UT and ORNL Senior NIMBioS Collaborators
The following individuals serve as a pool of possible postdoctoral mentors for NIMBioS as well as provide local expertise in a variety of fields related to possible working groups. All have agreed to assist the Institute as appropriate, with possible release-time funding provided by UT when needed to support Institute Activities.
Vasilios Alexiades, Professor, UT Department of Mathematics. Dr. Alexaides' research in applied computational mathematics includes modeling and analysis of physical processes involving systems of conservation laws (PDEs) in materials science, energy, and cell physiology, with emphasis on phase change processes (solidification), heat and mass transfer, and CFD. His biology interests include phototransduction and electrical propagation in excitable tissue, and his computational science interests include parallel (distributed) computing, uncertainty quantification, and parameter sensitivity analysis.
Jerome Baudry, Assistant Professor, UT Department of Biochemistry and Cellular & Molecular Biology. Dr. Baudry's research centers on providing self-consistent descriptions of biological phenomena across ranges of time- and length-scales. To pursue this major challenge in mathematical and computational biology, Dr. Baudry strives to integrate molecular-level and coarse-grained, mesoscopic descriptions of cell-scale systems behavior through development of parallelizable multi-scale methods and tools, including multigrid methods, continuum mechanics, graph theory, and covariance analysis. This work requires collaboration with researchers at the UT/ORNL Center for Molecular Biophysics, UT biological and mathematical groups, and numerous other national and international researchers.
Elissa Chesler, Scientific Program Director, ORNL Biosciences Division. Dr. Chesler's research emphasizes the integration of genomic and phenomic resources though implementation of statistical and combinatoric approaches to genetic systems analysis. Her current research centers on ontological discovery through extraction of sets of genes and phenotypes from large empirical data sets. Her postdoctoral research was conducted in association with the large collaborative Gene Network project, which successfully incorporates data from basepair to behavior.
Aimée Classen, Assistant Professor, UT Department of Ecology and Evolutionary Biology. Dr. Classen's research focuses on how abiotic and biotic factors interact to shape ecosystem structure and function and how natural disturbances and anthropogenic impacts such as climatic change, biofuel production, species invasions, and herbivore outbreaks may shape these interactions. Research in the Classen lab is highly collaborative and scales many levels of ecological organization, from microbial ecology to ecosystem ecology and links above- and below-ground interactions in a changing environment.
Charles Collins, Associate Professor, UT Department of Mathematics. Dr. Collins's research focuses on numerical analysis and scientific computing with applications to continuum mechanics and other areas.
Jack Dongarra, Distinguished Professor, UT Department of Electrical Engineering & Computer Science. Dr. Dongarra specializes in the development of numerical algorithms in linear algebra, the use of advanced-computer architectures, and the advancement of programming methodologies and related tools for parallel computing. He has designed, developed, tested, implemented and documented numerous high quality open source mathematical software packages and systems, including EISPACK, LINPACK, BLAS, LAPACK, ScaLAPACK, Netlib, PVM, MPI, NetSolve, Top500, ATLAS, and PAPI.
James Drake, Associate Professor, UT Department of Ecology & Evolutionary Biology. Dr. Drake's research interests focus on the nature of ecological complexity at the community level. Using both theory and experiment, Dr. Drake disassembles and reassembles community structure over space and time, in the process identifying rich and varied mechanisms and processes responsible for the shape of nature. Other research interests include biological invasions, hierarchical control of ecological systems, and time series phenomena.
Xiaobing Feng, Professor, UT Department of Mathematics. Dr. Feng's research in applied and computational mathematics focuses on the development and analysis of efficient and fast numerical methods and algorithms for partial differential equations and their applications to fluid mechanics, materials science, image processing/computer vision, general relativity, and mathematical biology. His research in mathematical biology involves mathematical modeling and numerical simulation for reverse engineering gene regulatory networks and functional prediction.
James Fordyce, Associate Professor, UT Department of Ecology and Evolutionary Biology. Dr. Fordyce's research focuses on factors that maintain variation within and among populations and the causes and consequences of phylogenetic and population divergence. This work includes the role of hybridization and gene flow in generating evolutionary novelty. His work also examines the costs and benefits of gregarious feeding by toxic organisms and the factors that determine optimal group size.
Matthew J. Gray, Associate Professor, UT Institute of Agriculture, Department of Forestry, Wildlife and Fisheries. Dr. Gray's expertise is wetland ecology, with emphasis on waterbird conservation and amphibian diseases. Dr. Gray's research interests include all aspects of wetland ecology, with past and current projects exploring wetland plant, amphibian, and waterbird communities. Three primary research focuses are (1) examining influences of humans on wetlands, (2) managing wetlands for sustainable use, and (3) studying the ecology of amphibian diseases. Dr. Gray also is involved in landscape conservation and is a former Team Leader for the USDA NRCS National Easement Assessment Project.
Hong Guo, Associate Professor, UT Department of Biochemistry & Cellular and Molecular Biology. Dr. Guo uses state-of-the art computational approaches to investigate mechanisms of enzyme- catalyzed reactions, inhibitor binding processes, and protein structural and dynamic properties. He is particularly interested in understanding the origin of high catalytic efficiency and selectivity of biological systems for enzymes. Techniques used include molecular dynamics (MD) simulations, free energy calculations, mixed quantum mechanical/molecular mechanical (QM/MM) methods, and other computational and mathematical approaches.
Kimberly Gwinn, Associate Professor, UT Entomology and Plant Pathology Department. Dr. Gwinn's professional interests include the use of natural products as pesticide alternatives, secondary metabolism of fungi, and the physiology of plant diseases. She is the Acting Science Director of the Bioactive Natural Products Center of Excellence, a collaborative research network incorporating several departments and divisions at the University of Tennessee (UT), The McClung Museum, and Oak Ridge National Laboratory (ORNL).
Thomas Hallam, Emeritus Professor, UT Departments of Ecology & Evolutionary Biology & Mathematics. Dr. Hallam's research centers on the use of mathematical models to help solve problems in ecology and ecotoxicology, with emphasis on the effects of toxicants at the population and community levels. His current research addresses the role of bats in agricultural systems, the diseases (especially rabies) for which bats serve as a reservoir, and the use of computer technology, including simulation visualization and 3D, to address pressing issues in ecology.
Elizabeth Howell, Professor, UT Department of Biochemistry & Cellular and Molecular Biology. Dr. Howell is conducting research on the structure, function, assembly, and folding of the enzyme Dihydrofolate reductase (DHFR). Inhibition of DHFR activity is the basis for cancer chemotherapy treatments using folate analogs and is also the basis for clinical treatment of a number of bacterial infections and malaria. Her research includes kinetic and physical studies as well as site-directed mutagenesis techniques and she uses X-ray crystal structures to evaluate mutant enzymes. In collaboration with RJ Hinde in Chemistry, she has built models of a new potential type of interaction between the quadrupole moment of aromatic rings and an anion and has done quantum mechanical calculations on this interaction and then probed the Protein Data Bank to determine if these types of interactions occur frequently in proteins.
Igor Jouline, Associate Professor UT Department of Microbiology & ORNL Computer Science & Mathematics Division. Dr. Jouline develops and applies computational genomics approaches to characterize biological processes. He addresses fundamental biological phenomena, such as signal transduction, gene regulation, and protein-protein interactions, through the prism of molecular evolution. His work, which is helping improve our understanding of biological system functioning, has direct applications in medicine, environmental science, bioenergy utilization, and agriculture.
David J. Keffer, Associate Professor, UT Department of Chemical and Biomolecular Engineering. Dr. Keffer has established and led the UT Computational Materials Research Group (CMRG). The UT CMRG uses an array of multiscale materials modeling tools, including quantum mechanical calculations, molecular dynamics simulation, Monte Carlo simulation, mesoscopic modeling and finite element modeling in order to develop relationships between molecular- level structure and macroscopic properties. A partnership between the expertise in the UT CMRG and the UT biological scientists would result in the application of this suite of multiscale modeling tools toward cutting-edge problems of interest to the UT biological community.
Michael A. Langston, Professor, UT Department of Electrical Engineering & Computer Science. Dr. Langston's research interests center on the synthesis of novel algorithmic tools and the development of highly-scalable implementations of such tools to help resolve the computational challenges presented by large volumes of complex biological data. During his twenty-five years of experience, he has worked in the areas of combinatorics, graph algorithms and complexity theory. He is a member of the UT's Genome Science and Technology faculty and also serves as a Collaborating Scientist in the BioSciences Division at ORNL.
Vena M. Long, Professor Mathematics Education; Associate Dean for Research, UT College of Education, Health and Human Sciences. Dr. Long's background and research are in mathematics and mathematics education with emphasis in the use of technology to teach and assess mathematical learning. She is currently on the Board of Directors of the National Council of Teachers of Mathematics. Her long history in the field has given her great contacts throughout the profession. As Associate Dean for Research, she can tap into the various areas of expertise that reside within our college, including evaluation (Institute for Assessment and Evaluation), mathematics education, science education, cognitive psychology, nutrition, and exercise science, and also excellent outreach connections with local schools and other service organizations.
Jaan Mannik, Assistant Professor, UT Department of Physics and Astronomy. Dr. Mannik's research focuses on self-organizing processes that take place in bacterial cell. The specific questions addressed in Dr. Mannik's lab are: How do bacterial cells position cell division proteins? How is bacterial DNA organized and how does it coordinate cell division? How robust are cell division and chromosome organization relative to perturbations in cell shape? A variety of approaches from experimental and theoretical biophysics, microchip engineering and molecular biology are used in this research.
Vasileios Maroulas, Assistant Professor, UT Department of Mathematics. Dr. Vasileios Maroulas' research interests include multi-target nonlinear estimation and filtering; large deviations and applications to image analysis; sequential analysis and applications to target detection and estimation; and biostatistics. His mathematical biology interests lie in the sphere of tracking intracellular movements and phylogenetic analysis
Wilfred M. Post, Senior Research Scientist, ORNL Environmental Sciences Division. Dr. Post's research focuses on global carbon cycling and the relationship of terrestrial ecosystem dynamics to environmental, edaphic, and biological conditions. Particular areas of interest include soil carbon dynamics, plant-soil nutrient relationships, and the role of species composition on terrestrial processes. He has developed novel approaches to incorporating land-use and climate changes in biogeochemistry models, as well as data assimilation methods and global data sets to help verify, validate and improve terrestrial ecosystem models.
Vladimir Protopopescu, Senior Research Staff, ORNL Computer Science & Mathematics Division. Dr. Protopopescu's research interests focus on the mathematical modeling of complex systems, functional analysis of transport-like equations, global optimization, and optimal control for point and distributed systems. His optimal control work involves models of populations interacting in various forms of competition and cooperation. Recent work includes improving pressure profiles for cardiopulmonary resuscitation.
Susan Riechert, Distinguished Service Professor, UT Department of Ecology & Evolutionary Biology. Dr. Riechert's NSF sponsored research has and continues to involve collaborative efforts with applied mathematicians in empirical tests of ecological and evolutionary constructs. Particular areas of interest have been in evolutionary game theory (collaborators: John Maynard Smith and Peter Hammerstein), social selection theory (Jason Wolf) and survivorship insurance models of social structure (Thomas C. Jones). Riechert also brings a major outreach program to the Institute: the Biology in a Box Project provides K-12 schools throughout the state of Tennessee materials and exercises that address biological concepts and that are designed to enrich science and math curriculum content.
Nathan Sanders, Associate Professor, UT Department of Ecology and Evolutionary Biology. Dr. Sanders's research focuses on the causes and consequences of spatial and temporal variation in diversity. A suite of projects examines how variation within plant species affects species diversity across trophic levels and ecosystem processes. Another project addresses how climatic warming will influence ant community structure and the processes ants mediate, from local communities to global-scale patterns of biodiversity.
Arnold Saxton, Professor, UT Department of Animal Science. For the past few years Dr. Saxton has been working in the area of statistical genomics, statistical methods applied to the large datasets generated by high-throughput biology. This has primarily been analysis of microarray data, but has also included gene mapping, eQTL and proteomics. His research also includes systems biology, the mathematical modeling of whole organisms at the molecular, cellular and tissue levels. The challenge is to develop a model that captures genetic and metabolic responses to environmental change and then derive useful information from this model that will have more parameters than observations.
Engin Serpersu, Professor, UT Biochemistry Cellular and Molecular Biology. Dr. Serpersu's research interest is in the investigation of structure, function, thermodynamics, and dynamics of enzyme-antibiotic interactions using several enzymes that modify aminoglycoside antibiotics. There is a large overlap between substrate profiles of these enzymes regardless of their sequence homology (i.e. the same reaction can be catalyzed by different enzymes using the same antibiotic as substrate). His work involves characterization of the global thermodynamic properties of various enzyme-ligand complexes and then uses different biophysical techniques to understand roles and contributions to these global parameters of different sites and functional groups on enzymes and the ligand.
Shih-Lung Shaw, Professor, UT Department of Geography. Dr. Shaw's research interests include geographic information science, transportation, and spatial modeling. His experience includes work with space- time geographic information systems and their application in the geospatial domain. Other relevant experience includes collaboration with Drs. Louis Gross, Mike Berry, and Suzanne Lenhart on an NSF-sponsored project entitled Grid Computing for Ecological Modeling and Spatial Control.
Michael L. Simpson, Professor, UT Department of Materials Science and Engineering. Dr. Simpson is the founding Principal Investigator of the Molecular-Scale Engineering and Nanoscale Technologies Research Group and the Thrust Area Leader for the Nanofabrication Research Laboratory that will be located at ORNL's Center for Nanophase Material Science. His research interests include analysis, modeling, simulation, and experimentation focused on stochastic processes in gene expression and regulation.
Ken Stephenson, Professor, UT Department of Mathematics. Dr. Stephenson's research focuses on conformal geometry of 2D and 3D surfaces, which has application in mathematics, engineering, scientific visualization, and biology. As a leader in the emerging topic of "discrete" conformal geometry, he has worked with neuroscientists on brain imaging, providing software for conformal flattening of cortical brain scans. Other work includes analysis of sensor arrays, 2D grid generation, graph embedding and manipulation, equidistribution of points, and most recently, the geometry of carbon nanotubes. His NIMBioS contributions would include assisting modeling and applications groups in development of unique capabilities for display and analysis of discrete 2D surfaces.
Chunlei Su, Assistant Professor, UT Department of Microbiology. Dr. Su's research focuses on population genetics and regulation of virulence in the protozoan parasite Toxoplasma gondii. The goals are to understand the origin, the global transmission patterns, the mechanisms of clonal expansion of a few predominant lineages of T. gondii and the evolution of virulence in this widespread parasite of humans and animals. Both experimental and mathematical approaches are to be employed to achieve these goals.
Michael Vose, Associate Professor, UT Department of Electrical Engineering & Computer Science. Dr. Vose holds PhDs in both Mathematics (analytic number theory) and Computer Sciences (combinational logic testing). His interests include: applied mathematical analysis of complex dynamical systems; computational applications for design optimization, algorithm development, simulation, and software engineering; data mining and pattern matching (including sequence alignment); probability and statistics applications, including Bayesian networks and experimental design; and hierarchical and interactive visualization. He is currently collaborating on the NIH-funded project New Approaches to Modeling Speciation.
Steven Wise, Assistant Professor, UT Department of Mathematics. Dr. Wise's research in computational mathematics focuses on development of efficient, adaptive multigrid methods to address interface problems in fluid, material, and biological sciences, as well as level-set and phase-field interface capture method development. His research in mathematical biology involves simulating tumor growth, while his work in computational materials science involves simulating crystal growth.
Russell Zaretzki, Assistant Professor, UT Department of Statistics, Operations & Management Sciences. Dr. Zaretzki's research focuses on the development of computational statistical methods and their application to the fields of bioinformatics and proteomics. His work includes collaborations with Mike Gilchrist of UT's Department of Ecology and Evolutionary Biology in the application of Bayesian methods to models of protein production, as well the development of improved inference methods for data extracted from Serial Analysis of Gene E.