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2016 Projects

 ARCHIVE of potential undergraduate research projects

Greg Asner and Emily Francis

Spatial Variation in the Drought Vulnerability of California Redwood Forest

California is home to the tallest, the oldest, and the most massive trees on earth, but the recent drought in California has led to widespread tree mortality across the state’s forests. Droughts are expected to become more frequent as climate change continues, therefore an understanding of the causes of spatial variation in forest vulnerability to drought is urgently needed to locate and protect valuable and threatened forest areas. The goal of the project is to study the causes of spatial variation in the vulnerability of redwood forests to future droughts. We will collect the branches and leaves from redwood trees in multiple different forest sites in California, and then analyze the samples in a lab to assess whether the structure, function, and chemistry of their leaves and branches indicates drought stress. This field data will eventually be paired with airborne remote sensing imagery.

The student will spend approximately four weeks doing fieldwork in California to assist a graduate student in collecting and processing redwood leaf samples, and the remainder of time at Stanford learning lab techniques and analyzing leaf samples. Depending on the student’s interests, the student could focus on a single source of variation in forest drought vulnerability (geology, topography, latitude, or forest age), or an aspect of leaf chemistry (water content, carbon isotope composition, and nitrogen content) and its relationship to tree health during drought. Previous experience doing fieldwork or other outdoor experience would be helpful but is not required. Enthusiasm and ability to work as part of a team are required.

Scott Fendorf, Steve Luby, E. Marie Muehe, Jenna Forsyth

Exploring the mechanism of lead contamination in food in Bangladesh

As a potent neurotoxin, lead poses a serious threat to public health and human intellectual capital worldwide. While there is no safe level of lead exposure for anyone, lead is most detrimental to children when their central nervous systems are still developing, before birth through three years of age.  Even low levels of lead can irreversibly lower IQ. Our past research in Bangladesh has identified food storage in lead-soldered cans as an implicated exposure route. The goal of this project is to gain a deeper understanding of this lead exposure route. We are looking for a motivated student to assist with field research in Bangladesh for 3-5 weeks as well as laboratory analyses of lead concentration at Stanford. In Bangladesh, the student will assist with in-depth interviews of relevant stakeholders and sample collection. The student will also help adapt a quick lead test to the field context as a confirmatory test for lead solder. At Stanford, the student will have the opportunity to conduct experiments that elucidate a possible mechanism of lead transfer from cans to food. If interested, another activity will be desk research to develop a database of information about the global lead industry: production, consumption and trade. Previous wet lab experience is desirable but not necessary.

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

Improving estimates of delta15N-PON in marine systems  

The availability of nitrogen (N) limits the productivity of phytoplankton throughout much of the ocean. As such, understanding the ocean’s N cycle is an important objective marine biogeochemists. The N isotope, 15N, of different marine N pools provides a wealth of information about microbial N transformations. Traditionally, methods for determining the 15N content particulate organic nitrogen (PON) in marine environments involves the filtration of large volumes of water to obtain enough material for accurate measurements using elemental analysis isotope ratio mass spectrometry. Likewise, marine biogeochemists often measure delta15N-PON as a proxy for plankton delta15N content, but in reality, the measurement includes not only phyto- and zooplankton, but also detrital matter. This is a joint project between the Arrigo and Casciotti labs and will explore a new pproach for measuring delta15N-PON that reduces detection limits and potentially allows for determining the 15N content of specific plankton populations.  The approach will combine persulphate oxidation of PON with the bacterial denitrification method for determining the delta15N-NO3-. Likewise, the student will use phytoplankton cultures and potentially flow cytometrically sorted natural samples to determine delta15N-PON of natural populations. Prior experience in the lab would be helpful but is not required. Enthusiasm for lab work, chemistry, biology, and biogeochemistry are absolutely necessary.

Gretchen Daily and Greg Bratman—SESUR

The impacts of nature experience on mood, emotion regulation, and cognitive function

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. We will be conducting experiments that involve human subjects as well as collecting data from pre-existing sources, as we employ a multi-method approach to investigating the role that emotion regulation may have in mediating environmental impacts on psychology.

Eric Lambin and Elsa Ordway—SESUR or SURGE

Measuring direct and indirect drivers of land use change in Cameroon

As agricultural and technological innovations surge, tropical regions continue to serve as a frontier for land conversion to meet global food, fuel, and fiber demands. Researchers have demonstrated the growing influence of global demands for commodities like soy, beef and palm oil on displaced forest conversion and agricultural expansion in South America and Southeast Asia. Yet the extent to which land use change in sub-Saharan Africa is driven by distant demands remains a major uncertainty. How are growing global demands for commodity crops impacting local land use change in sub-Saharan Africa? Ongoing research at Stanford aims to understand these land use and land cover change dynamics in the Central African country of Cameroon using satellite imagery, agricultural statistics, census data and household surveys.

The student collaborating on this project will be actively engaged in the research process, helping with both data entry and analysis. The student will also be supported in developing and testing independent research questions with the data. This project is suitable for students with an interest in GIS, remote sensing, spatial analysis, and economics. No prior research experience is required, although experience with or an excitement to learn R, ENVI and/or GIS software is desirable.

Jenny Suckale—SESUR

Quantifying the protective value of mitigation parks for tsunami risk mitigation

Coastal communities around the world are being encouraged to plant or restore vegetation along their shores for the purpose of mitigating tsunami and storm damage. A common setup for these projects is to develop ‘mitigation hills’ – an ensemble of vegetated hills along the coast – instead of one continuous stretch of vegetation. We have not yet quantified, however, how mitigation hills affect the behavior of the tsunami wave as it reaches the coast.  Because high resolution (and high order) numerical simulations may help better understand these complex phenomena, we have been developing a computational model for fluid flows based on high-order Galerkin methods which we would like to enhance via the use of high order grid generation tools.

There are different ways of getting involved in our work. Possibility to contribute include (i) adding high-order capabilities (i.e. use of curved elements;  this is a topic of active research in the computational fluid dynamics community) of an existing elliptic grid generator designed for domains with real topography, (ii) couple it to the high-order discontinuous Galerkin flow solver that we currently use to study inundation problems, and (iii) run a set of idealized simulations of the inundation caused by a tsunami. For this project, the knowledge of a programming language is recommended (possibly C and/or F90 if possible).

Kevin Arrigo and Matthew Mills—SESUR

New approaches to better understand individual algal cell responses to changing environments

About half of all photosynthesis on Earth occurs in the marine environment through the activities of morphologically and genetically diverse unicellular phytoplankton. These organisms include eukaryotic and bacterial taxa, ranging in size from 0.5µm to 10s of mm in diameter, that maintain different elemental compositions, metabolic capabilities and nutrient uptake strategies. As a group, phytoplankton are critical players in Earth’s carbon and nutrient cycles and form the base of a marine food web that all marine organisms rely on. Individually, different phytoplankton taxa control processes critical to the functioning of the Earth system. For example: 1) under some conditions, silica-containing diatoms in sub-Antarctic waters drew enough carbon dioxide out of the atmosphere to kick-start ice ages, 2) shifts in Antarctic phytoplankton taxa (from diatoms to prymnesiophytes) can double the amount of carbon transferred from the atmosphere to the ocean, and 3) dam construction has decreased silica in river runoff resulting in phytoplankton shifts toward harmful dinoflagellates that conservatively cost the US >$50 million per year alone (globally costs are much higher). Clearly, how different phytoplankton taxa adapt to future environmental conditions will significantly affect our World.

This project will explore two cutting edge techniques to quantify physiological status of individual algal cells.  The first, mass cytometry combines the advantages of single-cell, high-speed flow cytometry with the ability to resolve specific metabolisms (e.g. multiple protein concentrations) in >100k individual cells per day. While the second, explores macromolecular content of individual phytoplankton cells using Raman and Fourier transform infrared spectroscopy.  Both techniques offer great promise for improving our understanding of how multiple taxa respond physiologically to spatial and temporal differences in environmental forcing. Prior experience in the lab would be helpful but is not required.  Enthusiasm for lab work, biology, chemistry, and biogeochemistry are absolutely necessary. 

Gail Mahood and Molly Witter—SESUR

Investigating intermediate volcanics in the “bimodal” Yellowstone system

The oldest portion of the Yellowstone-Snake River Plain volcanic trend, located in northern Nevada and southeastern Oregon, has often been described as a bimodal province, but recent work has identified notable volumes of lavas of intermediate compositions. Bimodal volcanism is the term used to describe the presence of endmember lavas (basalts and rhyolites) and the lack of intermediate compositions (andesite or trachyte) in a volcanic province. We are conducting research in this area aimed at investigating the distribution of the intermediate lavas and their chemistry to try to constrain the relationship of the flood basalts and rhyolites in this region.

We are looking to collaborate with an enthusiastic undergraduate that will help conduct summer fieldwork (2-4 weeks) in northern Nevada and southeastern Oregon as well as get involved in sample preparation and laboratory analysis of the rock samples. The student will have the opportunity to develop a range of field and laboratory-based skills while contributing to our ongoing research. Before fieldwork begins, the student will have the chance to learn about compiling maps using ArcGIS and how to prepare for fieldwork. Some potential project ideas include (1) detailed geologic mapping of volcanic units in areas adjacent to where abundant intermediate lavas have been identified, (2) classification of newly sampled lavas and/or reclassification of previously misinterpreted units using whole-rock geochemistry through energy-dispersive X-ray fluorescence (ED-XRF) techniques, or (3) Nd isotopic analysis of volcanic products to classify the composition of the underlying crust. There is also potential for additional projects utilizing paleomagnetism techniques. Previous field mapping or geochemical laboratory experience is desirable, but not required. 

Eric Dunham and Leighton Watson—SESUR or SURGE

Seismic airgun bubble dynamics

Seismic imaging of oil and gas deposits beneath the ocean uses airguns as the source of acoustic waves. Airguns, towed behind a boat, are filled with pressurized air that is impulsively released to form a gas bubble that oscillates in the water. These bubble oscillations radiate acoustic (sound) waves. Our group has been modeling airgun bubble dynamics through statements of mass, momentum, and energy balances for the compressible gas in the airgun and bubble and for the water surrounding the bubble. The resulting system of nonlinear ordinary differential equations is solved numerically in Matlab. The frequency content of the acoustic waves is influenced by properties of the airgun (e.g., volume and pressure). Our current goal is to find the airgun properties that maximize low frequency waves (which are most useful for imaging) and minimize high frequency waves (that disturb marine mammals like dolphins). This summer project is to extend our modeling capabilities from a single airgun to a cluster of airguns, taking into account wave reflections from the water surface and interactions between the bubbles that occur when acoustic waves from one bubble alter the pressure field surrounding adjacent bubbles. This project requires a strong background in math and physics (ordinary differential equations, mechanics, thermodynamics, waves) and programming (Matlab or similar language). No prior experience in Earth Sciences is required. 

Eric Dunham—SESUR or SURGE

Acoustic-gravity waves in Earth's atmosphere

Explosions and volcanic eruptions excite acoustic (sound) waves in Earth’s atmosphere, which exist due to the restoring force from gas compressibility. But gravity also acts as a restoring force, giving rise to another type of wave known as an internal gravity wave. Gravity waves have been observed after several large volcanic eruptions. This project is to extend our wave propagation code, which can currently only model acoustic waves in an initially motionless atmosphere, to the general case of acoustic-gravity waves in a stratified atmosphere with background winds. The code is written in Fortran 95 and prior programming experience (in any language, not necessarily Fortran) and Unix skills (simulations will be run Stanford’s CEES computing cluster) are required. A strong background in math and physics (differential equations, mechanics, thermodynamics, waves) is also desirable. No prior experience in Earth Sciences is required.

Eric Dunham—SESUR or SURGE

Flexural-gravity waves in ice shelves

Understanding the stability and integrity of ice shelves is essential for predicting the response of the cryosphere to a changing climate. Several large ice shelves have catastrophically disintegrated in the past decade. Monitoring the thickness and material properties of ice shelves is possible using flexural-gravity waves. These are waves in both the floating ice layer and ocean beneath the ice. They involve bending of the ice (and associated elastic restoring forces) as well as gravitational restoring forces. Our group is developing a simulation code for flexural-gravity waves and this project is to explore flexural-gravity wave propagation and excitation by incident ocean waves. The latter is motivated by observations of ice shelf rifting following the arrival of major wave trains from storms or tsunamis. A strong background in math and physics (differential equations, mechanics, thermodynamics, waves) and prior programming experience (in any language) is required. No prior experience in Earth Sciences is required.

Scott Fendorf and Kristin Boye—SESUR or SURGE

Coupling organic matter decomposition to contaminant fate and groundwater quality

Floodplains are important contributors to a number of important environmental processes, such as greenhouse gas emissions, nitrogen cycling and metal contaminant cycling. They are also dynamic landscape features, with complex aquifer systems, offering challenges for understanding the underlying controls on elemental cycles, ranging from nutrients to contaminants. We are working on solving the mystery of persistent uranium groundwater plumes at former ore processing sites on floodplains in the upper Colorado River Basin. It was originally estimated that the uranium plumes would self-attenuate through natural flushing within a couple of decades, but monitoring shows that the elevated concentrations remain >20 years post cleanup. Our investigations so far have revealed that organic matter rich layers and lenses that are interspersed within the coarse-grained aquifer material are responsible for retaining and releasing uranium depending on the redox conditions. Therefore, we seek to resolve the fundamental controls of organic matter on uranium mobility. In particular, we need to determine the organic carbon compounds serving as fuel for microbially mediated processes that control both the fate of uranium but also the production of greenhouse gases. We are looking for 1 to 2 enthusiastic students to study the rates of organic matter decomposition in relation to different environmental conditions and help decipher which bacterial metabolic pathways are preferentially being stimulated. Students will conduct laboratory incubation experiments using natural sediments from uranium contaminated floodplain aquifers in the Colorado River Basin, and will become familiar with a multitude of different instruments and laboratory techniques. Previous wet laboratory experience is desirable, but not required.

Scott Fendorf and E. Marie Muehe—SESUR or SURGE

Assessing outcomes of rice cultivation on arsenic-contaminated paddies under a changing climate

With more than 50% of the global population consuming rice daily, rice is the staple food worldwide. Unfortunately rice productivity is postulated to decrease drastically due to climate change. Today’s rice productivity models for the year 2100 are based on higher annual temperatures and doubled atmospheric CO2 concentrations but do not include the presence of toxic arsenic in paddy soils of the biggest rice producing regions of the world. However, arsenic is currently being enriched in Asian paddy soils via irrigation with arsenic-bearing ground water. Within the soil, arsenic moves between the soil solution and the solid phase as a consequence of the prevailing environmental conditions. The mobile fraction of arsenic is easily taken up by rice plants and enriches in the grain, thereby not just reducing rice productivity but also grain quality. The goal of this project is to asses to what extent elevated temperature and atmospheric CO2 (parameters of climate change) affect the mobility of arsenic within rice paddies and ultimately arsenic uptake and accumulation in rice. To this end, the geochemistry of the soil solution and the release of greenhouse gases and volatile arsenic species will help to understand the fate of arsenic within the soil-rice-atmosphere continuum. A motivated student would be required to independently maintain rice pot experiments in greenhouses with different climates and collect and analyze pore water and atmospheric samples throughout the growth period of the rice. Previous laboratory experience in geochemical or environmental science would be useful.

Roland Horne and Jack Norbeck—SESUR or SURGE

Designing Strategies to Manage Injection-Induced Earthquakes

In 2014, the rate of magnitude 3 and larger earthquakes in Oklahoma exceeded that of California for the first time in recorded history. Other areas in the central and eastern United States that were previously considered at low risk of earthquake activity have also experienced unprecedented increases in observed seismicity in recent years. There is now a general consensus that many of these earthquakes have been associated with the disposal of large volumes of saltwater through injection into deep subsurface aquifers. Oil and gas regulators are actively placing restrictions on disposal wells that are thought to be linked to significant earthquake events, but there is not a clear procedure for how to most effectively manage injection well operations in order to reduce the seismic hazard.

In this project, an enthusiastic undergraduate will use a newly developed reservoir simulator to investigate how managing injection well flow rates and pressures influences seismicity. The student will test several operational response strategies that are currently being considered by regulatory bodies in order to quantify their effect on mitigating induced seismicity. Based on the results of the numerical experiments, the student will design and test an alternative management plan. This project is suitable for engineering and physical science majors, or students with an interest in math, physics, and their application to energy problems. Introductory mechanics of materials and fluid mechanics is recommended, and prior programming experience is desirable.

Eric Lambin, Tannis Thorlakson and Joann De Zegher—SESUR

Understanding Sustainable Sourcing Practices in the Food and Agriculture Sectors

Many large corporations, from Heinz to Whole Foods, have made significant commitments to source agricultural goods from sustainable sources. Yet each company has a different approach to defining ‘sustainably sourced.’ How are companies currently sourcing these goods? What are companies’ motivations for making sustainability commitments? This research, in combination with ongoing research at Stanford, will help to understand how sustainable sourcing commitments are impacting farmers, firms and consumers.

We are looking to collaborate with an undergraduate to conduct text analysis over the summer to address the questions outlined above. The student will play an active role throughout the research process, from data collection to analysis. The student will also be encouraged to develop and test additional hypotheses that emerge from the data. No prior research experience is necessary, but an excitement for the research topic and willingness to master new skills is required. 

Interested students should send a paragraph of interest and CV to Tannis Thorlakson directly at thorlaks (at) no later than Friday, Feb 12th. 

David Lobell and Meha Jain—SESUR or SURGE

Satellite mapping of agricultural regions

Food security is becoming increasingly threatened due to climate change, a growing population, and natural resource degradation. This is particularly true in India, which will likely become an increased food security hotspot over the upcoming decades. In order to identify which factors lead to reduced yields or potential interventions that may enhance food security, it is important to examine and obtain crop statistics to understand what factors are associated with high versus low yields through time. To do this, to date a large proportion of studies have relied on coarse-level district statistics provided by governments. However, satellite imagery can provide fine-level statistics, at the scale of a village or even individual fields. This project will work to quantify wheat and rice yields in Northern India using satellite imagery (e.g. Landsat, new high resolution microsatellites). We will then use this information to understand what factors (e.g. soil quality, irrigation access) are associated with low versus high yields and identify possible interventions (e.g. improved fertilizers) to enhance yields in this region. The student on this project will help us with any or all of the following: run crop models, process high-resolution satellite imagery, apply algorithms to satellite imagery to predict yield, and clean and process yield data from the field. Ideally the intern will have experience with or is excited to learn about using GIS, R project software, and/or crop models.

Kate Maher and Matthew Winnick—SESUR

Dynamic links between subsurface water and carbon in the Rocky Mountains

Soils, floodplains, and shallow aquifers are the least understood components of the global carbon cycle, yet they represent the largest reservoir of terrestrial carbon and are highly sensitive to shifts in climate, vegetation, and the resulting water balance. Small changes in the storage and cycling of carbon in the subsurface therefore may have very large impacts on the Earth’s climate system. We are currently conducting research at the Rocky Mountain Biological Laboratory (; Gothic, CO) aimed at addressing this critical knowledge gap by describing the interactions between water and carbon in the subsurface to better understand their sensitivity to future change. We use research techniques across a range of disciplines including stable isotope biogeochemistry, hydrology, microbial ecology, and GIS, and combine fieldwork with laboratory analyses and quantitative models.

An enthusiastic undergraduate will spend the summer conducting field research at the RMBL field station in Colorado and will have the opportunity to develop a range of projects to contribute to our ongoing research. Potential projects include (1) measurement of soil gas fluxes (CO2, CH4, H2O, N2O) across a range of scales within the East River watershed; (2) high spatial/temporal resolution stream chemistry measurements to characterize processes such as the effects of summer storm events on solute fluxes and topography on stream CO2 degassing; (3) soil description surveys across ecosystems, topography, aspect to characterize soil carbon stocks and guide hydrologic subsurface flow models. Projects will all involve a strong field component with ample opportunity to explore laboratory work and quantitative hydrologic and geochemical models depending on the student’s interests.

Paul Segall and Andreas Mavrommatis—SESUR or SURGE 

Testing for changes in vertical deformation rates before the Tohoku earthquake using GPS

The devastating 2011 magnitude 9 Tohoku-oki earthquake occurred offshore northeastern Japan, one of the most tectonically active and instrumented regions in the world. For two decades, Japan has operated a dense network of geodetic Global Positioning System (GPS) stations, which measures precisely how the Earth’s surface deforms in space and time in response to tectonic processes (plate motion, earthquakes, etc.). After analyzing horizontal position time series, we found that the rate of deformation in the period 1996 to 2011, prior to the Tohoku earthquake, did not accumulate at a constant rate as expected, but instead decreased by 30%. This change can be explained by an acceleration of slip on the fault that generated the M9 earthquake, an upward migration of the depth at which the fault transitions from partially locked to freely slipping ("transition depth"), or a combination of the two. However, the horizontal data allow for a wide range of models, and it is well known that vertical geodetic data can place tighter constraints on the transition depth and its temporal change. We are looking for a summer intern who will analyze vertical GPS time series from the Tohoku region in the period 1996-2011. The goals are: estimating average vertical deformation rates; looking for evidence of accelerating motion; and integrating the results with the previous analysis of the horizontal data. If the time series show evidence of acceleration this will help constrain further the spatial distribution of slip acceleration on the fault. The student will use MATLAB codes originally developed for analyzing the horizontal data. Prior programming experience and basic linear algebra knowledge is expected. The student will gain experience in working with GPS data, time series analysis and applied statistics, as well as basic models of crustal deformation and fault mechanics.

Erik Sperling—SESUR or SURGE

Environmental change in deep time and its effect on animal evolution

The Paleozoic is one of the most interesting times in Earth history, and during this interval there were important evolutionary milestones including major increases in animal body size and species-level diversity, the appearance of the first coral reefs in the geological record, the rise of fish, and the colonization of land by marine vertebrates. These evolutionary landmarks occurred against a backdrop of dramatic environmental change, including oxygenation of the oceans and several glacial events. There are currently many hypotheses relating environmental change to organismal evolution, but there have been few analyses directly relating the two in a statistical framework. This has been in part due to the lack of sufficient data from these time intervals.

In this laboratory-based sedimentary geochemical study, and student will work towards building a more complete record for either the Ordovician or Silurian periods. The student will analyze sedimentary rock samples (shale) from northwestern Canada, Great Britain, and the United States for their iron, carbon and sulfur geochemistry, and major- and minor-element composition. The student will learn the basics of sedimentary geochemistry and paleoenvironmental reconstruction, and will ultimately compile their data with other published data to compare against the paleontological record. There are no formal requirements for the research project, but background in Earth history and paleontology, sedimentary geochemistry, and the software package R will all be useful.  

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.

Marty Grove, D.K. Kimbrough, and Ziva Shulaker-SURGE

"Timing of Post-Laramide Erosional Denudation of the northern Peninsular Ranges batholith"

Detrital thermochronology to constrain basement erosion histories compliments direct measurements of presently exposed basement in that sedimentary rocks preserve a record of all previous erosional surfaces. Under the supervision of Drs. D.K. Kimbrough and Marty Grove, the student will collect three medium- to coarse-grained sandstone samples - one each from the base, middle, and top of the Silverado Formation in early April, 2016.  Sampling will be performed within the context of previous sampling for detrital zircon.  Based upon previously measured detrital zircon U-Pb age distributions, it is expected that K-feldspar age distributions yielded by samples at progressively younger stratigraphic positions within the Silverado Formation will record progressively slower denudation at the tail end of the Laramide phase of rejuvenated erosion of the batholith as expressed by a reduction in the lag time between K-feldspar 40Ar/39Ar and zircon U-Pb age distributions.  Standard crushing, sizing, hydrodynamic, density, and magnetic methods will be applied to concentrate basement K-feldspars from the sandstone using existing facilities at San Diego State University during the month of April.  If time permits, additional materials will also be produced from four previously sampled locations described in Lovera et al. (1999).  These mineral separates with be prepared for neutron irradiation at the USGS Triga reactor in Denver for irradiation in May 2016.  All irradiated material will be handled by M. Grove.  Once at Stanford University, the student will be instructed in the basics of 40Ar/39Ar analysis including how to program automated runs and reduce data and plot results.  Instruction in basic statistical analysis of the results will be provided by Grove and graduate student Ziva Shulaker.  The K-feldspar grains from the Silverado Formation will be analyzed using two different methods at Stanford University.  Most grains will be fused to obtain total gas (= K-Ar) age distributions.  Approximately 120 grains per sample for each of the three samples will be analyzed in this fashion.  An additional 20 grains per sample will be incrementally heated to produce detailed age spectra.  This analysis is estimated to require two weeks.  An additional two weeks will be required to interpret and model the results using previously developed numerical approaches with assistance provided by Grove and Shulaker.  The remaining time will be spent: (1) preparing a report describing the results and interpreting them in terms of the tectonic history of the Northern Peninsular Ranges batholith; and (2) preparing a poster presentation of the results.

Chris Field and Katharine Mach-SURGE or SESUR

Assessing Global Climate-Change Risks at 1.5°C to 2°C Temperature Increase

The December 2015 Paris agreement under the United Nations Framework Convention on Climate Change (UNFCCC) fixed a spotlight on climate stabilization at 1.5°C to 2°C above preindustrial levels. With the agreement, mitigation ambition intensified at the global scale: the long-term goal is now to hold global temperature increase to well below 2°C, while pursuing a limit of 1.5°C. Next steps, as the world marches forward with climate responses, will depend on understanding and communicating climate-change risks at 1.5°C to 2°C warming.

A compelling but incomplete scientific foundation underpins the tightened global temperature goal.  The risk assessment in the Intergovernmental Panel on Climate Change’s Fifth Assessment Report (IPCC AR5), provides a starting point, but it however, primarily contrasted outcomes in a world of continued high emissions (~4°C warming by the end of this century), as compared to ambitious mitigation (~2°C), based on available literature.  Refining the focus to contrast 1.5 and 2 will require a more sophisticated approach to the concept and interpretation of risk.

We are looking for a motivated student to undertake a synthesis on climate-change risks in one category (probably climate extremes or economic impacts) and analyze the projected impacts as a function of warming in the range of 1.5 to 2 through one of the sophisticated risk evaluation methods (for example, maxi-min or robust decision-making).  The project will provide an introduction to the broad area of climate-change impacts and a deep dive into next steps in refining the long-term climate goal under the UNFCCC.

Chris Francis and Bradley Tolar – SESUR or SURGE

Seasonal Dynamics of Nitrogen-Cycling Microbes in Monterey Bay

Monterey Bay is a dynamic system to study microbes, with shifts in nutrient abundance and primary production due to seasonal changes and upwelling.  Our lab focuses on the marine nitrogen cycle, which is driven by microbes, and specifically nitrification (oxidation of ammonia to nitrate).  We have collected samples from two locations in Monterey Bay for the past two years, and have quantified seasonal changes in nitrifying microbial communities.  This project will query other nitrogen transformations through functional gene-based quantitative PCR to get a glimpse of how the nitrogen cycle changes over time in Monterey Bay.  In addition to PCR, this project can involve a variety of techniques that are widely used in microbial ecology and other fields, including: DNA extraction, cloning, DNA sequencing, bioinformatics, chemical measurements (concentration of nitrogen compounds), stable isotope measurements (nitrification rates), and culture work.  Prior laboratory experience in molecular techniques or analytical chemistry is helpful but not required, and an enthusiasm for environmental science and microbiology is necessary.

Scott Fendorf and Hannah Naughton-SESUR or SURGE

Identifying chemical and biological factors controlling soil carbon storage and greenhouse gas emission

Soils play a critical role in the global carbon (C) cycle, storing more carbon than either the atmosphere or ocean.  In fact, soils store twice the amount of carbon in the atmosphere and Earth’s surface biomass combined.  It is imperative that we understand how soil carbon will respond to new temperature and precipitation regimes as climate change progresses.  Going into the future, will soils serve as a carbon sink that mitigates the negative effects of atmospheric CO2, or will soils release greenhouse gases and contribute further to climate change?  Microbes control carbon decomposition and thus greenhouse gas emissions from soil, but how rapidly microorganisms break down soil organic matter and release it as greenhouse gases is still poorly understood.  Past decomposition models based on carbon chemistry poorly predict soil carbon flux.  This project will therefore explore which chemical, biological and physical factors are most important for controlling carbon cycling in soils and parameterizing the next generation of soil carbon models.  We seek an enthusiastic student to carry out laboratory experiments using soil reactors.  The experiments will include reactor construction, sampling, chemical analysis, and data interpretation with the possibility of modeling.  We also have opportunities for a mechanical/electrically-oriented student interested in advancing an imaging system for capturing the anaerobic zone of soils.  The student will gain experience in environmental analytical chemistry and microbiology, and may have an opportunity to travel with the mentor to the Pacific Northwest National Laboratory to design and fabricate experimental equipment and perform micro-scale measurements. 

Adam Brandt and Emily Grubert-SESUR

How do communities prioritize social and environmental outcomes of energy development?

Large energy infrastructure, like oil fields, coal mines, and power plants, is societally necessary – but it is often socially and environmentally disruptive. Residents of areas affected by energy development note negative outcomes like increased traffic burden, crowding, and environmental degradation. Positive outcomes like increased diversity in relatively isolated towns, higher wages, and bigger local budgets also occur. However, at the national policy making level, details about local community priorities and tradeoffs are often lost, resulting in a separation between those making decisions and those affected. This project investigates how communities prioritize outcomes, with the goal of integrating that information to a decision support tool known as life cycle assessment to help improve policy and project designs. Up to two undergraduates are sought to aid in analysis of survey and interview data collected from community members in US and Australian regions that are currently undergoing large scale energy development. The ideal student enjoys having some freedom to make decisions (though help will be available!) and is interested in integrating social science and earth science. Especially if you think you might want to conduct a survey or interviews some day, this project will offer a great opportunity to learn how data are collected and help design and implement an analysis plan.  

Scott Fendorf and Sarah Fakhreddine-SESUR or SURGE

Determining groundwater quality changes during managed aquifer recharge

Recent widespread droughts have created a pressing need to diversify freshwater sources and develop innovative technologies to ensure water security. An increasingly popular technique to enhance local groundwater supplies is the use of Managed Aquifer Recharge (MAR). MAR projects have the potential to alleviate water deficits; however, they can also adversely impact groundwater quality by altering the native geochemistry of the aquifer and triggering the release of toxic contaminants native to the aquifer sediments. Naturally occurring contaminants of concern include arsenic, uranium and vanadium. Desorption and subsequent mobilization of these contaminants poses a serious challenge to maintaining local groundwater quality, and thus also to ensuring the viability of MAR as a water enhancement strategy. The goal of this research is to understand mechanisms of contaminant release to groundwater within managed aquifers, and to develop tools to aid in the prediction and prevention of arsenic release to groundwater. During this project, we will use laboratory experiments with aquifer sediments to simulate the effect of MAR with various recharge water chemistries. Additionally, depending on the student’s interests, the project can involve quantitative modeling of contaminant transport. Laboratory experience is beneficial, but not required.

Jonathan Payne and Xiaowei Li - SURGE

Assessing the impact of carbonate factory type on platform morphology

Carbonate platforms can be generally subdivided into high-relief rimmed shelves and low-relief carbonate ramps. A long-standing hypothesis states that “reef” development at margin-slope facies might transit low-relief ramp into high-relief shelf. Yet, the degree to which different carbonate factories that compose the reef (e.g. skeletal vs microbial factory) influence platform morphology remains poorly-constrained. Our project goal is to explore the relationship between carbonate factory types at margin-slope facies and their impact on platform morphology (e.g. height, width, slope curvature). This project plans to investigate the geometric parameters of different carbonate platforms from outcrops and subsurface analogs of different geologic ages through published literature and our studied outcrop analogs. No prior experience in Earth Sciences is required.    

Rebecca Niemiec and Anna Lee-SESUR

Understanding Residents' Engagement with Environmental Stewardship near the Arastadero Preserve

We are looking for a student interested in environmental behavior to work with us on a community engaged research project with Acterra (, an environmental education and action non-profit. The project will involve surveying and interviewing residents near the Arastadero preserve in the City of Palo Alto to understand residents' current engagement with the preserve and in environmental behaviors that may influence the preserve (such as weed control and taking actions on their property that influence the preserve's wildlife, such as bobcats). Specifically, we are hoping to understand: What are the barriers and motivators influencing neighbors' engagement in stewardship behaviors that influence the Arastadero preserve? How do neighbors conceptualize their relationship with Arastadero and Acterra, and how might their perceptions of and use of the reserve influence their behaviors on their own property? We are looking for someone who feels comfortable engaging with interviewees, including going door to door to hand out surveys and conduct interviews. The ideal candidate should also be willing to transcribe interviews and conduct analyses of interview and survey responses. 

Adam Brandt, Arvind Ravikumar and Jingfan Wang-SURGE or SESUR

Mitigating Methane Leakage For Natural Gas Sustainability

Methane is a powerful greenhouse gas (GHG). With the development and rapid growth of the unconventional gas from hydraulic fracturing (‘fracking’) industry, methane leaks from the US natural gas (consisting mainly of methane) infrastructure will contribute an increasingly larger percentage to US emissions. However, there are currently very few policies that regulate the amount of leakage that is considered ‘acceptable’. This is partly because, until recently, scientists and policy makers were not aware of the magnitude of the problem. Also, there is currently no consensus on the most cost-effective strategies to detect and repair leaks.

In this project, we will be analyzing the effectiveness of a leak detection technology – infrared optical gas imaging. We are looking to collaborate with 2 students to develop models and assist with experimental evaluation of optical gas imaging. The student(s) will help us better understand the limitations and advantages of infrared imaging techniques through simulation, modeling and experimental work. One student will focus on experimentation, while another will focus on modeling and simulation. This project is suitable for STEM majors, and students who have a broad interest in understanding how scientific results can be translated into policies. Prior experience with Matlab is a plus.


For SURGE inquiries please contact or call 650-724-6250.  If you have SESUR questions, please contact Undergraduate Program Director Sara Cina or call her at (650) 724-8899.

Page updated on January 31, 2016.