Stanford University
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Stanford Earth Summer Undergraduate Research

Photo by Kate Maher

2014 Projects

Kevin Arrigo and Kate Lewis- SESUR or SURGE

C:N:P Stoichiometry and Macromolecular Composition in Phytoplankton from Ross Sea, Antarctica

Macromolecules in phytoplankton cells exhibit unique stoichiometric ratios: nitrogen (N) rich components include primarily proteins, phosphorus (P) components are mainly nucleic acids and polyphosphates, and carbon (C) is affected by carbohydrates and lipids. Thus, phytoplankton cellular stoichiometry (C:N:P) is a reflection of its macromolecular composition, which phytoplankton adapt to achieve ideal growth strategies in given environmental conditions. Previous research suggests that within the Ross Sea, spatially and taxonomically distinct annual phytoplankton blooms occur, which are primarily correlated with varying mixed layer depth (MLD). Previous measurements of nutrient disappearance ratios by Arrigo et al. (2000) indicate the two dominant bloom taxa exhibit unique N:P stoichiometries; Ross Sea diatoms typically have a lower N:P ratio (~12) than Phaeocystis antarctica (~19). Climate change threatens to dramatically shift the phytoplankton community structure towards diatom dominance by increasing stratification and thus causing shallower MLD. Because of the unique taxonomic differences in nutrient stoichiometry, shifts in phytoplankton dominance could have a large impact on regional biogeochemistry by decreasing the effectiveness of the biological pump (CO2 drawdown and carbon export) by as much as 50%.

Macromolecular sampling on the NBP1310 cruise addresses two primary questions:

What is the cause at a macromolecular level for the difference in bulk C:N:P stoichiometry between diatoms and P. Antarctica?

How do phytoplankton adjust macromolecules pools to respond to different environmental factors (e.g. iron, light, mixed layer depth, stage of bloom etc.)?

Student will be working in the lab with samples gathered this winter from the Ross Sea in Antarctica. Experience working with biological lab techniques is preferred.

Gretchen Daily and Gregory Bratman- SESUR 

The Influence of Natural Environments on Human Cognitive Processes and Emotion 

After being present within natural environments, many individuals report feelings of “cognitive recharge”, decreased negative emotions, and increased positive emotions. Several previous studies have used tools from psychology to measure the impact on human cognitive abilities and mood that may result from experience in nature. But a great deal of research is still needed to further isolate and define these effects, and to answer the fundamental question: Do humans benefit in a measurable way from contact with nature? And if so, why, and in what ways? This study will employ a thorough and robust interdisciplinary experimental design, using tools and approaches from ecology and psychology, to consistently address the impacts that nature experience may provide for individuals’ cognitive function and mood. Students will be learning how to administer – and collaborate on the development of – confidential tests that measure some or all of the following capacities in subjects: memory, attention, impulse inhibition.

Greg Beroza- SESUR

Earthquake Detectability and Induced Seismicity

The usual earthquake detection threshold measure assumes Gutenberg-Richter size statistics (number of earthquakes as a function of magnitude) and has important disadvantages: it’s difficult to determine spatial variations in the detection threshold, it's difficult to document time-dependent changes (important as stations drop out/are added), and it’s uninformative about the detection threshold where no earthquakes are detected. Under this internship, we would pursue an alternative approach that uses earthquake arrival time observations to map the probability that an earthquake is detected as a function of assumed magnitude and location. This has the advantage of making no assumption about earthquake-size statistics. This is important because some studies have claimed that induced seismicity has different earthquake-size statistics. The focus of this internship would be to use this approach to explore whether or not induced earthquakes and natural earthquakes have different size statistics.

Rob Dunbar- SESUR 

Coral Paleoclimatology

Large coral colonies contain detailed records of past changes in climate as well as land-use change. The Dunbar lab holds one of the world’s largest collection of coral cores from the Indian and Pacific Oceans. This includes the longest known continuous coral record ever drilled, a 510 year time series from American Samoa. The SESUR student will work with Dunbar and Ph.D. student Neil Tangri to analyze and interpret climate records from the eastern Pacific (Galapagos) as well as the western Pacific (Samoa). The work involves stable isotopic analysis at Stanford. The project will also likely involve a 2 to 3 week trip to Perth, Australia, to collect trace element data using a state-of-the-art laser ablation ICPMS system. Learning outcomes will include knowledge of isotopic and trace element analytical techniques, modern climate dynamics, coral ecology, and tropical ocean circulation. 

Rob Dunbar and David Koweek- SESUR 

Coral Reefs and Climate Change: Impacts of Rising Temperature and CO2 levels

The project involves studying coral reef ecosystem response to global climate change, particularly to ocean acidification. One undergraduate intern will become involved in a combination of modeling and lab studies designed to enhance our understanding of coral reef biogeochemistry at several field sites in the Pacific. Most work will take place on campus, but an opportunity may exist for travel to one of these field sites as part of research team recovering, servicing, and redeploying an array of physical oceanographic instrumentation. The intern will be mentored both by the faculty member and a graduate student. Quantitative experience (esp. MATLAB) is preferred.

Rob Dunbar- SESUR 

Coral Paleoclimatology

Large coral colonies contain detailed records of past changes in climate as well as land-use change. The Dunbar lab holds one of the world’s largest collection of coral cores from the Indian and Pacific Oceans. This includes the longest known continuous coral record ever drilled, a 510 year time series from American Samoa. The SESUR student will work with Dunbar and Ph.D. student Neil Tangri to analyze and interpret climate records from the eastern Pacific (Galapagos) as well as the western Pacific (Samoa). The work involves stable isotopic analysis at Stanford. The project will also likely involve a 2 to 3 week trip to Perth, Australia, to collect trace element data using a state-of-the-art laser ablation ICPMS system. Learning outcomes will include knowledge of isotopic and trace element analytical techniques, modern climate dynamics, coral ecology, and tropical ocean circulation

Rob Dunbar and David Koweek- SESUR

Kelp Forest Biogeochemistry 

The Dunbar lab has begun a C system observational and modeling program focusing on the Hopkins Marine Station Kelp Forest Reserve. In collaboration with biological and physical oceanographers at Stanford we aim to determine the extent to which kelp forests modify their biogeochemical environment and the extent to which they may be susceptible to or may mitigate future ocean acidification. The project is based at Hopkins Marine Station and in the Dunbar Lab on the main campus. The student will work with Dunbar and graduate student David Koweek to collect samples, perform C system analyses and interpret complex data sets. Some knowledge of Matlab is preferred. Work at HMS will occur for periods of several days at a time over the summer and the student will participate in these field programs. Learning outcomes will include knowledge of kelp forest ecology and biogeochemistry, C system analytical techniques involving seawater, and modeling of ecosystem-scale C system dynamics.

Rob Dunbar- SESUR 

Patagonian Paleoclimate

Southern Patagonia is the world’s only land mass that intersects the most energetic wind system on Earth, the Southern Hemisphere Westerlies. The Dunbar lab has been actively coring lakes and fjords in Tierra del Fuego and southern Chile for the past 8 years. A new expedition will occur during March, 2014. This expedition will return to Stanford a unique set of sediment cores collected from a newly discovered anoxic marine basin near Puerto Natales. The student will work Dunbar and Ph.D. student Sverre LeRoy to analyze and interpret these sediment records. The student will work in part in the facilities of the US Geological Survey and also in several laboratories at Stanford. Tasks include sedimentological description, grain size analysis, microscopy, and geochemical/isotopic analysis. The goal is to reconstruct past variability in the strength and seasonality of the westerly winds with a view towards predicting possible changes in westerly associated rainfall in the coming greenhouse centuries. Learning outcomes will include knowledge of Holocene fjord sedimentology, isotopic analytical techniques, hydrological modelling, and fjord physical/biological oceanography. 

Eric Dunham and Brad Lipovksy- SESUR or SURGE

Earthquakes in Ice: Using Seismology to Study the Dynamics of Glaciers and Ice Sheets

The fate of the West Antarctic Ice Sheet is the most uncertain part of global sea level rise projections. The dynamics of fast flowing ice in this region are both scientifically fascinating and important for understanding future sea level rise. Seismic data similar to those used to understand tectonic earthquakes may provide new insights into these dynamics. Several projects are possible. (1) Seismographs recorded on the ice in Antarctica may be used to understand the physics at the bed of the ice sheet. In this project, small repeating earthquakes that occur during large-scale sliding will be used to estimate the coefficient of friction at the ice-rock interface. (2) Migrating waves of tidally modulated micro seismicity in Antarctica have been observed but the source of these events is not clear. A recently developed model of a resonating water-filled fracture will be used to analyze such microseismic catalogs to determine if they are due to the movement of fluid at the ice sheet bed. For both projects, prior programming experience in MATLAB or a high-level programming language will be essential, and introductory mechanics is recommended.

Eric Dunham and Sam Bydlon- SESUR or SURGE

Ground Shaking from Supershear Earthquakes Sam Bydlon 

A supershear earthquake is an earthquake whose rupture speed exceeds the shear wave velocity. During these events, we observe what is called a Mach front and Mach cone, similar to a sonic boom. These phenomena are associated with ground motion pulses that can lead to strong shaking at the surface. There are many questions concerning ground motions from supershear earthquakes that have important implications on seismic hazard assessments. Are ground motions from supershear earthquakes better or worse than subshear ruptures? How are the two scenarios different? What causes such differences? Our proposed project is to use 3D simulations of supershear earthquakes in homogeneous and heterogeneous media to confirm and quantify the reduction of ground motion amplitudes via seismic wave scattering and plastic strain in the near-fault area. Experience in MATLAB or other programming language, and understanding of basic UNIX commands, is desirable. 

Scott Fendorf and Marco Keiluweit- SESUR or SURGE

Assessing Soil Characteristics Controlling CO2 Efflux and Carbon Storage

Soils play a critical role in global carbon (C) cycling, having a C stock that is greater than the amount stored in biosphere and atmosphere combined. Of prime importance for future climate predictions is understanding the factors that control the rate at which soil C is mineralized by microbes and subsequently released to the atmosphere as climate-active CO2. What remains unclear is to what extent the limited availability of oxygen in soils affects overall rates of microbial C mineralization and associated CO2-release in upland soils.  We propose a project for an undergraduate researcher to determine the effect of soil texture (particle size) and structure on the formation of oxygen gradients within soil aggregates.  Soil pits will be dug and aggregates extracted at various field sites, which will be examined using a combination of wet-chemical techniques and micro-sensor technology to characterize biogeochemical gradients (oxygen, reduced iron and sulfur species, and organic C) within aggregates of varying size and mineralogy. The project may involve further analyses of microbial activity depending on the student interest and initiative. Experience in soil science and related laboratory work would be helpful.

Scott Fendorf and Annika Alexander-Ozinskas- SESUR or SURGE

The Chromium Project

Millions of people in California face elevated lifetime exposure to Chromium(VI), a known carcinogen, via drinking water from Californian aquifers. This project explores correlations between irrigation practices in California and Cr(VI) formation in order to call attention to the issue, inform water management decisions, and protect the public from Cr(VI) exposure. Students involved may work on any of the following: data acquisition, geospatial statistical data analysis, map making, results publication, and journalism to communicate the topic more broadly. The project may involve affected communities and stakeholders in future participatory research, depending on student interest and initiative. We aim to complete the first paper by June 2012, with ongoing research after June. We encourage students to apply who have experience or interest in the following areas: GIS, statistical analysis, groundwater contamination, public health risks, science communication, and participatory research.

Scott Fendorf, Eric Lambin, Samantha Ying - SESUR or SURGE

Impact of Fly Ash on Agricultural Yield in China

Poor air quality from coal combustion in China is a nation wide problem that is adversely affecting human health via many routes. One of the routes that we are interested in investigating is the effect and geography of coal combustion-derived particulates on crop production in China.  These particulates, often containing very high concentrations of toxic heavy metals, may deposit onto croplands and gradually release heavy metals into the soil aqueous phase, which can be taken up and accumulated in plant tissue during the growing season.  Unlike contaminated water and polluted air, which impact local populations the greatest, these crops can be harvested and distributed throughout the country, affecting both local and far reaching areas. However, aside from coal combustion by-products, other anthropogenic and natural sources of metals also contribute to the metal concentrations in soils. We propose a project for an undergraduate summer intern to determine the contribution of different sources of heavy metals in soil samples collected from farmlands near a power plant in Wuhan, China. The researcher will use a combination of laboratory and computer modeling techniques to accomplish this task. The undergraduate researcher will have the opportunity to acquire skills in the laboratory performing isotopic analysis followed by spatial analysis using GIS. Chemistry or related laboratory skills highly recommended.

Scott Fendorf and Debra Hausladen- SESUR or SURGE

Microbial Processes of Soil Carbon: Implications for Arsenic and Climate

Over 100 million people in Asia drink groundwater contaminated with arsenic, a result of microbial oxidation of organic carbon coupled to As(V) and Fe(III) reduction. What remains elusive, but essential for understanding and predicting arsenic release from sediments to groundwater, is how the spatial variation in functional microorganisms links the variation in flow fields of soils and sediments. In order to understand how specific microbial processes, or chemical reactions, shape the chemistry of transporting fluids and the release of greenhouse gases, we must gain an understanding of where functionally specific organisms reside within media having a complex architecture. We will couple microbiological techniques with chemical analysis to visualize how microbial community composition changes with proximity to diverse carbon phases and hotspots. Doing so will help determine the relevant carbon source and the specific microbial members responsible for arsenic mobilization and carbon dioxide or methane release. We seek an undergraduate researcher who is excited to combine techniques across disciplines in order to resolve the complex interactions of microorgansims with their resulting chemical environment. Chemistry, microbiology or related laboratory skills highly recommended.

Scott Fendorf, Annika Alexander-Ozinskas, and Cynthia McClain- SESUR or SURGE

What Controls the Spatial Distribution of Cr(VI) in California Groundwater? 

Millions of people in California face elevated lifetime exposure to Chromium(VI), a known carcinogen, via drinking water from Californian aquifers. This project explores correlations between irrigation practices in California and Cr(VI) formation in order to call attention to the issue, inform water management decisions, and protect the public from Cr(VI) exposure. Students involved may work on any of the following: data acquisition, geospatial statistical data analysis, map making, results publication, and journalism to communicate the topic more broadly. The project may involve affected communities and stakeholders in future participatory research, depending on student interest and initiative. We aim to complete the first paper by June 2012, with ongoing research after June. We encourage students to apply who have experience or interest in the following areas: GIS, statistical analysis, groundwater contamination, public health risks, science communication, and participatory research.

Chris Field and Kelly McManus- SESUR

Developing New Methods for Investigating Chemical Plant Defenses in Tropical Rainforests 

Plants may utilize a wide array of physical, chemical, and tactical defenses to mitigate damage from herbivores, and understanding how these defenses are distributed throughout plant communities can provide important clues into the role of plant-herbivore interactions in shaping and maintaining biodiversity.  The project described here is part of a larger study to investigate patterns of plant defense among 345 canopy trees in a tropical rainforest community on Barro Colorado Island, Panama.  We currently seek a highly motivated upper-level undergraduate student to assist in the development and execution of a study to measure two types of chemical defenses, serine and trypsin protease inhibitors, in previously collected leaf samples.  These are anti-herbivore defenses which are known to be widely distributed throughout the angiosperm phylogeny, but have not previously been examined in the context of tropical community ecology.   The goal of this project is to modify a protocol utilized primarily in agricultural pest studies of 1-2 species to provide accurate and reproducible quantification of protease inhibitors across a wide range of tropical tree species.  Prior chemical laboratory experience and completed coursework in an upper-division chemistry (particularly Organic or Biochemistry) are required.  This project will be based at the Department of Global Ecology at the Carnegie Institution for Science on Stanford campus.

Chris Francis and Jessica Lee- SESUR or SURGE

Ecology of Nitrogen-Cycling Microorganisms in San Francisco Bay

Ecology of nitrogen-cycling microbes in San Francisco Bay The San Francisco Bay-Estuary is an amazing place to study microbially-driven nutrient cycling, right in our own backyard. My research investigates the diversity of denitrifying bacteria in the sediments of the bay, and how their communities respond to changing environments. I also do a little bit of work with ammonia-oxidizing archaea. If you're interested in hands-on microbial ecology, our lab is the place for you! Depending on your interests, your project may involve any of the following: - culturing bacteria; isolating and characterizing novel organisms - molecular ecology techniques: PCR, cloning, DNA sequencing; bioinformatics - environmental chemistry measurements in sediment samples - measurements of denitrification rate potentials There may even be an opportunity for field sampling on the Bay. Prior biology lab experience is helpful but not required; absolutely necessary is an enthusiasm for DNA, microbes, environmental chemistry, or all three.

Chris Francis and Julian Damashek- SESUR or SURGE

What Factors Control the Biogeochemistry and Microbiology of Nitrification in San Francisco Bay Waters?

Eutrophication is one of the most salient ways humans are affecting estuaries and coastal oceans, with nutrient pollution leading to degraded ecosystems across the globe. San Francisco Bay is affected by both non-point sources of nutrient pollution from its agricultural watershed, and point sources from 42 wastewater treatment facilities that directly discharge into the bay. Yet, we understand little about the nitrogen cycle within this estuary’s waters. This project focuses on nitrification, the microbial conversion of ammonia to nitrate. An undergraduate will help analyze a set of water samples collected in summer 2013 from 41 sites throughout San Francisco Bay. Depending on interest, the student will help with one of two aspects of this project, working alongside graduate students from the Francis Lab: (1) analyzing nitrate isotopes to calculate nitrification rates throughout the bay; or, (2) extracting DNA and using molecular approaches (PCR/cloning, qPCR, etc.) to characterize the populations of microbial nitrifying organisms. If there is interest, additional samples may be collected by boat in summer 2014. Prior experience with genetic techniques or analytical chemistry is preferable, but not crucial. This work will greatly add to our knowledge of the biology and biogeochemical impact of nitrification in San Francisco Bay and estuaries in general.

David Lobell- SESUR or SURGE

Investigating Factors Affecting the Adoption of Drought-Tolerant Seeds in India

How farmers learn about new technologies and why they decide to adopt or not adopt them has long been a topic of research interest, particularly in developing country contexts. It has important implications for the food-security of smallholder farmers and for understanding their ability to adapt to a changing climate. In this project, the student would use the Rural Economic and Development Survey (REDS) panel dataset of input use over more than 200 villages in India with additional climate and weather datasets to explore the factors affecting adoption of drought-tolerant seeds. The student would gain experience in using and manipulating large spatial datasets and in statistical modeling. Some prior programming experience, preferably in R, would be essential.

Kate Maher, Scott Fendorf, and Cynthia McClain- SESUR or SURGE

How Does Cr(VI) Get into California’s Drinking Water?

In August 2013 California proposed the nation’s first drinking water standard for carcinogenic hexavalent chromium, Cr(VI). When this regulation comes into effect in 2014 or 2015, the cost for public utilities (capital investments and ongoing operation and maintenance of drinking water treatment facilities) is expected to be $156 million annually. California water agencies are currently struggling with increasing Cr(VI) concentrations in some groundwater wells and are interested in optimizing the placement of new wells to minimize Cr(VI) concentrations. However, the predominant processes governing the generation and distribution of naturally occurring Cr(VI) in California groundwater used for drinking have yet to be determined. This project explores coupled Cr-Mn oxidation, one of the most likely mechanisms of Cr(VI) generation in aquifer sediments in California. An undergraduate student will conduct experiments with simplified chemical systems as well as natural sediments to link the laboratory to field scale. Students will have the opportunity to synthesize minerals in the laboratory, conduct batch experiments, analyze water samples by mass spectrometry and spectrophotometry, analyze sediment samples using a BET surface area analyzer and work in a class 100 clean lab. Participation in water and sediment sampling at one of our established field sites is possible as well. As a part of the larger study on Cr in CA at Stanford, this undergraduate student will have the opportunity to interact with researchers working on multiple aspects of this local, timely issue. 

Kate Maher and Joey Nelson- SESUR or SURGE

Trace Metals in Tiny Places

Zinc and nickel are important components of catalysts for biological functions, yet are toxic at high concentrations in natural environments. Predicting the fate and transport of contaminants, such and Zn and Ni, hinges on understanding how aqueous solutes migrate through the subsurface and react with minerals. Nanopores (pore diameters < 100 nm) are abundant in soil profiles and rock types, but the effect of nanoporosity on geochemical reactions between solutes and minerals remains largely unexplored. The goal of the project is to decipher the effects of nanopores on cycling and mobility of Zn and Ni in nature. We are seeking a motivated undergraduate to (1) conduct experiments examining Zn and Ni partitioning to minerals with various pore sizes, (2) perform acidic leaches of Zn and Ni from these materials, and (3) measure cation concentrations from experiments using mass spectrometry. It is preferred that interested students have a general chemistry background. Prior laboratory experience is desired, but not required.

Wendy Mao, Mary Reagan, and Crystal Shi- SESUR or SURGE 

Nanoscale Imaging in a Diamond Anvil Cell

We are looking for a student intern to aid in Nanoscale Imaging in a Diamond Anvil Cell at the Extreme Environments Laboratory. Nanoscale x-ray computed tomography (nanoXCT) within a laser-heated diamond anvil cell has exciting potential as a powerful 3D probe for non-destructive, nanoscale (<40nm) resolution of multiple crystalline and amorphous phases which are synthesized under extreme conditions. One undergraduate intern will become involved in a combination of modeling and lab studies designed to map coordination and oxidation states, and provide quantitative composition information within the sample. The intern will be monitored by two graduate students and a faculty member.

Wendy Mao and Zhao Zhao- SESUR or SURGE 

High Pressure Study on Energy Related Materials

Under extreme conditions like high pressure, novel phenomena like solid to solid transitions, crystal to amorphous transition, and insulator to metal transitions can occur. Our group characterizes these changes in materials behavior using a variety of in-situ probes. We are looking for a summer intern student with interest or background in materials science and materials engineering to study the crystal structure and electronic transition in energy related materials like MoSe2 and WSe2. The intern student will have hand-on experience conducting experiments, analyzing data, and summarizing results under the supervision of a graduate student and a faculty advisor.

Elizabeth Miller and Abi Ruksznis-SURGE 

Tectonic history of the Snake Range Metamorphic Complex

The tectonic history of the Snake Range metamorphic core complex, shaped by Cenozoic extension and faulting related to the formation of the Basin and Range, remains enigmatic and debated even after years of research.  Our ongoing project integrates geologic mapping, geochronology, thermochronology and geochemistry to resolve this history.  A prime candidate to join this project for a summer would be interested in using one or more of these techniques, enjoy hard work and spending time in the desert, and be open to learning any aspect of science. This project will entail spending a month in the field collecting data and samples in order to compare and place time constraints on stratigraphic sections of Cenozoic sediments that inform the timespan of faulting.

Peter Vitousek- SESUR 

Nutrient Dynamics and Indigenous Agriculture Along a Rainfall Gradient in Kohala, Hawaii

The project seeks to integrate nutrient cycling/biogeochemistry and indigenous agriculture in sites along a rainfall gradient on the Island of Hawaii. Rainfall on the gradient ranges from 250 - 4000 mm/yr; indigenous Hawaiians intensified agriculture in the range from 700-1800 mm/yr. We understand that (and much of why) soils are particularly suitable for intensive agriculture in that range; however, we seek to understand how Hawaiian farmers managed to sustain intensive agriculture there for centuries. Also, we seek to understand the dynamics of nitrogen along this gradient. Other major plant nutrients are enriched by natural processes in the zone that Hawaiians cultivated; however we seek to understand why nitrogen - the element that most likely constrained ongoing agricultural production - could have supported sustained production there. 

Paula Welandar and Laura Meredith- SESUR or SURGE 

Investigations of the Microbial Imprint on Atmospheric Chemistry and Climate

Microorganisms have produced dramatic shifts in the composition of the Earth’s atmosphere. They continue to be important drivers of ocean- and land-atmosphere exchanges of gases that have a strong influence on atmospheric composition and climate. In this project, we are interested in understanding the significant yet poorly constrained consumption of atmospheric carbonyl sulfide (COS) by soil microorganisms. This is of importance because COS, a structural analog to carbon dioxide (CO2), has the potential to be a powerful carbon cycle tracer for disentangling the simultaneous and opposing photosynthetic and ecosystem respiration CO2 fluxes of the terrestrial biosphere. Efforts towards this end aid in predicting and monitoring the effects of climate change. The summer research associate will support our endeavors to link the microbial genes and pathways of COS consumption to the cycling of COS between the soil and atmosphere. This project provides an opportunity to learn a wide variety of techniques in molecular biology and environmental science: PCR; molecular cloning; DNA sequencing and sequence analysis; growing bacteria in culture; and measurements of microbe-mediated trace gas exchange rates. Prior microbiology lab experience is helpful but not required. We seek an applicant with enthusiasm for DNA, microbes, and/or atmospheric chemistry. 

Paula Welandar - SESUR or SURGE 

Linking Lipid Biosignatures in the Rock Record with Lipid Physiology in Modern Bacteria

In this project, students will utilize molecular and microbiological tools to study how bacteria produce and utilize two geologically relevant lipids, hopanoids and sterols. Both of these molecules are quite recalcitrant and are readily preserved in sedimentary rocks that are million and even billions of years old.  Hopane biosignatures are used as geological proxies for bacterial species while sterane biosignatures are primarily used as indicators for eukaryotic life deep in time. But our interpretation of these lipid biomarkers is limited by our lack of understanding of the physiological role of hopanoids and sterols in modern bacteria. In this project, students will undertake studies in bacteria that are capable of producing both hopanoids and sterols with the goal of trying to understand why these bacterial species produce both sets of lipids. Students will have exposure to a variety of techniques including bioinformatics, PCR, constructing gene deletions, bacterial growth experiments, and lipid analysis.  We are looking for students that are interested in microbiology and/or geobiology. Prior lab experience would be a plus but not necessary. 

Jennifer Wilcox and Shela Aboud- SURGE 

Carbon Dioxide and Methane Adsorption on Model Coal Surface

Geological carbon capture technologies with enhanced coalbed methane recovery is becoming an important research topic as carbon dioxide emissions and energy demand continues to increase. To understand the adsorption processes different research approaches must be considered, from the macroscale to the atomic scale. In the present study, binary system adsorption of CO2 and CH4 on graphene and bilayer graphite surfaces are used to model the adsorption mechanisms of these compounds on the organic coal matrix. Density functional theory with dispersion correction (DFT-D) calculations were performed to investigate the adsorption energy, molecular distance and electronic density of states for the binary system adsorption. Ab initio thermodynamics calculations were done to further investigate the adsorption mechanisms at finite temperatures and pressures. Adsorption energies of ~180 meV and ~160 meV calculated individually for CO2  and CH4 over a graphene sheet are close to experimental values and similar work. The binding energies for the single molecule systems over a graphitic bilayer are considerably close to those of single graphene. Ab initio thermodynamics calculations show that adsorption of either molecule is not thermodynamically stable at temperatures and pressures encountered in coal basins.

Jennifer Wilcox and Shela Aboud- SURGE 

Computational Quantum Chemistry for Environmental Applications

Computational approaches based on quantum chemistry such as density functional theory (DFT) provide detailed information about the physical structure, electronic properties, and vibrational characteristics of rocks and minerals, both manmade and in the natural environment.  These tools can also be used to examine how potentially harmful atoms or molecules will adsorb or dissociate on the surface of these materials, which can provide important information for a variety of environmental applications.  The following is a list of several topics available:

Natural sequestration processes of actinides (such as Uranium) in the soil.

Catalytic decomposition of Nitrous Oxide (a greenhouse gas with 310 times the global warming potential as Carbon Dioxide).

Nitrogen and/or Sulfur interactions with mineral dust in the atmosphere.

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