Research Projects by Subject

Note: If a research project is listed as having openings for more than one SIP intern, it should be assumed that the interns are expected to work collaboratively on the same project and/or data set. This may preclude rising seniors from submitting papers based on such projects to the Intel Science Talent Search competition.

Astronomy & Astrophysics

Code Research Project Descriptions
AST-01 Title: Stellar Isotope Survey at Lick Observatory (SISLO)
Primary Mentor: Dr. Evan Kirby
Secondary Mentor: Prof. Raja GuhaThakurta
Number of Interns: 2

Spectroscopy is an astronomer’s favorite tool for measuring the compositions of stars. Different elements absorb light at different wavelengths. Stars with a lot of carbon, for example, absorb lots of light around 430 nm. It is nice to know the amount of an element in a star, but the most detailed study of the composition of a star is to measure how each element is distributed among its constituent isotopes (atoms with the same number of protons but different numbers of neutrons). The SIP students will learn how to measure the isotopic compositions of stars and track how the isotopes change over the course of the Milky Way Galaxy’s history. The student will use data already collected from the Hamilton spectrograph at Lick Observatory. You can learn more about SISLO from the original proposal to use the Hamilton spectrograph. SISLO is seeking two highly motivated SIP students who are adept at independent learning. The students should work well together as a team. Previous computer programming experience or a desire to learn about computer programming is required. The primary mentor for this project, Dr. Evan Kirby, is a postdoctoral researcher at UC Irvine in southern California. The students should have the means and be willing to visit Irvine once or twice during the summer for 3-5 days per trip. The remainder of the communication with the primary mentor will be conducted over e-mail and Skype.

AST-02 Title: Cycling of Chemicals in the Gaseous Phase of the Large and Small Magellanic Clouds
Primary Mentor: Dr. Jessica Werk
[Faculty Contact: Prof. J. Xavier Prochaska]
Number of Interns: 2

Most of the atoms in your body were fused in the cores of stars. An understanding of their journey requires a picture of how gases cycle into and out of stars and, ultimately, into and out of galaxies. The Large and Small Magellanic clouds are our nearest neighbor galaxies — currently being cannibalized by the Milky Way halo — and serve as excellent laboratories in which to study the physical properties of gaseous material associated with stars and the interstellar medium. In this project, you will learn about emission line and absorption line spectroscopy. Ultimately, these experiments can tell us about what galaxies and stars are doing with their gas.

AST-03 Title: Modeling and Analysis of the Spectra of Exoplanets
Primary Mentor: Ms. Caroline Morley
Secondary Mentor: Prof. Jonathan Fortney
Number of Interns: 2

Over 1000 exoplanets — planets around stars other than the Sun — have now been discovered. This project will involve characterizing the atmospheres of exoplanets and determining their compositions. You will use computer simulations of planetary atmospheres to understand what a planet of a specific temperature and composition will look like. Each molecule has its own unique fingerprint; that is, based on the quantum physics of the molecule, it absorbs strongly at specific colors (called wavelengths) and more weakly at other wavelengths. Based on which molecules form as a function of height, we can calculate how bright the planet will be at different wavelengths, which we call a spectrum. Exoplanets are very challenging to observe because they are faint and extremely close to their stars, which are very bright. However, we know that giant planets and stars are actually made of the same basic building blocks: mostly hydrogen and helium, plus an additional assortment of elements that make up a few percent of the total mass. There is a class of objects called “brown dwarfs” that form like stars, but are much less massive, so they are never able to start the nuclear fusion of hydrogen that defines stars and makes them hot and bright. It turns out that these brown dwarfs can have the same temperatures as planets, but are floating by themselves in space instead of orbiting a star, so they’re much easier to observe. In this project, we will try to understand the similarities and differences between brown dwarfs and planets. In particular, we will look at the planetary-mass free-floating brown dwarfs which have recently been discovered, and compare those objects to planets of the same temperatures.

AST-04 Project cancelled!
The project “Hierarchy in Galaxy Groups: Separating Central and Satellite Galaxies over 8 Billion Years” has been cancelled due to the unavailability of the mentor.

AST-05 Title: Uranus and Neptune Interior Models
Primary Mentor: Dr. Nadine Nettelmann
[Faculty Contact: Prof. Jonathan Fortney]
Number of Interns: 1

Little is known about the interior structure of Uranus and Neptune, despite their importance in our understanding of the formation of the solar system and of the class of detected extrasolar Neptune-sized planets. Moreover, standard planetary structure models of the ice giants that have been developed since the Voyager era fail to agree with recent HST-and ground based atmospheric abundance measurements. Therefore, advanced ice giant planets models need to be computed. Such models will assume a super-adiabatic interior with a compositional gradient. The new interior models will be designed to match the observed CO and CH4 abundances of Uranus and Neptune. The prospective student is supposed to let a PC compute advanced Uranus and Neptune interior models. For that purpose the student will use an existing code and run it repeatedly. Programming language skills are not required but the student will get the opportunity to become familiar with the C++ language. Depending on interest and performance the student may develop sub-routines for generating compositional and temperatures profiles a priori, to be read-in by the main program for the structure calculation. The student will gain insight to the state-of-the art assumptions about planetary interiors including the bulk composition of the solar system planets. Perhaps most importantly, the student can learn how progress on a highly specific topic is at the mercy of progress in various fields and thus benefits from communication between different research groups.

AST-06 Title: Studying the Nature of Dwarf Elliptical Nuclei and Globular Cluster Satellites
Primary Mentor: Dr. Elisa Toloba
Secondary Mentor: Prof. Raja GuhaThakurta
Number of Interns: 2

The goal of this project is to learn about the origin of the nuclei observed in dwarf elliptical galaxies. Some theories suggest that these nuclei may have formed from the merging of globular clusters (groups of stars that orbit a galaxy) that have migrated to the center of the dwarf elliptical galaxy. We have obtained Keck/DEIMOS spectra of a sample of 300 globular cluster candidates around 21 different dwarf elliptical galaxies. The SIP student will analyze the properties of these globular cluster candidates to remove sample contaminants (objects that are not globular clusters). The student will then use the technique of spectral co-addition to analyze the spectroscopic properties of the globular clusters and compare them to the properties of the 21 dwarf elliptical nuclei.

AST-07 Title: Kinematic Anomalies in the Rotation Curves of Dwarf Elliptical Galaxies
Primary Mentor: Dr. Elisa Toloba
Secondary Mentor: Prof. Raja GuhaThakurta
Number of Interns: 2

The goal of this project is to quantify the degree of regularity and symmetry of the rotation curves of the stellar component of dwarf elliptical galaxies. Dwarf ellipticals are thought to have originated from star-forming disk galaxies that have been transformed into puffed up quenched galaxies by their environment. The anomalies and asymmetries in their rotation curves provide important constraints on how the environment transforms these galaxies. The SIP student will collect the rotation curves of the nearly 80 dwarf ellipticals published in the literature and will apply the new statistical analysis techniques that our team has recently developed to quantify the strength of these irregularities and asymmetries. The irregularities and asymmetries will be analyzed in the context of environmental and internal properties of the dwarf elliptical galaxies.

AST-08 Title: Supermassive Black Holes at the Centers of Galaxies
Primary Mentor: Dr. Martin Gaskell
Number of Interns: 3

This project involves studying the variability of the light emitted as supermassive black holes in the centers of galaxies swallow gas. These black holes are typically ten million to more than a hundred million times more massive than our sun. The role of the students is to measure the brightness from images taken with various optical telescopes, to compare these variations in brightness with data taken by satellites, and to work on related issues of data reduction and analysis so that the results can be published. The aim of the research is to understand why the energy output varies so dramatically with time. This project is part of an international collaboration.

AST-09 Title: How do Galaxies Grow in their Old Age?
Primary Mentor: Dr. Guillermo Barro
[Faculty Contact: Prof. David Koo]
Number of Interns: 2

Red elliptical galaxies are thought to be the final stage in the life-cycle of galaxies. They are the most massive galaxies in the nearby Universe, and appear red because they have ceased forming stars. How elliptical galaxies become so large, continuing to grow even after their star formation has ended, remains poorly understood. We aim to study the close environments of very distant galaxies, seen at a time when the Universe was only 2 billion years old, to determine if galaxy collisions play a key role in creating the most massive and oldest galaxies. This work will make use of very high-quality data products developed by astronomers in the CANDELS survey, including the visual analysis of deepest and highest resolution optical and near-infrared imaging data ever taken by the Hubble Space Telescope. This video illustrates the formation process of one of such galaxies showing the heavy bombardment of small systems at late times.

AST-10 Title: Galaxy Evolution
Primary Mentor: Mr. Hassen Yesuf
[Faculty Contacts: Profs. David Koo and Sandra Faber]
Number of Interns: 2

There are several interesting projects on the general theme of galaxy evolution that the two SIP students can work on. For instance, gas accretion onto galaxies and its ejection by galactic winds are two important processes in shaping the properties of galaxies but they are still poorly understood (read this paper for background information). The SIP students will use Python scripts to combine the spectra of 2000 distant galaxies from the DEEP3 survey. The galaxies are so distant that they are seen at a time when the Universe was about half of its present age. Another possible project will involve studying outflows in Active Galactic Nuclei (AGN, galaxies with active black holes) and green valley galaxies (GV, galaxies transition from star-forming to being quiescent). This project will involve using Python scripts to combine tens of thousands of spectra of nearby galaxies from the SDSS survey. The aim of the project is to check if there is a connection between outflows and galaxy quenching (i.e, transformation from star-forming to quiescent). For background information, the student can read this paper. A third possible project involves writing Python machine classification (learning) algorithm (in particular Neural Network) to automate and access the reliability of the on-going visual (human) classification of distant galaxies in the CANDELS survey. A fourth possible project involves studying the correlation between black hole mass and the central density of galaxies.

AST-11 Title: The Motion of Wisps in the Crab Nebular Supernova Remnant
Primary Mentor: Mr. Alexander Rudy
Secondary Mentor: Prof. Claire Max
Number of Interns: 2

The Crab Nebula is a supernova remnant, the remains of a giant star that exploded in the year 1050AD. At the center of the nebula is a neutron star, surrounded by gas left over from the massive explosion 1000 years ago. The rotating neutron star at the center of the nebula (called a pulsar, for the 33ms interval pulses it emits) lights up the large cloud of gas, and powers jets and ripples that move away from the pulsar. Here is a movie of this phenomenon. Although the movements of the ripples (called “wisps” in the Crab Nebula) has been measured over the course of a year before, we have data that suggest that the wisps move at a much faster speed when they are close to the pulsar. This project would develop an analysis and measurement technique for the moving wisps using data from the Keck telescopes in the near-infrared. The SIP interns will measure the wisp motion and attempt to connect the motion of the wisps that we measure when they are close to the pulsar with the published motion of the wisps when they are far from the pulsar. In the course of developing a novel analysis technique for the wisps, we may expand the scope of the project to consider motions in the nebula outside the wisps. Interested students should be prepared to get comfortable with linear algebra.

AST-12 Title: Flux Calibration of Keck/DEIMOS Spectra: Extracting Physically Meaningful Information for Andromeda and Milky Way Stars
Primary Mentor: Ms. Katherine Hamren
Secondary Mentor: Prof. Raja GuhaThakurta
Number of Interns: 1

The UCSC-based SPLASH survey (Spectroscopic and Photometric Landscape of Andromeda’s Stellar Halo) has to date collected ~15,000 spectra of stars in our nearest galactic neighbor, the Andromeda Galaxy. These spectra have so far been used for a variety of purposes, including understanding the kinematics of Andromeda’s various components, and pinpointing unusual stars. Before the spectra can be used to their fullest extent, however, they need to be “flux calibrated” – i.e., the spectra’s flux values must be converted to physically meaningful units. Flux calibration of an object depends on the details of the observation in which the spectra were obtained such as airmass, parallactic angle, seeing, and position of the object in the focal plane. We are looking for 1-2 SIP interns to flux calibrate the SPLASH spectra, thereby helping future astronomers understand both the properties of stars in Andromeda and the exact response of the DEIMOS spectrograph. The SIP interns will gain a deep understanding of the relationship between an instrument, an observation, and the final science.

AST-13 Title: Spectral Typing the SPLASH Sample
Primary Mentor: Ms. Katherine Hamren
Secondary Mentor: Prof. Raja GuhaThakurta
Number of Interns: 1

The Andromeda galaxy is a special laboratory in which astronomers can study a galaxy at all scales, as it is both close enough for us to resolve it into individual stars, but distant enough that we can see the entire galaxy at once. The UCSC-based SPLASH survey (Spectroscopic and Photometric Landscape of Andromeda’s Stellar Halo) has to date collected spectra of thousands of individual stars in Andromeda. With this data set, we can study stellar populations in Andromeda in a much more holistic sense than we can in any other galaxy. The first step of this process is to determine the physical properties of the stars for which we have spectra. There are a number of pipelines that do spectral typing in the Milky Way, but none that are tailored for stars as distant as those in Andromeda. We are looking for a student to start modifying existing codes to be used on the stars in our SPLASH survey database. The student will leave the SIP program with a deeper understanding of stellar properties, as well as statistics and scientific computing.

AST-14 Title: Finding Stellar Companions to Kepler’s Exoplanet Host Stars
Primary Mentor: Ms. Angie Wolfgang
[Faculty Contact: Prof. Greg Laughlin]
Number of Interns: 2

The Kepler Mission has discovered thousands of planets orbiting distant stars, the vast majority of them located much closer to their host stars than any of the planets in our Solar System are to the Sun. To understand how such planets could have formed, we must first fully characterize the current state of these planetary systems, including searching for any other stars which also orbit the planet-hosting star. The SIP students who work on this project will learn how to process and analyze high resolution images of stars in the search for these stellar companions, and will produce a catalog of nearby sources that they discover. There is also an opportunity to participate in acquiring this data at Lick Observatory, for those particularly interested in seeing how telescopes are used by professional astronomers.

Biomolecular Engineering

Code Research Project Descriptions
BME-01 Title: Curing, Managing, and Healing Cancer
Primary Mentor: Dr. Elinor Velasquez
[Faculty Contact: Prof. Jorge Soto-Andrade]
Number of Interns: 4

One non-invasive method for removing a patient’s cancer is the use of chemotherapy or application of cytotoxic drugs to destroy the cancer cells. The currently used cytotoxic drugs are designed to damage the DNA in a cancer cell, yet have produced mixed results for destroying the cancer cells and restoring good health to the patient. Cancer is currently thought to arise from a threshold number of gene mutations occurring in one or more cells. An alternative viewpoint, though not mutually exclusive of the gene mutation viewpoint, is that cancer is a metabolic disease. While metabolic pathway activity is similar across healthy patients or humans without cancer, metabolic pathway activity varies across cancer patients. Thus, each patient’s cancer is unique to that patient, giving rise to a need for a personalized medicine approach to ease cancer in that patient. Viewing cancer as a metabolic disease permits the possibility of designing novel drugs, intended to disrupt metabolic pathways in cancer cells, rapidly causing their death and quickly restoring good health to the patient. The summer project will involve working on the design and implementation of novel metabolic-based chemotherapeutic drugs. The student’s specific project will be focused in one of the following subject areas: biochemistry, computer visualization, math modeling, novel computer algorithm design, computer algorithm implementation, standard bioinformatics data analysis, or statistics. The student’s project supervisor is off-campus this summer, so the student will need to interact with supervisor virtually, using internet communication methods, such as Gmail chat, Google Hangout, Skype, etc. The student will have an office on-campus, as well as access to the campus library and the same facilities as the other SIP students. It is expected that the student will be a co-author of a future conference publication.

BME-02 Title: Lineage Bias and Long-term Persistence of Hematopoietic Stem Cells
Primary Mentor: Dr. Anna Beaudin
Secondary Mentor: Ms. Jessica Perez (MCD Biology)
[Faculty Contact: Prof. Camilla Forsberg]
Number of Interns: 1

Using a recently characterized in vivo lineage tracing model, I have identified a novel fetal hematopoietic stem cell (HSC) that, although capable of supporting reconstitution of the blood system in an irradiated adult recipient, does not reside in the adult bone marrow in situ. This novel fetal HSC exhibits a differential lineage bias and gives rise to unique immune cell subsets that mediate innate immunity. Current aims of my project including understanding the mechanisms regulating lineage bias and long-term persistence of this novel HSC population, as well as pursuing the possibility that this novel HSC may represent the cell-of-origin in pediatric leukemias. The SIP intern working in this lab will need to be at least 16 years old as of June 1, 2014 and will need to go through lab safety training before they can start working on their research project.

BME-03 Title: Characterization of the Proliferative Status of Hematopoietic Stem Cells
Primary Mentor: Ms. Jessica Perez (MCD Biology)
Secondary Mentor: Dr. Anna Beaudin
[Faculty Contact: Prof. Camilla Forsberg]
Number of Interns: 1

Using a recently characterized in vivo lineage tracing model, our lab has identified a novel fetal hematopoietic stem cell (HSC) that, although capable of supporting reconstitution of the blood system in an irradiated adult recipient, does not reside in the adult bone marrow in situ. This novel fetal HSC exhibits a differential lineage bias and gives rise to unique immune cell subsets that mediate innate immunity. We have also detected increased levels of several oncogenes within this novel HSC. Current aims of my project include characterization of the proliferative status of these HSC as well as any roles they may play in pediatric leukemias. The SIP intern working in this lab will need to be at least 16 years old as of June 1, 2014 and will need to go through lab safety training before they can start working on their research project.

BME-04 Title: Mining Phenotypic Data
Primary Mentor: Dr. Jingchun Zhu
Number of Interns: 2

Cancer genomics datasets hosted in the Cancer Browser are currently indexed by metadata, such as data type (e.g. gene expression), platform (e.g. RNAseq) and articles (e.g. PubMed identifiers). However, these structured information only captures a small portion of existing information we have on a tumor sample. Many phenotypic data, such as those exist in a patient pathological report, information in the dataset-associated articles, still only exist in unstructured data form, such as pdf reports. We need a method that can search both structured and unstructured data to identify samples of most interest to a biologist. The summer project is to adapt text mining tools to extract information from reports and perform sample search using a combination of structured and unstructured phenotypic data. More information can be found on the UCSC Cancer Genomics Browser website.

BME-05 Title: Primate-specific Non-coding RNAs
Primary Mentor: Mr. Andrew Field
[Faculty Contact: Prof. Sofie Salama]
Number of Interns: 1

In the Haussler molecular biology lab we use stem cells from humans and non-human primates to make cortical neurons in order to understand the molecular mechanisms underlying the early events in the development of the human brain. Graduate student Andrew Field has recently identified a number of primate-specific non-coding RNAs that are expressed at specific time points during cortical neuron generation. A SIP intern would work with Andrew to use standard molecular biology including PCR and DNA sequencing to characterize the transcript structure of these newly identified non-coding RNAs.

Chemistry & Biochemistry

Code Research Project Descriptions
CHE-01 Title: Metal Nanoparticles and Electrochemistry
Primary Mentor: Prof. Shaowei Chen
Secondary Mentor: Mr. Chris Deming
Number of Interns: 1

Ready availability of sufficient energy resources is critical in virtually every aspect of our life. Currently, fossil fuels (e.g., petroleum) constitute our primary energy sources; yet, they are of limited reserves and are being depleted rapidly, and exert negative impacts on the environment with the combustion products. Therefore it is of urgent importance to develop effective technologies for sustainable energy as well as energy storage for diverse applications. In this context, part of the research effort in the Chen lab is focused on the design and engineering of functional nanomaterials as effective catalysts for fuel cell electrochemistry and as electrode materials for high-performance supercapacitors. A variety of experimental tools will be used extensively in these activities including electron microscopy, spectroscopy, and electrochemistry. A detailed description of the research carried out in Professor Chen’s lab can be found at this website and links therein.

CHE-02 Title: Microbial Photoelectrochemical System
Primary Mentor: Ms. Hanyu Wang
[Faculty Contact: Prof. Yat Li]
Number of Interns: 1

The proposed study will focus on the development of a self-sustained and highly efficient microbial photoelectrochemical system (MPS) that could simultaneously address the increasing demand of clean water and energy due to the global population growth. Recently, we successfully demonstrated a microbial fuel cell (MFC) – photoelectrochemical cell (PEC) hybrid device, which proved the feasibility of chemical fuel (hydrogen) production, using municipal wastewater and sunlight as the sole energy sources. This reported MFC-PEC device not only achieved a decent solar conversion efficiency of 0.80% at zero external bias under one sun illumination, but also has a good soluble chemical oxygen demand (SCOD) removal rate of 186.67 mg/L/day. Click here for a report on this hybrid device. The preliminary success of this MFC-PEC device suggests that solar-assisted microbial technology holds great promise as a practical solution to energy sustainability. Now, we aim to transform this “solar-microbial” device concept into a practical microbial-photoelectrochemical system by addressing some fundamental limitations identified in the existing devices, such as, effective contact area between microbes and electrode, charge transfer at the bacteria/semiconductor interface, and the utilization of solar energy of photoelectrodes. We seek to address these limiting factors from a materials perspective through the rational design of device configuration as well as selection of photoelectrodes. Our goal is to produce chemical fuels in a sustainable and cost-effective manner by using MPS, with municipal waste water and sunlight as the sole energy sources.

CHE-03 Project cancelled!
The project “Sensitive and Molecular Specific Optical Detection of Biomarkers” has been cancelled due to the unavailability of the mentor.

Earth & Marine Sciences

Code Research Project Descriptions
EMS-01 Title: Seismic Imagery of Underwater Sediments in the Elkhorn Slough
Primary Mentor: Dr. Ana Garcia-Garcia
Number of Interns: 1

The mentor’s ongoing research aims to understand the infill of the last thousands of years in the Elkhorn Slough. While some cores and preliminary seismic lines were taken between 2008-2011, this project took off in 2011 with the collaboration of Monterey Peninsula College and has covered the northern-central part of the Slough so far. The mentor aims to complete the survey towards the ocean and will continue surveying this summer, and may involve the SIP student in the survey work, in order to have a better understanding on the whole area (we have some ONR funds). We also might get some extra cores during the summer to groundtruth the indirect data sets. Most of the software we will be using to acquire and interpret the CHIRP data is Triton Imaging Inc’s. The SIP student will learn how to use this software and interpret basic seismic data, as well as correlate it with direct samples.

EMS-02 Title: Sediment Production and Distribution on Midway Atoll
Primary Mentor: Ms. Anne Warner
[Faculty Contact: Prof. Donald Potts]
Number of Interns: 1

The goal of this project is to describe the present sediment distribution at Midway Atoll, a marginal coral reef in the North Pacific. Most of the sediment within a reef ecosystem is produced by organisms, and documenting both the sediment source and how it is subsequently altered and distributed across the atoll via oceanographic factors is the primary objective. Several research topics/projects (working with samples to examining relevant primary literature to introductory GIS techniques) supporting the larger project goal are available to a potential SIP student, depending on the student’s skills and interests. The SIP student’s research will be conducted primarily on the main UCSC campus.

EMS-03 Title: Ecological Effects of an Invasive Mudsnail and its Parasites
Primary Mentor: Ms. Rachel Fabian
[Faculty Contact: Prof. Donald Potts]
Number of Interns: 1

Trophically transmitted parasites commonly induce changes in host morphology and behavior to increase transmission to subsequent hosts. These changes can affect host distribution and resource use, so that infected hosts occupy an ecological niche distinct from uninfected individuals. Trematode parasites that use the Japanese mudsnail in its native range cause snails to move to lower tidal heights and grow larger. Large snails graze more, and exhibit different preferences than smaller snails. Thus, parasites can affect organic carbon cycling through an ecosystem, especially when host species are dominant invertebrates like Batillaria. This project will assess whether the subset of parasite species that infect Batillaria in its introduced range have similar effects on snail hosts as in Batillaria’s native range, and will characterize the differential effects of infected snails on microalgal resources.

Ecology & Evolutionary Biology

Code Research Project Descriptions
EEB-01 Title: Krill Population Dynamics and Trophic Interactions within the Central California Coastal Region
Primary Mentor: Prof. Baldo Marinovic
Secondary Mentor: Ms. Cynthia Carrion
Number of Interns: 2

Krill occupy a centrally important position in the marine food web of the California Current Ecosystem. Our work centers around understanding the physical and biological processes that influence krill populations through time. A variety of research topics/projects related to various aspects of these themes are available for potential SIP students. The SIP student’s research will be conducted at UCSC’s Long Marine Laboratory which is located outside the main UCSC campus in the city of Santa Cruz.

EEB-02 Title: Feeding Strategies in Marine Vertebrates
Primary Mentor: Ms. Sarah Kienle
Secondary Mentor: Prof. Rita Mehta
Number of Interns: 1

The research group is interested in the feeding strategies of marine vertebrates (fishes, sharks, marine mammals, etc.). The goal of the proposed project is to understand the diversity of feeding modes that have evolved in aquatic species and to determine the constraints to feeding imposed by the marine environment. The SIP student will mine the published literature for baseline information, assist in data analyses, and have opportunities to help in the lab/field on a variety of other projects. The SIP student’s research will be conducted at UCSC’s Long Marine Laboratory which is located outside the main UCSC campus in the city of Santa Cruz.

EEB-03 Title: Whisker Growth Dynamics of Seals and Sea Lions
Primary Mentor: Ms. Liz McHuron
Secondary Mentor: Prof. Dan Costa
Number of Interns: 2

Research in Prof. Costa’s lab focuses on the ecology, physiology, and conservation of marine vertebrates, primarily marine mammals (check this site for more details). The specific project that the SIP student will be working on is related to using whiskers of captive seals and sea lions housed at UCSC to understand the foraging behavior of wild populations. Specifically, the student would be using photogrammetry (pictures) to measure growth rates of whiskers to determine how quickly diet information is incorporated into whiskers. The student would be involved in both data collection and data analysis for one or more species, including harbor seals and California sea lions. The SIP student’s research will be conducted at UCSC’s Long Marine Laboratory, which is located outside the main UCSC campus in the city of Santa Cruz.

EEB-04 Title: The Evolution of Coloration Patterns in Wrasses (Labridae)
Primary Mentor: Mr. Vikram Baliga
[Faculty Contact: Prof. Rita Mehta]
Number of Interns: 1

One of the most striking aspects of reef fishes is the coloration pattern they exhibit. Selection operates on color patterns for myriad reasons, including predator avoidance, mate selection, and communication. Little is known whether functional groups exhibit convergent patterns, sometimes referred to as “guild colorations”. We will use the Labridae (wrasses and parrotfishes) as a model system, due to our extensive knowledge of the phylogenetic relationships between species, and the variety of functional groups contained therein. The SIP student will work with the primary mentor to collect and analyze colorimetry data on lateral photographs of labrids, using the program ImageJ (NIH). We will then use phylogenetic comparative methods to assess to what extent species with similar ecological roles have evolved to exhibit similar patterns in color. The SIP student’s research will be conducted at UCSC’s Long Marine Laboratory which is located outside the main UCSC campus in the city of Santa Cruz.

EEB-05 Title: Dietary and Habitat Variation Across Otters and Kin
Primary Mentor: Mr. Christopher Law
Secondary Mentor: Prof. Rita Mehta
Number of Interns: 1

Mustelids (otters, weasels, minks, and ferrets) are a diverse group of carnivores that exhibit great dietary variation—from rodents to hard-shelled invertebrates—as well as habitat variation—from aquatic to terrestrial habitats. The goal of this proposed project is to understand the evolution of dietary and habitat distribution across the mustelid family. The SIP student will learn to: (1) construct phylogenetic trees using published DNA sequences, (2) perform basic computational phylogenetic analyses to draw relationships between morphology, diet, and habitat distribution, and (3) reconstruct the evolution of these character traits. The SIP student’s research will be conducted at the Long Marine Laboratory, located outside the main campus of UCSC in Santa Cruz, CA.

EEB-06 Title: Conservation of Southwestern Atlantic Reef Environments
Primary Mentor: Mr. Hudson Pinheiro
[Faculty Contact: Prof. Giacomo Bernardi]
Number of Interns: 2

This project involves analyses of the prospect of conservation in coastal and oceanic areas of Brazil. In the coastal areas, the project aims to evaluate if Marine Protected Areas (MPAs) encompass biologically significant areas (BSAs). Data from marine habitats and BSAs come from fishermen’s traditional knowledge and are already available. In the oceanic areas, the project aims to evaluate shark communities in Trindade Island. The data come from the ancient literature (dating back to 1902, 1914, 1950) and it is still necessary to interview researchers who have recently (from the 1980s onward) visited the island. The main references for this project are: Pinheiro et al. 2010, Pinheiro et al. 2011, and Teixeira et al. 2013. The SIP student’s research will be conducted at the Long Marine Laboratory, located outside the main campus of UCSC in Santa Cruz, CA.

EEB-07 Title: Plant Phenology and Climate Change in Santa Cruz County
Primary Mentor: Ms. Juliet Oshiro
[Faculty Contact: Prof. Laurel Fox]
Number of Interns: 1

This project aims to understand how and why plants shift their blooming times with climate. The scope of the project for this summer includes: (1) collecting plant blooming data from the field, (2) comparing this data to historical observations, and (3) examining reproductive and physiological differences between species with different blooming times. The SIP student will assist with field observations, data entry, and plant trait measurements. The SIP student’s research will be conducted at field sites in Santa Cruz County, with lab work at the UCSC main campus.

EEB-08 Title: Does Increased Genetic Diversity Predict Positive Fitness-related Traits in Wintering Population of Golden-Crowned Sparrows?
Primary Mentor: Ms. Nina Arnberg
[Faculty Contact: Prof. Bruce Lyon]
Number of Interns: 1

Evolution is a change in characteristics of populations over generations. These characteristics must vary in fitness and that variation must be heritable. So, knowing how genetic variation relates to individual fitness in a population informs our understanding of evolution. A commonly used approach has been to relate individual genetic diversity (heterozygosity) to variation in fitness, or characteristics that may be related to fitness. In the past decade, access to good genetic data and more long-term studies of wild populations have resulted in many heterozygosity-fitness correlations papers. We are now beginning to understand why individual heterozygosity can be related to fitness and how this shapes evolution. This study focuses on understanding whether individuals with higher individual heterozygosity have higher fitness (as measured by fitness-related traits) during non-reproductive periods. We examined several potentially fitness-related traits in a wintering population of a migrant species, the golden-crowned sparrows (Zonotrichia atricapilla). In previous studies on other species, the various measures have been shown to be positively correlated with individual heterozygosity during reproductive periods. The SIP student will search the published literature and synthesize current understandings in the proposed area, assist in data analyses, and have an opportunity to visit field locations.

EEB-09 Title: Cascading Consequences of Rapid Trait Change in an Invasive Fish
Primary Mentor: Mr. David Fryxell
Secondary Mentor: Mr. Travis Apgar
[Faculty Contact: Prof. Eric Palkovacs]
Number of Interns: 2

We are examining how the invasive mosquitofish has changed since it was introduced to hot springs in the Owens Valley, and how those changes modify the impact of the species on freshwater environments. We will be using 36 experimental ponds at Long Marine Lab to understand how temperature and recent fish trait change interact to modify the pond communities and ecosystems. We will also be common rearing mosquitofish to understand the genetic basis of trait differences among different hot springs populations. In addition, other lab research projects will be underway for which intermittent help may be required, potentially including coastal estuary fish community sampling as well as sampling of juvenile coastal steelhead populations in collaboration with the genetics lab at the National Marine Fisheries Service. The SIP student’s research will be conducted at the Long Marine Laboratory, located outside the main campus of UCSC in Santa Cruz, CA.

EEB-10 Title: Researching Evolutionary Processes in Sea Urchins
Primary Mentor: Mr. Christopher Kan
[Faculty Contact: Prof. Grant Pogson]
Number of Interns: 2

The SIP intern will be assisting in sequencing and analyzing sequences of the genomes of sea urchins. The student will be looking for how evolutionary processes have shaped the genomes and evolution of sea urchin species. They will be introduced to whole-genome-sequencing and learn to use evolutionary theory to reconstruct the histories of these species.

Electrical Engineering

Code Research Project Descriptions
ELE-01 Title: Sun 2 Fibers (S2F)
Primary Mentors: Mr. Juan Jose Diaz Leon and Dr. Matthew Garrett
Secondary Mentor: Mr. Junce Zhang
[Faculty Contact: Prof. Nobuhiko Kobayashi]
Number of Interns: 3

The sun is a free and (virtually!) endless power source. There are many different ways to capture sunlight, but the lower efficiencies in most of these methods make it a more expensive resource than polluting combustibles like oil or coal. Here we propose a low cost, highly efficient method for collecting concentrated solar heat and light adiabatically. This challenging process requires high quality materials fashioned in an optimal profile both at the nanoscale and the macroscale, requiring an effort from materials science and engineering. This project will involve the modeling and characterization of optical thin films used in the S2F project, a revolutionary idea to concentrate light from the sun and couple it into optical fibers for different uses such as solar thermal power or daylighting. Succeeding on this project would dramatically decrease the costs on solar thermal power plants and would also enhance new technologies such as daylighting. The SIP intern will have the opportunity to assist with one or more of the Nanostructured Energy Conversion Technology and Research (NECTAR) group’s projects by working with material growth, characterization, and/or modeling. In particular the SIP intern will be working with optical thin films used for coupling solar light to optical fibers for novel energy applications. More information can be found at the research group’s website. The three SIP interns will work on three separate projects: (a) thin film synthesis/optical property measurement (Diaz Leon); (b) prism coupling measurement system set up/modeling (Schulkins); and (c) lateral loss measurement/modeling (Garrett). Note, this UCSC lab is located at NASA Ames Research Center in Moffett Field, CA.

ELE-02 Title: Nanowire Networks
Primary Mentor: Mr. Junce Zhang
Secondary Mentors: Mr. Juan Jose Diaz Leon and Dr. Matthew Garrett
[Faculty Contact: Prof. Nobuhiko Kobayashi]
Number of Interns: 1

Semiconducting nanowire networks are developed with the goal of understanding their electrical, thermal and optoelectronic properties while developing scalable, manufacturable solutions to a number of problems of contemporary interest to society, with particular emphasis on direct conversion of heat to electricity. Nanowire networks are grown by metal organic chemical vapor deposition (MOCVD) on flexible low-cost metallic substrates such as copper foils, leading to highly interconnected networks of nanowires capable of long-range three-dimensional transport while retaining many of the unique properties of highly confined nanowire structures and displaying advantageous and unique properties. The SIP student will work on device design and fabrication, thermoelectrics (TE) testing, and physical modeling by the software comsol for further study of the properties of nanowire networks. More information can be found at the research group’s website. Note, this UCSC lab is located at NASA Ames Research Center in Moffett Field, CA.

Note: The NECTAR group’s projects that were formerly labelled ELE-03 and ELE-04 have now been merged with the ELE-01 project above. That project will now take on three SIP interns with two primary mentors.

Microbiology and Environmental Toxicology

Code Research Project Descriptions
MET-01 Title: Evolution of Extended-Spectrum Beta-Lactamase (ESBL) resistance
Primary Mentor: Mr. Jay Kim
[Faculty Contact: Prof. Manel Camps]
Number of Interns: 1

There are about 2 million cases of bacterial infection each year in the US, which leads to 90,000 deaths [FDA]. The resistance to antibiotic treatment is becoming a serious health problem because pathogens have the ability to evolve resistance, which can be transferred across species, and because of a diminishing number of new antibiotics that are becoming available. Read a recent news article on the threat of antibiotic resistance at this link. Resistance in Gram-negative pathogens is largely due to the evolution of beta-lactamase mutants with an extended spectrum (known as ESBLs). These mutant enzymes degrade not only their original substrate (penicillin) but also newer antibiotics that were specifically designed to be resistant to beta-lactamase action such as cephalosporins or aztreonam. In the Camps lab, we use experimental evolution and computational techniques to analyze mutation trajectories that lead to increased ESBL activity. This work is producing predictive models of future ESBL evolution. In addition, ESBL evolution is used as a model for understanding, more generally, how proteins evolve new activities. The SIP intern will work closely with his mentor to analyze long mutation trajectories in ESBL obtained through clinical databases or experimental work. We will be applying statistical models to: (1) establish the order in which mutations appear and (2) determine whether certain mutation pairs are enriched or underrepresented. Previous experience in computer programming is optimal, but not required.

Molecular, Cell and Developmental Biology

Code Research Project Descriptions
MCD-01 Title: Genetic Characterization of Chromatin
Primary Mentor: Mr. Michael Doody
[Faculty Contact: Prof. Grant Hartzog]
Number of Interns: 2

All plant and animal cells package their genetic material into chromatin. This protein-DNA complex allows the two meters of DNA in our genome to be packaged within the cell’s nucleus, which is only a few microns in diameter! We are interested in understanding how packaging of DNA as chromatin affects its ability to be used by the cell. We study this problem in the baker’s yeast, Saccharomyces cerevisiae, which grows rapidly, is cheap, and packages and expresses its genes using a similar set of strategies and proteins as do human cells. We use both genetic approaches, in which we examine the effects of mutations on chromatin and gene expression, and also biochemical approaches, in which we purify and study proteins and DNA in the test tube. The SIP interns will be involved in the genetic characterization of chromatin mutants that we have isolated that we believe disrupt chromatin and make the ORF more fluid/permissive to transcription. In conjunction with this, the interns will also get hands-on experience of the molecular biology techniques mentioned above and an understanding of how to critically read scientific journal publications and present ones research.

MCD-02 Title: Chromatin Dynamics During Hematopoietic Stem Cell Differentiation
Primary Mentor: Ms. Rebekah Sousae
[Faculty Contact: Prof. Camilla Forsberg]
Number of Interns: 2

The primary mentor investigates the role of chromatin dynamics during hematopoietic cellular differentiation and self-renewal. The SIP intern’s research project will involve invitro treatment of hematopoietic cells with inhibitors of chromatin silencing (specifically inhibiting protein G9a capable of writing H3K9me2/3 histone modifications). Put simply, as cells divide and differentiate, important changes happen in terms of DNA organization. The goal of this research is to understand how DNA organization and DNA modifications affect and instruct blood development on the journey of a blood stem cell (hematopoetic stem cell) to fully developed mature cells such as white and red blood cells.


Code Research Project Descriptions
PHY-01 Title: Photoelectric Effect and High Temperature Superconductors
Primary Mentor: Mr. Kazue Matsuyama
[Faculty Contact: Prof. Gey-Hong Gweon]
Number of Interns: 1

In this project, you will learn how to apply the “photoelectric effect,” which underlies modern technologies from cell phone camera to solar cells, to tackle the one of the most mysterious problems in physics—the mystery of high temperature superconductors. You will learn to basic quantum mechanics (wave mechanics), superconductivity, and how the angle resolved photoelectron spectroscopy (ARPES)—the premier physics experimental tool based on the photoelectric effect—shed light on the mystery of high temperature superconductors at the forefront of physics. (For more information, visit this site and links therein.)

PHY-02 Title: Topological Insulators
Primary Mentor: Mr. Ahram Kim
[Faculty Contact: Prof. Gey-Hong Gweon]
Number of Interns: 1

In this project, you will learn the physics of the so-called “topological insulators” and participate in original research. Only recently discovered (2006), these materials are rapidly garnering interest by physicists and engineers alike, due to their special properties that may enable novel spintronics application in the future. Here in the Gweon group, we study the novel electronic structure of topological insulators using ARPES (angle resolved photoelectron spectroscopy—a very expensive photoelectric effect experiment), which is by far the best way to characterize the behaviors of the electrons in these novel compounds. You will learn basic quantum mechanics (wave mechanics), ARPES, and topological insulator physics, and will be able to participate in leading edge discovery in physics. (For more information, browse this site and links therein.)

PHY-03 Title: Analyzing and Visualizing Outputs from High-resolution Simulations of Galaxy Formation and Evolution
Primary Mentor: Prof. Joel Primack
Secondary Mentors: Mr. Miguel Rocha and Mr. Alex Bogert
Number of Interns: 3

The team led by Professor Primack has run about 100 high-resolution simulations of galaxy formation and evolution and have many more simulations in progress. In addition, the AGORA project that Professor Primack co-lead will produce many more such simulations. The SIP interns will help us understand these simulations and compare them with observed galaxies, especially using data from the CANDELS survey, the largest-ever Hubble Space Telescope project.

PHY-04 Title: Evaluation of Photosensors for Very-High-Energy Gamma-Ray Telescopes
Primary Mentor: Dr. Jonathan Biteau
Secondary Mentors: Prof. David Williams
Number of Interns: 1

In this project, the SIP intern will learn about the operation of state-of-the-art silicon photosensors and measure their performance, with a particular emphasis on those properties most closely related to the sensitivity of gamma-ray telescopes using these devices in the camera. These optical sensors are used to detect gamma rays indirectly, using the imaging atmospheric Cherenkov technique, in which telescopes collect and image the flash of light produced in the atmosphere when a very-high-energy gamma ray hits the atmosphere and generates a shower of lower energy (but still relativistic) particles. In doing the measurements, the SIP intern will learn about computer data acquisition techniques and programs for analyzing the resulting data, widely used in high-energy particle physics and astrophysics.