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Biogeochemistry Program

Harry Allcock, Evan Pugh Professor of Chemistry, Department of Chemistry
Research: Allcock's research is at the interface between inorganic and organic chemistry, polymer chemistry, biomedicine, and materials science.  It is based on the principle that new materials with hitherto unseen combinations of properties are accessible by the incorporation of inorganic elements into the backbone structure of polymers.  He was the discoverer of a major class of polymers known as polyphosphazenes which are based on a backbone of alternating phosphorus and nitrogen atoms with two organic, inorganic, or organometallic side groups linked to each phosphorus.  His research group has been one of the main sources of new discoveries in this field.  He also discovered a new class of molecular inclusion compounds (clathrates) that have been used to separate a wide variety of organic small molecules and high polymers, and which also serve as nano-scale templates for addition polymerizations.  A characteristic of his research program is its emphasis on long-range fundamental science, and on the utilization of this science to initiate new advances in medicine, aerospace materials, energy storage, fuel cells, solar cells, and photonic materials.

Doug Archibald, Research Associate, Department of Agricultural Sciences
Research: Dr. Archibald's tool-based research covers five broad areas within application of analytical chemistry in crop and soil sciences: 1) plant tissue evaluation, 2) fat quality assessment for commodities, 3) mycotoxin analysis, 4) soil organic matter evaluation, and 5) analytical laboratory training and education. He often focuses on the science of the chemical analysis while his collaborators focus on the biological, environmental or agricultural aspect of the research project. His principal areas of analytical expertise are multivariate analysis of instrumental data, and UV-vis, NIR, Raman and infrared spectroscopy. He has secondary expertise in many other analytical techniques such as chromatography, mass spectrometry, and microscopy. He manages a lab with capabilities in spectroscopy and conventional crop quality assessment methods, and maintains collections of agricultural materials and spectral-property databases. Dr. Archibald has a great depth of experience in applications of analytical chemistry as a result of his graduate work in industrial and biophysical chemistry, post-doctoral work in biomimetic materials and surface chemistry, research on analytical methods while serving as a scientist for the USDA Agricultural Research Service, and by way of his tenure as director of a Penn State University service laboratory known as The Crop Quality Lab. His research goal is to develop analytical methodologies that will catalyze improvement of agricultural and environmental systems through acceleration of research and development.

Iliana Baums, Assistant Professor, Department of Biology
Research: Molecular evolution and ecology encompasses studies of process on three different time scales - affecting populations, affecting species, and affecting long-term molecular evolution. People in the Baums laboratory test ecological and evolutionary hypotheses concerning all three time scales. They focus on research projects that can contribute to both our basic understanding of ecosystems and have applications in conservation biology. Currently, the Baums group develop and apply molecular tools to understand the influence of biogeography, population structure, and mating patterns on the survival and evolution of corals and other marine organisms. The degree to which coral reef systems are interconnected by larval exchange is one of the key issues in marine ecology and evolution today. Shallow water marine systems have experienced dramatic declines over the past few decades. Effective conservation of these systems requires knowledge on the spatial scale over which they are regulated. Traditionally, marine populations were thought to be open: passive larvae are transported long distances via ocean currents and so connect populations even at remote locations. However, recent methodological advances have produced evidence to the contrary. These results emphasize larval behavior as a means to increase retention around spawning grounds, resulting in closed populations on smaller spatial scales. Dr. Baum's research on coral reproduction was featured in News Focus Article published in the journal Science (14 Dec 2007): Vol. 318. no. 5857, pp. 1712 - 1717. DOI: 10.1126/science.318.5857.1712

Andre Boehman, Professor of Fuel Science and Materials Science and Engineering, Director of the Combustion Laboratory, Department of Energy and Geo-Environmental Engineering
Research: Prof. Boehman’s research interests are in alternative and reformulated fuels, combustion and pollution control.  His present research activities are focused on alternative diesel fuels, diesel combustion and diesel exhaust aftertreatment.  Additional research interests include: Clean and Efficient Diesel Locomotive, Determination of the Underlying Cause of the Biodiesels NOx Effect in Common Rail Diesel Engines, Pennsylvania Clean and Efficient Diesel Engine Program, and Research and Training of a Student in the Area of Thermal Oxidative Stability of Jet Fuel and Fabrication of Batch and Flow Reactor Systems.

Jean Bollag, Emeritus Professor of Soil Biochemistry, Department of Crop and Soils Science
Most of Dr. Bollag's research is focused on interactions of microorganisms and pollutants. His lab group is interested in determining the fate of pesticides and other xenobiotics in terrestrial and aquatic environments and they are studying the possible removal of pollutants by influencing their biodegradation or by provoking their complexation to humic material. Other topics of his research are concerned with the use of plant materials for bioremediating contaminated aquatic and terrestrial environments and with the study of the metabolism of imidazolinone herbicides. Other interests include: Microbial transformation of pesticides and other xenobiotics (particularly heterocyclic aromatic compounds, phenols, anilines); Incorporation of pollutants into soil organic matter as a detoxification method; Application of enzymes for pollution control; Transformation of heterocyclic compounds under anaerobic conditions; and, Use of plant material for decontamination of polluted environments.

Susan L. Brantley, Distinguished Professor, Department of Geosciences and Director of the Earth and Environmental Systems Institute
Research: Chemical, physical, and biological processes associated with the circulation of aqueous fluids in shallow hydrogeologic settings. Investigations incorporate field and laboratory work, and theoretical modelling of observations. Of particular interest are questions concerning the measurement and prediction of the rates of natural processes, including chemical weathering with and without micro-organisms. Recent work has focused on the effect of microbial life on mineral reactivity, and measuring and modelling how rock turns into regolith. Her current projects include: 1) Fe release and isotope fractionation during microbial alteration and weathering of shales, granites, and basalts; 2) Coupling between weathering and erosion; 3) Chemical, physical, and biological weathering in the Luquillo Critical Zone Observatory; 4) Chemical, biological, and physical weathering in the Susquehanna Shale Hills Critical Zone Observatory; The SSHO is one of six Critical Zone Observatories funded by National Science Foundation to study chemical, physical, and biological interactions in the Critical Zone. 5) Neutron scattering analyses of weathering rocks: and 6) Reactive transport modelling of weathering.

Jean E. Brenchley, Emeritus Professor, Department of Biochemistry and Molecular Biology
Research: Examination of the diversity and survival of microorganisms in cold environments and collection of information about their identity, habitats, and metabolism. A comprehensive picture was recently discovered of the microbial diversity in ice core samples from the 3 km deep Greenland ice sheet where microbial life and past climates have been preserved chronologically. A large collection of ultrasmall bacterial isolates was recovered that had remained viable for over 100,000 years at temperatures as low as minus 35°C and described novel bacterial species Herminiimonas glaciei and Chryseobacterium greenlandense.
Determining the extent and sources of contamination with exogenous microbes during ice core drilling that may compromise the authenticity of the indigenous microbial populations, Brenchely used the recent Greenland North Eemian (NEEM) drilling project as a first-time opportunity to assess potential microbial contamination throughout the drilling process by: a) microbiological and molecular analyses of the drilling fluid; b) tracking the penetration of the drilling fluid along the grain boundaries, and c) deployment of fluorescent microspheres as surrogates of potential microbial contaminants in the borehole at different depths representing major ice structures (bubbly, brittle and clathrated ice). Her research creates a comprehensive picture of the microbial populations within the largest ice sheet in the Northern hemisphere and helsp answer important questions about the limits of microbial life, mechanisms of survival, and metabolism within glacial ice. The development of strategies to detect contamination of ice cores during the drilling process will be valuable to both future microbiologists and others searching for extraterrestrial life and biosignatures.

William Brune, Distinguished Professor of Meteorology, Head of the Department of Meteorology
Research: Atmospheric photochemistry from Earth's surface to the stratosphere; atmospheric interactions between photochemistry and dynamics; chemical reactions in the gas-phase on surfaces; spectroscopic detection techniques; Atmospheric/Air Chemistry.

Mary Ann Bruns, Associate Professor of Soil Science and Microbio Ecology, Department of Crop and Soil Sciences
Research: Research in the Bruns lab aims to gain understanding of soil microbial responses to anthropogenic disturbance and of microbes’ roles in mitigating disturbance effects. Humans are constantly altering the face of the Earth—through forest clearing, urban development, agricultural cropping, strip mining. When soils are subjected to drastic disturbances, their complex biological networks are also disrupted. Well-established interactions among roots, fungi, other microflora, and micro- and macrofauna are all destroyed once vegetation is removed and soil is upturned, buried, or eroded away. Humans have little understanding of the ecosystem services performed by these underground biological networks or the impacts their losses may have on global biogeochemistry. Dr. Bruns lab group is studying nitrogen transformations in agricultural and urban soils; microbe-mineral-plant interactions and biological crusts that form and stabilize soils in acid mine drainage “kill zones” caused by overland flow of discharge from an abandoned underground coal mine; and carbon and nitrogen fixation by bacterial communities in soil crusts and in bedrock-regolith interface zones where soil formation is initiated. They combine molecular, microbiological, biochemical, microscopic, and mineralogical techniques to explore microbe-mineral-plant interactions.

Don Bryant, Pollard Professor of Biotechnology and Professor, Department of Biochemistry and Molecular Biology
Research: Genomics, structural and functional relationships, metabolism, physiology and ecology of chlorophototrophic bacteria. Photosynthesis, the chlorophyll-dependent conversion of light energy into chemical energy with the ensuing reduction of carbon dioxide to biomass, is arguably the most important biological process on Earth. Among prokaryotes, the ability to use chlorophylls to capture and convert light into biochemical energy was until very recently believed to occur in members of only five eubacterial kingdoms: Cyanobacteria, Proteobacteria, Chlorobi, Chloroflexi, and Firmicutes. The Bryant lab group recently discovered a previously unknown chlorophototroph, Candidatus Chloracidobacterium thermophilum, which is a member of the poorly characterized kingdom Acidobacteria (http://www.sciencemag.org/cgi/content/abstract/317/5837/523). Current research in the laboratory focuses on a wide variety of topics in photosynthesis in bacteria, including structure-function relationships of proteins, biogenesis of the photosynthetic apparatus, gene regulation, and photosynthetic physiology. The group principally study two model organisms, the unicellular, marine cyanobacterium Synechococcus sp. PCC 7002 and the moderately thermophilic green sulfur Chlorobaculum tepidum (Chlorobi), which can easily be manipulated genetically. Because Cyanobacteria perform oxygen-evolving photosynthesis but characterized Chlorobi are obligately photoautotrophic anaerobes, these two organisms provide an interesting contrast in physiology and metabolism. Dr. Bryant additionally studies natural phototrophic communities in Yellowstone National Park.

William Burgos, Professor, Department of Civil and Environmental Engineering
Research: Dr. Burgos' research interests include: 1) Bioremediation of soil, sediment and groundwater; 2) contaminant interactions with natural organic matter; biological iron(III) reduction; 3) biological uranium(VI) reduction; and 4) biodegradation of polycyclic aromatic hydrocarbons, and nano-scale systems. Research in the Burgos lab is focused on the bioremediation and biogeochemistry of organic contaminants, heavy metals and radionuclides. Current research projects examine iron(III) reduction and uranium (VI) reduction related to Department of Energy (link) legacy waste cleanup, and manganese(II) oxidation and low-pH iron(II) oxidation related to coal mine drainage. Research projects typically employ of series of cross-disciplinary and complementary techniques such as electron microscopy, X-ray diffraction and X-ray absorption spectroscopy for mineralogical characterizations; culture-based enumeration and DNA-based characterization of microbial communities; and, aqueous geochemical measurements for speciation modeling and kinetic analysis.

Fred Cannon, Professor, Department of Civil and Environmental Engineering
Research: Dr. Cannon's research interests are: Water, air, and hazardous waste treatment; activated carbon and surface chemistry. Tailoring of activated Carbon to remove specific compounds; Advanced oxidation/adsorption for reducing air pollution in foundries.

Hunter Carrick, Adjunct Associate Professor, Department of School of Forest Resources
Research: Dr. Carrick's research assesses how human activities influence aquatic assemblages, and ultimately how these changes alter the structure and function aquatic ecosystems. Major environmental concerns include- the addition of foreign chemicals (or increases above natural concentrations), introduction of exotic species and maintenance of biodiversity, and changes to the global gas balance. His research assesses the quantitative role of microbes in aquatic food webs, and identifies species complexes that are indicative of specific environmental conditions. He uses state of the art methodologies to estimate microbial abundance (fluorescence microscopy, remote-sensing), production (radioisotopic tracers, ultra-sensitive analytical methods), and assemblage shifts in time and space (inferential and multivariate statistical tools). Additional interests include: 1) Validation of In-Stream Metrics to Determine Phosphorus End-Points for Pennsylvania; 2) Water quality assessment for the Yellow Breeches, Beaverdam and Conestoga Watersheds, Pennsylvania; 3) Ecosystem ecology; 4) Effects of eutrophication on the biogeochemistry of lakes, streams, and wetlands; 5) Wildlife and Fisheries Science.

A. Welford Castleman, Jr., Evan Pugh Professor of Chemistry, Department of Chemistry, Eberly Distinguished Chair in Science
Research: Interests involve laser chemistry, spectroscopy; bonding, molecular properties, and reactivity of clusters and condensed matter of large finite dimensions; study of the influence of solvation on reaction dynamics using time resolved femtosecond laser techniques; applications of cluster research to unraveling important problems in catalysis and surface science, the science of nanoscale materials, atmospheric and interstellar chemistry, and reactions of biochemical interest. Discovery of a new class of molecular clusters termed Metallo-Carbohedrenes or Met-Cars for short. They are comprised of eight early transition metal atoms bound to twelve carbons. In view of their potential use as new electronic and optical materials, as well as predicted value as new catalysts, they have attracted wide interest in the chemistry community. Work is underway in Castleman's laboratory to investigate their molecular properties, reactivity, and routes for synthesis in the solid state. Excitation experiments using femtosecond lasers are providing new insights into the coupling of electronic and vibrational modes on the ultra short time scale, and are elucidating their photoinduced behavior. Studies of the reactivities of transition metal compound clusters of widely varying composition and types, with particular attention to oxygen transfer reactions. Investigations are also under way to learn how the small cluster building blocks lead to different morphologies of growing particles that are of interest in wide-ranging areas from photocatalysis to developing new cluster assembled nanoscale materials.

Wayne Curtis, Professor, Department of Chemical Engineering/Biotechnology Institute
Research: Dr. Curtis' research group works with Plant biotechnology using plants to make drugs, as well as the production of tissue-culture propagated superior clonal trees for wood production. Protein Production in Plants can be genetically engineered to produce proteins and fine chemicals.  His current work is developing a bioreactor-based transient expression system that will allow the rapid introduction of Human DNA into plant tissue to produce sufficient protein material for diagnostic testing. This project is in collaboration with other plant molecular biology research groups and the work presents a variety of research areas for undergraduates that range from bioreactor operation to genetic engineering. The Curtis lab focuses on the design of bioreactor systems to develop renewable fuels to achieve economic stability and a sustainable energy supply. His group has developed algae photobioreactors that can achieve continuous growth of algae at cell concentrations that are an order of magnitude higher than traditional systems (> 20 gDW/L). The research involves a broad range of refinements to operational strategy including on-line control based on incident light intensity, fluid dynamic studies to maximize liquid hold up and residence time distribution, nutrient management, and control of the algae and microbial populations.

Kenneth J. Davis, Professor, Department of Meteorology
Research: Dr. Davis' research group studies how the earth's surface interacts with the atmosphere. Most of their work in recent years has focused on study of the terrestrial carbon cycle using atmospheric flux and mixing ratio measurements via field projects including the NACP Midcontinent Intensive regional study, installation of highly calibrated CO2 mixing ration measurements on flux towers, the Indianapolis flux experiment, and the Chequamegon Ecosystem-Atmosphere study. These projects employ a synthesis of greenhouse gas mixing ratio and turbulent flux measurements, remote sensing of the earth's surface, measurements of the atmospheric boundary layer, and numerical models of both atmospheric transport and terrestrial fluxes to infer regional greenhouse gas budget at scales ranging from urban centers to continents. His group also studies the interactions between the earth's surface energy balance and the atmospheric boundary layer, most recently at the NSF's Susquehanna Critical Zone Observatory. He is Co-Chair of the North American Carbon Program (NACP) Science Steering Group and a member of the U.S. Carbon Cycle Science Steering Group. He served as a member of the working group that drafted the new U.S. Carbon Cycle Science Plan.

Dennis Decoteau, Professor, Department of Horticulture
Research: Dr. Decoteau is currently directing a research program on plant and ecosystem health and air quality. On-going major areas include:  Forest health monitoring program in rural PA sponsored by the USDA Forest Service, air quality monitoring in rural Pennsylvania sponsored by the Pennsylvania Department of Environmental Protection – Bureau of Air Quality, and sensitivity of Chambourcin grape to ozone.  Also responsible for the management, fundraising, and outreach activities of the Air Quality Learning and Demonstration Center in the Penn State Arboretum.

Brian Dempsey, Professor, Department of Civil and Environmental Engineering
Research: Research interest involve chemistry of trace metals, natural organic materials, production and use of chemical coagulants, removal of volatile chemicals from contaminated groundwater, coagulation and filtration processes, and mobility and removal of trace inorganic contaminants. Recent work focuses on design of solid phases for optimal performance and economics, especially relating to mine drainage wastes, water & wastewater treatment, removal of nutrients from industrial wastewaters, and immobilization of trace metals in soils. Additional research interests include: Aquatic chemistry with an emphasis on solid-liquid interfacial phenomena; manipulation of solid phases to enhance purity or density; stream monitoring and TMDLs;
removal of arsenic from potable water; uranium mobility and reactivity; arsenic removal by iron-modified sctivated varbon; arsenic removal from water with iron-tailored activated carbon: The arsenic removal project seeks to evaluate the mechanisms for very high removal capacities of arsenic (As) by granular activated carbon (GAC) that has been pretreated with iron-citrate. Previous studies have found this phenomenon of high capacity, which cannot be explained by conventional equilibrium models involving sorption onto ferric hydroxide or iron-arsenic precipitates. The study will test the hypothesis that removal of As(V) at a greater than 1:1 molar ratio of As:Fe is due to reduction and subsequent precipitation of arsenic sulfides within the pores of GAC. PIs will investigate the importance of various basic water quality/chemistry characteristics, such as pH, alkalinity, and concentrations of natural organic matter and dissolved oxygen, on rates and extent of As removal. The speciation of As after its removal by tailored GAC will be determined using extended x-ray absorption fine-structure spectroscopy (EXAFS) and Mossbauer spectroscopy.

David Dewalle, Emeritus Professor of Forest Hydrology, School of Forest Resources
Research: Forest hydrology; forest microclimatology; snow hydrology; and impacts of ecosystem disturbances: atmospheric deposition, urbanization, and climate change

Herschel Elliott, Professor of Agricultural Engineering, Department of Agriculture Sciences
Research: Fate of interaction of pollutants in soils and aquatic systems, land-based waste disposal systems, adsorption of pollutants at the solid-solution interface. Treatment and land disposal and recycling of municipal, agricultural and industrial wastes. Other interests are: Phosphorus runoff and water quality; soil decontamination; and odor management in agriculture and food processing.

Matt Fantle, Assistant Professor, Department of Geosciences
Research: The general objective of Fantle's work is to understand the global cycling of elements such as Fe and Ca at the surface of the Earth, but more specifically, weathering, fluvial transport, and marine sedimentation. He is interested in following processes affected by not only the mass fluxes of Fe and Ca, but also the isotopic composition of each in the natural environment: 1) Physical and chemical weathering of igneous, sedimentary, and metamorphic rocks (including the formation of dust); 2) Soil development, including organic complexation and redox reactions; 3) Fluvial transport and estuarine interactions; 4) Surface ocean processes (such as biological uptake of Fe), dissolution of dust, precipitation of secondary minerals, and cycling between the surface and deep ocean; and, 5) Deep ocean processes, such as particulate sinking and subsequent sedimentation and diagenesis. Fantle is also interested in combining geochemical data (either elemental or isotopic) with numerical models. He uses these techniques to investigate the fidelity of geochemical proxies, such as Sr and Ca, in marine carbonates. Combining modeling and geochemical measurements in marine carbonate sediments, he has found that chemical evolution of the ocean over the last 35 Myr, recrystallization rates over both million-year and 10 kyr time scales, diagenetic changes in carbonates over time (with regard to elemental concentrations of Sr, as well as Sr and Ca isotopes), the equilibrium fractionation factor between CaCO3 and dissolved Ca2+ in the marine sedimentary column, and mechanisms controlling Ca isotope fractionation during calcite precipitation. Such observations have direct implications for paleoclimate studies that use proxies such as Mg/Ca and Sr/Ca ratios to say something about sea surface temperatures. However, such techniques may also be applied to oxygen isotope studies, which have ice volume, as well as paleotemperature, implications.

James G. Ferry, Stanley Person Professor and Director of the Center for Microbial Structural Biology, Department of Biochemistry and Molecular Biology
Research: The Center for Microbial Structural Biology techniques include all methods for isolation and biochemical analysis of enzymes from microorganisms. Dr. Ferry and his group study the enzymology and molecular biology of anaerobic microbes from the Archaea domain.  Anaerobes--microbes living without oxygen--comprise nearly one-fourth of all living protoplasm on earth and are found in a variety of habitats. They are found in animals and plants that are healthy or diseased, such as human, animal, and plant infections, the rumen of cattle, and the intestines of humans and other monogastric animals. Anaerobes in the environment convert biomass to methane in a process that is critical to the global carbon cycle. The anaerobic decomposition of biomass to methane and carbon dioxide occurs in vast and diverse anaerobic habitats such as: 1) deep-sea hydrothermal vents; 2) marine and freshwater sediments; and 3) rice paddies and other agricultural environments. The process of methanogenesis impacts the environment and human health in other important ways: biologically produced methane is a major component of greenhouse gases, the process is used commercially to dispose of domestic and industrial wastes, many anaerobes are able to detoxify hazardous pesticides, and methane from renewable biomass is a clean-burning alternative energy source. Their research on ancient enzymes from the Archaea is contributing to an understanding of the origin and evolution of life and directly impacts the emerging field of Astrobiology.

Charles Fisher, Professor, Department of Biology
Research: Dr. Fisher's interests encompass the physiology and ecology of symbiotic autotrophic marine microbes and their invertebrate hosts. These types of symbiotic associations are important in the world's oceans, where symbiont dependent species are often the primary ecosystem-structuring organisms in both shallow tropical environments, such as coral reefs, and in the deep sea where biomass may be limiting. The importance of the symbioses between algae and tropical invertebrates (such as corals, clams, and anemones) has long been recognized, and has been studied by biologists for over 100 years. Much of his research begins with oceanographic expeditions conducted in conjunction with research submarines such as the deep submergence vehicles Alvin and Johnson Sea Link. He is currently involved in research projects at hydrothermal vents sites on the East Pacific Rise and hydrocarbon-seep sites in the Gulf of Mexico. Ecological studies designed to elucidate the relations between the animals, distribution and venting hydrothermal fluid, or reduced chemicals in interstitial waters, are conducted using submersibles. Physiological investigations (such as determination of condition, growth rate, or symbiont complement) of the animals and their symbionts are conducted in conjunction with the ecological studies in order to provide further insight into the physiological ecology of these symbiotic associations.

Katherine H. Freeman, Professor, Department of Geosciences
Research: Organic and isotopic biogeochemistry Laboratory: Techniques include organic extraction and separation methods, gas chromatography (GC), structural mass spectrometry (GC/MS), isotope ratio mass spectrometry (IRMS) and organic compound-specific isotope analyses (CSIA). Research interests encompass the use of indicator lipids (both their distributions and isotopic contents) for tracing giogeochemical processes in modern and ancient environments. Ongoing projects include establishing molecular records of acient climatic and hydrological change and redox-specific microbial signatures in modern and ancient settings. Dr. Freeman's lab group are involved in: Isotopic Signatures of Photosynthesis and Paleo-CO2 Reconstructions, Terrestrial Ecosystems, Paleozoic Climate, Microbial Biogeochemistry, and Applied Geochemistry. A new direction for her work employs precise analyses of the deuterium content of individual compounds. She is interested in using sediment records of deuterium variations in aquatic and terrestrial plant biomarker compounds to compare with paleoclimate reconstructions of isotopic patterns for meteoric water using regional models nested in models of the global atmosphere and she is also interested in carbon isotope fractionation by microbial phototrophs, and how these signatures are reflective of their growth environment. These organisms dominated photosynthesis prior to two billion years ago, and understanding their isotopic behaviors is essential to biogeochemical studies of early life on Earth.

Tanya Furman, Associate Professor, Department of Geosciences, Assistant VP/Assoc. Dean for UGED
Research: Using geochemistry of mafic lavas and phenocrysts to unravel melt generation, segregation and transport processes in the lithosphere and asthenosphere, with particular interest in continental rift zone magmatism and the development and maintenance of mantle reservoirs. My graduate students typically conduct field work and extensive laboratory analysis as they develop their own ideas into a research thesis. Current research efforts involve work in areas of continental extension (various localities in the East African Rift) and arc volcanism (Indonesia and Turkey).

Peter Heaney, Professor, Department of Geosciences
Research: Crystal structure analysis and processes of mineral growth and transformation; Environmental mineralogy and geochemistry; Phase transitions in rock-forming minerals. Techniques include powder X-ray and neutron diffraction and transmission electron microscopy.

Chris House, Associate Professor, Department of Geosciences, Director, Penn State Astrobiology Research Center and Director, Pennsylvania Space Grant Consortium
Research: Microbial diversity and cultivation, microbial paleontology, molecular evolution and genomics, astrobiology, & geomicrobiology.

Peter C. Jurs, Emeritus Professor, Department of Chemistry
Research: Prediction of Chemical, Physical, or Biological Properties of Organic Compounds from Molecular Structure by Computation. Jurs's research objective has been to develop and use interactive, computer-assisted methods to investigate relationships linking molecular structures of organic compounds with their physical-chemical properties, such as boiling points and the solubilities of substances in liquids, or biological activities such as drug potency and toxicity. For example, in one project he created an instrument that mimics the behavior of the mammalian nose in its ability to identify volatile organic compounds in an airstream. Jurs also has studied computational neural networks and genetic algorithms.

Tim Kane, Professor, Department of Electrical Engineering
Research: Dr. Kane works in the field of Optical Remote Sensing, with an emphasis on Laser Radar (or Lidar). His emphasis on optical propagation has also instigated current efforts in free-space optical communication as well as imaging. In addition to the design, development, and deployment of such instrumentation, he has current research interests in modeling of ionospheric, atmospheric, and oceanic dynamics and chemical processes.

Seogchan Kang, Professor, Department of Plant Pathology
Research: The goal of Dr. Kang's research program is to study plant- pathogen interactions at multiple levels, ranging from genes to ecosystems. One of his projects is to study root pathogenesis/defense using Arabidopsis thaliana as a host. He employs a diverse array of pathogens representing different infection strategies and tissue specificity so as to identify both general and pathogen-specific defense mechanisms in A. thaliana. He utilizes two soil-borne pathogens, Fusarium oxysporum and Verticillium dahliae, in these studies. These pathogens make it possible to compare pathogenicity and defense mechanisms in diverse plant species. Dr. Kang also studies Rice Blast, a disease which is the biggest threat to rice cultivation. Besides its economic significance, Rice Blast presents many advantages as an experimental model. Unlike most plant–fungal pathogen systems, the genome sequences of both M. oryzae and rice are available, providing a unique opportunity to study their interactions from both sides using functional genomics tools. Two areas of his research include the genetic mechanisms underpinning the breakdown of resistance in the field and the molecular and cellular basis of pathogenesis/defense. Dr. Kang's group has integrated a cyber-infrastructure for plant pathogens (CiPP) into their research. The goals of CiPP are to integrate existing genotypic and phenotypic information on plant pathogens with important environmental variables, and to engage the global community of plant pathologists to use state-of-the-art data mining and visualization tools for the advancement of science, education, and outreach.

Jason Kaye, Associate Professor of Soil Biogeochemistry, Department of Crop and Soil Sciences
Research: Kaye's lab focuses on changing biogeochemical cycles in terrestrial ecosystems (i.e. changes in the storage and movement of energy and nutrients). They are particularly interested in the nitrogen cycle.  In unmanaged ecosystems, a lack of nitrogen often limits plant growth and there are fascinating basic science questions regarding interactions among plants, microorganisms, soils, and hydrology.  In managed ecosystems, fertilizers alleviate nitrogen limitation, which helps feed the growing human population, but also generates water and greenhouse gas pollution. There are pressing applied questions regarding our ability to sustain yields while reducing nitrogen pollution. The goals of their research are to: 1) increase basic understanding of ecosystem element cycles, 2) help minimize nitrogen losses from managed ecosystems, and 3) discover how nitrogen losses from managed ecosystems affect and are attenuated by unmanaged ecosystems. They measure the flow and fate of nitrogen at scales ranging from individual microbial processes, to whole ecosystems and landscapes, to regions and they often study interactions between nitrogen and ecosystem carbon balance to understand how changes in carbon and nitrogen cycling are linked. 

Klaus Keller, Associate Professor, Department of Geosciences
Research: Dr. Keller's research interests include: oceanography, global carbon cycle, abrupt climate change, economic analysis of climate policy, climate change detection, decision-making under uncertainty. In his research group, they address two interrelated questions.  First, how to mechanistically understand past and potential future changes in the climate system?  Second, how they can use this information to design scientifically sound, economically efficient, and ethically defensible climate risk-management strategies?  They analyze these questions by mission-oriented basic research covering a wide range of disciplines such as Earth system science, oceanography, biogeochemistry, economics, and ethics.

Sridhar Komarneni, Distinguished Professor of Clay Mineralogy, Department of Agronomy
Research: Interests include: Cation Exchange Processes: (1) fundamental cation exchange (kinetics, equilibria and thermodynamics) in clay minerals, zeolites and tobermorites, and (2) separations of critical and strategic metals and hazardous radioactive species. Nuclear and Hazardous Waste Disposal: (1) ceramic waste from development; (2) leach testing of waste forms; and (3) immobilization of radioactive species by ion exchange. Ultrafine particles (powders): (1) preparation of ultrafine powders by hydrothermal and sol-gel methods, and (2) powder characterization of size, shape, composition and surface area by using different techniques. Sol-Gel Chemistry: (1) preparation of nanocomposite and single phase sol-gel bulk materials and thin films for structural and electronic applications; (2) structural investigation of sol-gels by TEM and NMR; and (3) preparation and characterization of nanocomposites of clays, gels and zeolites for use as desiccants.

Jim Kubicki, Professor, Department of Geosciences
Research: Dr. Kubickifocuses his research on determining atomic structures in non-crystalline systems and geochemical reaction mechanisms. Combining molecular modeling techniques with experiments and spectroscopic analysis, Kubicki and co-workers decipher molecular-level speciation on environmental interfaces. Using Molecular Dynamics (MD) and Quantum Mechanical (QM) computer simulations along with various spectroscopic techniques, Kubicki and his colleagues  study the interactions of the natural organic matter and oxyanions (e.g., arsenate, phosphate) with mineral surfaces, dissolution of minerals, and interactions of plant cell wall polymers. 

Gretchen Kuldau, Associate Professor, Plant Pathology
Research: Research in Dr. Kuldau's lab focuses on mycotoxigenic fungi and their interactions with plants. Mycotoxins are fungal secondary metabolites toxic to humans and animals. These toxins are of concern for both human and animal health since some are human carcinogens and others can cause fatal diseases in farm animals. While we have an understanding of the nature of many of the commonly found mycotoxins, often it is not known why they are made. One primary goals is to understand why fungi produce mycotoxins which should provide the basis for new strategies for prevention of accumulation of mycotoxins in food and feed. Her group is also exploring the role of fusaric acid in plant-fungus interactions using molecular genetic approaches. This mycotoxin has been implicated as a plant toxin so they are examining the role of fusaric acid in fungal virulence. They are also looking at the role of fusaric acid in asymptomatic infections of maize. Endophytes are microorganisms that live internal to plant tissues but cause no observable symptoms on their plant host. Some endophytic fungi can be pathogenic under certain environmental and or developmental conditions. Very little is known for any fungus about the genetic basis for asymptomatic colonization of plants or about why symptomless infections sometimes become symptomatic. Dr. Kuldau's lab is working to identify genes specifically expressed during endophytic colonization of maize by F. verticilloides. Their approach to this problem employs the tools of fungal molecular genetics.

Lee R. Kump, Professo, Department of Geosciences, Department Head of Geosciences
Research: Research focuses on the long-term evolution of the biosphere, especially the interplay between biogeochemical processes and oceanic and atmospheric composition. He is interested in studying the role of oceanic anoxia in mass extinction, an investigation of the cause of extreme warmth during the transition from the Paleocene to the Eocene, and the relative roles of tectonic and biotic evolution in the rise of atmospheric oxygen.  His current research interests include: Biogeochemical cycles, low temperature sedimentary geochemistry, atmosphere/ocean evolution; Modeling Anoxia and Euxinia in Earth History; Causes and Consequences of end-Permian Extinction; Carbon Cycle Perturbations during the Paleocene-Eocene Thermal Maximum; What Caused the Current Ice Age; Focus on the Eocene-Oligocene Transition; Weathering and Soil Formation before Land Plants; Fate of Wastewater Nutrients in Florida Keys Groundwaters; Interpreting Stable Isotope Excursions in Ancient Sedimentary Rocks; and Controls on Chemical Erosion.

Dennis Lamb, Emeritus Professor, Department of Meteorology
Research: Focus of environmental research is atmospheric chemistry. He develops and uses numerical models to diagnose and predict oxidant and sulfate episodes in Central Pennsylvania. Clouds and cloud physics is another interest of Dr. Lamb. What really goes on inside those spectacular clouds we see in the sky everyday? In the laboratory he measures the growth and evaporation of aerosol particles, cloud droplets and ice crystals.

Bruce E. Logan, Kappe Professor, Department of Civil and Environmental Engineering
Research: Bioenergy production: sustainability of the water infrastructure; environmental transport processes; bioremediation; bio-colloid adhesion and transport; molecular-scale studies of adhesion using atomic force microscopy. The main focus of the Logan lab is the development of  new bioelectrochemical technologies for achieving an energy sustainable water infrastructure. Logan and his collaborators have invented a method for sustainable hydrogen production using microbial electrolysis cells (MECs); invented a method for water desalination that does not require electrical energy from the grid or high pressures called microbial desalination cells; improved direct bioelectricity generation by several orders of magnitude in microbial fuel cells (MFCs). Other research has included the discovery of how large aggregates form in the ocean, called marine snow, that can help to sequester carbon to deep sediments; and molecular and nanoscale techniques to study particle dynamics and microbial adhesion in engineered and natural systems; microbial adhesion and transport. 

Serguei N. Lvov, Professor, Department of Energy and Mineral Engineering and Materials Science and Engineering
Research: Electrochemical Engineering - electrochemical sensors and pH measurements in high temperature aqueous environments; batteries and fuel cells; electrochemical kinetics in high temperature aqueous solutions. Surface Chemistry - electrolyte absorption on oxide surfaces, determination of zeta potential and pH of zero charge in hydrothermal systems, hydrothermal- electrochemical deposition of oxide films. Materials Science - corrosion of metals and alloys in hydrothermal environments, hydrothermal synthesis of new oxide materials. Thermodynamics and Kinetics - mosecular-statistical, irreversible and chemical thermodynamics of aqueous systems; electrochemical kinetics and transport properties; kinetics of hydrothermal dissolution of oxide materials.

James A. Lynch, Emeritus Professor of Forest Hydrology, School of Forest Resources.
Research: Research interests include: modeling changes in the chemical climate related to atmospheric deposition - effective linkages between global change parameters and environmental effects require detailed spatial patterns in deposition of toxic substances; current monitoring programs are spatially limited and extrapolation of point estimates to unmonitored regions results in errors that often limit cause-effect assessments; leading ridge experimental watersheds - this cooperative project is to study the effects of forest management activities on water resources and to support a graduate research program in forest hydrology and watershed management; evaluating the effectiveness of the clean air act amendments in reducing acidic deposition in the USA - the purpose of this study is to determine the effectiveness o the reductions in emission on precipitation chemistry and atmospheric deposition throughout the USA; assessing atmospheric deposition trends in Pennsylvania and their impact on stream chemistry - the objective of this project is to determine the effectiveness of national and state regulations designed to reduce acidic deposition in the state in reversing the long-term acidification of streams draining forested watersheds and to investigate nitrogen deposition contributions to nitrate export from both harvested and non-harvested watershed.

Jenn Macalady, Associate Professor of Geosciences and Director of CECG, Department of Geosciences
Research: Dr. Macalady, a geomicrobiologists, studies microbial interactions with earth materials: soils, sediments, solutes, atmospheric gases, minerals, and rocks. She sees microorganisms as agents of geologic and environmental change, and the earth system as a crucible for the evolution of life. Dr. Macalady and her research group explore how microorganisms shape earth's environment in the present and over geologic time scales, and are at the forefront of efforts to explore the uncharted microbial world (pdf download). They have found important links between geomicrobiology and astrobiology (the study of life in the universe), the origin of life, paleobiology, nanoscience, soil science, limnology, oceanography, global climate change, medical microbiology, and environmental engineering.

Tom Mallouk, Dupont Professor of Materials Chemistry, Department of Chemistry
Research: Professor Mallouk and his students are interested in several problems in materials chemistry, including photocatalysis, electrochemical energy conversion, nanoscale electronics, environmental remediation, chemical sensing and motion on the nanoscale. Their approach involves the synthesis of materials that contain both molecular and solid state components, and the study of their structure and properties by a variety of physical techniques. Research projects include: Chemistry of nanoscale inorganic materials; Solar photochemistry and photoelectrochemistry (developing new kinds of nanomaterials that will lead to efficient, inexpensive solar energy conversion devices); Using porous membranes as templates for growing nanowires and nanorods; Developing a set of soft chemical reactions that topochemically interconvert different structural families of layered and three-dimensional perovskites into functional inorganic layered materials; and, studying nanoparticle surface as a means of controlling core-shell structure and particle aggregation for optimized sub-surface transport, targeting of insoluble contaminants, and concentration of soluble contaiminants at the reactive nanoparticle surface.

Carmen Enid Martinez, Associate Professor Environmental Soil Chemistry, Department of Crop and Soil Sciences
Research: Testing a conceptual model of the terrestrial nitrogen cycle including rapid stabilization of nitrogen in soil

Sharon Miller, Research Associate, The Energy Institute
Research: BFB Biomass Fuels Characterization Testing at PSU/Energy Institute, Combustion and Emission Performance when Firing Coal/Biomass Blends, Research Boiler Testing, Tar Analysis Study, Effect of Catalysts on Coal Combustion and Emissions Performance, Evaluation of Biomass Feedstocks in a Traveling Grate Stoker Simulator

Ray Najjar, Professor of Oceanography, Department of Meteorology 
Dr. Najjar's work is in the broad areas of climate and oceanography.  Most of his work that directly involves climate is about the impact of climate change on coastal regions, especially estuaries of the Mid-Atlantic Region of the U.S.  He is particularly interested in how climate change, through changing streamflow patterns and sea-level rise, alters the salinity of estuaries and he is also interested in evaluating the skill of global climate models at regional scales.  Most of Dr. Najjar's oceanographic research has been in the field of marine biogeochemistry, with a particular focus on dissolved gases, like carbon dioxide, oxygen, carbon monoxide, carbonyl sulfide and dimethyl sulfide.  Ongoing research is with the USECoS project, which, through modeling, data analysis, and field observations, studies the carbon cycle of the continental shelf of the Eastern U.S.

Hiroshi Ohmoto, Professor of Geochemistry, Department of Geosciences
Research: Stable isotope geochemistry of sulfur, carbon, oxygen, nitrogen, and hydrogen in rocks, minerals, organics, and solutions; Geochemical processes of submarine hydrothermal mineralization; Geochemical cycles of redox-sensitive elements through the crust, oceans, oceanic crust, and mantle; Chemical evolution of the atmosphere, hydrosphere and biosphere on early Earth; Chemical evolution of the mantle and crust through geologic time.

Carlo G. Pantano, Professor, Department of Materials Science and Engineering and Director, the Materials Research Institute
Research: Glass Surfaces, Interfaces and Coatings Research: surface characteristics of glass by AFM, XPS, FTIR, etc; inverse gas chromatography (IGC) to measure the energy distribution of surface adsorption sites; weathering and dissolution of glass; surface treatments and coatings for strength; organic coatings and glass/polymer interfaces;  dielectric properties of thin commercial glasses;

Richard R. Parizek, Professor of Geology and Geo-Environmental Engineering, Department of Geosciences
Research: Hydrogeologic studies of fracture-flow dominated karst, coal and glacial-related aquifers. Solid and liquid waste management and pollution control.

Scott Philips, Assistant Professor, Department of Chemistry
Research: Dr. Philips research group is using organic chemistry to create “autonomous diagnostics” which provides all of the functions typically obtained with instruments (selectivity, sensitivity, quantitative measurements, and clearly displayed information), but using only organic reactions on a piece of paper. Their goal is to devise chemistry that forms the basis for exceedingly simple and disposable diagnostics devices. These systems will be useful in the developing world, emergency rooms, and other applications requiring portable and inexpensive devices for detecting disease or pollution. Another research project is to develop alternative chemicals to replace those derived from oil. One way is by developing reactions that use CO2 as an inexpensive carbon source (in place of oil) for making bulk chemical building blocks. A second project within this area focuses on reaction networks that are self-perpetuating, the simplest of which is an autocatalytic reaction (where a molecule makes more of itself). Dr. Philips group plans to expand autocatalytic behavior into more complex reaction networks, with the goal of developing systems that provide useful function and/or byproducts.

Sarma Pisupati, Professor of Fuel Sciences, Department of Energy and Geo-Environmental Engineering
Research: Air emissions from fossil fuel utilization systems; reduction of NOx by combustion modifications and down stream cleanup; SO2 reduction from stationary combustion sources, volatile organic compound (VOC) emissions from combustion systems trace metal emissions from combustion systems; combustion behavior of fossil fuels in fined; fluidized and pulverized modes.

John M. Regan, Associate Professor, Department of Civil and Environmental Engineering
Research: Biological processes with an emphasis on nutrient removal, regrowth in drinking water distribution systems, fermentative biological hydrogen production, microbial fuel cells, methanogenic systems, and molecular microbial ecology.

Beth Shapiro, Associate Professor, Department of Biology
Dr. Shapiro's research focuses on a wide range of evolutionary and ecological questions, mostly involving the application of phylogenetic and population genetic tools to try to uncover the dynamics of the molecular evolutionary process within populations and between species. A common theme to her research is that it involves some aspect of time, either using historical information from RNA viruses or ancient DNA to identify periods of population growth, decline or turnover, and integrating these analyses with climate and environmental data (ancient DNA) or epidemiological records (RNA viruses) to try to identify the causative factors behind the observed changes in genetic diversity.

William Sharpe, Emeritus Professor of Forest Hydrology, Department of Forest Resources
Research: Water quality in private drinking water supplies. The effects of acidic deposition to aquatic and terrestrial ecosystems. Restoration of damaged aquatic and terrestrial ecosystems.

Jorge O. Sofo, Professor of Physics, Assoc. Professor, Department of Materials Science and Engineering
Research: We develop and apply theoretical and computational methods to link properties and structures. Our work is devoted to understand properties like reactivity, molecular and electronic transport, stability, and optical response of solids, surfaces, clusters and molecules. Our most common tools are Density Functional Theory and other quantum mechanical methods to solve the many-body problem of electrons and atomic nuclei in mutual interaction. We use these tools to do molecular dynamics or Monte Carlo computer simulations at an atomic scale. We also use methods of quantum field theory in statistical mechanics (Green Functions) to study properties at a subatomic scale.

Richard Stehouwer, Professor of Environmental Soil Science, Department of Crop and Soil Sciences
Research: The extension program in environmental soil science serves a broad clientele including agriculture, industry, local municipalities, and state and federal regulatory agencies. Issues addressed in the program include soil-based recycling of agricultural, municipal and industrial and by-product materials, composting and compost utilization, mined land reclamation, brownfield restoration and remediation of contaminated soils. Dr. Stehouwer's research program in large measure is driven by the issues and needs that arise in the extension program. Recent and current research projects include: Characterization of dissolved organic carbon (DOC) in composts as a function of compost maturity, and the influence of DOC on metals binding and transport in soils and minespoils; Effects of long-term application of municipal sewage biosolids on the quality of agricultural soils and crops; Effect of biosolids used in mine reclamation on acid mine drainage and nutrient discharge; Fate and bioavailability of soil-applied Cu from dairy hoof baths.

Dan Sykes, Director, Analytical Instructional Laboratories, Department of Chemistry and Forensic Sciences Program
Research: Small Mobile Instruments for Laboratory Enhancement (SMILE); the development of new pyrene-phenyl- and phenoxy- based stationary silanes - the principal aim of the research is to develop a suite of silane coatings with a high-degree of selectivity towards specific nitro aromatics and/or develop a mixed-mode phase (PDMS/PAH) with broad selectivity and use multiple component analysis to recover individual analyte species; GC-MS and LC-MS screening and quantification of pharmaceuticals in water supplies as well as in blood and urine.

Ming Tien, Professor of Biochemistry, Department of Biochemistry and Molecular Biology
Research: The Tien lab has three active research areas. Initial impression is that the research areas are not related; however, they share a common theme of redox reactions: Fungal lignin biodegradation, Dissimilatory Iron reduction, and Methionine sulfoxide reductase.

Darrell Velegol, Professor, Department of Chemical Engineering
Research: Colloidal assembly, colloidal motors, colloidal forces. Dr. Velegol's group investigates the fabrication of colloidal assemblies and devices, with a specialty in understanding the interparticle forces and sorting processes. They use a wide range of experimental and modeling approaches, including electrophoresis, colloidal assembly techniques, the electrokinetic equations, and the colloidal force equations.

William B. White, Emeritus Professor of Geochemistry, Department of Geoscience/Material Research Lab.
Research: Aqueous chemistry, contaminant transport especially in karst aquifers, ground water chemistry.

Yuefeng Xie, Professor, Department of Civil and Environmental Engineering
Research: Disinfection byproduct analysis and control, wastewater reuse, ship ballast water treatment, crumb rubber filtration, and environmental chemistry and analysis.