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2019 Projects

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Understanding social-ecological rural transitions on rangelands in the American West through archival data and remote sensing

Mentors: Prof. Eric Lambin (ESS) and Briana Swette (PhD Candidate, E-IPER)
SESUR only

The use of rangelands in the American West is changing as part of an ongoing rural transition. Extensive ranching and livestock grazing are declining in some very rural places, while population grows, and exurban residential development expands explosively in other parts of the rural West. What are the impacts of these changes on ecosystems and communities? This project seeks to address this motivating question by looking closely at an ongoing rural transition in one region of the Northern Rocky Mountains—Idaho’s High Divide. We are currently investigating how extensive livestock grazing has changed across the landscape, the ecological impacts of that change, and the social and governance responses.

We are looking for a student to support an analysis of tree cover change using remote sensing techniques on historical and current aerial images. Previous experience with (or desire to learn) GIS, R, and/or image analysis software (e.g. ENVI, Google Earth Engine) will be helpful. Most of the work will be based on campus, but there might be an opportunity for fieldwork in Idaho’s Northern Rockies. The student will be encouraged and mentored to develop their own line of inquiry related to the overarching project if desired. Opportunities to continue work during the 2019 spring quarter or subsequent academic year might also be available. This is a great opportunity for students interested in remote sensing, GIS, landscape ecology, rural geography, and coupled human-natural systems.

Analyzing the coverage of a global network of flux towers to estimate methane emissions from wetlands

Mentors: Prof. Rob Jackson and Postdocs Gavin McNicol, Etienne Fluet-Chouinard
SESUR only

Wetlands are the largest natural source of methane, a powerful greenhouse gas, to the atmosphere. Despite their outsized importance, the global methane flux from wetlands is highly uncertain and field measurements are needed to better constrain this carbon flux across the world. Eddy flux-covariance towers are among the most reliable tools to measure ecosystem-level carbon fluxes. We compiled a large database of methane fluxes from sites across the world to produce a global map of wetland methane emissions using machine learning methods trained on these tower measurements. Generating reliable predictions of methane emissions over the global land surface requires a representative network capturing the full range of environmental conditions relevant for methane production (e.g. vegetation type, soil temperature, soil carbon content, surface hydrology).

We are looking for a motivated student with a background in environmental/earth science, statistics, and/or computer science that will develop and apply geostatistical methods to compare tower sites and globally-gridded remote sensing data. Day-to-day tasks will involve developing scripts for data exploration, analysis and visualization on a high-performance computing cluster. We will also plan 1-2 daylong fieldtrips during the summer to visit nearby flux tower sites. Preference will be given to a student familiar with scripting languages (e.g. preferably R, but also Python or MATLAB), and experience with geospatial data processing (e.g. GIS, remote sensing), machine learning.

The Effect of Groundwater Flow Rates on Naturally-occurring Trace Metal Mobilization 

Mentors: Prof. Scott Fendorf (ESS), Randall Holmes (PhD Student E-IPER), and Bobby McLean (MA Student SS&P)

With 30-46% of California's water demand met through groundwater, the impact of groundwater pumping on groundwater quality will become of increasing concern. California's Sustainable Groundwater Management Act (SGMA) of 2014 requires avoiding the undesirable result of degrading groundwater quality as one of the metrics for achieving sustainability. This will be especially important for California's irrigated agriculture, which according to the United States Geological Survey, used 18.9 billion gallons (71.5 million cubic meters) of water per day in 2015. As such, understanding the impacts fluctuating flow rates may have on groundwater quality will aid in developing best practices that avoid some aspects of degraded water quality, such as mobilizing naturally-occurring trace metals. The extraction of groundwater from aquifers that contain naturally-occurring trace metal elements, such as arsenic, vanadium, and uranium, has been shown to be sensitive to changes in acidity (pH), reduction/oxidation (redox) potential (measured as Eh), temperature, dissolved oxygen, organic carbon, other oxidizing chemicals, and residence time.

The objective of this study is to gain understanding of flow rate impacts on trace metal mobilization in aquifer systems. This is to assist in developing data on the natural background concentrations of these trace metals for select aquifers, and the geochemical conditions that lend toward (or prevent) degraded water quality. This project has both fieldwork and laboratory components. Fieldwork will periodically be conducted which entails collecting water and aquifer sediment samples at locations throughout California. The laboratory experiments will examine how fluctuating flow rates affect the mobilization of naturally-occurring trace metals. Multiple column flow experiments will be conducted by collecting water and sediments from the same location, and then flowing that groundwater at representative flow rates found near irrigation wells through the collected sediments. Trace metal concentrations in the column effluent and sediments will be monitored using a variety of techniques to include ultraviolet-visible spectrophotometry, inductively coupled plasma mass spectrometry (ICP-MS), X-ray diffraction (XRD), and X-ray fluorescence (XRF). Additional experiments may include introducing incremental changes in pH and/or Eh, or possibly introducing common contaminants such as those found in agricultural fertilizers and/or pesticides.

Basic understanding of college-level chemistry is recommended. The student will develop basic lab skills and will be expected to complete some repetitive (monotonous) tasks. No prior experience is required.

LCIG (Leave the Carbon in the Ground) Vitalization of Abandoned Oil Wells for Heat and Electricity Production 

Mentors: Prof. Roland Horne and Kewen Li (Senior Scientist)

Hundreds of thousands of oil wells have been or will be abandoned around the world. Yet a very large amount of oil still resides in abandoned reservoirs because of technological and economic limitations. The residual oil saturation is usually more than 40%. Both economic, climate and social benefits will be significant if these abandoned residual oil reserves could be vitalized for heat and electricity production.

The main idea of this project is to convert the abandoned or being-abandoned oil wells into thermal energy producers. The mechanism behind this would be to generate high temperature up to 350oC by using in-situ combustion, injecting air in order to oxidize a small part of the remaining immobile oil to generate heat that can be brought to the surface in the form of steam. Water could be injected after the high temperature zone has developed, or in many cases may be present naturally. High temperature and high-pressure steam will be produced for electricity generation. Hence the energy content of the abandoned or being-abandoned oil wells can be recovered, leaving the carbon in the ground and bringing only the energy to the surface in the form of heat.

In this project, the student will model the process of heat production by in-situ combustion as well as the recovery of the artificial geothermal energy for electricity generation and direct use of the heat. The student will also perform economic analysis for the system of artificial generation of heat and electricity. Some programming experience in Matlab or numerical simulation (for example, using CMG Star) is preferred, but most of the necessary skills will be developed during the project.

Investigating shock-metamorphism in meteor impacts

Mentors: Prof. Wendy L. Mao and Dr. Arianna Gleason

The objective of this project is to improve our understanding of the mechanics of deformation in shocked-materials. During a collision between two bodies, impact or shock wave metamorphism produces fracturing, and forms high-pressure mineral phases. As the second most abundant mineral in the Earth’s crust, SiO2 plays a fundamental role in meteor crater and planetary body collision mechanics, and we have been examining the behavior of quartz and quartzite under shock-compression to explore the phase transition kinetics and grain growth evolution. Our preliminary results indicate that we have evidence of pressure-induced amorphization of SiO2, with planar features that are associated with fracturing. However, the onset of amorphization and evolution of quartz across the transition from elastic to plastic still needs to be confirmed.

We are looking for an enthusiastic student to measure signals of different structures on shock-compressed SiO2 single crystals. The student will have an opportunity to perform Raman measurements on the samples and characterize the different structures formed from shock conditions. These measurements will be compared with the X-ray Laue transmission diffraction data, which will also be analyzed by the student with the help of their mentor. Some prior experience with data analysis and scientific programming skills, such as Python or Javascript are desirable.

Exploring the controls on global soil organic carbon storage

Mentors: Prof. Rob Jackson and Postdoc Katerina Georgiou

Soil organic matter (SOM) is the largest terrestrial pool of actively-cycling carbon, containing over three times the carbon in vegetation and over two times that in the atmosphere. The storage and cycling of SOM are governed by many co-varying factors, including climate, plant productivity, mineralogical properties, and disturbance history. Yet, it is still unclear which factors, and under what circumstances, drive observed SOM stocks and spatial variability. Elucidating these controls is essential for better informing Earth system models (ESMs) and making predictions under novel future conditions. 

This project will primarily involve data collection, processing, and analysis. Students will work with large globally-distributed datasets and/or ESM output, and will learn statistical techniques to analyze and draw significant conclusions from these datasets. Independent projects co-developed with the mentors are also possible, with an opportunity for projects to evolve with the students' interests as the summer progresses. 

Students with backgrounds and training in environmental/earth science, statistics, and/or computer science are encouraged to apply. Strong quantitative skills and experience with (and/or a strong desire to learn) programming languages (e.g., R, Python, MATLAB) are required. Students will also be mentored in science writing, with the opportunity to submit an abstract to a major conference at the end of the summer.

Do bacteria require sterol molecules to survive?

Mentors: Prof. Paula Welander, Jeremy Wei, Malory Brown, and Alysha Lee

In this project, students will use molecular biology techniques to determine if geologically relevant lipids are required for growth in bacteria. Sterols are lipid molecules that can be preserved in the geologic record for billions of years as sterane biomarkers. Given the important role of sterols in the physiology of eukaryotes, steranes detected in ancient sedimentary rocks are considered robust biomarkers for the occurrence of eukaryotic organisms deep in time. However, we have shown that bacteria can also produce sterol lipids and what significance sterol production by bacteria has on our interpretation of sterane signatures remains unclear. To address this, we need to better understand sterol physiology in modern bacteria.

Our preliminary data suggests that sterols are essential for growth in the methane-consuming bacterium Methylococcus capsulatus. To test this hypothesis, students will attempt to delete genes required for sterol synthesis in M. capsulatus. This project will teach students how to grow microbes in the lab, how to delete genes in bacteria, and how to utilize mass spectrometry to detect and measure sterol production. This is an excellent opportunity for STEM students from diverse fields who are beginning to explore the field of Earth and environmental sciences to experience the interdisciplinary nature of geobiology research. Prior experience in a microbiology lab would be helpful but not necessary.

Is the Past a Key to the Future? What Can We Learn from past Enhanced Geothermal Systems Projects?

Mentors: Prof Tapan Mukerji and Ahinoam Pollack

Sixty-five percent of greenhouse gas emissions result from fossil fuel combustion and industrial processes. To mitigate global warming, we must reduce the use of fossil fuels and transition into low carbon renewable energy sources. Geothermal energy is a clean renewable energy that can complement fluctuating renewable sources by operating at times when there is insufficient contribution from solar and wind energy.

Currently, geothermal energy is based on hydrothermal systems. Natural hydrothermal systems are rare, limiting the growth potential of the geothermal energy sector. First tested in Los Alamos National Laboratory in 1972, Enhanced Geothermal Systems (EGS) open the opportunity to engineer geothermal systems in locations without a natural geothermal system.

Enhanced Geothermal Systems have since been tested in 47 sites worldwide. Important lessons have been learned from each one of these projects; however, this knowledge is scattered in different papers in the published literature, making it difficult for people to access information that would lead to the development of new EGS projects. The most crucial lessons from these sites are often not even published since people do not publish information regarding mistakes.

In this project, we are collecting the lessons learned from these EGS projects to help developers and researchers better plan EGS projects. These lessons will help ensure EGS projects do not repeat past operational mistakes of other EGS projects and share the successful strategies in developing EGS projects.

We are looking for a student to research these EGS sites. Specifically, the student will review published literature, interview people who participated in EGS projects, compile statistics from different sites, write short reports on findings, and build a web site that presents information and findings. A student working on this project will have the opportunity to co-author a journal paper and perhaps present the results at a conference.

Biogeochemical Characterization in Soils of a Uranium-Contaminated Floodplain

Mentors: Prof Chris Francis, Dr. Bradley Tolar and Dr. John Bargar

Microorganisms play key roles in mediating biogeochemical cycles, especially in soils.  In addition to abiotic chemical reactions, microbes can impact the availability of metals, nutrients, and other important chemicals.  Our study focuses on a uranium-contaminated floodplain in Riverton, WY, and examines how seasonal changes in soil conditions (including soil moisture content, temperature, and oxygen availability) impact biogeochemistry in soils.  We have collected samples over multiple seasons under varying conditions at Riverton, and aim to use this data to develop predictive models for understanding water quality in impacted aquifers.  Our goal is to incorporate microbial community data into these models, using sequencing data collected from one field season at multiple depths to determine which microorganisms may be driving a given biogeochemical process.  This will allow us to characterize how seasonal microbial community changes impact water quality at the site.

The student will conduct microbial and chemical analysis of samples involving molecular biology (ex: DNA and RNA extraction, PCR, sequencing) and geochemistry approaches (ex: measurement of dissolved and solid-phase metals and carbon).  Prior laboratory experience is not necessary;  background knowledge in (micro)biology, (geo)chemistry, or Earth sciences is desirable.

Increasing environmental engagement through learning about changing fog patterns in coastal Redwood forests 

Mentors: Professor Nicole Ardoin, Dr. Diane Matar, and Emily Williams

This project brings together natural and social scientists to explore how shifting fog patterns on California coast are affecting redwoods ecosystems. As the social-science partners, we are examining how learning about potential impacts of fog-related shifts, through direct, place-based experiences, might affect visitors' climate-related perceptions, attitudes, and behaviors. 

We are looking for an enthusiastic undergraduate who will help with fieldwork, data analysis and data summaries. Fieldwork will be based in Bay Area redwood parks. Data will be collected through surveys and observations to measure changes in visitors' climate-related perceptions, attitudes, and behaviors in local redwood parks. Previous experience with fieldwork and data analysis software (NVivo or R) is preferred but not required. The ability to participate in a team and maintain a good attitude during inclement weather is necessary. The student will gain experience in fieldwork, quantitative and qualitative data analysis and organization, and working with a research team on a large-scale project.

Strategies for Connecting Research and Practice for Improved Environmental Literacy

Mentors: Prof. Nicole Ardoin, Dr. Mele Wheaton, and Emily Williams
SESUR only

The aim of this ongoing project is to train a cadre education professionals who have the knowledge, skills, and tools needed to deliver high-quality environmental education in formal and non-formal settings and to strengthen the environmental education field. To facilitate uptake and use of environmental education research by educators in the classroom as well as non-formal settings, we are developing workshops focused on the research-and-practice connection. We are using design-thinking strategies to create an innovative approach to these workshops. The initial design-thinking workshop, hosted at Stanford’s, involved a range of researchers and practitioners in a 2.5-day session to develop out-of-the-box thinking and approaches to connecting practice and research. The outcomes formed the core of the EE Research and Practice (EERAP) Workshops, which we have been offering in person, both regionally (in the San Francisco/Monterey Bay Areas), though our partners at ChangeScale, as well as nationally, at the NAAEE conference. We are also developing an online course that will synthesize in-person workshops.

We are seeking a motivated student interested in environmental education who will join our team to help evaluate and research the efficacy of our workshops and online course. The student will assist in conducting interviews with participants and in analyzing both qualitative and quantitative data.

GIS, Geochemistry & Geothermometry of Himalaya/Tibet to understand Continental Collision of India with Asia

Mentor: Prof Simon Klemperer 

Earth’s highest mountains and largest plateau, the Himalaya and Tibet, are created by continental collision between the Indian and Asian tectonic plates.  Many disagreements surround the details of the ongoing collision as it has evolved from initial contact 57 million years ago, including whether the Indian plate has been pushed horizontally beneath the Indian plate to double the crustal thickness; or whether the Indian plate subducts more steeply into the deep mantle.  Tibet is geologically active today, as signaled by hundreds of hot springs that span an area comparable to the western USA.  These hot springs contain a geochemical and isotopic fingerprint of underlying structure and process.  Over the last five years Stanford expeditions have sampled over 100 thermal springs across Himalaya/Tibet, many never previously visited by scientists, to develop the largest most comprehensive database yet available (see The student will search for patterns in temperature, pH, major and minor elements, H, He, C and O isotopes, and for correlations with local geology, topography and structure, regional tectonics, and geotectonic evolution of the Himalaya and Tibet.   S/he will analyze, visualize and interpret these patterns and correlations. Work will be computer-based, at Stanford or remotely.  

The ideal candidate (and unrealistic) is an expert in geochemistry, GIS, tectonics, and spatial geostatistics, with a comprehensive knowledge of regional geology and geophysics of Tibet and the Himalaya, and will read Chinese fluently. But that person doesn’t exist anywhere, so please apply if you have even minimal knowledge of some of these things, a willingness and interest to learn some of the others, and are ambitious to carry out original scientific research at or beyond a summer internship.  Appropriate for freshmen through seniors. Can be an 8-week or a 10-week project.  Suitable to develop into a senior or honors thesis, AGU conference presentation in Fall 2019, or even a peer-refereed scientific publication.  

Marine Biogeochemistry

Mentor: Prof Karen Casciotti and Colete Kelly
SURGE (or maybe SESUR)

Nitrate is an essential nutrient for phytoplankton growth and carbon export from the surface ocean on seasonal, annual, and millennial timescales. The isotopic composition of nitrate in the ocean provides a record of biogeochemical and physical processes on the time scales of years, decades, centuries, and millennia, with the shallow subsurface and deep ocean recording shorter and longer time scales, respectively. These are meaningful time scales in the efforts to (1) understand the feedbacks that structure the biogeochemistry of N in the ocean, ocean productivity, and the global carbon cycle, (2) reconstruct past changes in ocean biogeochemistry and carbon cycling, and (3) perhaps predict future changes.

This project involves analyzing the nitrate and nitrite isotopes in samples collected on a recent GEOTRACES cruise in the Pacific Ocean between Alaska and Tahiti. The project will involve learning sample preparation and analysis by isotope ratio mass spectrometry, as well as other laboratory equipment and skills, data analysis and interpretation.

These measurements will contribute to the investigations of three questions:

  1. What are the similarities and distinctions in nitrogen biogeochemistry among the different nutrient-rich regions in the Pacific basin: the Southern Ocean, equatorial Pacific, and subarctic North Pacific?
  2. How do they affect nitrate supply to low latitude surface waters?
  3. What sources of nitrogen fuel export production in surface waters across the Pacific?

Estimating the Temperature Dynamics of a Washcoated Gasoline Particulate Filter used for particulate emission reduction in modern gasoline vehicles

Mentor: Prof Simona Onori

Recent years have witnessed increasingly stringent legislations being imposed on the fuel economy and exhaust emissions of ground vehicles to address global warming concerns. A notable advancement in engine technology to meet current and future regulation targets is the transition from port fuel injection (PFI) to gasoline direct injection (GDI) systems. GDI systems offer an enhanced fuel economy, increased power output, and reduced greenhouse gas emissions compared to PFI systems. However, it under certain operating modes, GDI engines suffer from poor fuel-air mixing inside the combustion chamber. As a result, hazardous soot particulate matters (PM) are released into the atmosphere. As the number of vehicles using GDI engines increase, the reduction of PM emissions presents an increasingly significant technological and societal concern due to the health hazards they pose among humans and the environmental air quality.

Among different strategies to mitigate PM emissions, automotive manufacturers have identified gasoline particulate filters (GPFs) as the most promising and practically adoptable emission control devices in the exhaust system. As the exhaust gas enters the GPF, soot particulates are trapped within its channels. Over time, this accumulation of soot increases the back pressure on the engine. To minimize this negative performance impact, the soot trapped in the GPF is  periodically cleaned. This is accomplished via regeneration, i.e. oxidation of soot at elevated temperatures and oxygen concentration. Recent advancements in GPF technology have led to the development of washcoated GPFs, in which a catalytic washcoat is applied across the channels. In comparison with uncoated GPFs, washcoated GPFs an enhanced soot oxidation ability at relatively lower temperatures. Research and development efforts until now have focused only on uncoated GPFs. Accurate, computationally efficient models must be developed for wash coated filters for on-board vehicle applications. This will enable future vehicles to benefit from the use of GDI engines without suffering from increased soot emissions. The aim of this project is to capture the thermal and soot oxidation dynamics in a washcoated GPF during regeneration.

A highly motivated and meticulous student is sought for this task. A physics-based mathematical model that is used to predict the internal GPF dynamics, provided to the student, will be used to develop an estimator to monitor internal states of the device. Previous experience in Matlab and Simulink is desired. The successful outcome of this project will help in the control and optimization of GPF performance, and develop strategies to enhance the longevity of GPFs through health monitoring and prognosis. This project is an excellent opportunity for the student to publish his/her research findings in conference proceedings, and showcase them in the form of a poster presentation. Finally, the student will have the opportunity to present his/her findings to an automotive industry partner.

How do ice sheets change? Ice penetrating radar design and data analysis

Mentor: Prof Dustin Schroeder

Ice penetrating radar design and data analysis The Stanford Radio Glaciology research group focuses on the subglacial and englacial conditions of rapidly changing ice sheets and the use of ice penetrating radar to study them and their potential contribution to the rate of sea level rise. In general, we work on the fundamental problem of observing, understanding, and predicting the interaction of ice and water in Earth and planetary systems Radio echo sounding is a uniquely powerful geophysical technique for studying the interior of ice sheets, glaciers, and icy planetary bodies. It can provide broad coverage and deep penetration as well as interpretable ice thickness, basal topography, and englacial radio stratigraphy. Our group develops techniques that model and exploit information in the along-track radar echo character to detect and characterize subglacial water, englacial layers, bedforms, and grounding zones. In addition to their utility as tools for observing the natural world, our group is interested in radio geophysical instruments as objects of study themselves. We actively collaborate on the development of flexible airborne and ground-based ice penetrating radar for geophysical glaciology, which allow radar parameters, surveys, and platforms to be finely tuned for specific targets, areas, or processes. We also collaborate on the development of satellite-borne radars, for which power, mass, and data are so limited that they require truly optimized designs. Student projects are available in support of both ice penetrating radar instrument development and data analysis.

Climates of Rocky Planets through Time

Mentor: Prof Laura Schaefer

The atmospheres and hydrospheres of rocky planets like Earth, Mars, and Venus as well as many newly discovered exoplanets evolve with time.  This is due to both geochemical interaction with the solid planet as well as interaction with stellar radiation. Internal inventories of some atmosphere/hydrosphere components, such as water and CO2 may match or exceed present day surface inventories. Surface climate will vary on long timescales as a result of geochemical cycling through the planet's interior and variability in stellar radiation.

In this project, the student will modify existing Matlab codes to incorporate additional volatile components and develop simple climate models. The student will use these models in order to study the variability of climate on the Solar System terrestrial planets as well as rocky exoplanets around other stars and compare the relative habitabilities of these different worlds. Some programming experience in Matlab or Python is preferred, but most of the necessary skills will be developed during the project. 

California's forest carbon GHG inventory

Mentors: Prof Chris Field and Dr. Christa Anderson

California's forest lands are an important source and sink of greenhouse gas emissions in the state, and California is a global leader on climate change policy and greenhouse gas emissions quantification. The state recently completed two inventories that include emissions sources and sinks on California forest lands, along with a set of implementation goals for reducing forest carbon emissions and enhancing sinks. 
This project seeks an enthusiastic student to work on two aspects of California's forest inventory: 
1) Quantitatively analyze the differences between the two existing forest carbon inventories and make recommendations on the strengths and limitations of each of the inventories. 
2) Assess different options for climate mitigation on California forest lands and other Natural and Working Lands using the state's CALAND model.

These analyses will contribute to research on Natural and Working Lands in California.
Background knowledge in Earth Science and ability to program in R are desirable.

Soil Chemistry in Fire Zones

Mentors: Prof Rob Jackson and Dr. Adam Pellegrini
SURGE only

Changes in fire frequencies in the Western United States have the potential to alter the storage and cycling of carbon and nutrients in forests. Although much research has gone into understanding the response of the plant community, changes belowground in soils, specifically the microbial communities, are less well understood. Sequoia and Kings Canyon National Parks in the Sierra Nevada mountains of California have several permanent plots that have been burned at different intervals since the 1960s, presenting a unique opportunity to gain insight into the long-term effect of fire on ecosystems. Repeated measurements of plants and fuels have been occurring, but data on soil chemistry and microbial activity and community composition are largely lacking. We are currently undertaking a project to measure carbon and nutrient content, microbially produced enzyme activity, and microbial community composition to more completely understand the implications of repeated burning on ecosystem function. Our goals are to characterize the soils in different vegetation types (ponderosa pine and sequoia groves) that have experienced different fire frequencies. The relationship between soils and fire would be linked with vegetation responses using the long-term monitoring data from the fire effects plots. The summer research would include trips to the Sequoia and Kings Canyon National Parks to collect field soil samples followed by lab analyses at Stanford. 

The student(s) will learn field sampling methods as well as chemical analysis methods on several different instruments at Stanford (measuring carbon, nitrogen, phosphorus, calcium and other elements). Sampling can be adjusted slightly if a student has a particular question in mind that they would be interested in addressing.

Mountains and mole-hills: How does topography influence climate-driven extinction?

Mentors: Prof Page Chamberlain and Tyler Kukla

When the Earth plunged into its present “icehouse” climate (34 million years ago), mammals went extinct globally, but not uniformly. While mammals near the west coast of the US suffered a long extinction event, their counterparts within the Rockies escaped this climate transition largely unscathed. Did the mountains save these mammals?

The answer to this question lies in fossils and chemical signatures of rocks that formed during this time. With the aid of sophisticated numerical models, this information will elucidate how mountains, the water cycle, and atmospheric circulation influenced ecosystems and extinction during the most pronounced climate event of the last 50 million years.

We are seeking an enthusiastic student to tackle these questions with laboratory analyses of isotopic signatures in ancient rocks, large fossil datasets, and computer simulations of ancient landscapes and ecosystems. The student will acquire all necessary skills during the program; no prior experience required.

Exploring Uranium Contamination in Groundwater through an Isotope Tracer Test

Mentors: Prof Kate Maher, Dr. John Bargar and Zach Perzan

Uranium is a major pollutant at hundreds of abandoned mines and other contaminated sites throughout the western U.S., the result of a long legacy of uranium mining. The groundwater contaminant plumes at many floodplain mill sites are subject to strong seasonal fluctuations, but the processes behind these variations are not well understood. This project will examine uranium transport during seasonal floods, with research centered around a series of field experiments using artificial groundwater tracers. Our study has immediate relevance to water quality concerns at the field site -- a uranium-contaminated floodplain in Wyoming -- but has much broader implications as well. Isotopically labeled nitrate will allow us to track denitrification and the formation of nitrous oxide (a powerful greenhouse gas), deuterated water (D2O) could map plant water uptake, and visible dye will be used to answer questions regarding unsaturated zone flow.

The research student will develop strong lab and fieldwork skills throughout this project. Early summer will include one or more short trips to Wyoming to help conduct tracer tests, while the remaining time will be spent on labwork analyzing soil, water and gas samples for contaminants, artificial tracers and other solutes of interest. Previous laboratory experience and a strong interest in soil science or hydrogeology is highly recommended, but not necessarily required.

Using machine learning to identify and map environmental regulation violations

Mentors: Prof. Steve Luby, Nina Brooks

Over the past 25 years Bangladesh has experienced rapid economic growth, declines in poverty, and improvements in health. Bricks are central to this development. Bangladesh lacks other construction materials and depends heavily on bricks to support construction. However, bricks are produced in highly polluting, traditional kilns that burn substantial amounts of coal contributing to poor air quality locally and to global climate change.

The Government of Bangladesh has attempted to regulate brick manufacturing, by altering the permitting processes to open kilns, placing restrictions on where kilns can be constructed, mandating technological changes, and restricting fuels that can be used. Evidence on the ground suggests that these regulations have been minimally enforced at best, but there is almost no official data on where kilns are, what kind of technology is being used, or even how many kilns there are to assess compliance with existing laws. Generating this data and making it public is an essential first step to support our team’s long-term goal to make brick manufacturing cleaner.

We have been working to overcome these data limitations by combining satellite imagery and machine learning algorithms to visually detect brick kilns. We seek 1-2 motivated students with a quantitative and computational background—preferably with experience in python or R, some experience with machine learning, and/or experience with website development. The student(s) will work together and with our team to 1) apply and refine the algorithms to detect brick kilns in Bangladesh over the past 15 years, 2) assist with spatial analysis to assess compliance with government regulations, and 3) support the development of a publicly available website that spatially and dynamically presents the information on kiln location, type and proximity to human populations.

DNA Tracers for Subsurface Reservoir Characterization

Mentors: Prof. Roland Horne, Prof. Anne Dekas and Yuran Zhang

Geothermal energy is an important member of the clean energy portfolio, counterbalancing limitations caused by the intermittent nature of other renewable energy like wind and solar. The exploitation of geothermal energy relies on a good understanding of the subsurface fracture system. Tracer testing is one of the key tools to characterize subsurface reservoirs, mainly by injecting into the reservoir a tracer distinguishable from naturally occurring substances, then recovering the flowed tracer with time. The return profile of the tracer depends on the formation properties (reservoir volume, fracture aperture, etc.) between the injection and production wells, hence provides valuable insights in understanding those formation properties. The larger number of distinct tracers available, the more well pairs could be investigated simultaneously, and the better constrained a reservoir model is. Our study explores the use of DNA technology as a novel tool to aid the characterization of the subsurface. Specifically, synthetic DNA will be evaluated as a novel reservoir tracer, which allows unlimited number of unique tracers to be applied in the field and distinguished unambiguously. Flow properties of DNA tracers as well as potential interference with conventional chemical tracers will be evaluated to better inform field applications.

We are looking for a motivated student to spend the summer at Stanford Earth performing experiments that characterize properties of available DNA tracers in a tracer testing context. Prospective student will be involved in: 1) Bench interference test between DNA tracer and conventional chemical tracers, using qPCR (quantitative polymerase chain reaction) and ICP-MS (inductively coupled plasma mass spectrometry) as analytical techniques; 2) Lab flow experiments transporting DNA tracers with chemical tracers through defined porous/fractured media, measuring effluent concentrations using qPCR and/or ICP-MS; 3) (depending on project progress and method development) Environmental DNA extraction and sequencing on deep subsurface samples to utilize indigenous DNA fingerprint to guide reservoir characterization. Laboratory experience/interest is preferred. Background knowledge in molecular biology, reservoir engineering, hydrology and/or (geo)chemistry is useful but not required.

A Window into the Deep: Visualizing Deep-Dea Microbes

Mentors: Prof Anne Dekas and Nestor Arandia
Marine microbes (including bacteria and Due to their enormous abundance and functional diversity, microbes play a key role in all marine biogeochemical cycles, particularly in carbon and nitrogen cycling. Yet, due to their enormous diversity, the community composition of marine microbes may largely determine the amount of nitrogen and carbon recycled in the water-column. Although microbial community composition has been well studied in the surface ocean, the dominant bacterial and archaeal groups in the deep ocean and their impact on the biogeochemical cycling of the ocean are still largely unknown.

In an ongoing project in the Dekas Lab, we analyze the effect of community composition in the carbon and nitrogen cycling of the waters of the deep ocean. The project will involve microscopy, and in particular cell hybridization techniques, in order to identify and quantify different phylogenetic groups of pelagic marine microbes. By the end of the project, the student will acquire laboratory skills using fluorescence in situ hybridization techniques, microscopy and data analysis.

We are seeking an enthusiastic student interested in marine microbial ecology, with some background in biology.

Microbiology and Geochemistry of Deep-sea Sediments: Who is there, and what are they doing? 

Mentors: Prof. Anne Dekas and Nicolette Meyer

In deep-sea sediments, archaea and bacteria play a fundamental role in carbon cycling. Carbon dioxide is fixed by phytoplankton in the photic zone, and the organic matter they produce eventually settles on the seafloor. In marine sediments, microorganisms respire some of the organic carbon, while the remaining organic matter is stored on 1000 year timescales, acting as a regulator of climate. Thus, investigating the microorganisms that live in marine sediments and their activity is important to understanding climate stability and the marine biogeochemical cycle of carbon.

The student will work with deep-sea marine sediments (<4500 m below sea level) previously sampled from the Californian coast. These sediments were collected at different water and sediment depths, spanning a suite of physical and chemical gradients. They will use geochemical and/or molecular techniques to characterize the microbial community composition and their activity. Prior research experience is not necessary, but an enthusiasm to perform lab work, high attention to detail, and interest in Earth science, geochemistry and microbiology is required.

Predicting root system response to climatic and environmental conditions

Mentors: Prof. Rob Jackson and Shersingh Tumber-Davila

Root systems have the ability to affect many different processes, and can alter the environment greatly. They also respond differently to certain climatic and environmental conditions. Therefore, it is crucial that we understand the importance of rooting systems to different processes such as soil characteristics, hydrology, climate, and carbon sequestration. This summer project will seek to give insight to and answer the following questions:  1). Do above-ground plant extents and functional traits serve as predictors for below-ground rooting extents? 2). Do large-scale climatic indices of water availability serve as predictors for relative rooting extents? 3). At the individual plant scale, which local and sub-climate factors most influence rooting extents?

Answering these questions will help us better understand the processes determining the coarse root distributions of plants globally. In particular, these analyses will examine the climatic and environmental mechanisms controlling below-ground investment. Understanding these mechanisms is necessary for predicting how this system may change in the future, the potential impacts to the global carbon cycle, the local hydrologic cycle, and may inform Earth Systems Models (ESM) on how plants invest their carbon below-ground.

The student will have the opportunity to test the relationship between root canopies, and the above-ground environment of an individual plant. This will include the analysis of a global database of individual plant root systems. The primary task of this project is to measure below-ground root system volumes and other root system measurements, as well as above-ground plant sizes by digitizing detailed plant profile drawings using the ImageJ software. Additional fieldwork to local California sites may be included as part of the project, measuring root systems directly. The student must have an interest in forest ecology, and a willingness to learn different field measurement, and analysis techniques. The data analysis will be mostly using R and excel.

Effects of Soil Properties and Land Management on Oxygen in Upland Soils

Mentors: Prof. Scott Fendorf and Rob Rossi
SURGE only

Soils are the largest terrestrial store of carbon (C), containing up to 3,000 Pg of C which can be transformed by microbial activity into greenhouse gases. Because soil greenhouse gas efflux is partially controlled by oxygen supply, anaerobic microsites, which form when oxygen demand outpaces oxygen supply, likely exercise a

This research project will answer the following questions:  1. What is the anaerobic volume of upland agricultural soils? 2. How do land management practices (e.g., tillage) affect oxygen distribution in these soils? 3. Can we use land management to minimize soil greenhouse gas emissions and maximize soil C storage?

Tasks will include extracting soil pore water with pressure cells, measuring trace element and oxygen content of collected pore waters, measuring soil gas efflux, and performing bulk soil property analyses (e.g., organic matter content, texture, bulk density). Previous lab experience is a plus but not required. Ideal applicants will have an eye for detail while performing laboratory work, and most importantly, are eager to learn more about and participate in Earth/soil science research.

Exploring American Public Opinion on Climate Change

Mentor: Prof. Jon Krosnick
SESUR only

For more than a decade, my team has been studying what the American public thinks about climate change. And in numerous surveys, we have found that the vast majority of Americans are on the "green" side of the issue. But in recent surveys, we have conducted numerous experiments exploring how survey question wording influences responses. This is an opportunity to study the impact of question wording generally in surveys (can survey results be believed? Or are they so fragile and easily manipulated by question wording that they should not be trusted?) and the robustness of Americans' opinions on the issue. We will conduct statistical analyses of the data collected in these experiments, and write up a paper for publication.

The undergraduate will build the databases for analysis using many survey datasets, and then the student will conduct statistical analyses of the data using Stata or R and will draft a manuscript. The student will benefit in the following ways: (1) gaining understanding of the structure and nature of survey research, (2) gaining understanding of procedures to design and conduct objective data collection, (3) gaining understanding of conducting elementary statistical analysis of quantitative data, (4) gaining understanding of how to write up research findings in ways suitable for publication in academic journals, and (5) gaining understanding of how to design and conduct experiments embedded in surveys to document the causal impact of news stories on people’s opinions. The student will work as part of a large team of post-docs, graduate students, and undergraduates working with Professor Krosnick and will participate in regular meetings with the team, which will provide exposure to scientific careers and offer resources on which to draw when learning how to do work. And the student will meet weekly with Professor Krosnick to review and plan research activities.

We welcome all students who are interested in understanding how to use scientific methods to document public opinion about climate change and to learn about the science of survey research. It would be desirable for the student to have experience with statistics and data base management, but these skills are not necessary.

What are the Main Barriers to Better Accounting our Carbon and Greenhouse Gas Emissions?

Mentors: Prof. Rob Jackson, Prof. Chris Field, Dr. Katherine Mach and Leehi Yona

Adequately calculating greenhouse gas inventories is important to action on climate change, because any climate action is rooted in policy that is grounded in our knowledge of carbon stocks. The ways in which we calculate greenhouse gases can influence the sectors in which we choose to reduce our emissions (for example, in sectors such as energy and transportation, land use, or food systems). Yet, despite this importance, there are many remaining knowledge gaps within carbon accounting, particularly when it comes to land use, forests, and soil carbon.This research project aims to fill some of these knowledge gaps around soil carbon and forest soil carbon. Work will be primarily focused on developing better guidelines to calculate soil carbon. As countries participating in the United Nations Paris Agreement will all be required to report greenhouse gas inventories for the first time in 2020, answering these questions is directly related to policy decisions.

We'll be working on interdisciplinary research grounded in ecology and carbon cycling that also has real-world policy implications. The main project consists of developing a more accurate model for calculating soil carbon stocks on a national level. The student will have the opportunity to work on various components of the research project depending on interest, focusing on soil carbon, carbon accounting, and land use. The student must be independent and enthusiastic about learning new analysis and ecological techniques.

Outdoor Air Pollution and Adverse Birth Outcomes in California

Mentors: Prof. Marshall Burke, Prof. Gary Shaw, and David Gonzalez

Preterm birth is a critical public health issues, affecting 1 in 10 births in the United States. Infants born preterm have higher risk of death or long-term health problems. The causes of preterm birth are not well understood. Recent research has focused on the role of air pollution in increasing risk of adverse birth outcomes. Our objectives are to study the reproductive health effects of outdoor air pollution, examining pollution from sources that have not been well-characterized. The research involves applying methods from epidemiology, quantitative social sciences, environmental science, and data science.

We’re looking for a student interested in applying quantitative skills to study the intersections between environmental science and public health, with a specific focus on air pollution exposures and preterm birth. If the student is interested, we can also explore the role of environmental injustice in shaping exposures and outcomes. With guidance from research mentors, the student will gather and work with data related to outdoor air pollution and population health. Work will involve data gathering, processing, analysis, interpretation, and, possibly, communication to community partners.  Depending on the student’s interests, we may be able to pursue field work in impacted communities in the California Central Valley. We are particularly interested in students seeking to build data analysis skills in R or similar statistical packages (you don’t need to have extensive experience, but familiarity with statistical packages is helpful). Background in the environmental sciences, public health, and/or quantitative social sciences is also helpful, but not required.

Simulating Volcanic Eruptions through Physics-based Models

Mentors: Prof. Paul Segall and Ying-Qi Wong

As magma ascends during a volcanic eruption, it undergoes many changes that affect the way it flows.  Magma solidifies and releases dissolved gas as the confining pressure declines, causing its viscosity to greatly increase.  To capture this and some other complexities in the magma ascent process, our group has developed a 1D numerical code specialized for effusive, dome-forming type eruptions and applied, as a test case, to the 2004-2008 Mount St. Helens eruption.  Current efforts to rigorously compare predicted results from the model with real observations from the eruption have been limited by the speed of the code, thus we hope to move to a lower-level programming language to enhance the code's efficiency.

In this project, the student will find ways to translate parts of a Matlab code into a lower-level language, e.g. C/C++/Fortran, measure the performance improvement, and rigorously check the output of the code using convergence tests, as well as verification methods including the Method of Manufactured Solutions.  We are looking for a keen student with some experience in scientific computing (Matlab and C/C++/Fortran), linear algebra and calculus (including differential equations).  This project involves a standard process in developing a numerical code to model physical processes, thus students interested in computational aspects of fluid dynamics and solid mechanics should consider applying, irrespective of whether they have experience in the Geosciences.

Changes in the Land Surface during Volcanic Eruptions

Mentors: Prof Paul Segall and Ying-Qi Wong

Highly localized ground deformation patterns have been observed in many volcanoes around the world, including Tungurahua in Ecuador, Masaya in Guatemala, Merapi in Indonesia and Usu in Japan.  A growing network of instruments, from Global Positioning System (GPS) and tiltmeter networks on the ground, as well as the satellite-based Interferometric Synthetic Aperture Radar (InSAR), has enabled volcanologists to study the change in the land surface (the field of geodesy) at many restless volcanoes to learn more about the eruption process.  While broader-scale deformation offers insight into the depth, shape and pressure change of a magma reservoir, localized deformation reflects shallow processes as the magma undergoes the final stages of magma ascent.  Understanding magma behavior in this last stage is critical for forecasting the volcanic hazard. 

For this project, the student will use numerical models to simulate ground deformation due to normal and shear forces exerted by the magma as it moves through a pipe connecting the magma reservoir to the surface, and compare with surface observations (specific study volcano TBD).  A key question is what conditions are needed for magma movement to cause measurable deformation, and at which volcanoes these conditions would be met.  We are looking for a keen student with experience in scientific computing (preferably Matlab), as well as some understanding of linear algebra, calculus (including differential equations) and modeling of physical processes.  Interest in the Geosciences is preferred, but no prior experience in this field is necessary. 

Molecular Ecology of Nitrogen-cycling Microorganisms in San Francisco Bay

Mentors: Prof. Chris Francis and Anna Rasmussen

San Francisco Bay is the largest estuary on the west coast of the US and has been highly altered by human activity. The bay receives high anthropogenic nitrogen input from wastewater treatment plants and agricultural runoff. Despite receiving high levels of nitrogen, San Francisco Bay does not suffer classic symptoms of eutrophication such as large algae blooms or seasonal hypoxia. We are interested in understanding the ecology of microorganisms that metabolize nitrogen in San Francisco Bay and connections between microbial ecology and biogeochemical cycling. We are particularly interested in nitrifying organisms, which are responsible for the conversion of ammonia to nitrate. Nitrification is generally carried out by two groups of organisms, ammonia oxidizing archaea or bacteria and nitrite oxidizing bacteria. Our project aims to address questions such as: Which nitrifiers are present and abundant in bay waters? Can we observe co-occurrence patterns between ammonia and nitrite oxidizers? Are there connections between microbial ecology (abundance, diversity, etc.) to nitrification rates? Which environmental factors most strongly influence nitrifier ecology and nitrification rates?

The student will work closely with the graduate student, Anna, on samples recently collected during biweekly cruises on San Francisco Bay and should have a general interest in microbial ecology, biogeochemistry, molecular biology, geobiology, or biological oceanography. The student will use molecular biology techniques (e.g. DNA extraction, PCR) and possibly culturing or geochemical techniques to understand nitrifier ecology in San Francisco Bay. Prior laboratory experience is not necessary. Some background knowledge in biology, microbiology, earth sciences, or biogeochemistry is desirable.

Reassessing the Rice Yield in the Future: Coupled Impact of Soil Contamination and Climate Change

Mentors: Prof. Scott Fendorf and Tianmei Wang

Rice is a staple for more than 50% of the world population. Thus, it is crucial to accurately estimate rice productivity in the future for a growing population. Arsenic contamination is a major concern for rice because of soil biogeochemistry resulting from paddy flooding. Anaerobic conditions destabilize arsenic bound to soil minerals and enhance arsenic availability for plant uptake. Arsenic poses a chronic threat to human health when consumed. It also retards growth of rice plants, threatening rice yield and grain quality. Current climate and crop models projected a decrease of rice yield under climate change conditions. However, they did not include arsenic, a common contaminant in paddy soils especially in south and southeast Asia where more than 90% of the world rice is produced.

The goal of this project is to assess to what extent elevated temperature and atmospheric CO2 (parameters of climate change) combine with soil arsenic to affect rice yields and grain quality within South and Southeast Asia. We will conduct highly-controlled greenhouse experiments with different soil arsenic concentrations and climatic conditions. The geochemistry of soil porewater and physiological changes of rice plant will be analyzed to understand the fate of arsenic in the soil-rice continuum.

We’re looking for a highly motivated student to maintain greenhouse pot experiment in fully climate-controlled chambers; collect and analyze porewater samples; and assess changes in rice physiology throughout the growth period. Previous laboratory experience in geochemical or environmental science would be helpful.

Simulating the Carbon Cycle: Can imitating complex models with a simple model reveal the most likely future?

Mentors: Prof. Alexandra Konings and Dr. Gregory R. Quetin

Changing climate associated with global warming can change ecosystems, water flow in rivers, and more. But changes to the world’s ecosystems (also known as ‘the carbon cycle’) also feed back to the climate and the amount of temperature rise and changes in rainfall. To understand future ecosystem changes, scientists use a collection of complex so-called Earth System models representing the atmosphere, oceans, and land. However, these models do not agree on the future of the carbon cycle. In some models, the carbon cycle absorbs ever more CO2 - slowing global warming - while in others large amounts of carbon return to the atmosphere as CO2 - accelerating global warming. Indeed, although the basic trends associated with climate change are well understood, how much CO2 will be taken up by ecosystems is one of the main uncertainties surrounding exact temperature and rainfall predictions for future climates.  Part of the challenge with these models is their complexity, with each model having hundreds of uncertain mathematical parameters values (e.g. how much photosynthesis changes with temperature, or how long carbon stays in the soils). The parameters can be estimated by comparing present-day simulations from these models to measurements of ecosystem properties today, but because there are so many parameters the mathematical problem is intractable.

In this project you will use a new tool – CARDAMOM – to try to mimic these complex Earth System models with a much simpler alternative that has fewer parameters. With a simpler model – and fewer choices – we can test different choices millions of times to determine which choices best emulate the complex Earth System models and the real world. The results will be analyzed to discover whether 1) a simpler model can successfully emulate the complex dynamics in the Earth System model, 2) whether the choices in the simpler models imitating the Earth System models can be used to help determine which Earth System models best represent the real world. Determining which Earth System models most realistically represent the carbon cycle will help predict the speed and consequences of global warming.

The student will have the opportunity to gain experience with Earth system models, mathematical parameter fitting techniques, and ecosystem models. Some prior programming experience (preferably Python) is required, but specific experience in related fields is not necessary.

Environmental change of Cretaceous ocean basins in Patagonia during the rise of the Andes

Mentors: Prof. Matthew Malkowski and Tom Boag

The Cretaceous period (145 to 65 Million years ago) encompasses one of the most dynamic paleoenvironmental time intervals in Earth's Phanerozoic history (past 550 million years). For example, the Cretaceous is one of the hottest time periods during the Phanerozoic and it includes several different events of global marine anoxia which had profound effects on the fossil record of marine life. Major events such as these in the Cretaceous are most commonly inferred from studying the stratigraphic fill of sedimentary basins (Earth's record-keepers). Therefore, in order to understand the magnitude of extreme climatic conditions of both terrestrial and marine environments we must be able to constrain the physical and chemical characteristics of the paleoenvironments of deposition in the basin. Doing so requires excellent, continuous exposure of basin fill stratigraphy with the appropriate lithologies (mudstone, volcanic ash beds, and index fossils) over the time interval of interest. The student will have the opportunity to work with rocks from the southern Patagonian Andes, where there is a nearly complete record of Cretaceous stratigraphy that accumulated over two different basin phases: The Early Cretaceous Rocas Verdes Basin and the Late Cretaceous Magallanes' Austral Basin.

In this laboratory-based sedimentary geochemical study, the student will work as part of a group project to analyze shale samples from the Rio Mayer and Zapata Formations from Cretaceous rocks collected in southern Patagonia. The student will analyze shale samples for their organic carbon isotope and major- and trace-element composition. The student will learn to interpret these data they generate and integrate it with both the stratigraphic record and existing geochemical and paleobiological trends at that time. The student will learn the basics of how make measurements of the global carbon cycle, and learn how global and local climatic and tectonic forces interact to produce the chemical and physical environments of deposition in sedimentary basins. There are no formal requirements for the research project, but a general background in chemistry and geology will be useful.

Mountain building in the Alaska Range: Deconvolving the forces of climate, topography, and sediment transport from mountain belts to ocean basins

Advisors: Prof. Matthew Malkowski and Colin White

The growth of mountains occurs over geological timescales (millions of years) and as mountains evolve they are continuously subject to weathering and erosion. Consequently, these destructive forces are removing the mountains as they grow. But because the removed material (sediment) ultimately gets transported by glaciers, rivers, and streams and deposited into sedimentary basins, we can use the stratigraphic rock record of sedimentary basins to reconstruct the timing and magnitude of mountain building, and even the forces acting to erode them. The Alaska Range hosts North America's highest topography and much of the sediment removed from the growth of the Alaska Range is carried out to the Bering Sea basin along the Kuskokwim and Yukon Rivers. This project will focus on addressing two related questions: 1) What is the uplift and unroofing history of the Alaska Range? 2) How did the Yukon-Kuskokwim drainage evolve in response to Alaska Range mountain building? To help answer these questions the student will work on sediment from modern rivers and sedimentary rocks from cores drilled in the submarine Navarin Basin in the Bering Sea, Alaska. The combination of subsurface and surficial samples will facilitate the reconstruction of sediment erosion, transport, and deposition in Alaska and the Bering Sea.

This project will provide an opportunity for the student to examine existing data while acquiring new results from a previously unsampled, deeply penetrating, legacy drill core. The student will prepare, analyze, and interpret geochronological and petrographic data taken from samples systematically collected in a drill core from the Navarin Basin in the Bering Sea. Lab work will primarily consist of heavy mineral separations for zircon extraction. Samples will be analyzed by a laser ablation inductively coupled plasma mass spectrometer. Interpretation of the data will be conducted by comparing U-Pb age populations in detrital zircons extracted from the core with samples previously collected along modern drainages feeding into the Bering Sea. Although there are no strict prerequisites, the preferred candidate will have a basic chemistry background, ideally coupled with courses in mineralogy, geochemistry, and/or sedimentology. Some previous lab experience is also favored.

Soil Carbon Protection in Agricultural and Natural Soils

Mentors: Prof. Scott Fendorf and Emily Lacroix
SESUR only

Soils are the largest dynamic reservoir of carbon (C) on Earth, storing more C than the atmosphere and vegetation combined. Microbial conversion of soil C into carbon dioxide (CO2) accounts for ¼ of annual global CO2 emissions.  Recently, oxygen depletion in soils, leading to zones termed anoxic microsites, has been identified as an important soil C protection mechanism, slowing the rate of CO2 production in upland soils. While anoxic microsites likely exert an important control on soil CO2 efflux, surprisingly little is known about their prevalence in soil, and how they change with soil properties and management practices.

Our project will examine the role anoxic microsites play in various agricultural soils and nearby ‘natural’ soils in storing carbon. Moreover, the results of this work will inform land management strategies to maximize soil C storage in cropland soils and ultimately help mitigate global climate change.

As a summer researcher, you will work to collect soil samples, analyze soil properties, and conduct incubations and water extraction experiments to measure greenhouse gas production and oxygen content. In order to capture a range of soil and climatic factors, field sampling will likely involve spend time driving across the United States (with Emily Lacroix) to collect and analyze soils and gas efflux from both agricultural and natural systems. We expect the position to involve long car trips and many hours working outside. Lab work includes elemental analysis by combustion, density fractionation, texture analyses, and more. A driver’s license and lab or field experience would be nice but are not required. Most importantly, the student must have a sense of humor and willingness to learn!

Deep Learning Applied to Seismic Data Recorded by the Stanford Fiber Seismic Observatory

Mentors: Prof. Biondo Biondi and Ariel Lellouch 

Seismic sensing using fiber-optics cables is an emerging technology, already proving useful for downhole seismic monitoring and infrastructure monitoring. This sensing technology may be also applied using conventional telecommunication fibers, which are shallowly buried and usually have poorer coupling to the ground. While data quality is often lower, the prevalence, low cost, and wide coverage of telecommunication fibers make them an ideal candidate for an earthquake monitoring system.

Such a system, consisting of a 4.8 km telecommunication fiber and an optical interrogator, has been in place under Stanford Engineering Quad. It has been continuously recording data for the past two and a half years. In this project, students will work on customizing an existing catalog of recorded earthquakes, and analyzing them using seismological and machine-learning tools. Eventually, earthquake detectability, location, and characterization, using telecommunication fibers, will be quantitively assessed, laying the foundations for fiber-based large scale monitoring.

Prof. Biondo Biondi will supervise the project; Dr. Ariel Lellouch, a post-doctoral researcher in Geophysics, will provide mentorship. Candidates from a geophysical, seismological or CS background are welcomed, and their contribution to the project will be adjusted accordingly to their experience.

Earthquake and Volcano Modeling

Mentors: Prof. Eric Dunham and Chao Liang

Earthquakes and volcanoes pose immediate hazards to human society. Our research group develops computational codes to model a wide range of physical processes associated with these hazards. Summer interns have multiple opportunities to apply the theory of mechanics to understand phenomena in both earthquakes and volcanoes. Students who enjoy mathematical analysis can help to derive equations and solve analytical problems; experience with differential equations, continuum mechanics, and Fourier transform would be useful. Students who enjoy programming can assist with code development; prior programming experience in MATLAB, Python, C++, or another language is required. A strong background in mechanics is a must for all applicants since they will mostly work with solid and fluid mechanics problems. Students may also perform simulations using existing codes to understand the theory behind physical processes or assist in analyzing data from seismometers to validate models. Previous experience with earth science is not required.

Unsupervised and semi-supervised machine learning for crop mapping

Mentors: Prof. David Lobell and Sherrie Wang

Remote sensing is becoming increasingly important to applications from land use monitoring to sustainable development. Combined with recent advances in deep learning and computer vision, there is enormous potential for monitoring global issues through the automated analysis of remote sensing and other geospatial data streams. However, recent successes in machine learning have largely relied on supervised learning techniques and the availability of large annotated datasets. Remote sensing provides a huge supply of data, but many downstream tasks of interest are constrained by a lack of labels.

Our research group is working on developing unsupervised and semi-supervised methods for remote sensing data, particularly applied to cropland and crop type mapping. The student would help develop these methods by using public/private satellite datasets and geotagged crop datasets in different countries, as well as working with various machine learning algorithms and neural network architectures. Background in computer programming (preferably Python) is required. Familiarity with satellite datasets and Pytorch/TensorFlow is desired but not required.

Understanding the sustainability of irrigated agriculture

Mentors: Prof. David Lobell and Jillian Deines

Irrigation for agriculture is the largest water use on the planet. Irrigation enhances crop yields and price stability, but overexploitation of surface and groundwater resources has caused considerable water stress in many regions around the world. Moving towards agricultural water sustainability requires better data on when and where irrigation occurs, as well as the relative impacts on crop yields, water resources, and food security. Our research group uses a suite of tools to study this food-water nexus, including satellite remote sensing data, crop modeling, and synthesis of agricultural and water use statistics. In this project, the student would contribute to one or more of the following depending on skills and interests: 1) compare different satellite methods to detect irrigation activity and trends; 2) acquire and analyze regional and national datasets on irrigated area, yield, and water stress; or 3) run crop models to evaluate yield impacts of different irrigation regimes. Preferred qualifications include experience in at least 1 of the following: programmatic data manipulation and analysis (R, Python, or similar), GIS, satellite data, and crop modeling.

Thermal History of the Boulder Batholith, Montana

Mentors: Prof Marty Grove and Ginny Isava, Geological Sciences
SURGE only

The Pacific Northwest’s tectonic history of terrane accretion and translation can be extrapolated by linking the erosion of sediments from older regions of the continent to sedimentary basins formed by the addition of accreted terranes. By comparing the ages and thermal histories of sources and sinks, we can interpret the relative positions of landmasses during the time of sediment transfer. The Nanaimo Group, a sedimentary unit in Vancouver Island of British Columbia, received most of its detrital material from the Coast Mountains, a plutonic belt on the mainland of British Columbia that formed during Late Cretaceous subduction of the Farallon plate. However, isotopic study of the Nanaimo Group indicates a shift in sediment source around 80 Ma.

This project will analyze one potential extraregional source for the Nanaimo Group, the Boulder Batholith in southwestern Montana. The SURGE student will analyze the history of the Boulder Batholith using Ar-Ar thermochronology, a method in which argon-39 is used as a proxy for potassium-40 in the potassium-40/argon-40 radioactive dating of rocks. This project is designed to introduce an undergraduate student to the entire process of Ar-Ar thermochronology. They will process rock samples for irradiation (crushing, sieving, magnetic grain separation, LMT, etc. – the steps required to go from a bulk rock to ~0.5 mm grains of separated K-feldspar), analyze irradiated samples in Stanford’s noble gas lab, and write up their results in the context of the regional geology of Idaho and Montana, which they will be reading about during the duration of their SURGE summer.

While a background in earth sciences (geology, oceanography, etc.) is preferred, this project may also be suitable for students with chemistry or environmental science backgrounds. It is specifically designed such that even a rudimentary knowledge of radioactive dating will be sufficient for the student to understand the research they will be performing, although they are expected to significantly improve that knowledge through reading and research. No prior lab experience is required, but the student must be able to work independently while carefully following PPE (personal protective equipment) and safety procedures in order to minimize risk when handling radioactive material, hazardous chemicals, and machines that release silica dust.

Environmental change in ancient and future oceans: understanding the role of marine oxygen and temperature change across timescales

Mentor: Prof Erik Sperling
SESUR only

Due to anthropogenic increases in CO2 the world is becoming warmer and oceans are also becoming more acidic and less oxygenated. The geological record demonstrates that oxygen and temperature change are the two main levers controlling both evolutionary radiations and mass extinctions. Yet because changes to oxygen levels and temperature often co-occur (along with still other effects), causal inferences are often limited to simple temporal correlation, and it is unclear which specific environmental factor was most influential.

Recently, we have used an ecophysiological model (the Metabolic Index) to understand the drivers of habitat loss in the oceans during the Permian-Triassic mass extinction, when up to 96% of marine species went extinct (Penn et al., 2018, Science). A noted issue with this study is that currently available physiological data mainly comes from arthropods and fish--we lack physiological data from organisms that actually make up the bulk of the marine fossil record—brachiopods, bryozoans, echinoderms, cnidarians and molluscs. If the physiological traits of these five phyla differ substantially from the available arthropod and fish data, our understanding of the extinction magnitude and its effects are incomplete. This SESUR project will make the first measurements of oxygen tolerance across temperature ranges in these five phyla and compare them to the arthropod/fish dataset. These results will also be used to examine how oxygen and temperature changes in the California Current ecosystem over the next 100 years will impact the viable habitat distribution of these organisms. Over the course of the project, the student will learn marine invertebrate biology and physiology, global change biology, and how environmental change in the geological past has affected life on Earth.

Experimental protocol: The experiments themselves will involve closed-cell respirometry experiments. These techniques are relatively straightforward but do require careful attention to detail.

Location: This SESUR project will take place at marine labs in the Pacific Northwest, specifically Friday Harbor Marine Lab (San Juan Islands, Washington State), Bamfield Marine Lab (west coast Vancouver Island, Canada) and Quadra Island (Inside Passage, British Columbia).

Requirements:  The project does not require any specific background knowledge or skills and is open to all levels of experience, although previous experience with R or marine biology/oceanography would be useful. However, some of the work will be conducted independently by the SESUR student at the marine stations, and we want to ensure the student is competent with the protocols prior to the summer. The ideal candidate will be available in spring term for at least 5 hours per week for a paid research assistant position to gain experience with the protocol. Please contact Dr. Sperling for more information.

Groundwater Quality and Geology in the Central Valley

Mentors: Prof Steven Gorelick and Arden Wells, Earth System Science

Groundwater pumped from some wells in California’s Central Valley contains high concentrations of uranium. This uranium is naturally-occurring, derived from the eroded granites and other sediments that make up much of the Eastern San Joaquin Valley Aquifer. Our study’s goal is to understand and model why uranium concentrations have been increasing in Central Valley groundwater. We are seeking a student to help us analyze well logs in public well completion reports. We have water quality data from most public supply wells in the region, but we don’t know from which sediment layers and formations each well pumps. For this project, the student will match well completion reports to public supply well data and identify correlations between sediment layers and water quality. They will also identify locations where wells are screened at multiple intervals and groundwater from different aquifers may mix. One question we hope this project can answer is "Do wells pumping groundwater from volcanic sediments have worse groundwater quality?" This work will be done on a computer at Stanford over 8-10 weeks during Summer 2019. The ideal candidate has a basic understanding of geology and chemistry (preferably has taken a college-level course in each subject) and an interest in learning more about groundwater quality and hydrogeology. Students with skills with GIS or statistics are encouraged to apply. We will work with the student to tailor the project to their research interests, emphasizing geology, GIS, or statistics.

Exploring the source mechanism of oceanic microseisms with big data

Mentors: Prof Greg Beroza, Lise Retailleau, and Yixiao Sheng

Natural or artificial activities radiate seismic energy in addition to just earthquakes. For example, oceanic activity generates seismic signals that can be recorded by seismometers far inland. These weak seismic signals, though previously treated as a nuisance, carry information about Earth structure. This has led to multiple applications in geophysics studies, ranging from Earth structure tomography, monitoring, to earthquake hazard analysis. Despite these successful applications, our knowledge of the origin of these signals is still limited, especially the source mechanism for Love wave (waves guided across the Earth’s surface with horizontal-transverse motion). A starting point to understand better the source mechanisms is achieving accurate source locations of these microseismic signals. Understanding how far away from the coast these signals are generated gives information about the influence of water depth, and examining whether different types of waves are generated at the same location and time may reveal intrinsic connections. Recent studies have demonstrated promising array techniques to improve the locations of ocean-generated waves. Thanks to the long term operation of seismic arrays in California, we can combine the advanced array techniques with seismic data continuously recorded over 15 years, to constrain the location and migration of these sources.

We are seeking an enthusiastic student to help us implement the developed techniques on the pre-processed data. We anticipate the student will develop some understanding of oceanic microseisms and their source mechanisms. The student will develop basic skills in seismic data analysis. A background in geophysics is not required, but some prior experience with scientific programming, preferably with Python or MATLAB would be very helpful.

Data Science to quantify Uncertainty in Geologic Basin Modeling

Mentors: Prof. Stephan Graham and Tanvi Chheda

To decipher the Earth's past, we use present day evidence and clues, and find the past scenarios that could've resulted in what we see today. Data science and geology put together make a powerful tool to tackle this challenge. One way to quantitatively model a geologic basin is using Basin and Petroleum System Modeling. It integrates geology, geochemistry, and physics to predict hydrocarbon generation and accumulation, among other things. Because of the large number of uncertain input parameters and insufficient data constrains, there exists inherent uncertainty in modeling results. The objective of this project is to quantify uncertainty, risk, and value of information.
An enthusiastic undergraduate student will get an opportunity to work on a rich dataset from offshore East Coast of Canada. A modeling program will be used to run simulations and compare pressure, temperature, and other modeling outputs to those actually measured in the field using Bayesian statistics. To accelerate scientific analysis and automate repeated tasks, you will get a chance to write scripts for automation and data analysis. A strong background in statistics and fluency in MATLAB (Python is acceptable in lieu) are required. Writing and Illustrator/ Photoshop skills and coursework in Object Oriented Programming are desirable. Students from any major are welcome to apply: those new to Earth sciences or geology can be introduced to these areas.