Stanford University
Students on hike

Stanford Earth Summer Undergraduate Research

Photo by Kate Maher

2015 Projects

Kate Maher, Simon Klemperer, and Chris Castillo—SESUR

Catalina Island Marine Terrace Chronology

Marine terrace sequences provide critical information about past climates and active tectonics.  These wave-cut marine terraces mark paleo sea-level, while fossils contained within terrace deposits provide paleoclimate information regarding past ocean temperature and ocean circulation. Dating of fossil material from marine terraces also allows us to estimate tectonic uplift rates, which in turn provides information about the development of fault linkages over time.  We propose an undergraduate research project to date shells and foraminifera recovered from Catalina Island to correlate with our high-resolution seismic dataset.  In June 2014, we collected several bottom samples from offshore Catalina Island (offshore Los Angeles, Southern Californian Continental Borderlands), along with an extensive seismic dataset with 50 cm resolution at the near surface.  We have also obtained core samples collected by USGS and USC that contain dateable shells and foraminifera.  

An enthusiastic undergraduate will assist us in collecting dateable material from cores and bottom samples and will prepare them for 14C or U/Th chronology using ICPMS (inductively coupled plasma mass spectrometry).  The student will gain substantial lab experience preparing the samples and running them on our Nu Plasma HR Multi-collector ICPMS.  After the material is dated the student will assist in correlating samples with seismic data.  This multidisciplinary project incorporates geochemistry, marine geophysics, and quaternary geology.  The learning outcome will be knowledge of radiometric dating techniques, dynamics of oceanic circulation, California coastal fauna, and applications of seismic stratigraphy.  There is the possibility of a one-week science cruise for coring and high-resolution profiling.

Peter Vitousek—SESUR

Biogeochemistry and Traditional Rainfed Agriculture in Hawaii  

Prior to European contact, Hawaiian cultivators created remarkably large and intensive rainfed agricultural systems on fertile on the younger islands. Peter Vitousek is working with colleagues at Stanford and in a community NGO in Hawaii to restore examples of that system in the Kohala District, Island of Hawaii, to understand how it worked, and to develop educational materials for the local community.  At the same time, we are studying the biogeochemical context within which that system was embedded - working to understand why soils in the zone where Hawaiian intensified production were so fertile.

David Lobell and Meha Jain—SESUR or SURGE

Adapting to Climate Change in India

Warming temperatures are already negatively affecting wheat yields, particularly in the Indo-Gangetic Plains region of India. Agronomists suggest that two of the best ways to reduce the negative impacts of heat stress are to plant certain wheat varieties that are better suited to warming temperatures and planting wheat earlier so that the crop matures before heat stress occurs at the end of the growing season. However, it is unclear whether farmers alter their sowing date and wheat varietal choice in response to weather fluctuations, and if so, whether these alterations actually confer some benefit in terms of yield. The summer student will help contribute to this project by analyzing panel district-level data on percent area under different wheat varieties and yields of those varieties over the last few decades. We will combine these datasets with rainfall and temperature datasets to identify whether farmers alter wheat varieties in response to weather shocks, and whether certain varieties are more tolerant to terminal heat stress.

George Hilley and Sam Johnstone—SESUR or SURGE

How Does Rock Type Affect the Sensitivity of Landscapes to Erosion?

Earth’s topography is an integrated record of tectonic deformation and the processes that break down rocks and transport them across Earth’s surface.  Understanding how these surface processes shape landscapes may allow us to use landscape forms to infer something about changes in tectonics or the aspects of climate that control surface processes, but only if landscape forms are sensitive to such changes.  We are looking for a student to help us as we try to understand if some landscapes forming over mud-rich sedimentary rocks are armored by the soils that separate these rocks from the Earth’s surface.  If this hypothesis is true, changes in the style or intensity of surface processes that expose these mud-rich rocks may cause landscapes to become unstable, while less significant changes may yield no response in landscape forms at all.

The exact nature of this work is relatively flexible.  We hope that the project will provide you, the student, the opportunity to learn about or strengthen your abilities in one or more of the following areas, depending on your own goals and interests:  1) the interpretation and analysis of high-resolution topographic data and aerial photography to determine styles and relative rates of erosion; 2) producing and or utilizing computer simulations of landscape development; 3) development and/or use of physical experiments to investigate the resistance of rocks to erosion. Through direct experience and discussions you will become familiar with common principles and active research in geomorphology, techniques for geospatial analysis of landscapes, and general techniques and strategies for data analysis. Students should either be comfortable learning new software or have some experience with ArcGIS, Matlab, or Python.  This project includes the possibility of complementing observations made in elevation data and imagery with field observations from a site in the California Coast Ranges.

Jonathan L. Payne and Caitlin Keating-Bitonti—SESUR or SURGE

How Do Marine Shelled Protists Get Big?

Benthic foraminifera are common single-celled protists that live on or within the seafloor sediment throughout the world’s oceans.  Carbonate species of benthic foraminifera secret tests (shells) similar to mollusks and grow by incrementally adding new chambers to their tests. Geochemical analyses of foraminiferal tests are readily used to reconstruct past ocean conditions, but we know relatively little about how foraminifera grow and how variations in chamber number and/or test size relates to the ambient environment.  We seek a student to help better understand the growth history of foraminifera by studying variations in test size and number of chambers along a bathymetric and oxygen gradient from a Southern California borderland basin.  

Potential research questions to be addressed include: Do large individuals within a species have more chambers or do larger tests have increased chamber size relative to individuals with smaller-sized tests?  Is there a relationship between chamber size or the number of chambers to oceanographic variables, like dissolved oxygen concentrations?  Student will make measurements on foraminiferal tests and photograph specimens that have been previously processed and identified to the species level.  Student will learn to work with foraminiferal specimens, to process and statistically analyze paleontological data in R, and will gain knowledge of organisms living in oxygen minimum zones.

Pamela Matson and Laura Hess—SESUR

Climate Change Effects on Nitrogen Losses from Midwest Agroecosystems

As a consequence of climate change, rainfall patterns are changing across the globe, and especially in the U.S. Midwest, with an increase in the frequency of large storms and the length of dry periods in between them. These changes in climate may have especially important consequences for rain-fed agriculture.

We are exploring how these changes in rainfall patterns may influence nitrogen (N) losses from agricultural soils through a large-scale rainfall manipulation experiment at the Kellogg Biological Station Long Term Ecological Research site in southwest Michigan.  N is an essential crop nutrient, but it is easily lost from soils to the environment, where it causes a host of environmental harms.  For instance, N leached from soils in water can cause algae blooms and dead zones in rivers, lakes, and coastal areas.  In addition, N lost in gaseous form is a precursor to ozone and a potent greenhouse gas.

We are looking for a highly motivated undergraduate student to work on a project helping to understand mechanisms driving the response of N losses to changing rainfall patterns.  This student would measure rates of soil microbial processes contributing to soil N concentrations, which are a primary factor explaining N losses from soils.  However, depending on the student’s interests and skills, additional projects could also be developed, for example involving a computer simulation model, analyzing the nutritional quality of grains, or measuring crop root distribution.

The project will involve a combination of field and lab work based at the Kellogg Biological Station.  Previous laboratory experience is a plus. Interested students should contact Laura Hess at

Scott Fendorf and Marco Keiluweit—SESUR or SURGE

Assessing Soil Characteristics Controlling Greenhouse Gas Emissions and Carbon Storage

Soils play a critical role in the global carbon (C) cycle, 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 metabolized by microbes and subsequently released to the atmosphere as climate-active greenhouse gases (e.g.. carbon dioxide or methane). What remains unclear is to what extent the limited availability of oxygen in soils affects overall rates of microbial C oxidation and associated greenhouse gas-release in upland soils. We propose a project for an undergraduate researcher to determine the degree of microbial C oxidation across a soil series exhibiting a natural variation in oxygen availability.  Soil samples will be collected at an Oregon field sites and will be examined using a combination of wet-chemical and density fractionation techniques to characterize differences in C transformation among the soils.  The project may involve further analyses of abundance and activity of soil microbes depending on the student interest and initiative.  Experience in soil and/or environmental science and related laboratory work would be helpful.

Gretchen Daily and Gregory Bratman—SESUR

The Influence of Natural Environments on Emotion

After contact with natural environments many individuals report feelings of 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’ affect and emotion regulation strategies.  Students will be learning how to administer – and collaborate on the development of – confidential tests that measure these capacities.

Eric Dunham and Brad Lipovsky—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.

Kevin Arrigo, Karen Casciotti, Matthew Mills—SESUR or SURGE

Understanding the Pre-Bloom Nitrogen Cycle of the Chukchi Sea, Arctic Ocean

The Arctic Ocean is a highly productive, seasonally ice covered sea with an expansive shallow continental shelf.  This high productivity fuels high rates of sediment denitrification and results in one of the largest nitrogen deficits relative to phosphorus in the global ocean.  These high rates of denitrification in the Arctic potentially have large impacts on other ocean basins, such as the Atlantic Ocean.  This project will use data and samples collected during a research expedition to the Chukchi Sea during May – June, 2014 to examine aspects of the Arctic N cycle.  Specific attention will be given to analyzing the stable isotopes of nitrate from both the water column and experimental manipulations.  Prior experience in the lab and/or with stable isotopes would be helpful but is not required.  Enthusiasm for lab work, biological and chemical oceanography, and biogeochemistry are absolutely necessary.

Kevin Arrigo, Chris Francis, Matthew Mills—SESUR or SURGE

Understanding the Important Microbial Players in the Pre-Bloom Nitrogen Cycle of the Chukchi Sea, Arctic Ocean

The Chukchi Sea in the Arctic Ocean is a highly productive, seasonally ice covered sea with an expansive continental shelf.  High rates of denitrification and nitrification, as well as, nitrogen limitation of the phytoplankton community in the summer time make the Chukchi Sea an ideal system for studying the microbially-mediated nitrogen cycle.  This project will focus on using molecular techniques to investigate the diversity and structure of the microbial community involved in the nitrogen cycle of the Chukchi Sea water column and sediment.  Samples from a research expedition to the Chukchi Sea in May – June, 2014 will be analyzed using a wide variety of techniques standard to molecular biology and environmental science: PCR; molecular cloning; DNA sequencing and sequence analysis.  Prior biology lab experience is helpful but not required; absolutely necessary is an enthusiasm for DNA, microbes, environmental chemistry, or all three.

Rosemary Knight and Jingyi (Ann) Chen—SESUR

The Subsidence Signature Due To Groundwater Extraction as Inferred from Remote Sending Data in Mexico City

Mexico City is undergoing large amounts of land subsidence and, at the same time, is facing a severe water shortage.  This land subsidence has damaged building foundations, wells, streets, and the sewer system and, additionally, has led to flooding as the city now lies almost 6 feet beneath the nearby Lake Texcoco.  It is known that groundwater pumping is the major cause of land subsidence and, because of this, water resource managers in Mexico City need to monitor land subsidence in order to efficiently and sustainably allocate water resources. Interferometric Synthetic Aperture Radar (InSAR) is a radar remote sensing technique that retrieves surface deformation to millimeter-level accuracy at meter-scale resolution over very wide regions.  Achieving this level of accuracy requires complex radar signal processing techniques such as the Persistent Scatters (PS) and Small Baseline Subset (SBAS) method to compensate for the effects of decorrelation and atmospheric noise.  Here we propose to combine long sequences of InSAR data from different radar satellites in order to reconstruct comprehensive long-term and seasonal surface subsidence map over the Mexico City.  We will explore the temporal and spatial links between the change in subsidence pattern and key elements in a fresh water cycle, e.g. how changing precipitation or pumping leads to change in the aquifer groundwater levels and surface subsidence.  The resulting temporal and spatial correlations between subsidence pattern and principal fresh water cycle elements can inform decisions related to the use of groundwater, allowing time to take actions that impact the withdrawal of water from the aquifer or the recharge of the aquifer.

Kevin Arrigo—SURGE or SESUR

Phytoplankton Community Composition in Coastal Antarctic Waters

The Southern Ocean, surrounding Antarctica, is a biologically productive region responsible for a significant amount of carbon dioxide drawdown from primary production by phytoplankton.  Two major phytoplankton functional types, Phaeocystis antarctica and diatoms, compete to dominate the phytoplankton community in the region.  Because the two groups are distinct in their nutrient needs, the relative abundance of the phytoplankton impacts the nutrients and carbon present in the surrounding environment.  Hydrographic changes from climate change are likely to shift the current phytoplankton community composition, which in turn could have a major impact on regional biogeochemical cycling and carbon dioxide drawdown, however the direction and magnitude of possible change is still largely unknown. 

This project will help characterize the phytoplankton community composition along the coast of Antarctica.  The student will work with a graduate student to learn the taxonomy of Antarctic phytoplankton and analyze photographs of phytoplankton from a recent cruise to determine the phytoplankton community composition.  This data will be compared regionally and to physical and chemical data collected during the cruise, including ocean temperature, salinity, dissolved oxygen, and pCO2.  Attention to detail is important, as well as an excitement for biological oceanography.

Chris Field and Grayson Badgley—SESUR or SURGE  

Remote Sensing of Nutrient Limitation

Nutrients, like nitrogen and phosphorous, are an essential part of the global carbon cycle.  When nutrients are readily available, natural ecosystems help draw down the amount of carbon dioxide in the atmosphere.  This allows natural ecosystems to slow the rate at which atmospheric greenhouse gases accumulate.  However, the productivity of most vegetation is thought to be limited by nutrient availability.  This raises the possibility that the carbon capturing ability of natural ecosystems might diminish in the future as nutrient stores become depleted. Understanding the future of the terrestrial carbon sink requires that we better quantify the severity, as well as the spatial extent of nutrient limitation at the global scale.  We are working on an approach to estimate total nutrient availability by combining principles from plant physiology with data derived from satellites.  We are looking for an undergraduate researcher interested in helping us refine our method.  The summer student will be responsible calculating nutrient limitation from satellite images and comparing their results against ground validation data.  The student will learn the basics of remote sensing, statistical analysis using R, and the fundamentals of plant physiology.

Scott Fendorf and Sarah Fakhreddine—SESUR or SURGE

Capturing Scalable Parameters of Carbon Flow in Soils for Global Climate Models

Global climate change models depend on our understanding of the biogeochemical processes regulating carbon flow in soils, which represent the largest terrestrial pool of carbon.  A critical factor controlling terrestrial carbon flow is the oxygen content (determined by the competing rates of delivery versus microbial consumption).  Our project aims to (1) determine a scalable measure of soil oxygen content, (2) link the oxygen content to scalable soil characteristics such are particle size distribution and moisture content, and (3) develop a model to predict water and oxygen content based on available soil parameters.  We propose an undergraduate research project to help better understand the effect of varying physical properties such as texture, water content and carbon content on pore water oxygen concentrations.

Specific project tasks are flexible depending on student’s interest.  Potential projects involve a combination of fieldwork and subsequent laboratory analysis of soils.  Students can focus on soils from a particular region or a specific soil property of interest.  Additionally, depending on the student’s goals, the project can also involve data analysis and computational modeling.

Stephan Graham, Nora Nieminski, Lauren Shumaker—SESUR or SURGE

Detrital Zircon Provenance Analysis of a Forearc Mini-Basin, East Coast Basin, New Zealand

Sedimentary basins are the accumulations of sand, mud, and gravel transported by wind and water over millions of years.  Detrital zircon provenance analysis allows us to trace out the sources of these sediments, providing critical information about changes in the landscape through which sediment was transported over geologic time.  What portions of the landscape were exposed to erosion and contributed sediment to the basin?  Was there any significant change in sediment supply and/or transport directions through time?  Answering these questions can have implications for broad-scale tectonic evolution in the region.

We propose an undergraduate project to analyze a suite of detrital zircon samples from a sub-basin of the East Coast Basin, New Zealand, spanning Miocene through Pliocene time (~20 million years).  Acquiring the detrital zircon age spectra for these samples and comparing them to data from ongoing research and published literature will constrain the possible sediment sources that fed the basin over that time span.  Trends in these data may help illuminate the effects of west-directed subduction along the Pacific-Australian plate boundary, and the onset of slip on the plate-bounding, transpressional Alpine Fault.

We seek a student with interests in sedimentary basin analysis, tectonics, and/or detrital zircon provenance analysis.  No experience with this dating technique is needed, as this project will provide the opportunity to learn U-Pb detrital zircon dating and provenance analysis from start to finish – including mineral separations, grain analysis by laser ablation, data reduction, and statistical assessment of results.  The student will generate a workable dataset of 3-5 samples, which will be incorporated into a larger, ongoing research effort for publication.  U-Pb dating of detrital zircon is a highly popular and quickly growing field, and this project will educate the student in some of the opportunities and limitations of the technique while providing hands-on experience working with data.

Stephan Graham and Lauren Shumaker—SESUR or SURGE

Mapping Submarine Gullies with High-Resolution Seafloor Bathymetry Data

Submarine gullies are small (tens to hundreds of meters wide), straight channels found in a wide variety of settings on the seafloor, typically where slopes are relatively steep (such as canyon walls, mass failure scarps, and continental slopes).  The presence of submarine gullies on continental slopes worldwide implies that they are an integral part of sediment transport from shallow waters to deeper ocean basins.  Despite this, the conditions of gully formation are poorly constrained, and even the definition of a submarine gully varies widely across publications.

We propose a seafloor mapping project with the goals of (1) generating a large, widespread dataset of gully geometries in the context of regional tectonics, sediment supply, and slope character; and (2) using these data alongside published research on gullies and other seafloor channels to develop a robust definition for “submarine gullies.”  The student will take advantage of publicly available, high-resolution seafloor bathymetry data from continental margin locations including northern California, Costa Rica, New Zealand, the Gulf of Alaska, New Jersey, and others.  Additional, published data from seafloor bathymetry, outcrop, and subsurface studies should be incorporated.  No prior experience working with bathymetric data is necessary, but the student should be comfortable learning new software and/or have experience with ArcGIS or similar.

Rob Jackson and Mary Kang—SESUR or SURGE  

Methane Emissions and Potential Groundwater Contamination from Abandoned Oil and Gas Wells

Abandoned oil and gas wells can be pathways for fluid migration, leading to potential groundwater contamination and greenhouse gas emissions.  Recently, my measurements of methane emissions showed that abandoned oil and gas wells could be an important source of methane to the atmosphere (Kang et al., PNAS, 2014).  Millions of abandoned oil and gas wells exist across the U.S. in states such as California and Texas with a long history of oil and gas development.  The student project will be to work with geospatial databases and to help with field and laboratory research on abandoned wells. 

Paula Welander 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.

Scott Fendorf and Michael Schaefer—SESUR or SURGE

Assessing the Impacts of Climate and Land-Use Change on Soil Carbon Dynamics and Arsenic Contamination in Tropical Asian Deltas

The tropical deltas of South and Southeast Asia represent nearly half of the global terrestrial deltaic area, yet their carbon fluxes have not been adequately quantified to incorporate into global climate models.  Deltas are dynamic systems with the potential to store or release large quantities of carbon due to high primary productivity and decomposition rates, respectively.  A major control on these rates in low-lying regions is the extent of flooded area, which may largely determine carbon decomposition pathways. Different degradation pathways have implications for atmospheric CO2 concentrations as well as rates of arsenic release to groundwater across the deltas of Asia.  The goal of this project is to determine under what conditions carbon is released and stabilized in the Mekong Delta, and to further determine what mechanisms control carbon dynamics in the Delta.  Understanding the various carbon pathways will help determine and predict current and future CO2 flux from sediments as well as spatial and temporal variations in groundwater arsenic concentrations.  This project will require an undergraduate researcher to learn and perform various laboratory techniques including bulk elemental analyses of sediments and wet chemical sediment extractions as well as the opportunity to assist in laboratory manipulation experiments of Mekong sediment by making solid, aqueous, and gas phase measurements.  Previous laboratory experience in environmental science or chemistry are a plus.

Scott Fendorf and Ivan Carabante—SESUR or SURGE

Remediation of Abandoned Mine Wastes in Native American Southwestern Communities

More than 1,000 mine waste sites remain abandoned in the Western US, as part of the legacy from uranium mining since the 1950s.  Placement of permeable covers comprising soil and rock on waste piles at abandoned mines continues to be the most widely used “interim” containment method to reduce health risks.  Yet, the release of uranium from a mining site in northeastern Arizona recently contaminated  groundwater with uranium at concentrations 5-fold higher than the guideline recommended by the the U.S. EPA.  The release of metals compromises the environment and, more importantly, human health since these metals are lethal upon acute poisoning and carcinogen upon long term exposure.  Worryingly, an overwhelming number of these contaminated sites are located in the proximity of rural Native American communities.

A cost-effective method to reduce the risk, i.e. mobility and bioavailability, of metals in a contaminated site is to apply in situ stabilization techniques, keeping the soil on site.  We are examining the feasibility of adding chemical amendments, both metallic iron and phosphate, to simultaneously decrease uranium, arsenic, and vanadium released from an abandoned mine waste site near Native American Southwestern Communities.  The addition of the chemical amendments will be experimentally studied in confined pot trial in the laboratory.  Pore water samples (analogue to ground water) will be routinely collected and analyzed from the trial pots to assess the released of uranium, arsenic and vanadium before and after the chemical amendment.  Changes in the metals partitioning of the mine waste after chemical amendment addition will be followed as well using advanced spectroscopic methods.

Roland Horne and Anna Suzuki—SESUR or SURGE

Characterization of 3D Printed Fracture Network

Fractures in deep rocks represent only pathway for groundwater flow, which is essential for several appreciations, such as geothermal and petroleum engineering, nuclear waste repositories, environmental remediation.  As complex fracture distributions are not accessible directly but only at their intersections with boreholes or outcrops, understanding and quantifying the fracture geometry using limited data remains the main task for reservoir engineering.  Tracer testing provides a valuable diagnostic service for measuring hydraulic properties and may obtain inter-well information directly controlled by the fracture geometries between the wells.  A series of geophysical investigations have confirmed that subsurface fracture networks can commonly be described by fractal geometry.  Fractal geometry is a branch of mathematics and has great potential for characterising and simulating the geometry of complex shapes.  One of promising model to analyse mass transport based on fractal geometries can reproduce anomalous tracer behavior often obtained from fractured reservoir.  If the tracer analysis model can provide useful information to evaluate fracture geometries using tracer responses, it will contribute to estimate geological and physical structures in a fractured reservoir.  The summer student will help to clarify the unknown quantitative relationship between the tracer response and the mass transport model by conducting tracer experiment in laboratory.  3D printed fracture network samples based on fractal geometry will be designed and used for tracer flow test.  Student will learn to work with designing 3D model for 3D printing and conducting flow experiments, and will gain knowledge of fluid flow in fractured rocks.

Paula Welander—SESUR or SURGE

The Role of Hopanoid and Sterol Lipids in Stress Survival of Methane Consuming Bacteria

Aerobic methanotrophic bacteria utilize oxygen to consume methane for growth and thus play a critical role in the global carbon cycle.  These organisms have been discovered in a variety of methane containing environments including freshwater, marine, terrestrial and even more “extreme” ecosystems such as hot springs, deep sea mud volcanoes, and Arctic ice lakes.  Although much effort has been put forth to study the phylogenetic diversity and metabolic aspects of aerobic methanotrophs from these diverse environments, very little is known about how these organisms are able to survive and thrive in their natural habitats. In this project, students will utilize molecular and physiological tools to explore the role hopanoid and sterol lipids have in stress survival in the alkaliphilic halotolerant methanotroph, Methylomicrobium alcaliphilum 20Z. 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.

David Lobell—SESUR or SURGE

Testing New Satellite Approaches to Crop Yield Mapping

A combination of new sensors and data processing platforms are opening up new opportunities for measuring and predicting crop yields from space. These estimates of yields can then be used to understand how crops respond to different management and environmental changes, and how to improve overall productivity of agriculture. In this project, the student will work on applying approaches developed for the US Corn Belt to other crops and regions, most likely wheat in the Great Plains and Northwest Mexico. The work will include running large numbers of simulations with crop models, interacting with Google’s Earth Engine Platform, and performing detailed tests against available ground-based measurements. Prior programming experience, especially in R or Javascript, is desired.

Eric Dunham and Kali Allison—SESUR or SURGE

Computer Science and Earthquakes

Many cities in California, such as Los Angeles, are at risk for earthquakes from nearby faults.  The properties of the material on which these cities are built affects the earthquake cycle in ways that are not well understood, however.  To explore this, we have programmed a parallelized system to simulate the earthquake cycle over thousands of years.  The student can work on different aspects of this project depending on interest.  Possible projects:  1. The most time-consuming step in the simulation involves solving a large system of equations.  We are looking for an undergraduate to implement different algorithms from a suite of available techniques to determine the fastest.  This will involve researching various algorithms to determine the tunable parameters and analyzing system performance.  Students should have at least introductory knowledge of linear algebra and some computer programming experience.  2. Change the current I/O implementation to use a file format for storing and managing a high volume of data efficiently.  This will involve choosing an organizational scheme for simulation results from a parameter space search, including metadata, implementing the output in the existing code (C++), and developing code to search and load results through either Matlab or Python.  Students must be comfortable with C++ or a comparable language.

Jessica Warren and Katie Kumamoto—SESUR only

Mantle Shear Zone Structure and Microstructure in the Josephine Peridotite, SW Oregon

The Josephine Peridotite is the mantle section of a 150-my-old ophiolite located in the Klamath Mountains of southwestern Oregon.  One small section of the peridotite, an outcrop known as Fresno Bench, contains numerous easily-observed shear zones that represent small-scale mantle deformation.  These ductile shear zones have a relatively consistent orientation and are believed to have formed around the same time. Just outside Fresno Bench, there is another small shear zone.  We seek a student to characterize this previously unanalyzed shear zone in terms of orientation and microstructure. This shear zone will then be compared to the nearby shear zones in the Fresno Bench outcrop.  The student will learn the basics of photogrammetry using “Structure-from-Motion” software to create a 3D model of a hand sample from the shear zone.  The student will also analyze oriented thin sections from the sample using electron backscatter diffraction and energy dispersive spectroscopy to characterize the microstructures and chemical composition of the deformed rock.

Marty Grove and Miguel Francisco Cruz—SESUR or SURGE

Potassium, Calcium, and Argon in Mantle Minerals

The tectonic processes expressed at Earth’s surface also extend to great depths, such as when subducting plates plunge oceanic crust soaked in salty water and other volatiles into the Earth’s mantle.  Those fluids interact with the mantle in complex and mysterious ways.  Rare mantle fragments provide opportunities to learn about these processes.  Phlogopite, a mineral from the mantle, holds information about mantle fluids.  The potassium in phlogopite decays to calcium and argon, which leak out of the phlogopite via diffusion, at different rates depending on pressure, temperature, and the nature of the fluid surrounding the phlogopite.  We have phlogopite from controlled laboratory experiments as well as from the mantle.  To gain insights to the pressure-temperature history of the mantle phlogopite as well as to the nature of the fluids that surround the phlogopite and permeate the mantle, we must simulate and compare diffusion in both the laboratory and the mantle.  This work will have implications for the relationships between fluids, tectonic processes, and geochemical cycles.  We seek an undergraduate who will run a Matlab code to simulate diffusion of calcium and argon in phlogopite under different pressures, temperatures, and with different fluid compositions.  This project will also involve using a scanning electron microscope to image natural and synthetic phlogopite.  If these questions about mantle minerals and fluids have piqued your curiosity, we look forward to hearing from you.

Greg Asner and Dana Chadwick—SESUR

Nutrient Retention and Cycling in the Peruvian Amazon

The Amazon basin is home to some of the most biodiverse forests on the planet.  However, large regions of these forests in the western amazon basin exist on ancient soils, which are extremely depleted of many essential nutrients.  Many of these essential nutrients are retained in the ecosystem through tight biological cycling at the soil surface.  In addition, they can be reintroduced to the system when erosion acts to remove surface soils that are depleted of mineral nutrients, exposing more nutrient rich soils for use by the forest biota.  These factors, biota and topography, are two of the five state factors that influence how soils form, and determine the soil characteristics.

The goal of this project is to consider the relative importance of topography and local tree species in dictating local soil nutrient concentration. The project would involve characterizing nutrient concentrations in surface soils, collected during 2014 from across a terra firme forest in the Peruvian Amazon and working with us to analyze the variability within and between collection sites.  The samples were collected from a series of sites on both flat and sloping areas, and were collected from beneath known tree species.  We are seeking an undergraduate who is interested in gaining laboratory and research experience, and is excited to learn about tropical biogeochemistry and nutrient dynamics.  Prior experience in a laboratory environment would be helpful but is not required.  Interested students should contact Dana Chadwick at

Steven Gorelick and P. James Dennedy-Frank – SESUR

Hydrologic Ecosystem Services in a Tropical Watershed

The goods and services that ecosystems provide to people vary strongly across gradients in climate, ecosystems, and intensity of human use.  Conservation organizations are using the value of these goods and services to support the conservation and restoration of these ecosystems, but a systematic understanding of these ecosystem services and the tradeoffs between them and human infrastructure remains a challenge.  We are pursuing a project to globally estimate the value of these services, with a focus on the services from water and biodiversity.  We propose an undergraduate research project to evaluate the hydrologic ecosystem services provided in a Puerto Rican watershed by building a hydrologic model and investigating the changes in ecosystem services under distinct development scenarios.  Puerto Rico provides an ideal testbed for evaluating the ecosystem services provided in tropical environments because of the easily-available, high-quality standard US data.  This ecosystem services assessment will stand alone as a coherent analysis but will also fit into the larger context of a project to understand hydrologic ecosystem services globally.

The enthusiastic student will learn and use a conceptual rainfall-runoff computer model to simulate the hydrologic processes in this tropical watershed.  A familiarity with ArcGIS and some high-level computing language (e.g., Matlab) will be useful for this task.  The student will select appropriate development scenarios in consultation with the advisors to better understand the tradeoffs in ecosystem services with potential development scenarios.  According to the interests of the student, the project could branch out to examine the demand for ecosystem services in this area or the likely effects of development scenarios on biodiversity.  The outcome of the project will be a site study of the production of ecosystem services in a tropical environment, an area for which high-quality studies are in short supply.

Greg Beroza and Yihe Huang—SESUR or SURGE

Detecting Induced Seismicity

As the injection and withdrawal of fluids become increasingly common in the energy industry, the observations of injection-induced seismicity have increased too, and they present an urgent need to understand the physical mechanism. A complete catalog of induced earthquakes is critical for studying the evolution of induced seismicity and for assessing the risk of ongoing fluid injection; however, due to the sparse permanent seismic instrumentation in most areas, induced earthquakes, especially small ones, are usually missing in traditional catalogs.

We would like to work with an undergraduate student to detect induced earthquakes using high-resolution methods. The first method is template matching based on matching the waveform similarity of earthquakes. The second method is subspace detection, which exploits features common to a design set of earthquakes. Once assembled, we will develop a complete catalog by estimating magnitude for the earthquakes as well.  The results of the project will assess detection capabilities of the two methods and will apply them to a region of induced seismicity. The project will involve tools of seismic data analysis and Matlab, including modifying scripts for template matching and subspace detection. 

Peter Vitousek—SESUR

Biogeochemistry and Traditional Rainfed Agriculture in Hawaii  

Prior to European contact, Hawaiian cultivators created remarkably large and intensive rainfed agricultural systems on fertile on the younger islands. Peter Vitousek is working with colleagues at Stanford and in a community NGO in Hawaii to restore examples of that system in the Kohala District, Island of Hawaii, to understand how it worked, and to develop educational materials for the local community.  At the same time, we are studying the biogeochemical context within which that system was embedded, by evaluating soils and biogeochemistry along a rainfall gradient from 280 mm/yr of rain up to 3400 mm/yr.  This summer we will be focusing on the distribution of plants with nitrogen fixing symbioses along the gradient, and determining the fraction of their nitrogen that they derive from fixation

Karen Casciotti & Matthew Forbes—SESUR

Nitrogen Cycling and Loss in the Eastern Tropical North Pacific Oxygen Deficient Zone

The Eastern Tropical North Pacific Ocean (ETNP) contains one of three large natural oxygen deficient zones (ODZs). Nitrogen cycling in ODZs leads to production of nitrous oxide (N2O), accumulation of nitrite, and loss of bioavailable nitrogen from the deep ocean nutrient reservoir. We use stable isotopic measurements of nitrate (NO3-) and nitrite (NO2-) to trace the balance of nitrite oxidation and reduction, which dictates how much bioavailable nitrogen is retained or lost from the region. This summer, we are looking for a student to help process and analyze the isotope ratios of N and O in nitrate samples collected from the ETNP. The project will involve learning nutrient analyses, isotopic analyses, operation of laboratory equipment, and data analysis in Microsoft Excel. Depending on the interests of the student, further data analysis and modeling in Matlab is also possible.

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