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: How Supermassive Black Holes Grow
Primary mentor: Martin Gaskell
Location: UCSC main campus
Number of interns: 2

Project description: Astronomers now believe that every large galaxy contains a supermassive black hole in its center. Because of the tremendous energy released as the black hole grows by swallowing gas, these black holes can be readily detected as so-called “active galactic nuclei” (AGNs) back to very early times in the Universe. The details of how supermassive black holes form and grow and how this is related to the formation of normal galaxies is one of the central mysteries of contemporary astrophysics. The mentor’s research group is analyzing spectra and spectral variability to try to understand how AGNs produce the intense radiation seen and how supermassive black holes grow.

Tasks: SIP intern involvement in the project will consist of analyzing multi-wavelength spectral observations of relatively nearby actively accreting supermassive black holes to try to understand the emissions and how the black holes grow. This work will involve compiling data sets, applying corrections, making statistical estimates of parameters, and comparing the results with theoretical models of how black holes grow. The aim is to present the results at a meeting of the American Astronomical Society and publish them in a paper in a major international journal.

Required skills for interns prior to acceptance: None
Skills intern(s) will acquire/hone: Statistical data analysis
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: ON ON ON ON ON ON ON ON ON ON


Code Research Project Descriptions
AST-02 Title: Galaxies and Dark Matter - I
Primary mentor: Christoph Lee
Other mentors: ,
Location: ISB, UCSC Main Campus
Number of interns: 2

Project description: Several research projects are available studying galaxy formation and evolution and the properties of the dark matter halos in which galaxies form. The mentors’ research group is providing theoretical support for CANDELS, the largest-ever Hubble Space Telescope (HST) program. The group is doing a large suite of high-resolution galaxy formation simulations and comparing them with HST and ground-based telescope observations in order to determine how galaxies evolve. The group’s simulated galaxies are often elongated and clumpy in the early universe, and the group is determining why this is the case and to what extent these features agree with the observations. The group is also measuring the velocities of the stars and gas in the simulations and comparing to observations. The group has also run the most accurate simulations of the Universe on large scales, and is studying how the features of the dark matter halos that host galaxies correlate with other properties of the halos such as their mass, internal structure, shapes, spins, and location within the cosmic web.

Tasks: SIP interns will help the mentors’ research group: (1) analyze observations of galaxies and compare them with the simulations, or (2) analyze how the properties of dark matter halos in the group’s cosmological simulations correlate with each other and with their locations within the cosmic web. SIP interns who work on this project will have access to powerful computers and to the group’s 3D Astronomical Visualization Lab.

Required skills for interns prior to acceptance: Computer programming
Skills intern(s) will acquire/hone: Computer programming; statistical data analysis
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: ON ON ON ON ON ON ON ON ON ON


Code Research Project Descriptions
AST-03 Title: Galaxies and Dark Matter - II
Primary mentor: Dr. Aldo Rodriguez
Other mentors: ,
Location: ISB, UCSC main campus
Number of interns: 1

Project description: Several research projects are available studying galaxy formation and evolution and the properties of the dark matter halos in which galaxies form. The mentors’ research group has run the most accurate simulations of the Universe on large scales, and the group is studying how the features of the dark matter halos that host galaxies correlate with other properties of the halos such as their mass, internal structure, shapes, spins, and location within the cosmic web. The group is providing theoretical support for CANDELS, the largest-ever Hubble Space Telescope (HST) program. Using halo occupational models for connecting galaxies to dark matter halos and data with HST and ground-based telescope observations, the group is determining how galaxies evolve across the cosmic time.

Tasks: The SIP intern will help the mentors’ group: (1) analyze how the properties of dark matter halos in the cosmological simulations correlate with each other and with their locations within the cosmic web, or (2) improve existing halo occupational models in order to constrain how galaxies evolve. The intern who works on this project will have access to powerful computers and to the group’s 3D Astronomical Visualization Lab.

Required skills for interns prior to acceptance: Computer programming; statistical data analysis
Skills intern(s) will acquire/hone: Computer programming; statistical data analysis
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: ON ON ON ON ON ON ON ON ON ON


Code Research Project Descriptions
AST-04 Title: Exotic Molecules in Exoplanet Atmospheres
Primary mentor: Caroline Morley
Other mentors:
Location: UCSC main campus
Number of interns: 2

Project description: The mentors’ research group works to understand exoplanets (planets around stars other than the Sun). One of the ways one can learn about exoplanets is by simulating their spectra; the group calculates using computer simulations what a planet of a given composition and temperature will look like. One can then compare these modeled spectra to observations of a particular planet. This analysis can be used to figure out what planets are made of, how warm they are, and other parameters. Right now the group mostly studies giant planets like Jupiter and Neptune, but in the future these techniques will be used to study object like our own Earth! The SIP interns this summer will investigate the importance of exotic molecules in exoplanet atmospheres. It is already known that one can detect very abundant molecules like water and methane. Can “weird” molecules like hydrogen sulfide, benzene, and phosphine also be detected? Using a combination of existing modeling tools and their own analysis, the interns will determine which exotic species can be detected, and at what wavelengths. They will also figure out whether other scientists who have ignored these molecules have inaccurately inferred properties of the planets they have studied.

Tasks: (see above)

Required skills for interns prior to acceptance: Computer programming; statistical data analysis
Skills intern(s) will acquire/hone: Computer programming; statistical data analysis
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: ON ON ON ON ON ON ON ON ON ON


Code Research Project Descriptions
AST-05 Title: Looking for Extended Wind Emission in Very Distant Galaxies
Primary mentor: Hassen Yesuf
Other mentors:
Location: ISB, UCSC main campus
Number of interns: 2

Project description: 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: http://arxiv.org/abs/1304.6405 for background information). Last summer, this mentor supervised two SIP interns who worked on developing a python script to combine hundreds of 2D galaxy spectra to achieve better signal-to-noise. The aim of the project was to look for faint wind signatures at the outskirts of galaxies. The mentor is now seeking two interns with computer programing experience who will work together on the next phase of this research project.

Tasks: The task this summer is for the SIP interns to develop the python script further and to apply it to simulated 2D spectra first as a check and then to real data. The mentor has new and better data since last summer. The interns will generate fake data using a theoretical model described in this paper (http://arxiv.org/abs/1102.3444). If the SIP interns finish this project early, they can apply their python script to study star formation and dust gradients (dust distribution as a function of radius) across galaxies.

Required skills for interns prior to acceptance: Computer programming
Skills intern(s) will acquire/hone: Computer programming; statistical data analysis
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: ON ON ON ON ON ON ON OFF ON ON


Code Research Project Descriptions
AST-06 Title: Constraining Convection Physics through Eclipsing Binaries
Primary mentor: Tuguldur Sukhbold
Other mentors: ,
Location: UCSC main campus
Number of interns: 1

Project description: Stars create the majority of the elements in the Universe through nuclear burning, spread them back into space through winds and explosions, and, when they finally die, they leave behind exotic compact objects like white dwarfs, neutron stars, and black holes. Though astronomers have a good general understanding of how stars evolve and die, there are some details that they still do not understand well enough that are known to have a large impact on stellar evolution. One such missing piece is how material is mixed inside a star as it ages. Without a good understanding of this process, astronomers will never be able to accurately predict how long a given star will live, the quantity of heavy elements it is going to produce, how it will die, what it will leave behind, etc... Today, mixing is an active area of research and, while there are several competing theories, astronomers still do not know which theory is the best. It is possible that some theories work for certain types of stars at certain stages of their lives, while other theories work for other types of stars. In order to address these issues through this research project, the mentors’ groups aims to use modern high-precision observational data coupled with statistical methods to compare and test these theories/models.

Tasks: The SIP intern will do a literature search to compile relevant observational data, and contribute to the programming of the statistical test, the calculation of stellar models, and the writing of the paper.

Required skills for interns prior to acceptance: Computer programming
Skills intern(s) will acquire/hone: Computer programming; statistical data analysis
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: ON ON ON ON ON ON ON ON ON ON


Code Research Project Descriptions
AST-07 Title: Studying Orphan Globular Clusters in the Virgo Cluster of Galaxies
Primary mentor: Dr. Elisa Toloba
Other mentors: ,
Location: UCSC main campus
Number of interns: 2

Project description: The goal of this project is to learn about the spatial distribution, kinematics, chemical composition, and mean stellar age of globular clusters (GCs; small groups of stars that orbit around a galaxy) in the Virgo cluster of galaxies (large collection of galaxies gravitationally bound to M87, a very massive elliptical galaxy sitting at the cluster center). Of particular interest is a subset of GCs dubbed “orphan GCs”. The mentors’ group has spectroscopically observed a sample of 300 globular cluster candidates in the Virgo cluster. Of these, 82 are confirmed GCs that are gravitationally bound to Virgo cluster dwarf elliptical galaxies while 68 are candidate orphan GCs that are not obviously associated with any of the dwarf galaxies or normal galaxies in the Virgo cluster but are instead likely to be remote GC satellites of M87.

Tasks: The SIP interns will analyze the photometric and spectroscopic properties of these candidates orphan GCs to remove likely sample contaminants (e.g., non-GCs) and test whether all of the remaining objects or only a subset are likely to be remote satellites of M87. For those objects that are likely to be remote M87 satellites, the interns will study the number density of GCs as a function of distance from the center of Virgo, the velocity dispersion of these GCs, and will compare their stellar populations to those of GCs that are gravitationally bound to other galaxies in Virgo. The interns will use existing computer programs and write some programs of their own to carry out these tasks.

Required skills for interns prior to acceptance: Computer programming
Skills intern(s) will acquire/hone: Computer programming; statistical data analysis
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: OFF ON ON ON ON ON ON ON ON ON


Code Research Project Descriptions
AST-08 Title: Big Bang Meets Big Data
Primary mentor: Dr. Guillermo Barro
Other mentors: ,
Location: UCSC, ISB
Number of interns: 1

Project description: The most recent advances in extragalactic astronomy are data driven. New surveys that unlock a new spectral domain or provide improved spatial or spectral resolution are key for obtaining ground-breaking results. However, these breakthroughs are rarely based on an individual new data set. In the era of big data, it is the synergy between new data sets and the wealth of other high quality data sets that have been accumulating over the years that really makes the difference. Such richness of data, however, comes at the price of complex data sets with many layers of information. While much of this information is available to the community through online archives and virtual-observatory services, it requires a lot of effort on the user’s part to collect and prepare all the data for analysis. Multipurpose image viewers or catalog tools allow access to the primary data products of deep extragalactic surveys but there are no specific resources to inspect or mine all the available information for a galaxy that combines all the primary products in a consistent way. Given this data bottleneck, a simple eye-to-mind visual inspection tool becomes an invaluable resource.

Tasks: The SIP interns will help the mentors’ group create a one-stop-shopping online resource to collect, inspect and analyze the increasingly complex data products of deep cosmological surveys. The primary goal is to improve and expand the existing infrastructure of the Rainbow Database by creating new applications such as: (1) Data plotter — make interactive plots on-the-fly using the web browser (similar to http://filtergraph.com/); and (2) Google Sky maps — generate sky maps for the HST images using the well-known Google Map interface.

Required skills for interns prior to acceptance: Computer programming; statistical data analysis
Skills intern(s) will acquire/hone: Computer programming; statistical data analysis
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: ON ON ON ON ON ON ON ON ON ON


Code Research Project Descriptions
AST-09 Title: Design and Characterization of Silver-based Mirror Coatings for Astronomical Telescopes
Primary mentor: Dr. Andrew Phillips
Other mentors:
Location: UCSC main campus (UC Observatories Advanced Coatings Lab)
Number of interns: 1

Project description: The Advanced Coatings Lab (ACL) is a research group formed by the University of California Observatories (UCO) in an effort to develop improved optical coatings for Earth-based astronomical equipment. ACL’s work focuses on superior broad-band optical properties and robust mechanical/chemical properties of highly reflective silver-based mirrors. Successful mirror coatings require careful understanding of the material deposition parameters and physical properties of thin films located both below and above the silver layer. Mirror coatings must be optically tested for broadband reflectivity and optical density, mechanically tested for strong adhesion and scratch resistance, and chemically tested against corrosive environmental conditions such as heat and humidity. This project will require the SIP intern to understand these characterization mechanisms and draw conclusions for potentially strong mirror coating materials and then design her/his own mirror coating recipe.

Tasks: The SIP intern will learn the background physics of optical response in various materials across the broad spectrum that astronomers study. She/he will also gain an understanding of thin film deposition techniques, how process parameters affect material properties, and how these material properties are measured. After conducting studies and measurements on a variety of materials and mirror coating recipes, the intern will design her/his own experiment to fabricate and test a unique mirror coating recipe. The intern should have some basic understanding of and experience with experimental methodology, but no specific background knowledge is required. The intern should expect to spend most of her/his time in lab (on the UCSC campus) with hands-on measurements and observations.

URL: http://http://coatings.ucolick.org/
Required skills for interns prior to acceptance: Lab work; statistical data analysis
Skills intern(s) will acquire/hone: Statistical data analysis
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: ON ON ON ON ON ON ON ON ON ON


Code Research Project Descriptions
AST-10 Title: Gamma-ray Cosmology Using Splines
Primary mentor: Dr. Jonathan Biteau
Other mentors: Nina3 Arnberg
Location: UCSC main campus (SCIPP/NatSci II)
Number of interns: 2

Project description: In this project, the interns and mentors will learn about the journey of the most energetic gamma rays known to mankind from distant sources called blazars down to the atmosphere of Earth where they are detected by imaging atmospheric Cerenkov telescopes. These gamma rays interact with the pool of light that permeates the voids of the Universe, called the extragalactic background light (EBL), through a particle physics process known as pair creation. The gamma-ray astronomy group at SCIPP has developed an analysis framework to extract crucial characteristics of the EBL. The SIP interns will work on upgrading this framework using splines to model the intensity of the EBL as a function of wavelength. Skills required: mathematics, some experience with programming  

Tasks: The SIP interns’ role will be to understand the mathematical concept of splines, develop a C/C++ program to approximate any curve with a spline, and include this piece of code in an existing framework. The interns and mentors will then study the impact of this tool on their understanding of the extragalactic background light and exotic particle physics processes.

Required skills for interns prior to acceptance: Computer programming; statistical data analysis; other
Skills intern(s) will acquire/hone: Computer programming; statistical data analysis; C/C++, a glimpse of fundamental physics (particle physics, high energy astrophysics, and cosmology)
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: ON ON ON ON ON ON ON ON ON ON


Code Research Project Descriptions
AST-11 Title: Separating the Stars Belonging to the Halos and Disks of the Andromeda and Milky Way Galaxies
Primary mentor: Dr. Raja Guhathakurta
Other mentors: Sample Sue, Sue Grasso
Location: UCSC main campus (ISB) & Google (Mountain View)
Number of interns: 3

Project description: The goal of this project is to learn how galaxies form and evolve by studying the assembly history, dynamics, and chemical composition of their stars. Andromeda and the Milky Way are the only two large galaxies that can be studied star by star; other galaxies are generally too far away for their stars to be seen individually. Both Andromeda and the Milky Way have disks comprised of mostly young stars and large, diffuse halos of old stars. However, when looking at Andromeda through the Milky Way, it is not trivial to determine which galaxy and which component (disk or halo) a star belongs to. It is also of particular interest to identify populations of ”rare” stars in the Andromeda galaxy.

Tasks: The mentor’s group has put together a rich and extensive database containing many photometric and spectroscopic characteristics of individual stars in the direction of the Andromeda galaxy. This database contains proper motions, brightnesses, and colors of stars from the Hubble Space Telescope, and stellar spectroscopic characteristics such as velocities from the Keck telescope and DEIMOS spectrograph. The SIP interns will use all this information to classify each star to look for groups of stars belonging to the same class. This will provide valuable information about the different components of the Milky Way and Andromeda. The interns are expected to carry out some computer programming using the Python language.

URL: http://www.astro.ucsc.edu/faculty/profiles/singleton.php?&singleton=true&cruz_id=pguhatha
Required skills for interns prior to acceptance: Computer programming; statistical data analysis; other
Skills intern(s) will acquire/hone: Computer programming; statistical data analysis
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: ON ON ON ON ON ON ON ON ON ON


Biomolecular Engineering

Code Research Project Descriptions
BME-01 Title: Precision Immunotherapy for Cancer Treatment
Primary mentor: Arjun Rao
Other mentors:
Location: UCSC main campus
Number of interns: 3

Project description: Cancer is a generic term used to describe a group of diseases characterized by uncontrolled cell growth in the body. It is one of the leading causes of human deaths (8.2 million casualties in 2012 — World Health Organization). The standard of care to treat cancers involves chemo- or radio-therapies. Both these methods are extremely effective in their cell-killing potential; however, they are also extremely toxic to healthy normal cells in the vicinity of the tumor. The immune system is geared to protect the body from infection. Tumors develop ways to inhibit the immune system and the body is unable to fight them off by itself. The mentor’s research involves looking for ways to boost the immune reaction to a tumor in an attempt to provide a non-toxic therapy for cancer.

Tasks: The SIP intern will: (1) study immune reaction modulating functions of tumors from the literature and identify genes of interest; (2) parse microarray and RNA-sequencing data for genes identified in the previous step; and (3) run pipelines to detect immune targets in tumors.

Required skills for interns prior to acceptance: Computer programming; other
Skills intern(s) will acquire/hone: Computer programming; statistical data analysis; working knowledge of the human immune system
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: ON ON ON ON ON ON ON ON ON ON


Chemistry & Biochemistry

Code Research Project Descriptions
CHE-01 Title: Synthesis of Advanced Ternary Transition Metal Oxides Nanomaterials and Their Applications in Supercapacitors
Primary mentor: Tianyi Kou
Other mentors:
Location: UCSC main campus
Number of interns: 1

Project description: Recently, “supercapacitors” have attracted a lot of attention because of their excellent power density (high-rate charging/discharging) and extended cycling life (more than 100,000 cycles of charging/discharging). They are regarded as the promising next-generation energy storage devices to replace traditional batteries. Based on their charge storage mechanism, supercapacitors can be divided into two categories: electrical double-layer capacitors (EDLCs), which store charge via the electrical double-layer at the electrode/electrolyte interface, and pseudocapacitors, which depend on the reversible faradic reactions (redox-reaction pairs) to store charge. EDLCs exhibit appealing cycling capability but have relatively low energy density due to their charge storage mechanism (which only occurs at the electrode/electrolyte interface). By comparison, pseudocapacitors store charge in bulk materials and therefore display a relatively high energy density while also having a high power density. Ternary transition metal oxides such as Ni-Co-O with nanostructures can provide rich redox reaction sites and display excellent energy density. The mentor’s research projects include exploring new ternary transition metal oxides systems, finding ways to modify existing systems (e.g., improving electrical conductivity, enhancing their cycling stability, and increasing the energy density even further).

Tasks: The SIP intern will: (1) try to understand the working mechanism of supercapacitors; (2) master routes to synthesizing ternary transition metal oxides with nanostructures; (3) learn to characterize or estimate the capacitive performances of the materials using an electrochemical workstation; (4) learn to characterize the nanostructures of materials using SEM (scanning electron microscope), XRD (X-ray diffraction), TEM (transmitting electron microscope), etc. technologies.

Required skills for interns prior to acceptance: Statistical data analysis
Skills intern(s) will acquire/hone: Statistical data analysis
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: ON ON ON ON ON ON ON ON ON ON


Code Research Project Descriptions
CHE-02 Title: Carbonaceous Materials for Supercapacitors
Primary mentor: Tianyu Liu
Other mentors:
Location: UCSC main campus (PSB 198)
Number of interns: 1

Project description: Supercapacitors, also known as ultracapacitors, are emerging as a new class of electrochemical charge storage devices that can be used in powering electric vehicles. In comparison to lithium ion batteries, the advantages of supercapacitors are ultra-fast charging rate (can be fully charged in seconds) and ultra-long life time (can be charged and discharged for more than 100,000 cycles without degradation). However, the energy densities of supercapacitors are still substantially lower than that of lithium ion batteries, which limits their applications as energy storage devices. Therefore, improving the energy density of supercapacitors is highly desirable. Previous studies have shown that the specific capacitance of an electrode is directly related to its effective surface area and electrical conductivity of electrode material. This project aims to boost the energy density of supercapacitors by developing novel porous and conductive carbonaceous materials as supercapacitor electrodes.

Tasks: The SIP intern will design her/his own novel nanostructured electrodes and gain hands-on experience in synthesis and characterization of nanomaterials (electron microscopy and spectroscopy), supercapacitor fabrication, electrochemical testing, and data analysis.

Required skills for interns prior to acceptance: Lab skills
Skills intern(s) will acquire/hone: Lab work; statistical data analysis
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: ON ON ON ON ON ON ON ON ON ON


Code Research Project Descriptions
CHE-03 Title: Hematite Photoanode on Photoelectrochemical Water Splitting
Primary mentor: Yi Yang
Other mentors:
Location: UCSC main camus (PSB 198)
Number of interns: 1

Project description: Photoelectrochemical water splitting is a promising method of transforming solar energy into chemical energy stored in the form of hydrogen. Hematite (α-Fe2O3) has attracted much attention due to its favorable optical band gap (2.2 eV), extraordinary chemical stability in oxidative environments, low cost, and abundance. However, this research project will focus on addressing the limitations of hematite.

Tasks: The SIP intern will design their own novel nanostructured electrodes and gain hands-on experience in synthesis and characterization of nanomaterials (electron microscopy and spectroscopy), supercapacitor fabrication, electrochemical testing, and data analysis.

Required skills for interns prior to acceptance: Lab skills
Skills intern(s) will acquire/hone: Lab work; statistical data analysis
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: ON ON ON ON ON ON ON ON ON OFF


Code Research Project Descriptions
CHE-04 Title: Long-Range Electron Transport in Organic Semiconductors
Primary mentor: Vincent Duong
Other mentors: Marie Wingyee Lau
Location: UCSC main campus (PSB); possibly Berkeley National Lab
Number of interns: 1

Project description: The premise of this project is to understand how electrons traverse through organic semiconductors. The mentor’s goal is to design more efficient solar cells. Most of our understanding of semiconductor physics comes from inorganic materials, such as silicon. A key factor in the study of inorganics is the repetition of individual atoms to form a crystal lattice. To ensure these lattices are pure, expensive conditions are often deployed (high temperature, high purity, etc.). Organic solar cells offer a low-cost alternative to leading the green revolution. In particular, this project studies how organic small molecules orient themselves relative to other molecules and how these orientations influence electron transfer.

Tasks: The SIP intern should expect to fabricate organic solar cells using a technique known as spin-coating. The intern will then help characterize the cells using techniques such as current-voltage measurements and various X-ray scattering measurements. Lastly, the intern will develop some familiarity with the Matlab language to manipulate and plot data. Because the laboratory is new, the intern may be asked to help with other tasks such as seting up a nitrogen glovebox or designing circuits to optimize the current-voltage measurements. Depending on availability and passing a background check, the intern may accompany the mentor to the Advance Light Source at Berkeley National Laboratory to perform X-ray scattering experiments.

Required skills for interns prior to acceptance: Lab skills
Skills intern(s) will acquire/hone: Computer programming; statistical data analysis
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: ON ON ON ON ON ON ON ON ON ON


Code Research Project Descriptions
CHE-05 Title: Nanoparticle Electrocatalysts for Oxygen Reduction in Fuel cells
Primary mentor: Peiguang Hu
Other mentors: Vicky Yuan, ,
Location: UCSC main campus (PSB)
Number of interns: 1

Project description: With the rapid depletion of fossil fuels, extensive studies have been carried out to search for sustainable energy resources. Among these, fuel cells have been considered as one of the most promising technologies. A fuel cell is a device that converts the chemical energy from a small molecule fuel directly into electricity through a chemical reaction with oxygen. At a fuel cell anode, the fuel is oxidized and generates electrons, the electrons are drawn from the anode to the cathode through an external circuit, and the electrons reduce oxygen at the cathode. The efficiency of fuel cells could be as high as 60% in practice and 85%–90% theoretically, and they are also environment-friendly, especially for hydrogen-oxygen fuel cells that produce only water. However, to promote the oxygen reduction reaction (ORR; O2 + 4e– + 2H2O —> 4OH–), a large amount of Pt is generally required, due to the complicated reaction mechanism and sluggish kinetics. This makes fuel cells expensive and impedes the widespread commercial applications. In this context, our research project will focus on surface-functionalized nanoparticles as ORR catalysts, either to improve the efficiency of Pt catalysts or to synthesize Pt-free ORR catalysts. Experimentally, a variety of preparation methods will be developed for nanoparticle synthesis, and a range of experimental tools will be used.

Tasks: The SIP intern will search and read relevant portions of the scientific literature, learn synthetic methods and characterization techniques, learn tools for graphing and analyzing data, write reports, prepare slides to present experimental results, and lead discussions.

URL: http://chen.chemistry.ucsc.edu
Required skills for interns prior to acceptance: Lab skills
Skills intern(s) will acquire/hone: Lab work; statistical data analysis
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: ON ON ON ON ON ON ON ON ON ON


Code Research Project Descriptions
CHE-06 Title: Nitrogen Doped Graphene Quantum Dots For Improved Electrocatalytic Oxygen Reduction
Primary mentor: Chris Deming
Other mentors: Vicky Yuan, Rene Mercado,
Location: UCSC main campus (PSB)
Number of interns: 1

Project description: Scarcity of fossil fuels and growing environmental concerns demand a source of clean, renewable energy. Fuel cells utilizing renewable resources such as hydrogen, methanol, and formic acid have provided sufficient energy output for many applications such as personal and commercial vehicles. Currently, this technology is not commercially available due to the large amount of precious metal catalyst required for efficient operation. Recently, graphene quantum dots (GQD), especially those with nitrogen doping, have exhibited activity approaching that of commercial metals. Our goal is to improve the activity of N-doped GQDs by controlling the amount of nitrogen introduced into the GQD structure as well as modification with organic ligands.

Tasks: The SIP intern will review literature articles related to the research topic to better understand the scope of the research. The intern will perform synthesis from start to finish. This will include determining and weighing out appropriate amounts of chemical reagents, performing desired chemical reactions, and purifying the resulting product in a safe, professional manner. In addition, the intern will utilize spectroscopic and electrochemical equipment to collect data and analyze this data for the extraction of desired parameters. Furthermore, the intern will be expected to explain their results in the context of experimental design and previous work found in the scientific literature and develop a presentation that conveys her/his results and scientific implications.

URL: http://chen.chemistry.ucsc.edu
Required skills for interns prior to acceptance: Lab skills
Skills intern(s) will acquire/hone: Lab work; statistical data analysis
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: ON ON ON OFF ON ON ON ON ON ON


Code Research Project Descriptions
CHE-07 Title: Network Formation and Charge Transport of Thin Film Organic Semiconductors
Primary mentor: Michael Roders
Other mentors: Marie Wingyee Lau
Location: UCSC main campus (PSB)
Number of interns: 1

Project description: Photovoltaic systems, otherwise known as “solar power”, stand as one of the premiere technologies for alternative energy generation. Organic semiconductors (i.e., chemicals that mostly contain carbon atoms) are an advantageous material because they are inexpensive to produce and less toxic than other inorganic-based photovoltaic systems and also provide the opportunity to deploy solar power as a flexible, transparent, thin film coating that can be used almost anywhere. Instead of just rooftops, this solar power system could be used to cover windows or even clothing! This project will examine how different types and shapes of organic molecules form microstructural networks within thin films and how these networks affect the path along which electrical energy can be transported in the form of electrons.

Tasks: The SIP intern will begin by developing a strong foundation of working within a wet chemistry lab by learning how to use an analytical balance and prepare solutions of various organic chemicals. As the project progresses, the intern and mentor will begin building solar power devices by a process known as spin coating that deposits a very thin layer of a chemical mixture onto an electrode. The devices will then be characterized by current-voltage measurements and related to the structure of the thin film from X-ray scattering data collected at nearby synchrotron light sources. Throughout the process, the intern will be tasked using Matlab programming software to manipulate, analyze, and present data.

Required skills for interns prior to acceptance: Lab skills
Skills intern(s) will acquire/hone: Computer programming; statistical data analysis
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: ON ON ON ON ON ON ON ON ON ON


Computational Media

As of yet, no mentors have submitted projects for this field of research. Mentors are still in the process of submitting projects so please keep posted for more projects to be submitted.
 

Computer Science/Computer Engineering

Code Research Project Descriptions
CSE-01 Title: Network Modelling for Extreme Conditions
Primary mentor: Daniel Alves
Other mentors:
Location: UCSC main campus
Number of interns: 2

Project description: Initially created to model interplanetary communication, Delay- and Disruption-Tolerant Networks (DTNs) have also found applications in a variety of other fields, such as sensor networking, vehicular communication, and emergency response, to name a few. Those kinds of networks have characteristics that distinguish them from traditional networks that form the Internet. In DTN, delays are common and often long, disconnections are expected, and error rates and asymmetrical data-rates are high. An important issue is to ensure that the network operates correctly and efficiently under these “extreme” conditions. Due to the difficulty of replicating these “extreme” conditions in real testbeds, DTN algorithms are usually tested in simulation environments. These simulation environments provide functionalities to better control the desired aspects of the system to be tested, subject the system to a wide range of conditions, as well as reproduce experiments. This project aims to study and implement network protocols for DTNs in a simulation environment.

Tasks: The SIP intern will work with the modelling and analysis of DTN algorithms in simulation environments. The intern will first learn about the working of the algorithms and the simulation environment. Later, the intern will need to implement the studied algorithms and then study their operation in the simulation environment.

URL: http://skynet.cse.ucsc.edu/inrgwiki/Projects
Required skills for interns prior to acceptance: Computer programming
Skills intern(s) will acquire/hone: Computer programming; statistical data analysis
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: ON ON ON ON ON ON ON ON ON ON


Code Research Project Descriptions
CSE-02 Title: Describing Human Behavior in WiFi Networks
Primary mentor: Larissa Oliveira
Other mentors:
Location: UCSC main campus (Engg 2)
Number of interns: 1

Project description: In this project, the aim is to study the behavior of human movement by analyzing data collected from mobile WiFi users. Data are obtained from recordings of users’ laptops, smartphones, and other similar wireless mobile devices. The data are then stored in public repositories where they can be accessed by the community. By studying the data, one expects to be able to predict human behavior, in order to answer questions such as: how many antennas should be installed in a given school so all students will have access to WiFi? Recent studies indicate that human movement is symmetric, that is, the number of people that tend to go from the cafeteria to a classroom, is the same as the number of people that tends to go from a classroom to the cafeteria. Also, given the data collected, one can observe that humans tend to form different groups and are attracted to different geographical areas.

Tasks: The development of models capable of describing and capturing human behavior is extremely important for the implementation and analysis of wireless networks. The SIP intern will have the opportunity to work with data analysis, statistical modeling of data, and computer programming by aiding the mentor in the analysis of results obtained from the study of WiFi data records.

URL: http://skynet.cse.ucsc.edu/inrgwiki/Projects
Required skills for interns prior to acceptance: Computer programming
Skills intern(s) will acquire/hone: Computer programming; statistical data analysis
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: ON ON ON OFF ON ON ON ON ON ON


Code Research Project Descriptions
CSE-05 Title: Crowdsourcing System for Policy Development and Moderation
Primary mentor: Rakshit Agrawal
Other mentors: Samantha Sweeney
Location: Mostly remote, using personal computers; some meetings on the UCSC main campus or the Silicon Valley campus
Number of interns: 2

Project description: This project resides in two primary domains, crowdsourcing and policy moderation. Crowdsourcing systems can be defined as platforms where multiple users contribute very little effort to perform certain tasks that together combine to fulfill larger tasks. Policy moderation includes maintaining checks on progress of public policies and help ensure growth and development of policies with time. The interns and mentor will develop a crowdsourcing platform where some policy domain experts will first contribute their knowledge on certain public policy and then, with the help of a large number of users, will ensure successful implementation of policies in real-world systems. At the same time, our system will keep track of user performance to improve overall system quality.

Tasks: The SIP interns will assist this project in the following ways: (1) data collection — this will involve collection of data from public policy websites and news websites; (2) help develop the frontend web system — this will involve creation of HTML and CSS elements of web page, and working on Javascript and JQuery; (3) help design system interface — this will involve designing artwork and themes for the system (mostly Photoshop or SVG graphics work required); (4) assist development of backend server system — this will be the entire Python based web system and will include all functionalities. Interns will be provided with guidance on all technical details and will be provided with assistance whenever needed.

URL: https://rakshitagrawal.wordpress.com/
Required skills for interns prior to acceptance: Computer programming
Skills intern(s) will acquire/hone: Computer programming; statistical data analysis
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: ON ON ON ON ON ON ON ON ON ON


Code Research Project Descriptions
CSE-06 Title: Smartphones for Hybrid Estimation and Control in Mobile Robotics
Primary mentor: Ryan Rodriguez
Other mentors: Jia Lu
Location: UCSC main campus
Number of interns: 1

Project description: With the computational power of smartphones and tablets fast approaching the capabilities of traditional workstations, the Hybrid Systems Lab (HSL) at UC Santa Cruz seeks to understand how one can utilize smart sensors and actuators to improve existing infrastructure. This research has vast implications in the fields of water and energy conservation, power generation and conversion, and robotics. The project seeks to leverage mobile computational power of the latest iOS devices with the versatility of the RFduino, a small, general purpose microcontroller with built-in Bluetooth Low Energy capabilities.

Tasks: The SIP intern will work alongside graduate students at the HSL and aid in the development of robust code frameworks for the iOS and Arduino platforms. The intern and graduate mentor will work together to specify, design, and build a robotic or sensing platform utilizing the RFduino microcomputer and an iOS device. This is an excellent opportunity for interns wishing to learn to write code, or to advance their existing abilities. Apart from the software domain, this project will have a significant hardware component allowing interns to become more well-versed in designing and building non-trivial electric circuits.

URL: https://hybrid.soe.ucsc.edu
Required skills for interns prior to acceptance: Computer programming
Skills intern(s) will acquire/hone: Computer programming; circuit design/impementation; iOS microcontrollers
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: ON ON ON ON ON ON ON ON ON ON


Economics

Code Research Project Descriptions
ECO-01 Title: Quantitative Analysis of the Asset Price Bubbles Using REITs
Primary mentor: Dalia Terleckaite
Other mentors:
Location: UCSC main campus about three times a week, can meet near Los Gatos other days.
Number of interns: 3

Project description: Asset price bubbles (or overpricing, fluctuations above asset’s fundamentals) is an important topic in modern economics.  There is no compelling theory fully explaining the creation, growth and burst of asset price bubbles.  Characteristics of a classical equity bubble (high share price, volatility and turnover) are not always present in bubbles. They may be different for different asset classes.  Quiet Bubbles by Hong and Sraer (2013 JoFE) is a new theory attempting to explain bubble episodes with low turnover.  The project involves doing quantitative research of the asset price bubbles, currently focusing on the equity and mortgage REITs and possibly expanding into other assets. This research is quantitative in nature, relying on statistical and econometric techniques.  There is particular interest in behavior of asset prices and trading measures during the different stages of a bubble cycle, and the mentor is testing some new bubble theories using trading data of two types of REITs (Real Estate Investment Trusts) - mortgage REITs and equity REITs.    So far the research has focused on monthly data and only the U.S. REITs market, but it will include international markets as well (Europe, Asia, and possibly Australia) and higher frequency data (most likely daily).  The core of the research will be rigorous econometric analysis (e.g., panel regressions, event study regressions), so SIP interns will have an opportunity to learn some advanced econometric techniques.

Tasks: SIP intern tasks will include: (1) Reading and summarizing academic papers and industry research publications on the asset price bubbles and REITs, (2) Identifying and collecting REITs trading and other data (from the Bloomberg terminal, reit.com, sec.gov, bls.gov, and other sources) for the U.S. and international markets, (3) Doing in-depth research of individual REITs and comparative analysis of equity vs. mortgage REITs, (4) Learning and applying advanced econometric techniques, (5)Assisting with statistical programming, such as SAS, STATA, or R, and (6) Presenting results using tables and graphs.

Required skills for interns prior to acceptance: Computer programming; statistical data analysis
Skills intern(s) will acquire/hone: Computer programming; statistical data analysis
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: ON ON ON ON ON ON ON ON ON ON


Ecology & Evolutionary Biology

Code Research Project Descriptions
EEB-01 Title: Plant Phenology and Climate in Santa Cruz County
Primary mentor: Juliet Oshiro
Other mentors: Kingsley Odigie
Location: UCSC main campus; Arboretum; various field locations in Santa Cruz County
Number of interns: 2

Project description: Phenology is the timing of life cycle events, and one expects that it will change in response to climate change. For example, many studies have found that blooming times are becoming earlier in the year due to increased temperature. The mentor is broadly interested in how and why plant phenology responds to climate. The mentor’s PhD research focuses on flowering phenology in the grasslands and sandhill habitat types of Santa Cruz County. She has three goals: (1) discover how flowering phenology relates to climate in the field, (2) determine if flowering phenology responses to climate are related to certain plant traits, and (3) replicate the patterns she sees in the field using a greenhouse experiment. She is also interested in promoting citizen science as a way to collect phenology data; therefore, she created the UC Santa Cruz Arboretum Phenology Walk. For this project, the mentor provided infrastructure and resources for visitors to the Arboretum to collect phenology data on permanently marked plants in the gardens. The goal of this project is to engage the public in science research, and to create a long-term dataset for research use.

Tasks: The SIP interns will be in charge of their own project that uses data collected by the UC Santa Cruz Arboretum Phenology Walk. The interns can choose their own research question and are encouraged to present their findings at a phenology workshop. The interns will also assist with the mentor’s PhD research, including: (1) spend 1–3 days per week collecting data in the field; (2) assist with data management including: entering data, summarizing climate and flowering data, performing basic statistical analyses, counting seeds, and analyzing photographs; and (3) assist with greenhouse experiment: including measuring plant size attributes, and collecting and counting seeds.

URL: http://borg5.ucsc.edu/research/eeb/fox/?page_id=80
Required skills for interns prior to acceptance: Computer programming; statistical data analysis
Skills intern(s) will acquire/hone: Statistical data analysis; field work; leadership; communication skills
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: ON ON ON ON ON ON ON ON ON ON


Code Research Project Descriptions
EEB-02 Title: Investigating Evolutionary Consequences of Speciation in Sea Urchins
Primary mentor: Christopher Kan
Other mentors: Patrawat Samermit
Location: UCSC Main Campus (EMS)
Number of interns: 2

Project description: Our lab seeks to investigate the forces that create species and the consequences of speciation. The project that the SIP interns will assist with specifically focuses on two areas: temperature adaptation and reproductive isolation. Temperature adaptation in proteins is a burgeoning topic because of climate change. Our lab seeks to understand which proteins adapt and why. The results have obvious applications for human and planetary heath. Secondly, the project will investigate reproductive isolation genes in sperm and eggs. Speciation as a process is incompletely understood and the SIP intern will assist in investigating how this process occurs.

Tasks: The SIP interns will be taught how to use software to obtain answers from genetic data. They will assist with collecting information about key proteins in sea urchin genomes. Past SIP interns have improved their critical thinking, data analysis and computer programming skills.

URL: christopherkan.com
Required skills for interns prior to acceptance: Computer programming; statistical data analysis
Skills intern(s) will acquire/hone: Computer programming; lab work; statistical data analysis
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: ON ON ON ON ON ON ON ON ON ON


Code Research Project Descriptions
EEB-03 Title: Human-induced Effects on Species Interactions
Primary mentor: Justine Smith
Other mentors: Christoph Lee
Location: UCSC main campus
Number of interns: 1

Project description: Pumas in the Santa Cruz Mountains live among towns and roads, and must adapt to human presence to survive. However, they are fearful of humans and alter their behavior to avoid risky interactions with them. In the mentor’s work, she has found that pumas spend less time consuming their kills and as a result have to kill more deer when they are disturbed by people. The mentor is currently investigating if this relationship leads to greater food availability for scavengers, such as opossums and skunks. To do this, she put motion-sensored video cameras on puma kills to track consumption of the prey by both pumas and other species. This study will provide new insights into the indirect effects of human disturbances on wildlife through changes in top predator behavior.

Tasks: The SIP intern will gain new skills in the study of animal behavior primarily by examining video footage at puma kill sites. The intern will learn how to identify carnivore behaviors in the videos and explore how species interact at a shared food source. There will also be opportunities to visit kill sites in the field, and a student with permission to go to active kill sites is preferred for this position. Visiting kill sites will entail hiking off-trail and possibly being exposed to ticks, poison oak, and steep slopes. Finally, the student will engage in preliminary analysis of the data and will learn fundamentals of GIS (geographic information systems).

URL: http://santacruzpumas.org
Required skills for interns prior to acceptance: Computer programming; statistical data analysis
Skills intern(s) will acquire/hone: Statistical data analysis; field work; animal behavior and natural history training; spatial analysis in GIS
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: ON ON ON ON ON ON ON ON ON ON


Code Research Project Descriptions
EEB-04 Title: Climate Impacts on Species Distributions in a Desert Ecosystem
Primary mentor: Sarah Skikne
Other mentors: Claire Masteller
Location: UCSC main campus
Number of interns: 1

Project description: Globally, climate change has already caused shifts in species ranges, with species moving polewards and upwards in elevation in parallel with suitable climate conditions. Understanding how such range shifts have unfolded will help conservation biologists predict and respond as species react to accelerating climate change in the future. The mentor’s research investigates species range shifts using records of animal and plant distributions collected since the 1970s along an elevational gradient in Boyd Deep Canyon, a UC Natural Reserve near Palm Desert, California. The mentor is building on this unique dataset to test whether species have shifted their elevational ranges, and if so, what ecological processes have unfolded to create these shifts.

Tasks: The SIP intern will be involved in one or more potential projects to support this project, depending on their skills and interest, and project status. For example, the intern may: (1) mine published literature to create a database on the physiological tolerances, natural history, and ecological interactions of these species, (2) analyze photographs using GIS to quantify changes in plant species distributions, and/or (3) analyze local climate data to quantify historic climate change in the area. The intern may also have the opportunity to help with re-photography over an approximately 5-day trip to the field site in Southern California.

Required skills for interns prior to acceptance: Computer programming; statistical data analysis
Skills intern(s) will acquire/hone: Statistical data analysis; field work; GIS
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: ON ON ON ON ON ON ON ON ON ON


Code Research Project Descriptions
EEB-05 Title: Plant Defense Syndromes in the Mustard Family (Brassicaceae)
Primary mentor: Julie Herman
Other mentors:
Location: UCSC main campus (greenhouses, EMS)
Number of interns: 2

Project description: Plants use a variety of quantitative and qualitative defense traits to discourage or escape from their herbivores. These include toxic chemicals, physical impediments to consumption such as leaf coatings or thorns, and growth rate. However, it is unknown whether these traits are interrelated — for example, if a plant has thorns, does it also need chemical toxins? The goal of this project is to assess plants in the mustard family (Brassicaceae) for evidence of clustering of defense traits, or syndromes.

Tasks: The SIP interns will monitor physical traits and defense characteristics of experimental plants in the mustard family, including growth rate, physical leaf attributes, and leaf chemistry. The interns may also assist with statistical and phylogenetic analysis of the data, depending on interest and skill level.

Required skills for interns prior to acceptance: Computer programming; statistical data analysis
Skills intern(s) will acquire/hone: Lab work; statistical data analysis
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: ON ON ON ON ON ON ON ON ON ON


Code Research Project Descriptions
EEB-06 Title: Assessing the Evolutionary Convergence of Cleaner Fishes
Primary mentor: Vikram Baliga
Other mentors: Talia Waltzer
Location: UCSC Long Marine Lab
Number of interns: 1

Project description: “Cleaner fishes” are species that consume ectoparasites by picking them off other organisms. Over 120 species of saltwater fishes from diverse groups exhibit this behavior, including species of wrasses, gobies, damselfishes, and angelfishes. It is unknown whether cleaner fishes show convergence in anatomical traits, but one can predict that cleaners clearly must possess traits that allow them to find and remove ectoparasites. The goal of this project is to discover whether the evolution of cleaning behavior within several families of reef fishes is associated with the same suite of traits. Do these distantly-related species converge on similar anatomical form, or is there more than one way to build a cleaner?

Tasks: The SIP intern will collect gene sequences from online repositories (e.g., GenBank) in order to assemble phylogenetic trees for two families of reef fishes. The intern and mentor will quantify variation in body shape for different species via geometric morphometrics. Finally, the intern and mentor will use phylogenetic comparative methods to assess how convergent in body shape cleaner fishes are. The mentor is happy to teach the SIP intern basic programming in the R and Python languages in order to accomplish all of the above. The intern may also choose to occasionally be involved in another study involving the use of high-speed cameras to capture slow-motion sequences of feeding behaviors of animals in captivity. All of this research will be conducted at UCSC’s Long Marine Laboratory.

Required skills for interns prior to acceptance: Computer programming; statistical data analysis
Skills intern(s) will acquire/hone: Computer programming; statistical data analysis
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: ON ON ON ON ON ON ON ON ON ON


Code Research Project Descriptions
EEB-07 Title: Evolution in Acid: Contemporary Evolution in a Drilling Predator
Primary mentor: Gina Contolini
Other mentors: Audun Dahl, Sam Mansfield
Location: UCSC Long Marine Lab
Number of interns: 2

Project description: In this project, the mentor seeks to understand how ecological and evolutionary factors influence the interaction between dogwhelk predators and their local prey, California mussels. Dogwhelks (also known as whelks) are intertidal snails that prey on mussels by drilling a hole through the mussel’s shell. The mentor hypothesizes that ecological factors, such as predation, competition, and planktonic food availability as well as abiotic variables such as pH influence the interaction between dogwhelks and mussels. The mentor is especially interested in how pH affects the interaction, since highly acidic water can reduce shell thickness in mussels, thereby affecting the ability of dogwhelks to prey on them. The mentor also hypothesizes that evolutionary factors, such as the ability of dogwhelks to adapt genetically in response to the environment and prey defenses, specifically mussel shell thickness, influence the interaction. Finally, the mentor hypothesizes that ecological and evolutionary factors interact to influence the dogwhelk-mussel interaction. For example, seawater pH (an ecological factor) may affect the thickness of mussel shells, which in turn may cause the dogwhelks to adapt genetically to mussel shell thickness (an evolutionary factor).

Tasks: The SIP interns will get to do the following tasks: (1) help collect mussels and whelks in the field at beautiful intertidal sites around California (and Oregon, if possible); (2) set up and organize the tanks where the mentor’s research group will be keeping the live whelks and mussels that are collected; (3) measure the length, width, and mass of the whelks that are collected; (4) measure the shell length, width, and thickness of the mussels that are collected; (5) measure and describe the whelks’ radulas (the radula is the feeding aparatus whelks use to drill – this involves dissections); and (6) go on field trips to intertidal sites nearby to learn about intertidal ecology.

URL: http://rediscoveringevolution.blogspot.com
Required skills for interns prior to acceptance: Field work; other
Skills intern(s) will acquire/hone: Lab work; statistical data analysis; field work; learning how to apply and test questions in evolutionary biology
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: ON ON ON ON ON ON ON ON ON OFF


Code Research Project Descriptions
EEB-08 Title: Cows, Birds and West Nile Virus: Impact of Local Host Communities on Pathogen Transmission
Primary mentor: Tony Kovach
Other mentors: Jennifer Bellik
Location: UCSC main campus
Number of interns: 1

Project description: Mosquitoes are important vectors of many pathogens. Where mosquitoes get blood from can change the amount of local pathogen transmission. Particular sites with certain animals that are highly infectious and fed upon frequently can lead to hotspots of pathogen transmission, whereas other sites with less infectious animals that are fed upon frequently may reduce local transmission of pathogens. The contribution of each host to transmission intensity varies depending on host infectiousness and vector/host contact rates. If mosquitoes alter feeding behavior in response to host community composition, local transmission may be dampened or amplified. This project examines the effect of local host community changes on West Nile virus (WNV) transmission in 60 small wetland sites, half of which are surrounded by large herds of cattle. For each of the 60 small wetland sites, we already have data on mosquito abundance, local host abundance, and infection rates of WNV in mosquitoes. We have also collected blood-fed Culex mosquitoes at each site. The intern in this project will use lab techniques to analyze blood meal compositions of collected mosquitoes in order to analyze mosquito feeding preferences, and determine how variation in host communities may influence transmission of WNV.  This project will contribute to a greater understanding of mosquito biology, help identify hotspot locations where management efforts can be focused, and examine the potential use of cattle as a way to reduce WNV transmission.   

Tasks: This project will be mostly lab based. The SIP intern will work closely with the mentor using genetic techniques to determine the source of blood in individual mosquito abdomens. Blooded mosquitoes have already been caught from various field sites and are in the freezer awaiting processing.  The source of blood in individual mosquito abdomens will be tested using PCR amplification of the cytochrome b gene, nucleotide sequencing of the amplified product, and matching the sequence to known vertebrate species on GenBank using BLASTn. The project will address: (1) How do the feeding preferences of Culex tarsalis change when exposed to drastically different local host communities? (2) How strong is the link between local mosquito feeding preferences and local WNV infection rates in mosquitoes? (3) Does the presence of cattle reduce the local transmission of WNV by diverting mosquito bites away from more competent hosts?

Required skills for interns prior to acceptance: Lab skills
Skills intern(s) will acquire/hone: Lab work; statistical data analysis
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: ON ON OFF ON ON ON ON ON ON ON


Code Research Project Descriptions
EEB-09 Title: Assessing Craniodental Shape Variation in Sea Otters
Primary mentor: Chris Law
Other mentors: Jason John
Location: UCSC Long Marine Lab
Number of interns: 1

Project description: Despite the recognition that many species populations exhibit intraspecific dietary specialization, the consequences of this phenomenon on individual fitness are poorly known. Within the central California coastline, southern sea otters (Enhydra lutris nereis) exhibit great intraspecific dietary specialization in response to a limited resource environment. In addition, sea otters also exhibit variation in tool-use during feeding; while some individuals use rocks and shells as anvils or hammers, others do not use tools yet still feed on the same hard-shelled prey. Despite the large number of studies on sea otter life history and ecological role as an apex species, the relationship between individual dietary specialization and tool use variation and its affects on optimal foraging efficiency remains unknown. The goal of this project is to project the maximum feeding capability of sea otters in the absence of tool use through biomechanical modeling of sea otter bite forces and craniodental (skull) shape analyses. To learn more, please visit the mentor's website!  

Tasks: The SIP intern will: (1) Perform computational geometric morphometric analyses to quantify craniodental shape between male and female sea otters, (2) Photograph skull specimens at the California Academy of Sciences in San Francisco, (3) Take linear measurements of skull specimens, and (4) Help with sea otter dissections (optional)  

URL: http://research.pbsci.ucsc.edu/eeb/cjlaw/
Required skills for interns prior to acceptance: Lab skills
Skills intern(s) will acquire/hone: Computer programming; lab work
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: ON ON ON ON ON ON ON ON ON ON


Code Research Project Descriptions
EEB-10 Title: Fish in Geothermal Waters: How do Invasive Mosquitofish Change Traits After Introduction to Extreme Thermal Conditions?
Primary mentor: David Fryxell
Other mentors: Audun Dahl
Location: UCSC marine lab
Number of interns: 1

Project description: Mosquitofish are a globally invasive freshwater fish that were introduced to springs ecosystems in California within the past century. In order to understand how organisms deal with novel environmental conditions, the mentor is investigating how mosquitofish characteristics have changed among populations after their introduction to springs of a variety of thermal and ecological conditions. These fish were collected at sites ranging from 18 celsius to 38 celsius over the past year. The SIP intern will assist in dissecting the preserved fish in the lab. We will determine if fish traits like body size, body shape, body condition, number and size of developing embryos, gut length, and diet are different among populations, and whether those differences correlate with environmental characteristics like spring temperature and presence of predators.

Tasks: The SIP intern can expect to spend the majority of time in an indoors lab setting using basic lab equipment such as a microbalance and a dissecting microscope. This work requires a team of two people; the SIP intern will therefore be largely working alongside the mentor or an undergraduate student.

URL: http://people.ucsc.edu/~epalkova/Palkovacs_Lab/Palkovacs_Lab_Home.html
Required skills for interns prior to acceptance: Lab skills
Skills intern(s) will acquire/hone: Lab work; statistical data analysis
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: ON ON ON ON ON ON ON ON ON ON


Code Research Project Descriptions
EEB-11 Title: Evolution of Reef Fishes in an Oceanic Island of the Atlantic Ocean
Primary mentor: Hudson Pinheiro
Other mentors: Anna Isi
Location: UCSC marine lab
Number of interns: 1

Project description: This research addresses the evolutionary history of reef fishes found at Trindade Island, situated 1200 km offshore in the South Atlantic. The main question is related to speciation processes, genetic diversity and age of the species. The SIP intern will learn laboratory procedures of DNA extraction and genetic data analysis. More information about the fish fauna of Trindade is found at:      http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0118180   https://www.youtube.com/watch?v=ZsV3AkDvvvE&feature=youtu.be     http://journals.plos.org/plosone/article/asset?unique&id=info:doi/10.1371/journal.pone.0118180.s001  

Tasks: The SIP intern will learn laboratory procedures of DNA extraction and genetic data analysis. Thus, at the end of the summer the student will be able to estimate the age of speciation/isolation of the species, and the genetic diversity of continental and island populations. The SIP intern will study different kinds of speciation, such as allopatric, parapatric and ecological.

URL: http://bernardi.eeb.ucsc.edu/people/hudsonpinheiro/
Required skills for interns prior to acceptance: Lab skills
Skills intern(s) will acquire/hone: Computer programming; lab work; statistical data analysis
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: ON ON ON ON ON ON ON ON ON ON


Code Research Project Descriptions
EEB-12 Title: Feeding Diversity in Apex Marine Predators
Primary mentor: Sarah Kienle
Other mentors: Jason John
Location: UCSC Marine Lab
Number of interns: 1

Project description: All animals need to feed to survive. Despite the fact that feeding is of paramount importance to an organism's life history, for some vertebrates, we know little about what they feed on, how often they feed, and exactly how they get their food. One of the foci of the Mehta lab is the evolution of feeding behaviors in vertebrates. The lab has many ongoing behavioral projects that focus on understanding how animals feed and what they feed on in the wild. The main project the SIP intern will focus on relates to prey apprehension behaviors in captive marine mammals. We are using video to quantify the prey capture behavior of pinnipeds (seals and sea lions). 

Tasks: For this project, the SIP intern will learn how to digitize and analyze video of feeding behaviors of multiple species of pinnipeds (seals and sea lions). The intern will also learn how to anayze behavioral data.  Additionally, there will be some opportunities to help out on other lab projects including field work with elephant seals at Ano Nuevo State Park, recording video trials of captive marine mammals, and prepping muscle samples for stable isotope analysis. 

URL: http://mehta.eeb.ucsc.edu/
Required skills for interns prior to acceptance: Lab skills
Skills intern(s) will acquire/hone: Statistical data analysis; field work
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: ON ON ON ON ON ON ON ON ON ON


Code Research Project Descriptions
EEB-13 Title: Understanding How Fish Evolve in Fluctuating Environments
Primary mentor: Ben Wasserman
Other mentors: Audun Dahl
Location: UCSC Long Marine Lab
Number of interns: 2

Project description: The mentor is investigating evolutionary responses of the short-lived threespine stickleback fish (Gasterosteus aculeatus) to an ever-changing environment. Due to the seasonal pattern of rainfall in central California, sand bars form at the mouths of rivers and streams during the dry season, disconnecting these waterways from the ocean. Throughout the dry season the water in these bar-built estuaries becomes increasingly fresh, but when winter rains come the high flows breach the sandbars and are inundated with salt water. By repeatedly collecting fish and measuring their characteristics we can observe the pace and direction of evolution. 

Tasks: The SIP interns will measure traits in stickleback caught in these estuaries at different times of the year. This includes staining, measuring, and photographing fish. There will also be opportunities to assist in field work including catching fish using nets and traps, and maintaining time lapse cameras that record whether the estuaries are open or closed. 

Required skills for interns prior to acceptance: Lab skills
Skills intern(s) will acquire/hone: Lab work; statistical data analysis; field work
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: ON ON ON ON ON ON ON OFF ON ON


Code Research Project Descriptions
EEB-14 Title: SMURF: Small Mammal Undergraduate Research in the Forest
Primary mentor: Tina Cheng
Other mentors: Jennifer Bellik
Location: UCSC Main Campus/Forest Ecology Research Plot
Number of interns: 1

Project description: The SMURF program is a collaboration between graduate students, the Natural History Museum, and the UC Natural Reserve System that monitors long term small mammal population dynamics in the UCSC Forest Ecology Research Plot. SMURF interns trap small mammals every quarter (including summer) and then use the data to examine environmental and ecological questions. The internship is an introduction to small mammal surveying and handling, data entry and management, and project organization. SIP interns will have the opportunity to design and conduct a research project, analyze existing data, review scientific literature, and practice public speaking, in addition to furthering their development of field skills. Previous interns who have conducted independent research with the project have worked with endangered species, parasite load counts, habitat specialization, and stable isotope analysis. SIP interns will be encouraged to pursue an independently-derived research question, or investigate one of several potential ongoing projects under graduate student mentorship relating to small mammal population biology and ecology.

Tasks: A rough timeline including SIP intern tasks: Weeks 1 & 2 (June 8-19th): Literature Review and Design Research Question SIP interns will research the scientific literature and write short reviews on studies investigating the natural history, ecology, and population biology of small mammals, with particular focus on species found on the FERP – Neotoma fuscipes, Peromysces californicus, Peromysces boylii, Peromysces maniculatus, Sorex spp. Interns will work with the mentor to choose amongst several research questions or develop a research question to pursue during the summer program. Weeks 3 & 4 (June 22 – July 3rd): Field preparation for trapping session SIP interns will assist in organizing field-sampling materials to prepare for the summer trapping session. Duties will involve cleaning and preparing small mammal traps, proofing and printing datasheets, preparing bait and trap materials, organizing trapping schedule. SIP interns will work with mentors and other SMURF undergraduate interns to complete these tasks.   Week 5 (July 6-10th): Data entry and management SIP interns will work under mentor supervision to enter data from the trapping session and proof prior data.   Weeks 6 & 8 (July 13-31st): Data analyses SIP interns will work under mentor supervision to analyze data.

URL: http://research.pbsci.ucsc.edu/eeb/cheng/
Required skills for interns prior to acceptance: Statistical data analysis; field work
Skills intern(s) will acquire/hone: Lab work; statistical data analysis; field work
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: ON ON ON ON ON ON ON ON ON ON


Code Research Project Descriptions
EEB-15 Title: Investigating Kinematics and Behavior in Domestic Dogs and Wolves
Primary mentor: Caleb Bryce
Other mentors: Karen Duek
Location: UCSC Long Marine Lab
Number of interns: 1

Project description: The mentor's research interests focus primarily on the physiological constraints of locomotion for terrestrial carnivores, namely top canid predators such as grey wolves. My research is centered on how the elevated energetic demands of these elusive carnivores structure the ecological communities they inhabit. Top carnivores are rare and particularly vulnverable to anthropogenic disturbance because of their high energy requirements. We need to understand their resource requirements and activity patterns in order to predict their likely response to ongoing ecosystem change (e.g, prey availability, habitat fragmentation). If their energetic needs are not met and their populations decline, the landscapes they inhabit could change profoundly.  The mentor uses innovative wildlife collar technology to remotely monitor the activities and energetic demands of wolves and other carnivores. In order to be useful for investigators and wildlife managers, the mentor calibrates these collars via treadmill experiments and ground truthing in the field. Ultimately, this techonlogy enables scientists to monitor behavioral and energetic diaries of free-ranging animals, thereby affording a more mechanistic understanding of why top carnivores are so ecologically important. 

Tasks: The mentor currently needs assistance in video analysis of the videos they have of dogs running on a treadmill (i.e. kinematics) and wolves moving around freely in large enclosures (constructing an ethogram/annotating videos). The mentor may or may not complete these analyses before the summer, but if so can find other roles for the SIP intern. 

URL: https://sites.google.com/a/ucsc.edu/canid-energetics/
Required skills for interns prior to acceptance: Statistical data analysis; field work
Skills intern(s) will acquire/hone: Statistical data analysis; other
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: ON ON ON ON ON ON ON ON ON ON


Code Research Project Descriptions
EEB-16 Title: An Investigation of Juvenile Salmon Behavior and Habitat Use
Primary mentor: Katie Mcelroy
Other mentors: Shelley Sianta
Location: UCSC Long Marine Lab and NOAA's Southwest Fisheries Science Center (on the UCSC Long Marine Lab campus)
Number of interns: 1

Project description: To implement successful restoration strategies, the relationships between juvenile Chinook salmon and their physical environment must be better understood to provide direction for managers. Juvenile Chinook occupy a wide range of freshwater habitats, from clear, high velocity mountain streams to turbid, slow moving delta waters, with their habitat requirements changing along this gradient. The mentor's study seeks to understand how these habitat requirements change with location and age, by using an artificial stream channel to evaluate individual response to varying conditions. 

Tasks: The SIP intern will assist in behavioral analysis from video trials of individual fish. He/she will collect data from these videos to inform on habitat use such as time spent in each location, angle of fish, and position in water column. The intern will also help with artificial stream channel maintenance and behavioral trials as needed. 

Required skills for interns prior to acceptance: Statistical data analysis
Skills intern(s) will acquire/hone: Lab work; statistical data analysis
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: OFF ON ON ON OFF ON ON ON ON ON


Code Research Project Descriptions
EEB-17 Title: Assessing Stream Restoration Outcomes
Primary mentor: Bronwen Stanford
Other mentors: Claire Masteller
Location: UCSC main campus (or remotely)
Number of interns: 1

Project description: Hundreds of stream restoration projects take place in California each year, but in many cases there is a lack of information on how effective these projects are. In those cases, we find that restoration may not have the desired effects, and that there is a lot of variation in the amount of benefit from these projects. The mentor's research investigates the influence of surrounding land use on restoration outcomes in streams, both locally in California and using a global dataset of restoration projects. Using a combination of field work and spatial analysis the mentor is investigating how we can better target our restoration efforts. 

Tasks: The SIP intern will help with tasks related to a few different projects. The mentor will provide appropriate background readings for any topics of interest to help the intern put this work in context. Any of these projects could become more of a focus of the internship depending on intern interest. There is also the potential for stream field work depending on the interest of the intern. Tasks include: (1) Restoration outcomes meta-analysis: The intern will assist me in compiling a global database of restoration projects using published scientific papers. I will teach the intern how to read and extract information from these papers. Depending on intern interest we can also begin quantitative analysis of the results from these papers. (2) Insect identification: The intern will learn how to use a dichotomous key to identify aquatic insects collected this spring in Marin County. I will also guide the intern in using statistics to analyze initial patterns in the data. (3) Spatial analysis of restoration locations: The intern will assist with the compilation of a database of restoration projects on the California Central Coast. (4) If the intern has skills or interest in GIS we can also develop an approach for conducting spatial anlaysis of land uses surrounding my field sites. This would involve digitization and use of spatial analysis tools in GIS.

URL: http://people.ucsc.edu/~zavaleta/
Required skills for interns prior to acceptance: Statistical data analysis
Skills intern(s) will acquire/hone: Statistical data analysis
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: ON ON ON ON ON ON ON ON ON ON


Code Research Project Descriptions
EEB-19 Title: How Do Ant Diets Change With Seasonal Variation?
Primary mentor: Katherine Ennis
Other mentors: Christy Starr
Location: UCSC main campus
Number of interns: 1

Project description: Coffee is a globally important export crop supporting hundreds of thousands of farmers across the world, but is constrained by a number of ecological factors, including pest damage. Ants are ubiquitous in coffee agroecosystems and, while omnivorous, are also well documented as important predators of multiple coffee pests. However, ants and other species often attempt to shift foraging patterns depending on resource availability that varies with rainfall. The mentor's study aims to assess the differences in ant diet across the dry and rainy seasons. It is expected that ants in the dry season should have more limited diets due to reduced resource availability. However, the impact of the dry season on diet may not occur if the ant is able to shift foraging patterns more readily. To test for differences in ant diets, the mentor and SIP intern will perform a stable isotope analysis on gut content of several ant species. Carbon and Nitrogen isotopes, specifically, can provide a measure of how predaceous a species is relative to others. The ratio of heavy to light N isotope increases with increased predation because heavy N isotopes are incorporated into animal tissue more rapidly than light N isotopes. By measuring the relative proportions of the heavy and light Nitrogen isotopes it is possible to quantify differences in consumption of animal and plant tissues between individuals and thus determine if an ant's diet changes over a season. The mentor has collected the ant specimens and will be performing the diet analyses over the summer.    

Tasks: The SIP intern will be involved with the following: (1)Data management - For all studies, the SIP intern will learn how to organize data spreadsheets for efficient calculations and will be asked to enter data from identification or chemical analyses for future statistical analyses. (2) Chemical analyses - The SIP intern will learn how to conduct a stable isotope analysis. He/she will help prepare the ant specimens for analysis at the UCSC Stable Isotope Laboratory. (3) Statistical analyses - The SIP intern will gain a background in several commonly used statistical approaches. The mentor will guide the intern in learning how to code specific statistical analyses in the programming language, R. The intern will be asked to perform basic statistical analyses learned. (4)The SIP itnern will become proficient in scientific writing.     

URL: http://people.ucsc.edu/~sphilpot/Philpott_Lab/Research.html
Required skills for interns prior to acceptance: Statistical data analysis
Skills intern(s) will acquire/hone: Computer programming; statistical data analysis
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: ON ON ON ON ON ON ON ON ON ON


Code Research Project Descriptions
EEB-20 Title: The Effect of Reduced Rainfall on Pest Predation Rates
Primary mentor: Katherine Ennis
Other mentors: Christy Starr
Location: UCSC main campus
Number of interns: 1

Project description: The future production of coffee is increasingly threatened by a more variable climate. This is in part due to seasonal variations in temperature and precipitation that will affect coffee plant growth, but these variations may also increase population growth rates of a major coffee pest, the coffee berry borer (Hypothenemus hampei). This study focuses on how precipitation variation may impact pest populations and predation rates of the coffee berry borer (hereafter, borer). With this project the mentor will be comparing the predation of the coffee pest by ants and how seasonality (dry vs. rainy season) and rainfall may affect predation rates. The results obtained from these questions will help inform how shifting climatic effects may change the regulation of a global coffee pest. The mentor's preliminary study of ant predation of the borer provide evidence that ground-foraging ants do prey on the borer and that predation rates of the borer are higher in the dry season and that greater litter accumulation is associated with higher predation rates. This study seeks to further investigate these findings to determine the mechanism behind seasonally changing predation rates by ants. To do so, the mentor has conducted a simulated drought experiment using rainfall exclusions for a six-month period during the rainy season in two coffee farms in Chiapas, Mexico to see how limited rainfall affects predation interactions.   

Tasks: The SIP intern will be involved with the following: (1)Insect identification - The SIP intern will be taught and guided in insect identification with use of camera microscopes and insect keys. The SIP intern will then be asked to identify insect samples from the rainfall exclusion project. (2) Data management - For all studies, the SIP intern will learn how to organize data spreadsheets for efficient calculations and will be asked to enter data from identification or chemical analyses for future statistical analyses. (3) Statistical analyses - The SIP intern will gain a background in several commonly used statistical approaches. I will guide the student in learning how to code specific statistical analyses in the programming language, R. He/she will be asked to perform basic statistical analyses learned. (4) Scientific writing - The SIP intern may be asked to write or edit portions of manuscripts and to find relevant literature resources.  

Required skills for interns prior to acceptance: Statistical data analysis
Skills intern(s) will acquire/hone: Computer programming; statistical data analysis
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: ON ON ON ON ON ON ON ON ON ON


Code Research Project Descriptions
EEB-21 Title: Using Krill Eggs to Estimate Adult Krill Abundance in the California Current Pelagic Marine Ecosystem
Primary mentor: Cynthia Carrion
Other mentors: Susan Grasso
Location: UCSC marine lab
Number of interns: 2

Project description: Euphausiids (krill) are a protected forage species within EEZ waters of the west coast of the United States.   The characterization of the spatial and temporal distribution of key forage species including euphausiids, market squid, and sardines/anchovies is an important step in an ecosystem-based management strategy.  Krill distribution and abundance demonstrate a high degree of spatial and temporal heterogeneity and existing measurement protocols are both expensive (ship time, equipment costs) and problematic. These problems range from a lack of species specific data (i.e. hydroacoustic techniques) to inaccurate measurement of abundance due to patchiness and/or avoidance (traditional net sampling). Schooling fish such as sardines and anchovies  present similar sampling challenges but one alternative approach has been to utilize egg distribution and abundance as an independent measure of spawning stock distribution and abundance). Euphausiid eggs share many features with sardine and anchovy eggs: They have relative short hatching intervals and thus are an excellent indicator of recent and proximate spawning activity, they are easily distinguished in plankton samples, and their small size and near surface distribution make them relatively easy to sample with a variety of techniques including low tech, easily deployed nets. The current project will provide key data that will permit such an approach to be adopted. 

Tasks: SIP interns will analyze samples collected in 2014 and 2015 from a variety of locations off the California coast and enumerate both adult krill and krill egg abundance. These data will be utilized in the development of predictive hindcast fecundity models designed to estimate adult krill biomass as a function of krill egg abundance.

Required skills for interns prior to acceptance: Statistical data analysis
Skills intern(s) will acquire/hone: Statistical data analysis
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: ON ON ON ON ON ON ON ON ON ON


Code Research Project Descriptions
EEB-22 Title: Examining the Estuarine Fish Communities of California's Central Coast
Primary mentor: Travis Apgar
Other mentors: Audun Dahl
Location: UCSC Marine Lab
Number of interns: 1

Project description: Intermittent bar-built estuaries are unique aquatic habitats that occur only in coastal regions with seasonal rainfall patterns, including California’s Central Coast. These estuaries undergo seasonal cycles of repeated openings (breaching) and closures, which cause periodic connections to the ocean and have important implications for water temperature, depth, salinity, dissolved oxygen, and water clarity in the estuary. These variables, in turn, impact the organisms inhabiting the estuary. Bar-built estuaries on the Central Coast are home to threatened and endangered aquatic species that rely on the estuary habitat for all or part of their life cycle. Some of these species include tidewater goby, threespine stickleback, coho salmon, and steelhead trout. The tidewater goby is an estuarine-specialist and California endemic that has evolved unique adaptations to survive in bar-built estuaries. Anadromous fishes such as salmon and steelhead must time their migrations around the breaching cycle of bar-built estuaries. Understanding the temporal dynamics of estuary opening and closing would inform the recovery plans for these protected species.      

Tasks: The SIP interns will measure traits of the fish caught in bar-built estuaries at varying times of year. This will mainly include processing samples in the lab using techniques such as staining, measuring, and photographing fish. There will also be opportunities to assist in field sampling that will include catching fish using seine nets and traps.           

Required skills for interns prior to acceptance: Statistical data analysis
Skills intern(s) will acquire/hone: Computer programming; statistical data analysis; field work
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: ON ON ON ON ON ON ON ON ON ON


Electrical Engineering

Code Research Project Descriptions
ELE-01 Title: Demystifying Electromagnetic Coupling within Antenna Arrays
Primary mentor: Patrick Ellis
Other mentors: Heather Sully
Location: UCSC Main Campus
Number of interns: 1

Project description: Antenna arrays have long been used to detect objects by retrieving information within impinging electromagnetic (EM) waves.  Locating ships, airplanes, and even lost adventurers in remote areas are all tasks that antenna arrays are used for.  As such, the accuracy in which these arrays can predict locations is vital.  Various factors contribute to the accuracy of this task:  Whether there are objects around the antenna array, whether the EM waves have bounced off layers of the atmosphere or the surrounding ground, and if there is significant coupling.  Coupling is parastic EM radiation - an example - when an EM wave hits an antenna and then bounces off and hits another antenna.  The bouncing, or re-radiation, upon another antenna is coupling and it can greatly hinder the antenna array's ability to correctly detect objects.  It is a well known but not completely understood phenomena that this project looks to investigate thoroughly.  

Tasks: The SIP intern will learn antenna basics, and how antenna arrays can gather electromagnetic waves and intuit such things as location and speed of objects in the air.  The intern will become familiar with a powerful electromagnetic modeling software called 4NEC2, and use MATLAB to draw preliminary results and further physical insight on coupling for a half wavelength dipole or monopole antenna arrays in various physical scenarios.

Required skills for interns prior to acceptance: Statistical data analysis
Skills intern(s) will acquire/hone: Computer programming; statistical data analysis
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: ON ON ON ON ON ON ON ON ON ON


Code Research Project Descriptions
ELE-02 Title: CANCELLED: Image filtering for enhancing the quality of images
Primary mentor: Amin Kheradmand
Faculty advisor: Prof. Peyman Milanfar
Location: UCSC main campus
Number of interns: 0

Project description: This project has been cancelled due to the unavailability of the mentor. These days with ever increasing image data produced by cameras, filtering images to get more visually pleasant outputs is necessary. Understanding the underlying mechanism for manipulating and enhancing (filtering) images makes it easier to come up with tools for improving the quality of images. As such image filtering has found lots of applications in differnt disciplines where one needs high quality images.

Tasks: The SIP intern will get familiar with the filtering operations for image processing. The intern will also study the concepts like low pass filtering for removing noise in the image, high pass filtering for emphasizing some details in the image. Also, the intern works with either MATLAB or OpenCV programming tools to apply different filters to an input image and see their effects visually.

URL: https://users.soe.ucsc.edu/~aminkh/
Required skills for interns prior to acceptance: Computer programming
Skills intern(s) will acquire/hone: Computer programming; statistical data analysis
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: ON ON ON ON ON OFF OFF ON ON ON


Code Research Project Descriptions
ELE-03 Title: Robust Renewable Energy Conversion for Smart Grids
Primary mentor: Jun Chai
Other mentors: Jia Lu
Location: UCSC main campus
Number of interns: 1

Project description: The use of power from renewable energy sources is a promising solution to meet increasing electricity demands. This is one of the cornerstones of the future “smart grid.” However, a particular challenge anticipated by a “smart grid” is the high variability of the power provided by the renewable resources, mainly due to their high dependence on environmental conditions. The Hybrid Systems Lab (HSL) at UC Santa Cruz is developing algorithms for DC (power from a solar panel) to AC power conversion/inversion. New technologies are being developed to complete the task with less power loss than current conversion methods, as they do not require intermediate conversion, and produce accurate AC power with low harmonic distortion. 

Tasks: The SIP intern will be working with a hardware prototype (a standard H-bridge-based inverter) that implements the new technology, and assisting in the testing of several algorithms. With help from the mentor, the intern will gain an understanding of the algorithm, gain basic knowledge of control systems, and learn about the operation of electronic circuits and solar panels.

Required skills for interns prior to acceptance: Computer programming
Skills intern(s) will acquire/hone: Computer programming
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: ON ON ON ON ON ON ON ON ON ON


Code Research Project Descriptions
ELE-04 Title: Characterization and Modeling of Metal Oxide Thin Films
Primary mentor: Nobuhiko Kobayashi
Location: UCSC main campus
Number of interns: 2

Project description: The mentor's research group, Nanostructured Energy Conversion Technology and Research (NECTAR), focuses on studying state-of-the-art inorganic thin films in terms of their structural, electrical, and optical properties with emphasis toward energy harvesting/conversion (e.g. sunlight and waste heat), microelectronics (e.g. memories in computing systems), and small/large-scale optics (e.g. small optical waveguides, large telescope mirrors). Design, development, and optimization of thin films made of a wide range of materials (e.g. metal oxides) require complementary scientific tools. This project aims at studying both optical and electrical properties of thin films to experimentally obtain the association between these two basic properties. The SIP interns will learn; (1) how to measure basic optical properties (e.g. refractive index and extinction coefficient) of thin films using an advanced spectrometric ellipsometer-reflectometer and (2) how to measure basic electrical properties (e.g. electrical conductivity as a function of temperature) of thin films using a sophisticated  electrical transport measurement set up. The interns will also gain an understanding of the basic working principles behind these measurement techniques to assess implications of collected experimental data.

Tasks: The SIP interns will be conducting the following tasks: (1) learn how to use the spectrometric ellipsometer-reflectometer, (2) learn how to model thin film structures to obtain basic optical properties from the measurement, (3) set up an electrical transport property measurement system (i.e. four-probe measurement system) with a cryogenic probe station and a semiconductor parameter analyzer, (4) learn how to use the electrical transport measurement system, (5) learn how to assess the obtained electrical properties by parametrically studying electrical properties of various thin films, (6) complete the project by correlating optical and electrical properties of thin films.  

URL: http://https://nectar.soe.ucsc.edu/
Required skills for interns prior to acceptance: Computer programming
Skills intern(s) will acquire/hone: Computer programming; lab work; statistical data analysis
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: ON ON ON ON ON ON ON ON ON ON


Code Research Project Descriptions
ELE-05 Title: Measuring Surface Energy of Thin Films and Nanostructures by Water Droplet Contact Angle
Primary mentor: David Fryauf
Other mentors: Katie Hellier
Location: UCSC main campus
Number of interns: 1

Project description: The mentor's research group, Nanostructured Energy Conversion Technology and Research (NECTAR) is developing novel and innovative thin films and nanostructured materials for several areas of competitive technology, including thermoelectrics, transparent conducting films, anti-reflective coatings, and chemical corrosion barriers.  Design, fabrication, and characterization of such materials requires many types of scientific tools, and one important tool for characterization is a water droplet contact angle profiler for measuring surface energy of materials.  This project includes full design and testing of the custom measurement system using simple precise hardware and open source image processing software.    

Tasks: The SIP intern will learn the background chemistry/physics of the surface energy measurement and its significance for understanding novel advanced nanomaterial properties.  With this understanding, software will be designed for calibration, automated measurement, and analysis of contact angle for water droplets on various thin film samples.  We will be comparing the chemical and mechanical durability of experimental thin film materials fabricated under different conditions.  The intern will be working hands-on with custom hardware in our lab space at our Santa Cruz lab at 2300 Delaware Ave as well as on campus.   

URL: https://nectar.soe.ucsc.edu/
Required skills for interns prior to acceptance: Computer programming
Skills intern(s) will acquire/hone: Computer programming; lab work; statistical data analysis; other
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: ON ON ON ON ON ON ON ON ON ON


Environmental Studies

Code Research Project Descriptions
ENV-01 Title: Ecology of the Bee Microbiome: Local and Landscape Drivers of Gut Variation in the Blue Orchard Bee
Primary mentor: Hamutahl Cohen
Other mentors: Christy Starr
Location: UCSC Main Campus; Field work in Urban Gardens in Santa Cruz, San Jose, and Monterey
Number of interns: 1

Project description: Bees are important pollinators in many agricultural ecosystems but their populations are declining on a global scale due to a complex set of interacting stressors. While there has been an incredible amount of research on the impact of pesticides, parasites, and pathogens, one oft-overlooked factor is the impact of land-use change on bee health. As bees forage across vast distances, they rely on the landscape for pollen, nectar, and nesting resources. Bee populations are thus sensitive to landscape composition, benefiting from natural habitat. But what is the relationship between landscape and the actual health of these bees?  The first step to answer this question requires defining the somewhat vague concept of bee health. For bees, the gut microbial community plays a role in health. Each bee has a unique collection of bacteria, fungi, and other gut microbes called the microbiome, which supports pathogen defense, digestion, and even insecticide resistance. Many of these important microbes are only available from the surrounding environment. For example, bees acquire beneficial species of the bacterial genus Lactobacillus from flower pollen. Habitat has been shown to impact gut diversity in some insects, but for bees the relationship is unclear. The mentor's research is motivated by how environmental factors impact the bee microbiome. The hypothesis is that bees from urban gardens situated in heterogeneous, diverse landscapes host a more abundant and species-rich microbiome compared to bees in gardens with landscapes dominated by urbanized and simple landscape features.

Tasks: The SIP intern will join the research team to conduct research in urban gardens in San Jose, Santa Cruz, and Monterey throughout the summer. Field work occurs every 3 weeks, and takes 3 days to visit all the sites. These are full field days, leaving from campus. At each garden field site, the intern will be supervised to conduct vegetarian surveys or collect insects.  In between field days, there will be lab work identifying bee species. Additionally, the SIP intern will have their own project, which the mentor will supervise. The mentor would like the student to make a printed guidebook to all the bees found along the central coast of California. The guidebook will include pictures (that the student can take without microscope camera of the specimes), illustrations, and information about the ecology of each species. The guidebook will be used as a teaching material for agroecology students at UC Santa Cruz, and will be given to the management at each of the 20 urban gardens in which we work.  Although this is the project suggested for the intern, they are encouraged to develop their own project.  Finally, this research is part of a larger colloboration of urban garden research between Santa Cruz, CA and San Cristobal, Mexico. At the end of July, a multicultural team of students and faculty from the University of San Cristobal, Mexico, will be visiting our research lab in Santa Cruz for a week-long short course and agroecology tour. The SIP intern will be encouraged to participate during this week. There will be short lectures, tours of local gardens and farms, and some joint research work during the meet that the intern will be encouraged to join. 

URL: http://envs.ucsc.edu/about/singleton.php?&singleton=true&cruz_id=hcohen1
Required skills for interns prior to acceptance: Computer programming
Skills intern(s) will acquire/hone: Lab work; field work
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: ON ON ON ON ON ON ON ON ON ON


Code Research Project Descriptions
ENV-02 Title: Federal Lands Multiple Use and Extractive Industries Analysis
Primary mentor: Jeffrey Jenkins
Other mentors: Emily Entress
Location: UCSC main campus (and remote)
Number of interns: 1

Project description: Nature-society geography focuses on the relationship between populations, natural resources and the environment, through both temporal (time) and spatial (space) scales, from the household to planet earth.  In the western United States a subset of this work is related to the relationship between economies for extractive industries (e.g. oil, gas, mining) and multiple use amenities (e.g. ranching, hiking, timber) that take place throughout federal lands (e.g. national parks, forest service, etc). Recently, President Obama, like his predecessors, has designated new national monuments (e.g. San Gabriel Mountains near Los Angeles) with the specific intent of protecting natural landscapes that are accessible to urban populations. At the same time the Obama administration has opened up new lands for oil, gas and mineral development throughout Alaska and the American west. This research analyzes the change in land use associated with extractive and amenity economies to answer questions about environmental trade-offs, social justice, economic growth, and conservation priorities. Questions include: What are the patterns of energy project investment throughout the western U.S.? What is the median household income for residents within a 1 hour drive of a national monument, how many residents will these new and proposed monuments serve, and what will lead the local economy to boom? Are there more endangered species on federal lands or private lands, what type of species are these, and will these lands be sufficient for species with climate change-induced range shifts? Are property value, biodiversity, and jobs equally valued between land that has been acquired for future extractive industry pollution and other parcels it was traded for?

Tasks: The SIP intern(s) will work on acquiring, compiling, and analyzing data related natural resources management on federal lands throughout the western U.S., most specifically data having to do with extractive industry development, related amenity economies, landscape-scale ecological impacts, and conservation strategies. The type of data sets to be collected include geospatial, socioeconomic, and ecological. Intern(s) will learn to use openly accessible programs and web interfaces to collect, organize, and make sense of information, including demographic statistics from the Census Bureau, geographic information system use in such programs as Google Earth and ArcGIS, federal natural resource agency online archives, and publically available corporate data-sets. While intern(s) are not expected to have long-standing experience with these particular programs, it would helpful that they show an interest in preparing with these applications prior to the summer research experience and that they bring a willingness to problem solve and think critically. These skills will come in handy throughout the second half of the summer research experience when intern(s) have transitioned from map, policy document, and population data collection to preliminary steps of data analysis.

URL: http://scwibles.ucsc.edu/Profiles/JeffJenkinsProfile2014.html
Required skills for interns prior to acceptance: Other
Skills intern(s) will acquire/hone: Statistical data analysis
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: ON ON ON ON ON ON ON ON ON ON


Code Research Project Descriptions
ENV-03 Title: Puma Project Camera Trapping
Primary mentor: Veronica Yovovich
Other mentors: Abigail Walsh
Location: UCSC main campus; possibly some field work in the Santa Cruz Mountains (transport provided)
Number of interns: 1

Project description: Mountain lions hold the dubious distinction of being California’s last top carnivore, and are a vital part of natural ecosystem balance and integrity. Human development threatens their future persistence by encroaching on habitat and disrupting important dynamics. The mentor’s research group has been GPS-collaring mountain lions in the Santa Cruz Mountains since 2008 and studying how they interact with their environment as well as with other species. The group also uses motion-sensitive camera traps as an effective, non-invasive way to document the activity of mountain lions, humans, and other species, to research how we all use our shared environment.

Tasks: The SIP intern can expect to be involved in lab and field work here associated with data processing and maintaining our camera trap array. Interns will become familiar with the photo-processing program Picasa, as well as get hands-on experience with field work setting camera traps and puma kill site investigations. Interns will be encouraged to pursue research questions about species interactions and/or habitat use and apply basic statistics to help answer their question.

URL: http://santacruzpumas.org
Required skills for interns prior to acceptance: Other
Skills intern(s) will acquire/hone: Statistical data analysis; field work; Excel; Picasa
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: ON ON ON ON ON ON ON ON ON ON


Code Research Project Descriptions
ENV-04 Title: Remote Sensing of Soilborne Pathogens in Strawberries
Primary mentor: Graeme Baird
Other mentors: Julia Soares
Location: UCSC main campus; field sites in Watsonville
Number of interns: 1

Project description: The use of remote sensing and spectral imaging techology in agriculture is a rapidly expanding field. This project aims to develop the use of hyperspectral imaging (from satellites and near-ground technology, possibly UAV "drones") for evaluating general plant health characteristics, as well as detecting and identifying soilborne plant pathogens in strawberry cropping systems and field experiments. The primary scope of the project will focus on linking remote-sensed data with samples collected directly from experiments and on-farm trials, both at the UCSC farm and at field sites in Watsonville. 

Tasks: The SIP intern will assist with: collection of remote-sensing data, field monitoring and collection of soil and plant samples, sample processing, data analyses, and image processing.

Required skills for interns prior to acceptance: Computer programming; statistical data analysis; field work
Skills intern(s) will acquire/hone: Computer programming; statistical data analysis; field work
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: ON ON ON ON ON ON ON ON ON ON


Code Research Project Descriptions
ENV-05 Title: Climate Change and Hydropower Development Along the Brahmaputra River in Northeast India
Primary mentor: Costanza Rampini
Location: UCSC main campus
Number of interns: 2

Project description: All of Asia's main rivers originate in the glaciers of the Himalayas and depend at least partially on summer monsoon rains to supplement their flows.  As increased temperatures due to anthropogenic climate change cause the accelerated melting of Himalayan glaciers and alter the South Asian summer monsoon, Asia's main rivers, such as the Yarlung-Tsangpo-Brahmaputra, are experiencing changes in their flows and summer flood regimes. The Yarlung-Tsangpo-Brahmaputra is one of the world's largest rivers both in terms of volume and sediment load.  It originates in the glaciers of Tibet and flows through China, Northeast India and Bangladesh before emptying out into the Bay of Bengal. In Northeast India, it is considered the lifeline of the region and its people as it provides numerous ecosystem services including irrigation and fertilization, food sources, groundwater recharge, transportation and cultural services. Changes in the river's flow and flood regime as a result of climate change have cascading impacts on downstream communities and ecosystems. At the same time, the Brahmaputra has been identified as India's 'future powerhouse' and over 130 new dam projects are planned in the river basin in an effort to harness the enormous and yet-untapped hydropower potential of the river.  The combined impacts of dam building and climate change on the river and the riparian communities that depend on it have not yet been studied.  This project uses interviews, dam planning documents and hydrological data to understand the impacts of dams along the Brahmaputra River on the vulnerability and adaptability of local riparian communities to floods, which are expected to increase in both frequency and magnitude as a result of climate change. 

Tasks: The SIP intern(s) will be primarily involved in the analysis of interview data. The interview data consist of 74 semi-structured interviews conducted with riparian communities in Northeast India and includes information on demography and livelihoods, flood vulnerability, adaptation strategies, and dam impacts. The intern(s) will learn to code and analyze data, and will be encouraged to come up with their own questions to guide their analysis. 

Required skills for interns prior to acceptance: Other
Skills intern(s) will acquire/hone: Computer programming; statistical data analysis; other
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: ON ON ON OFF ON ON ON ON ON ON


Earth & Planetary Sciences

As of yet, no mentors have submitted projects for this field of research. Mentors are still in the process of submitting projects so please keep posted for more projects to be submitted.
 

Molecular, Cell & Developmental Biology

Code Research Project Descriptions
MCD-01 Title: Investigating the Mouse Visual System
Primary mentor: James Shanks
Other mentors: Jongchan Lee
Location: UCSC main campus
Number of interns: 1

Project description: The vertebrate visual system relies on a number of molecular cues to ensure proper development. The Feldheim lab is very interested in the molecules responsible for the accurate development of the retina as well as molecules necessary for the precise guidance of retinal axons to their proper targets in the brain. The mentor is using transgenic mice to investigate the role that adhesion molecules play in the developing retina and visual system.    

Tasks: The SIP intern will work directly with the mentor and utilize transgenic mice to identify the need for specific adhesion molecules in the development of the mouse visual system.  The intern will have the opportunity to learn about the vertebrate visual system as well as gain experience using molecular biology techniques such as immunofluorescence, PCR, histology, injection labeling, and microscopy.

URL: http://people.ucsc.edu/~anistori/index.html
Required skills for interns prior to acceptance: Other
Skills intern(s) will acquire/hone: Lab work; statistical data analysis
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: ON ON ON ON ON ON ON ON ON ON


Code Research Project Descriptions
MCD-02 Title: Transcriptome Analysis of Primate Neocortical Neuron Development
Primary mentor: Andrew Field
Other mentors:
Location: UCSC Main Campus (Biomedical Sciences Building)
Number of interns: 2

Project description: The Haussler lab is using 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. The mentor has recently identified a number of primate-specific non-coding RNA elements that are expressed at specific times during human and rhesus macaque cortical neuron generation. The mentor is currently in the process of generating more neural tissue from great ape species, sequencing their transcriptomes, and interpreting expression data to isolate candidate human-specifc non-coding RNA elements that may contribute to the creation of our larger brains.

Tasks: The mentor has had great success with a prior SIP intern who created several crucial RNA-sequencing libraries from orangutan induced pluripotent stem cells. This year, we are expanding the project, having SIP interns process more samples for RNA and DNA sequencing, test in vitro grown tissues with immunofluorescence staining, and use computational tools to process bioinformatic data. The SIP interns will learn strategies to tie together the many seemingly disparate ends of the rapidly growing field of modern genomics research into one cohesive story. Their efforts will lead us to a greater understanding of the changes in the transcriptome as neural tissue develops, and provide a snapshot into what makes us unique as humans.

Required skills for interns prior to acceptance: Computer programming
Skills intern(s) will acquire/hone: Computer programming; lab work; statistical data analysis
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: ON ON ON ON ON ON ON ON ON ON


Code Research Project Descriptions
MCD-03 Title: Exploring the Role of a Developmentally Restricted Hematopoietic Stem Cell in Infant Leukemia
Primary mentor: Perez-cunningham Jessica
Other mentors: Hyejin Han
Location: UCSC Main campus, Biomedical building
Number of interns: 1

Project description:     The mentor's goal is to understand the cause of infant leukemia. This project focuses on infant B cell acute lymphoblastic leukemia (B-ALL) which is believed to arise from an oncogenic transformation in utero. The five year survival rate for this extremely early onset leukemia is less than 20%. As the disease arises from a mutation at an early developmental time point, the mentor's laboratory has begun investigating fetal blood development. Using a lineage tracing model the laboratory has discovered a novel, developmentally restricted hematopoietic stem cell (HSC). It is believed that the normal function of this HSC is to specify early innate-like lymphoid cells during fetal development.  Given its lymphoid bias, the mentors hypothesize that this HSC which exists during early development but does not persist into adulthood is the cell of origin in infant B-ALL. With this project the mentor will investigate the cell intrinsic and extrinsic mechanisms of leukemic transformation using a unique model that the mentor's laboratory has developed. He hypothesis is that the fetal microenvironment provides signals essential to leukemic transformation and progression, and that hematopoietic stress during development decreases disease latency and worsens prognosis. Here the mentor proposes using a transgenic mouse model to express oncogenic fusion proteins to test the leukemic potential of our developmentally restricted HSC. While it is hypothesized that these HSC will generate an infant B-ALL phenotype, any information that can be gained about the leukemic potential of these cells will be informative as they are currently a novel, uncharacterized population.  

Tasks: SIP interns working on this project will learn skills in necropsy, flow cytometry, PCR, and genotyping. The interns will work on growing hematopoietic cells in culture to better understand their oncogenic potential.

Required skills for interns prior to acceptance: Computer programming
Skills intern(s) will acquire/hone: Lab work; statistical data analysis
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: ON ON ON ON ON ON ON ON ON ON


Code Research Project Descriptions
MCD-04 Title: Genetic Analysis of Chromatin in Baker's Yeast
Primary mentor: Michael Doody
Other mentors: Brittany Young
Location: UCSC main campus
Number of interns: 2

Project description: 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!  The mentor is interested in understanding how packaging of DNA as chromatin affects its ability to be used by the cell. The mentor will 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. The mentor will use both genetic approaches, which examine the effects of mutations on chromatin and gene expression, and also biochemical approaches, in which the SIP intern and mentor will purify and study proteins and DNA in the test tube.  

Tasks: The SIP intern will be involved in the genetic characterization of chromatin mutants that have been isolated which are believed to disrupt chromatin and make the ORF more fluid/permissive to transcription. Additionally, the SIP intern will conduct a genetic screen on a conserved and essential transcription factor- Spt5- to isolate new mutations that disrupt chromatin strucutre. In conjunction with this, the SIP intern will also get hands on experience with primary molecular biology techniques and an understanding of how to critically read scientific journal publications and present research in a group meeting.

Required skills for interns prior to acceptance: Computer programming
Skills intern(s) will acquire/hone: Lab work; statistical data analysis
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: OFF OFF ON ON ON ON ON ON ON ON


Code Research Project Descriptions
MCD-05 Title: Molecular Factors in Hematopoietic Stem Cell Trafficking
Primary mentor: Susan Calhoun
Other mentors: Hyejin Han
Location: UCSC main campus
Number of interns: 1

Project description: Hematopoietic stem cells (HSCs) form blood and immune cells and are responsible for the constant renewal of blood in the body. HSCs have been successfully used in transplantaiton therapies for more than 50 years and can be used to treat both genetic and aquired disorders of the blood system including cancers and immune diseases.  Adult HSCs are primarily found in the bone marrow. When a transplantation needs to occur, the HSCs from the donor must be able to travel out of the bone marrow and into the blood where they can be collected and put into the recipient. Once in the recipient, the reverse process must occur in that the HSCs must travel from the blood and into the bone marrow where they must settle in to their respective niches where they can begin to make more cells. However, despite all of the advancements made in regenerative medicine, we stil do not have a complete mechanistic understanding of the factors that regulate the ability of HSCs to travel into and out of the bone marrow and what helps them engraft in their respective bone marrow niches. Recent findings in the Forsberg lab indicate that the vascular endothelium plays important roles in regulating HSC trafficking into and out of bone marrow niches. These findings led to the discovery that a distinct subpopulation of bone marrow endothelial cells in wild type mice express high levles of vascular cell adhesion molecule 1 (Vcam1). Further characterization of this Vcam1+ population revealed that these cells are likely sinusoidal endothelial cells (SECs). SECs have a unique expression of adhesion molecules, which are thought to play a role in HSC trafficking and engraftment. We hypothesize that SECs marked by Vcam1 mediate the trafficking of HSCs from the blood to the bone marrow. 

Tasks: The SIP intern working on this project can expect to learn many useful lab skills including: antibody dilutions, mice necroposy, mice genotyping, immunohistochemistry, flow cytometry, cell culture, data analysis   

Required skills for interns prior to acceptance: Computer programming
Skills intern(s) will acquire/hone: Lab work; statistical data analysis
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: ON ON ON ON ON ON ON ON ON ON


Microbiology & Environmental Toxicology

Code Research Project Descriptions
MET-01 Title: Investigating Photosynthetic Arsenite-Oxidizing Microorganisms from Extreme Environments
Primary mentor: Jaime Hernandez
Other mentors: Matthew Clapham
Location: UCSC main campus (PSB)
Number of interns: 2

Project description: Recent scientific studies discovered that arsenic could be metabolized during anoxygenic photosynthesis by microbes inhabiting extreme environments containing high arsenic levels, such as Mono Lake California.  These photosynthetic bacteria form dense blooms in hypersaline alkaline lakes and can also grow as red colored biofilms in hot springs. Our current project is to investigate the ecology, physiology, and genetics of these "novel" photosynthetic bacteria. One of these extremophilic bacteria, Ectothiorodospirae sp. str. BSL-9, was isolated from an arsenic rich hypersaline alkaline lake in Nevada.  This microbe can grow using light energy coupled to arsenite oxidation thus representing a "novel" form of anoxygenic photosynthesis linked to the toxic metalloid arsenic. The mentor is working to determine the genetic mechanisms for light-fueled arsenite oxidation. In addition, the mentor is also developing methods to investigate the impact of anoxic photosynthetic arsenite oxidation on the arsenic geochemical cycle. These studies will be informative for broadening our understanding of how microbial metabolisms can contribute to arsenic contamination known to occur in various freshwater environments.      

Tasks: The SIP interns will be able to work on several aspects of the project such as: (i) determine how changing environmental factors affects how BSL-9 oxidizes arsenite coupled to photosynthesis or (ii) developing a genetic system to determine what genes are required for light-dependent growth on arsenic.  While working on this project, interns may learn one or more of the following methods: anaerobic microbiology culturing methods; how to grow photosynthetic bacteria; how to analysis arsenic concentrations in growth media using HPLC-ICP-MS methods; gene amplification by PCR, molecular cloning techniques, quantitative mRNA analysis; and learning how to analyze DNA/genomic sequence information for downstream genetic investigations.  

URL: http://www.metx.ucsc.edu/research/saltikov.html
Required skills for interns prior to acceptance: Statistical data analysis
Skills intern(s) will acquire/hone: Lab work; statistical data analysis
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: ON ON ON ON ON ON ON ON ON ON


Code Research Project Descriptions
MET-02 Title: Analysis of Epistatic Interactions in Extended-spectrum Beta Lactamase Evolution
Primary mentor: Jay Kim
Other mentors: Sarah McKay Strobel
Location: UCSC main cmapus
Number of interns: 1

Project description: 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. The Camps lab uses 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.

Tasks: The SIP intern will work closely with the mentor to analyze epistatic interactions (non-additive interactions between two or more mutations) in ESBL obtained through clinical databases or experimental work. They will be applying statistical and machine learning models to: (1) investigate the link between epistasis and protein structure (2) apply what we’ve learned about epistasis in ESBL to HIV protease and reverse transcriptase inhibitor resistance. Previous experience in computer programming is preferred, but not absolutely required. A strong desire to learn programming skills works as well.

URL: http://www.metx.ucsc.edu/research/camps.html
Required skills for interns prior to acceptance: Statistical data analysis
Skills intern(s) will acquire/hone: Computer programming; lab work; statistical data analysis
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: ON ON ON ON ON ON ON ON ON ON


Ocean Sciences

As of yet, no mentors have submitted projects for this field of research. Mentors are still in the process of submitting projects so please keep posted for more projects to be submitted.
 

Other

As of yet, no mentors have submitted projects for this field of research. Mentors are still in the process of submitting projects so please keep posted for more projects to be submitted.
 

Physics

As of yet, no mentors have submitted projects for this field of research. Mentors are still in the process of submitting projects so please keep posted for more projects to be submitted.
 

Psychology

Code Research Project Descriptions
PSY-01 Title: Latina/o Children, Mural Making, Sense of Belonging, and Empowerment
Primary mentor: Jesica Fernandez
Other mentors: Colleen Reichmuth
Location: Live Oak Elementary School (Santa Cruz)
Number of interns: 2

Project description: The research team teaches 4th and 5th grade students how to conduct social science research to create change in their school and community. The students have decided to focus on creating a stronger connection between the school and community by collecting community stories, analyzing the stories, and creating murals that represent the themes and stories. This summer, the students will create their third mural, which is focused on hopes and dreams for the school and community. In addition to guiding the students, our research team studies how the students move through this process, in terms of their literacy development, empowerment, and connections to people in the school and community.

Tasks: In June, SIP interns will meet weekly with their mentor to read studies and receive instruction on fieldnotes. In July, they will participate in the program, including instructing 4th and 5th graders and taking fieldnotes. The summer program runs Mon-Th from 8:30 am through 11:30 am at Live Oak Elementary School (transportation being determined). In August,SIP interns will meet weekly to learn to analyze their fieldnotes. Statistical analyses (e.g., t-tests, ANOVAs) are possible. The SIP interns need not have experience with art or murals, but should be comfortable working with children in a flexible environment. Also, Spanish language skills are a plus.

URL: http://cogmodlab.ucsc.edu
Required skills for interns prior to acceptance: Statistical data analysis
Skills intern(s) will acquire/hone: Statistical data analysis; field work
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: OFF OFF ON ON ON ON ON ON ON ON


Code Research Project Descriptions
PSY-02 Title: Examining Motivation, Performance, and Persistence
Primary mentor: Sara Goodman
Other mentors: Justine Smith
Location: UCSC Main Campus (Social Sciences 2)
Number of interns: 1

Project description: Students often engage in activities (sports, clubs, etc.) that serve as a source of social and developmental growth during their secondary school years.  However, many students who start participating eventually quit these activities and may not be able to reap the same benefits as their peers.  Why do some students quit and others persist?  The current study assesses students' experiences in Extracurricular Activities, and investigates the relationship between motivation to keep participating, persistence, social factors (including support from family and friends), and level of performance or ability.  Using a large database of self-report information from our participants, this project aims to explain why and how some students "stick to it", while others simply quit.

Tasks: Much of the work for this project involves statistical data analysis.  The SIP intern will be asked to complete several different analyses, draw preliminary conclusions about the findings, and communicate them to the research team. While some statistical or data analysis experience would be helpful to start with, it is not necessary. The intern will learn to manage large data structures containing human subjects data, and use different types of statistical software packages to conduct analyses that will answer the major research questions.  The SIP intern may also be asked to provide suggestions and ideas for future directions and new research questions in order to expand and continue this line of research!

URL: http://cogmodlab.ucsc.edu/cogmodlab/
Required skills for interns prior to acceptance: Statistical data analysis
Skills intern(s) will acquire/hone: Statistical data analysis
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: ON ON ON ON ON ON ON ON ON ON


Code Research Project Descriptions
PSY-03 Title: Divided Attention in Mobile Multitasking
Primary mentor: Spencer Castro
Other mentors: Justine Smith
Location: UCSC Main Campus (Social Sciences 2)
Number of interns: 2

Project description: Screen displays today are more ubiquitous, varied in appearance, and deployed in novel situations than ever before. As a result they potentially affect people’s abilities to attend to and perform everyday tasks. The new situations that this research can impact include human performance at work, training the ability to attend to multiple stimuli optimally, and distractedness while operating vehicles. Previous research shows that a split in attention can have detrimental effects on goal-directed behavior. It also suggests that display-size can impact performance as well as holding the display compared to having it mounted. It is important to discuss how multiple screens affect attention as it becomes more commonplace in developed communities.

Tasks: First, SIP interns will be asked to read relevant material for the study. Then they will be trained to run human participants and learn the purpose of an Institutional Review Board. Next, the SIP interns will learn to use the application Eprime and the programming language Python to design and build experiments. Interns will collect data and we will discuss organizing data for analysis, which analyses apply to the experimental design, and what conclusions we are allowed to draw from them. Finally SIP interns will learn how to write an academic paper in APA formatting, and will write a section of this paper.

Required skills for interns prior to acceptance: Lab skills
Skills intern(s) will acquire/hone: Computer programming; statistical data analysis
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: ON ON OFF ON ON ON ON ON ON ON


Code Research Project Descriptions
PSY-04 Title: Race/Ethnicity in College and High School Contexts
Primary mentor: Alexandra Merritt
Other mentors: Gepoliano Chaves
Location: UCSC main campus
Number of interns: 2

Project description: This research is aimed at examining the influence of race in the college and high school contexts. The mentor has several projects that cover topics including microaggressions, culturally relevant teaching, and various aspects of school climates. The term microaggressions refers to brief commonplace transgressions against a person based on some aspect of his/her identity. The microaggressions study uses a crowd mapping iphone/android application as an innovative way of collecting data regarding such experiences of discrimination when they occur. The work involving culturally relevant teaching aims to understand how teaching that incorporates students’ backgrounds is perceived by students, thus affecting psychological and academic outcomes. Lastly, the study that addresses high school climate uses interviewing as a method of understand student’s experiences of their high school’s racial climate.

Tasks: The SIP interns that work in our lab will have the opportunity to learn how to transcribe interviews collected during the regular school year from the high school climate project. Additionally, SIP interns will also gain experience in coding qualitative data from the incidental reports collected from the microaggressions mobile app as well as aid in the development of the iphone app. Those interested in the effects of culturally relevant teaching will have an opportunity to research the ways that such practices are incorporated into teaching resources as well as assist with coding of the literature. Lastly, the SIP interns will receive training on how to use statistical software by aiding the mentor in running preliminary analyses. Interns that choose to work in this lab will have the opportunity to gain a wealth of experience in the different project areas.

Required skills for interns prior to acceptance: Lab skills
Skills intern(s) will acquire/hone: Statistical data analysis
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: ON ON ON ON ON ON ON ON ON ON


Code Research Project Descriptions
PSY-05 Title: Do Toddlers Attend to Speakers' Interactions when Overhearing a Conversation?
Primary mentor: Neda Namiranian
Other mentors: Baldo Marinovic
Location: UCSC main campus
Number of interns: 1

Project description: Young children can learn words from overhearing conversations between others. They selectively accept or reject information from linguistic sources. Although they tend to accept new words from accurate and familiar speakers, it is unclear what cues children attend to when overhearing conversations between unfamiliar people with no past record of accuracy. To address this question, the research group will present children with videos in which an adult labels new objects and another adult either agrees or disagrees nonverbally with the speaker. We will measure children’s word learning by asking them to identify the new objects labeled by the adult in the video.  

Tasks: This is a collaborative research project between a developmental and an adult psycholinguistic lab, which will allow the SIP intern to engage in hands-on experience of the psychological research process. The intern will be involved in recruiting participants, assisting with data collection, coding videos, and organizing data. Additionally, they will gain the skill of communicating findings to a general audience through presenting the project.  

URL: http://people.ucsc.edu/~nakhtar/
Required skills for interns prior to acceptance: Lab skills
Skills intern(s) will acquire/hone: Statistical data analysis; other
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: ON ON ON OFF ON ON ON ON ON ON


Code Research Project Descriptions
PSY-06 Title: Learning from Games
Primary mentor: Barrett Anderson
Other mentors: Justine Smith
Location: UCSC main campus
Number of interns: 2

Project description: Games have played an important role in learning since well before the beginning of modern education. Uniquely among educational tools, games have a "mechanical" or "system" component that is responsive to a player's agency, and can be discovered though interaction.  The implications of a game's system has been described as that game's "procedural rhetoric." Currently, the mentor is investigating factors that influence the transfer of information from these mechanical aspects of games, and comparing the effectiveness of learning from game mechanics with learning from other information channels.  This work can inform the design of more engaging and effective educational games.

Tasks: The bulk of the work is expected to be statistical analysis of data from completed experiments.  The SIP intern will learn to run analyses, generate reports, and communicate their findings.  This will involve using a statistical software package (R), learning some aspects of APA style, and (depending on need and comfort level) possibly some simple programming in Python.  The SIP intern may also have the opportunity to assist in data collection from research participants.  The intern will be involved in ongoing discussions about what conclusions we can draw from existing work, and plans for future research.

Required skills for interns prior to acceptance: Lab skills
Skills intern(s) will acquire/hone: Computer programming; statistical data analysis
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: ON OFF ON ON ON ON ON ON ON ON