experimental bedforms (bars) in meandering channels.
Figure 2: Secondary flow in the presence of migrating dunes.
Chemical Engineering
Anna Balazs' research involves theoretical and computational modeling of the thermodynamic and kinetic behavior of polymer blends and composites. She is also investigating the properties of polymers at surfaces and interfaces.
Image 1: The sample is irradiated by a fixed light source at the right end; the rest of the sample is kept in the dark. The gel moves towards the dark region.
Image 2: The light source is fixed at the two ends of the sample while the center is kept in the dark. The ends of the sample move towards the dark center and hence, cause a bending of the gel.
Computational Biology
Modeling and simulations of the structure and dynamics of biomolecular complexes and assemblies; statistical mechanics of macromolecules; molecular aspects of biochemical and biophysical networks; computer modeling and engineering of enzyme-substrate, protein-DNA and protein-drug binding and interactions; mathematical modeling of cell cycle signaling and regulation, statistical analysis of gene expression arrays.
Ivet Bahar's Research: Computational analysis of interactions of MAP kinase phosphatase 1, a cell signaling enzyme targeted in high-throughput screening studies, with a selective inhibitor, PSI2106, is displayed. Analyses of molecular details of protein-inhibitor interactions assist in explaining inhibition mechanism of small-molecules and designing more potent and selective compounds in drug-discovery.
Otolaryngology
The goal of Dr. Balaban's research is to develop a rational basis for understanding the neurobiology of the vestibular system so that new therapies for vestibular disorders can be designed. This goal is approached by: (1) identifying the organization of central vestibular circuits that mediate autonomic and somatic motor responses to vestibular stimulation; (2) identifying neurotransmitters and intracellular signal transduction proteins that are important in these brain circuits; (3) examining the role of these biochemical constituents in responses to challenges from toxins; and (3) identifying contributions of these mechanisms to the clinical linkage among balance disorders, anxiety disorders (panic with agoraphobia), and migrainous vertigo.
Department of Chemical Engineering
Dr. Ipsita Banerjee received her PhD from Rutgers University, MS from Indian Institute of Science, and BS degree from Jadavpur University, all in Chemical Engineering. Her primary research interest is in the area of process systems engineering and its application in different chemical and biomedical problems. She is currently developing novel methods for differentiating embryonic stem cells to pancreatic lineage and applying systems engineering principles to the analysis of regulatory network of the differentiating cells population. She is also interested in reaction network modeling and development of reduced reaction networks for energy efficient combustion processes.
Human and Computational Genetics
Dr. Barmada is an associate professor of Human Genetics in the Graduate School of Public Health, University of Pittsburgh, Director of the Center for Computational Genetics at GSPH, and an Associate Director of the Center for Simulation and Modeling at the University of Pittsburgh.Through his involvement with multiple research projects, including large multi-center epidemiologic and genetic studies, Dr. Barmada has extensive experience with the informatic and analytical issues involved in complex multi-disciplinary studies. His particular research interests lie in the analysis of high-throughput data-intensive genomics data sets, including multivariate genetic data and the pleiotropic effects of individual genes or gene networks. More recently, he has worked on the application of systems biology to the analysis of genetic and genomic data, and the integration and analysis of data from multiple experimental platforms. He is an integral part of ongoing efforts on campus to develop translational applications of data-intensive genomics methods (such as next-generation sequencing). He is an active member of the graduate faculty at the University of Pittsburgh, and teaches in several classes covering statistical genetics and computational methods for genetics and bioinformatics, as well as risk analysis for the genetic counseling program, and the genetics module for the university's medical school.
Industrial Engineering
Professor Bidanda is the Co-Director of the Manufacturing Assistance Center at the University of Pittsburgh. He has industrial experience in manufacturing systems, tools, and precision manufacturing. His research focus includes Computer Integrated Manufacturing Systems and Robotic Applications, Time Compression Technologies such as Rapid Prototyping and Reverse Engineering, traditional Industrial Engineering, Automated Data Collection and Shared Manufacturing. He works closely with manufacturing industries in Western Pennsylvania in the area of cellular manufacturing, work measurement, automatic data collection, and shop floor information systems.
John Brigham
Department of Civil and Environmental Engineering
John Brigham received his BE in civil and environmental engineering and mathematics from Vanderbilt University in 2003, followed by his PhD in civil and environmental engineering from Cornell University in 2008. Then in the fall of 2008 he joined the Department of Civil and Environmental Engineering and the Department of Bioengineering at the University of Pittsburgh as an assistant professor.
Dr. Brigham's research is focused on fundamental concepts in computational mechanics and inverse problems. His work includes developing computational tools to better simulate the behavior of manmade and biological structures in their natural environments, as well as approaches to inversely assess the current state and future behavior of such structures.
Graduate School of Public Health
Since 1999, Dean Burke has been principal investigator of a National Institutes of Health-funded HIV Vaccine Trials Unit, a consortium based at the Johns Hopkins Center for Immunization Research and involving clinical trial sites in China, India, and Thailand. Much of his research on epidemiology of infectious diseases is conducted in the field. He established and directs a project on cross-species transmission of infectious diseases in rain forest populations in Cameroon, Central Africa, and is principal investigator of a multicenter effort that is developing computational simulations and predictive models of infectious disease epidemiology and evolution, focusing on influenza, dengue, measles, and bioterrorist attacks. In addition, he is coprincipal investigator of the Mid-Atlantic Regional Center for Biodefense and leads a program that seeks to enable Thai epidemiologists with new theoretical and computational tools to more effectively plan and respond to outbreaks of avian flu.
The Graduate School of Public Health has received a $10 million grant from the Bill & Melinda Gates Foundation to fund the creation of computer simulations of epidemics, showing worst- and best-case outbreak scenarios. These will be used to evaluate new vaccine technologies and modes of vaccine delivery. The models will be designed to fit the prevalence, incidence and geographic spread patterns of past epidemics in developing countries worldwide, and will help prevent future infectious disease epidemics by optimizing vaccine strategies for particular diseases and regions.
Chemistry
The central goal of the Chong lab is to use theory and simulation to understand how proteins fold, bind their partners, and catalyze reactions, with an emphasis on how malfunctions at the molecular level can be linked to clinical data for various diseases. To achieve this goal, they develop accurate approaches for simulation and subsequent analysis of protein structure and function.
The Chong Lab uses simulations to study protein dynamics. Shown are snapshots from a simulation exhibiting the mechanically-induced unfolding that results from the fusion of two proteins.
Chemistry
Rob D. Coalson investigates ion channels as they play crucial roles in the processes of life. His group is studying many aspects of their function and role in nature.
Image 1:Molecular dynamics simulation of water flow through the Aquaporin 1 protein channel.
Image 2: Time-evolution of counterion cloud formation around a charged spherical colloid particle. In this Dynamic Monte Carlo simulation, the mobile ions are confined to a sphere (inscribed in the indicated cube) and distributed randomly at time t=0 (left panel). Right panel shows steady state cloud of counterions around the macroion; center panel shows the counterion distribution at an intermediate time.
Graduate School of Public and International Affairs
Louise Comfort uses simulation and modeling tools to research organizational theory, innovation, and behavior; complex adaptive systems; policy analysis, design, and program implementation; and information technology policy and management; and disaster response management.
Physics and Astronomy
We explore non-equilibrium dynamics in systems of ultracold atomic and molecular gases. Over the last decade, advances in experiments with these gases have made possible the realization of strongly interacting quantum systems, which exhibit many interesting penomena, some of them related to superconductivity and more exotic behavior in solid state devices. Using recently developed numerical methods, we are able to compute the time-dependent dynamics of these systems in parameter regimes directly relevant for ongoing experiments, and make predictions for novel phenomena that could be observed in the laboratory.
Computer Science
Robert Daley works in the theoretical foundations of computer science, computational complexity, learning algorithms, and philosophical aspects of computer science. The major thrust of Professor Daley's current research effort is directed towards establishing mathematical tools which can be used to analyze various learning algorithms (viz., heuristics) that have been and are being developed by researchers in artificial intelligence, and also towards the determination of the fundamental relationships between the various parameters of the learning paradigm. Of particular interest currently are: the development of cooperative strategies for multi-agent learning systems; use of Genetic Algorithms in reinforcement learning problems.
Economics
David DeJong research economic cycles and macroeconomics, econometrics, and transition Economics using simulation and modeling tools.
He uses computer simulations to reconcile two branches of the field that don’t always communicate with one another—theory and statistics—by mapping theoretical models of economic behavior onto statistical models.
Mathematics
Bard Ermentrout's research centers on dynamical systems, nonlinear differential and integral equations, mathematical biology, neuroscience and mapping the immune system using simulations and modeling.
Two snapshots in time of the response of a simple laterally inhibitory cortical network to spatially uniform flickering light. This is meant to model a phenomenon known as flicker phosphenes. When a human subject looks at a uniform flickering field, at a critical frequency, the visual field spontaneously breaks into colorful moving geometric patterns. The simulation here consists of a two-dimensional array of differential equations coupled via lateral inhibition and with a local negative feedback.
Mechanical Engineering
Peyman Givi investigates thermal-fluid science, turbulence, combustion, computational methods and numerical algorithms, applied mathematics, spectral analysis, stochastic processes.
Load balancing applied at an instance of time during the simulation. 3D turbulent scalar fields (rendered on top left) affect CPU load distribution over solution domain. Each color on the 3D solution blocks represents a separate computational domain. A uniform decomposition (top block) leads to poor load distribution, while the balanced irregular decomposition (bottom block) overcomes this severe scalability bottleneck and paves way to much shorter simulation times.
Biology
Michael Grabe works on voltage-sensing, ion selectivity and conduction, network dynamics in ion regulation, and bilayer mediated protein interactions.
The voltage-dependent anion channel (VDAC). It facilitates the flow of ions and metabolites across the outer mitochondrial membrane. Work in the Grabe and Coalson labs shows that the recently solved x-ray structure of VDAC from mouse is selective for anions with a high single-channel conductance both properties indicate that the structure represents the physiologically relevant, open state of the channel. The channel (green) is pictured on the left with ions (yellow) passing through it. The right panel shows a stacked view of the electrostatic potential at 3 different levels. The electrostatic potential is mostly positive, which is one of the clues indicating that this channel is open.
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