2025 JT-SURF Research Projects - Descriptions
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Simone Baumann-Pickering - Professor, Marine Physical Laboratory Research Areas: Marine Ecology, Acoustics
Passive acoustic long-term autonomous monitoring data has been collected in US waters since 2006, amassing an acoustic archive of ~500 cumulative years of continuous high-frequency acoustic data. Ongoing analyses focus on improvements of AI-based algorithms to automatically extract signals of interest from the archive, conduct spatio-temporal analysis of occurrence, translate acoustic presence into animal density, and infer habitat preferences based on oceanographic conditions relative to presence and density.
JT-SURF fellows will work with a postdoctoral fellow, a staff researcher, or graduate student directly on a project, likely to either improve or run automated routines for signal detection and classification, and to evaluate output for accuracy. They will evaluate time series generated from this effort and provide scientific figures for reports or manuscripts. Day-to-day supervision will be through the direct mentor, with weekly interactions with the principal investigator through lab meetings.
Valentina Di Santo - Assistant Professor, Marine Biology Research Division. Research Areas: Biomechanics and Physiology of Fish Locomotion
In the Di Santo Lab, students will contribute to research exploring fish movement, performance, and adjustment to changing environments. Participants will have the opportunity to:
- Analyze the movement of schooling fishes using video tracking and kinematic analysis to study collective behaviors.
- Quantify metabolic rates of fish during locomotion under varying environmental conditions, such as warming or hypoxia, using respirometry techniques.
- Study the kinematics of walking fishes, investigating how certain species transition from swimming to underwater walking through biomechanical experiments.
This interdisciplinary work integrates physiology and biomechanics to answer fundamental questions about fish locomotion. Students will gain hands-on experience with experimental design, data collection, and analysis.
Activities include: analyzing and digitizing movement of fish in 3D, analyzing metabolic rates of fish locomotion. Supervision by me and postdocs
**This project includes a remote/virtual option.
Yassir Eddebbar - Assistant Research Scientist, Climate, Atmospheric Science and Physical Oceanography. Research Area: Climate Sciences
The equatorial Pacific is the largest source of natural carbon to the atmosphere, but the processes driving this carbon outgassing are poorly know. Using autonomous measurements and satellite data, this project aims to identify the impacts of tropical instability waves, which are large eddies that propagate along the equatorial Pacific, on carbon fluxes and primary production.
JT-SURF fellows will gain hands-on skills analyzing multiple data streams using python and shell coding. Data analysis skills will include learning how to import and process data from different sources, conduct various types of time series analysis to characterize variability and relationships between variables, and create figures for visualization and communicating results. JT-SURF fellows will also gain communication skills by creating a poster and preparing progress talks through the project. The PI and a graduate student will be the main mentor for the student.
Sarah Giddings – Associate Professor, Physical Oceanography. Colleen Petrik – Assistant Professor, Integrative Oceanography Division. Research Areas: Physical Oceanography, Biological Oceanography
The California Current System is an eastern boundary upwelling system well-known for its high productivity and importance to fisheries. Recent research campaigns have sought to address the temporal and seasonal variability of this region’s productivity through high resolution measurements of mesoscale and submesoscale features (from ~200km to less), particularly in the relatively undersampled transition zone between the high upwelling region of the Northern CCS and the countercurrent region of the Southern California Bight. Understanding physical-biological coupling in the region is important for fisheries, biodiversity, and conservation efforts.
Potential research projects will address drivers of productivity in the California Current System at these local scales of 200km or less. Using in-situ measurements from recent research campaigns, satellite data, and regional models, a JT-SURF fellow could investigate topics like upwelling anomalies or internal wave features and their biological impacts in the “transition zone” in recently designated marine sanctuary, the Chumash National Marine Sanctuary offshore from Point Conception. Projects on the region could shape future reports and conservation for this sanctuary or inform physical-ecological studies of the area recently leased for offshore wind farms.
The JT-SURF fellow will be mentored primarily by a graduate student for day-to-day support, with further advising from postdoctoral and PI assistance. Typical research is computer-based analysis of data and therefore interested fellows should be competent/motivated in coding (python, MATLAB). JT-SURF fellows will gain data analysis skills and science communication skills via lab meetings and progress talks through the project.
**This project includes a remote/virtual option.
Sarah Gille – Professor, Physical Oceanography. Research Areas: Physical Oceanography, Polar Science.
Possible research projects will address circulation in the California Current System and the Southern California Bight. In the 1970s, the toxin DDT was dumped into the San Pedro Basin. As part of a multi-disciplinary project, we are using models and data to try to understand how DDT might have been distributed initially, where it might be distributed in the future, and how to mitigate further contaminant dispersal. The project as a whole has broader goals to assess impacts on ecosystems and humans. Other research opportunities could examine observations from the Surface Water and Ocean Topography satellite, which measures sea surface height along a 120-km wide swath, providing new insights into small-scale ocean processes.
Saulo Soares (project scientist) will provide day-to-day supervision. Typical research is computer-based analysis of data and requires coding skills, persistence, and problem-solving skills. The numerical models that we analyze are based on the Navier-Stokes equations and solve partial differential equations, so we seek students with a foundation in physics and math, including calculus, multi-variable calculus, and hopefully linear algebra and ordinary differential equations.
Jamin Greenbaum - Researcher, Institute of Geophysics and Planetary Physics. Research Area: Geophysics
The Scripps Polar Geophysics Lab is composed of researchers and engineers dedicated to improving predictions of global sea level rise by revealing and understanding processes that drive rapid melt of the Antarctic Ice Sheet. Our research involves analyses of data and integration of data into numerical ice, ocean, and subglacial hydrology models. This particular research project involves the analysis and use of high resolution digital elevation models acquired by satellites over Antarctic ice shelves to estimate floating ice thickness --and thickness change over time driven by ice melt. The outcomes of the project will inform the accuracy of numerical ocean models that attempt to predict melt rates based on measured ocean properties.
The student will be trained to locate, organize, and process satellite data products using a Linux operating system. They will also use data collected by aircraft to perform error estimates where the satellite and airborne overlap. They will use Python and Matlab tools to perform computations on the data, with guidance from the principal investigator and his group. Day-to-day guidance will be provided by members of the Polar Geophysics Lab, including the principal investigator, Postdoctoral Fellow Tyler Pelle, Ph.D. student Briar Conger, and Applications Programmer Daniel Auerbach.
**This project includes a remote/virtual option.
Jennifer Haase - Professor, Institute of Geophysics and Planetary Physics. Research Area: Atmospheric Science, Geophysics
Atmospheric Rivers have significant impacts on the water supply in the western US and also on flooding hazards in extreme rainfall events. We are making new aircraft observations that sample the environment of the storm while offshore. Analysis of the information from these new measurements should shed new light on the vertical structure of the storm. Several case studies of AR events will be studied to describe AR features in better vertical detail.
JT-SURF fellows will be reviewing the case history of several impactful AR events, then writing simple programs to visualize the cross-sectional structure of the Atmospheric River. Simple programs to create composite views of ARs will be used to quantify their description. JT-SURF fellows should be able to program in MATLAB or be willing to learn.
Ilysa Iglesias - Postdoctoral Scholar, Integrative Oceanography Division. Research Area: Deep-Sea Ecology, Fisheries Acoustics.
The deep pelagic ocean is one of the largest, yet least understood, environments on earth. In this project, we will explore how animals inhabiting these deep depths (from ~200-1500 m), are vertically distributed in the water column during different life stages. Using fisheries acoustics data (EK80) in combination with biological catch data collected previously on Scripps research cruises (led by Dr. Anela Choy), as well as publicly available datasets and primary literature, the SURF fellow will generate knowledge about the depth range of deep sea fish species in the Southern California Bight.
JT-SURF fellows will gain background knowledge in and experience with deep-sea ecology, fisheries acoustics, working with large biological datasets (including accessing and analyzing publicly available data) and using the programming language R to explore the vertical distribution of deep pelagic animals. We plan to develop these skills with the fellow and do not require previous knowledge in these topics, although we do require a willingness to learn! In addition to building the fellow’s analytical skills, we plan to provide advice and guidance on developing independent scientific questions, obtaining background knowledge from primary literature and building a fulfilling scientific career. JT-SURF fellows will be mentored by a Postdoctoral fellow (Ilysa Iglesias), and will also be invited to participate in lab meetings and events within the Choy Lab. This position is primarily computer-based, with a preference for remote (or hybrid) work options.
**This project includes a remote/virtual option.
Paul Jensen - Professor, Center for Marine Biotechnology & Biomedicine. Research Area: Marine Natural Products
We study microbes in the ocean and the natural products they produce. The goal is to find new medicines. This project targets the discovery of new natural products with activity against the malaria parasite and other neglected diseases. It will involve learning basic techniques in microbiology, analytical chemistry, and the genetics behind natural product biosynthesis.
Activities will include preparing media, growing bacteria, generating organic extracts, submitting them for screening, analyzing active extracts, and isolating active compounds. Molecular taxonomy and genome sequencing may also be involved. The JT-SURF fellow will be mentored by a postdoctoral scholar.
April Lukowski- Assistant Professor, Center for Marine Biotechnology & Biomedicine. Research Areas: Environmental Toxicology, Genomics, Metagenomics, Bioinformatics
The Lukowski Lab looks to the ocean for proteins that install bromines onto their substrates, as marine environments are a richer source of bromine than terrestrial environments. Marine cyanobacteria produce such enzymes; however, they demonstrate unique preferences for the type of substrate on which they will install bromines. This phenomenon of substrate specificity has yet to be understood. This project will focus on how these enzymes perform their mechanisms on different substrates by mutating residues likely responsible for substrate specificity.
A JT-SURF Intern in the Lukowski Lab will gain hands-on experience learning molecular biology and protein biochemistry techniques, including DNA cloning, mutagenesis, and protein expression, purification, and characterization. Weekly meetings are held to discuss research topics; an intern can expect to gain presentation and communication skills in this format. A graduate student, Anna Skrip, and the PI, April Lukowski, will supervise the intern.
Tyler Pelle - Postdoctoral Green Scholar, Institute of Geophysics and Planetary Physics. Research Areas: Geophysics, Geosciences
The Antarctic Ice Sheet is the largest reservoir of freshwater on Earth. The glaciers that drain it have undergone rapid acceleration, thinning, and retreat over the past few decades in response to climate change, raising global mean sea level by 14 mm between 1979-2017. This behavior is driven by interaction of the ice sheet with components of the climate system, in particular the adjacent ocean and underlying bedrock (including freshwater systems that exist beneath the ice sheet, termed “subglacial hydrology”). Our lab uses numerical ice sheet, ocean, and subglacial hydrology modeling to investigate these ice-climate interactions and better understand how they might impact the future fate of Antarctica and its corresponding contribution to global sea level rise.
Potential research projects include applying data analysis techniques on numerical model output to explore how warm ocean waters drive melt of the periphery of the East Antarctic Ice Sheet and how these simulated rates of melting compare to satellite observations. We also have large quantities of ice sheet model projections of the entire Antarctic Ice Sheet through 2300 available, where interested students can investigate the future demise of particularly vulnerable regions (e.g., drivers of collapse of the West Antarctic Ice Sheet, ocean driven melt of the world’s largest floating ice shelves, etc.). Given the diversity of ice sheet projections that we have available, there is considerable room for development of a model output-analysis project that conforms to the students’ interests and strengths. Additionally, for qualified applicants, there is potential to develop and run ice sheet model projections of individual glaciers, including the Thwaites and Pine Island Glaciers in West Antarctica as well as Totten and Denman Glaciers in East Antarctica.
The JT-SURF student will be primarily mentored by PI Pelle with support from graduate students and others in the Polar Geophysics Lab, led by Jamin Greenbaum. Weekly group meetings will be held to share updates on ongoing research, discuss and resolve any project bottlenecks, and provide general updates on project progress. Given the nature of proposed work, students should have some familiarity with coding (MATLAB or Python) and an interest in polar regions. By conclusion of the project, SURF students will gain experience in data analysis, navigating clustered computing environments, oral/visual science communication, and working in a dynamic science lab.
Day-to-day activities of the JT-SURF student will include but is not limited to: (1) getting set-up and familiar with the IGPP-hosted JKB-computing cluster infrastructure; (2) reading key literature to gain knowledge in the field of Antarctic science evaluating; (3) modifying and running pre-written MATLAB scripts to gain experience in how to upload, work with, and process numerical model output; (4) developing their own scripts and techniques to analyze model output and create figures; (5) depending on student qualifications, possibly run pre-existing ice sheet models of select glaciers; and (6) engage in weekly group meetings to share weekly research/progress updates and stay up-to-date on work within the lab. The JT-SURF student will be primarily mentored by PI Pelle with support from graduate students and others in the Polar Geophysics Lab, led by Jamin Greenbaum. Weekly group meetings will be held to share updates on ongoing research, discuss and resolve any project bottlenecks, and provide general updates on project progress.
**This project includes a remote/virtual option.
Stuart Sandin - Professor, Marine Biology Division. Research Areas: Conservation Biology, Mathematical Ecology, Coral Reef Ecology
The JT-SURF fellow will work with a postdoctoral fellow, graduate students, and staff scientists to analyze coral reef imagery from a project that uses genetic sampling in combination with large-area imaging to assess adaptations of the coral holobiont in its environmental context and through time. This project involves using this imagery of coral reef habitats to track changes in reef ecosystems through time and focuses on the development of a ‘bio-bank’ of genetic samples from coral colonies that can be used to investigate molecular adaptations and changes in population structure through environmental disturbances (e.g., marine heatwaves, disease outbreaks, anthropogenic disturbances).
JT-SURF fellows will gain experience in computer-based and AI-assisted imagery workflows, with opportunities for hands-on lab work. Fellows will work with a postdoctoral fellow and several staff researchers to segment and annotate benthic data from reef imagery for percent cover and demographic analyses, and help to organize a ‘bio-bank’ of collected genetic samples from coral. Day-to-day supervision will be through the postdoc, graduate student and staff scientists, with weekly interactions with the principal investigator through lab meetings.
Dave Stegman - Professor, Institute of Geophysics and Planetary Physics. Research Areas: Geophysics, Geosciences
Activities include: numerical modeling of planetary interiors using high performance computing. PI, Dave Stegman will be the primary supervisor and will also have support from a Postdoc and PhD student.
**This project includes a remote/virtual option.
Aaron Thode - Researcher, Marine Physical Laboratory. Research Areas: Marine Mammal Acoustics, Advanced Acoustic Signal Processing
Applying machine learning techniques to identify bowhead whale and gray whale calls in underwater recordings. Students will learn how to convert sounds into spectrograms, and participate in helping deploy small acoustic recorders offshore San Diego.
Under day-to-day supervision of a graduate student, summer interns will be processing acoustic data, annotating presence/absence of whale calls in the data, and helping test and evaluate machine learning algorithms for identifying the calls. Much of this can be done on a local laptop and even remotely. I'm also interesting in having students help snorkel to deploy and recover acoustic recorders around the SIO Pier to help test and calibrate directional acoustic instrumentation.
Daniel Wangpraseurt – Associate Researcher, Marine Biology Research Division. Research Area: Coral Ecophysiology, Coral Restoration and Engineering, Aquatic Benthic Photosynthesis
Coral reefs are under increasing threat from climate change, with rising sea temperatures triggering widespread coral bleaching events. This project focuses on the development of innovative nanomaterials designed to reduce bleaching susceptibility and enhance coral resilience. By integrating bio-nanoengineering approaches, we aim to create biomimetic materials that interact with coral microhabitats to mitigate thermal stress and optimize environmental conditions for coral health. This work combines advanced nanotechnology, environmental sensing, and coral physiology, offering a transformative approach to reef restoration and conservation in a rapidly changing climate.
JT-SURF fellows will work closely with a postdoctoral researcher who is developing these materials and collaborate with another student investigating coral stress responses. The primary responsibility of the undergraduate will be to set up and run controlled coral bleaching experiments, evaluate coral health using physiological and imaging techniques, and assist in data analysis to assess the effectiveness of the nanomaterials.
A typical work week will involve preparing and maintaining experimental aquaria, monitoring coral health metrics (e.g., photochemical efficiency, polyp behavior, and visual indicators of stress), and contributing to weekly team meetings to discuss progress and troubleshoot challenges. Day-to-day supervision will be provided by the postdoctoral fellow, ensuring consistent guidance and mentorship throughout the project, with additional input and oversight from the principal investigator as needed. This hands-on experience will provide valuable insights into coral biology, climate resilience strategies, and cutting-edge bio-nanoengineering techniques.