Project labs are listed below.

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Updated August 31, 2021

Chemical & Biological Engineering

Department: Chemical & Biological Engineering

Research group: Weimer Lab

Project title: Particle Atomic Layer Deposition

Due to funding limitations, preference will be given to student applicants from Chemical & Biological Engineering.

Brief Project Overview​: The overall goals of the project are (1) to obtain reaction kinetics data for the synthesis of a film on particles produced by atomic layer deposition, the kinetics being useful for chemical reactor design and (2) the ability to assess the impact of a Particle atomic layer deposition film on particles used to fabricate Li-ion battery cathodes.

Department: Chemical & Biological Engineering

Research group: Hayward Lab

Project title: Stimuli-responsive nanostructured polymer materials

Due to funding limitations, preference will be given to student applicants from Chemical & Biological Engineering.

Brief Project Overview​: The Hayward group conducts research related to the development of ‘smart’ materials that can change their structures and properties on demand or in response to environmental cues, and in particular on strategies to form such materials through self-assembly of nanometer or micrometer-scale building blocks. Depending on the interests of the Uplift student, and the availability of near-peer mentors, specific topics may include: (i) soft, ionically-conducting polymer networks that respond to electrical fields and mechanical deformation, (ii) light-responsive polymers and hybrid materials that efficiently harvest light energy to produce mechanical work and motion, and (iii) frustrated self-assembly of polymeric building blocks whose geometries are incompatible with the formation of well-ordered structures.

Department: Chemical & Biological Engineering

Research group: Medlin Lab

Project title: Bifunctional catalysts for coupling of biomass-derived oxygenates to jet fuel

Due to funding limitations, preference will be given to student applicants from Chemical & Biological Engineering.

Brief Project Overview​: The overall goal of this research is to develop improved catalysts for upgrading of biomass-derived sugars to aviation fuel. Specifically, we are focusing on a key reaction late in the jet fuel synthesis process that involves forming C-C bonds between small oxygenated compounds to create higher-molecular weight species that have appropriate energy density and combustion properties. To carry out these reactions at industrially relevant rates, we are utilizing bifunctional catalyst materials that contain two types of sites: sites capable of hydrogen activation (e.g., palladium) and sites capable of acid-base chemistry (e.g., tungsten oxide). The focus of our research is identifying how the properties of the individual sites and the interface between those sites influences the overall process performance. Students working on this project will gain experience working with catalytic materials and bench-scale versions of industry-relevant flow reactors.

Mechanical Engineering

Department: Mechanical Engineering

Research group: Borden Lab

Project title: Microscale Gas Delivery Vehicles for Hypoxia Rescue

Brief Project Overview​: COVID has highlighted the need for extrapulmonary oxygen delivery: In the case of acute respiratory distress, timely intervention saves lives.

Our Lab has developed a microscale gas delivery platform capable of delivering oxygen through a variety of routes.  This semi-liquid, semi-gas suspension, called Oxygen Microbubbles, shows promise as an expedient therapeutic that can be administered at the first-responder level to provide an immediate increase in patient oxygen levels. These 1-10 micron oxygen gas spheres are stabilized in storage with a mono-atomic layer of lipid.  In the body, oxygen microbubbles dissolve over the course of minutes to hours, delivering oxygen and scavenging carbon dioxide from the bloodstream.  Whether administered intravenously, or into the GI tract, oxygen microbubbles interact with the body in a way that addresses and majorly circumvents a decrease in lung function.

Students will contribute towards novel measurements and revisions of the Oxygen Microbubble system, from
1) Testing new formulations to improve stability and delivery, to
2) Measuring Oxygen Microbubble gas transport in student-engineered and designed instruments, and
3) Presenting observations and novel insight at meetings here and abroad.

A note to Students: Many of your mentors started as undergraduates in the lab!  We know your classes come first, and we want to make sure you have enough time with us to meaningfully learn what science and high-level research is all about.  That means around 10–15 hours in the lab a week and an appreciation for new sights, sounds, skills, and challenges.

Department: Mechanical Engineering

Research group: Pellegrino Lab

Project title: Static Mixer Crystallization

Brief Project Overview​: The goals of the project are to make a static mixer that will induce crystallization in prepared salt solutions. Normally, surface crystallization or scaling occurs on everyday surfaces such as the hard water buildup in shower heads and coffee pots, but it also occurs in pipes of water treatment systems. This scaling must then be removed through various means, but there are ways to mitigate and slow down surface scaling. One such way is to use controlled mixing such that crystallization occurs in the water itself instead of on the surfaces of the system. Impellers can mix the water in a tank to promote crystallization, but static mixers can mix the water with lower energy and a more defined efficiency: they sit in the flow while their shape and the water flow across their surface induces mixing.

To that end, the goal of the project is to make a static mixer to be placed in a pipe and mix prepared salt solutions to induce crystallization. The student will be introduced to and involved in the many tasks that this can take inside and outside the lab, including modifying the geometry of the static mixer in a CAD-like environment, 3D printing the static mixer elements, preparing salt solutions, testing the static mixer elements, and changing parameters in the testing apparatus. In the end, the student will get to experience the research and development process on a real-world challenge.

Department: Mechanical Engineering

Research group: Animal Inspired Movement and Robotics Laboratory

2 Project Options (please list only one project from each lab you are interested in)

Project title: Development of Wireless Robotic Processing Circuit Board for use on Electroadhesion Rover

Brief Project Overview​: Our lab's research is focused on building micro-robotic platforms that are capable of autonomous navigation, sensing and power generation.  We are currently developing a light weight tank like robot with treads that when excited with high voltage allow the robot to stick to conductive surfaces through the process of electroadhesion.  With a high enough voltage, and a light enough design, this robot can drive on steep inclines, and potentially up walls or onto ceilings.  The ability to stick to steep or inverted surfaces will allow our robots to navigate environments traditionally off limits to most robots.  Our goal is to use these robots in a variety of applications such as engine inspections, search and rescue, space exploration and infrastructure monitoring.  

While the mechanical portions of this robot are actively being developed, we need help designing the robots electronic control board.  This circuit board will serve as the backbone of the robot providing wireless communication, controlling the two drive motors, generating high voltages for electroadhesion and measuring vehicle orientation.  Working alongside the mechanical team, a complete printed circuit board will be designed, fabricated, assembled and integrated into the final robot platform for testing.  Ultimately, the final platform will be evaluated in a number of environments and scenarios to evaluate performance.

Much of this circuit board's design can be leveraged from existing or other parallel electronic developments in the lab, and regular advising will be provided by a graduate mentor.


Project title: Towards the design of a spider inspired micro robot

Brief Project Overview​: The Animal Inspired Movement and Robotics Lab (AIMRL) builds micro scale robots that take inspiration from animals. The robotic systems are manufactured using multi-laminate composite materials and origami folding techniques with our femtosecond laser system. Current focus is to develop an eight-legged robot that is capable of multimodal locomotion (running, climbing, etc).

In the project the student will initially learn the manufacturing process of laminate rigid origami. Focusing on learning 2D to 3D spacial thinking and digital CAD designing of new robotic features. Prototypes for new leg mechanisms will be innovated, designed, manufactured, calculated and tested. Providing the student with exposure to the full cycle of design to final robot systems. Final robotic leg mechanisms will be programmed and the dynamics of motion analysed under high frame rate video footage for further optimisation.

Department: Mechanical Engineering, ATLAS

Research group: Emergent Nanomaterials Lab

Project title: UV-Sensing Biomedical Tattoos

Brief Project Overview​: Our lab creates UV-sensing tattoo pigments that address unmet needs in several application domains, including UV protection, dermatologic surgery, and body art.

Despite decades of public UV protection campaigns, skin cancer is the most common malignancy in the US, claiming 2 lives/hr and costing >$5B to treat >5M cases/yr. 1 in 5 Americans will get skin cancer by age 70, and these rates continue to rise. 90% of non-melanoma and 60–70% of melanoma skin cancers are caused by UV exposure. Sunscreen is the only protectant available for unclothed areas (head, neck, hands) where >80% of skin cancers occur. However, <30% of US adults use sunscreen correctly, usually because the distribution, amount, and frequency of application falls short of guidelines. There is an urgent need for products that facilitate correct sunscreen use and other risk mitigation (shade, clothing, etc.). Wearable on-skin UV sensors are limited by short lifetimes (hours) and discomfort, whereas UV photography requires expensive, bulky equipment. Our skin-implantable UV nanosensors overcome these limitations because they are (i) semi-permanent (~1-5 years), (ii) implanted in a single, fast, minimally-invasive procedure, and (iii)  seamless and completely comfortable inside the skin. Our pigments have a second application in dermatologic surgery as improved biopsy site markers for skin cancer patients. and a third application as photoreactive tattoo ink for body art.

The goal of this project is to optimize and validate a new kind of permanent, in-skin UV dosimeter that can be reset and reused on an hourly or daily basis. These UV-dosimeter tattoos will count and record cumulative UV exposure in the form of a graduate color change that can be read by a smartphone app. The student who joins this project will learn to create color-changing UV-activated pigments, formulate them into inks, implant them in skin models via tattooing, characterize and model the colorimetric response of these nanosensors in different lighting conditions. The student will work with other lab members to build up an interdisciplinary set of skills and techniques including polymer and nanoparticle synthesis, dynamic light scattering, scanning electron microscopy, UV-Vis spectroscopy, quantitative photography, data modeling and fitting, and shear rheology.

Department: Mechanical Engineering

Research group: Neuromechanics Lab

2 Project Options (please list only one project from each lab you are interested in)

Project title: The effect of reward on gripping

Brief Project Overview​: Combining ideas from cognitive science, behavioral economics, and biomechanics, the Neuromechanics Lab explores how subjective costs and rewards affect movement control. Our research tries to reverse engineers how the brain controls movements using computational models and experimental designs based on robot interfaces and virtual reality. These studies explore interactions between biomechanical and sensorimotor processes in the brain that underlie decision-making and movement control.
This project aims to explore how people modify movements in the presence of reward. In previous reaching studies, findings suggest that subjects move faster toward rewarded targets. Over the course of the Uplift project, the student will work directly with subjects, collecting and analyzing data related to the force and velocity in gripping movements using a robot in the Neuromechanics Lab. The student collect data, refine and expand the experimental design to explore effort valuation, and develop analyses applying economic principles of decision-making to examine how the brain evaluates the costs associated with gripping.


Project title: The influence of added mass on preferrred walking speed

Brief Project Overview​: Combining ideas from cognitive science, behavioral economics, and biomechanics, the Neuromechanics Lab explores how subjective costs and rewards affect movement control. Our research tries to reverse engineers how the brain controls movements using computational models and experimental designs based on robot interfaces and virtual reality. These studies explore interactions between biomechanical and sensorimotor processes in the brain that underlie decision-making and movement control.
Why do we choose to walk at the speeds we do? This project aims to better understand the mechanisms underlying our this choice by exploring the effect of added mass on preferred walking speed. Previous research has established that humans prefer to walk at energetically optimal speeds and that added mass increases the energetic cost of walking. The influence of added mass has not been explored with respect to preferred walking speed and has important implications for the sensitivity of humans to energetic cost. Over the course of the Uplift project, the student will design an experiment to determine preferred walking speed for subjects carrying additional mass. The student will work directly with subjects, collecting and analyzing gait kinetics and kinematics using a force-sensing instrumented treadmill and motion capture system in the Neuromechanics Lab. Based on preliminary findings, the student will refine the experimental design to best explore how added mass changes the kinematics, kinetics and energetics of the walking task and may influence preferred speed.

Computer Science

Department: Computer Science

Research group: Kann Lab

2 Project Options (please list only one project from each lab you are interested in)

Project title: Improving Engineering Education with the Help of Natural Language Processing

Brief Project Overview​: We are looking for a student to contribute to the natural language processing side of a project which aims at learning about the effect of different engineering teaching styles on students. It is based on collected surveys of engineering classes taken at the University of Colorado, and its long-term objective is to look into ways to diversify and increase student graduation rates in STEM. The student's role will be to implement machine learning (including deep learning) models capable of automatically analyzing the data, thus enabling the evaluation of course surveys at a larger scale than what would be possible manually. The student will be part of an interdisciplinary team consisting of engineering education and natural language processing researchers. We are looking for candidates with an interest in learning python, deep learning, and pytorch.


Project title: Exploring the Cognitive Plausibility of Deep Learning Models of Morphological Inflection

Brief Project Overview​: The goal of this project is to explore the cognitive plausibility of models of morphological inflection. Looking at the task of morphological inflection (i.e., generating specific forms of words, such as "walked" as the past tense form of "walk"), we ask: do state-of-the-art deep learning models learn and behave in ways similar to humans? The selected student will be part of an interdisciplinary team, consisting of linguistics and computer science researchers. They will be responsible for implementing the deep learning models which we will investigate. We are looking for candidates with an interest in learning python, deep learning, and pytorch.

Department: Computer Science

Research group: Brown Lab

Project title: Verification, validation, and efficiency in computational fluid dynamics

Brief Project Overview​: Solving real life problems in computational science and engineering in areas such as fluid and solid mechanics, materials science, and geoscience require developing innovative mathematical algorithms. At the Physical Prediction, Inference, and Design group, we develop methods and open source software to meet the needs of an ever-changing research and engineering community. In this project, we'll be working on verification, validation, and efficiency analysis of new methods in a fluid dynamics mini-application built using libCEED and PETSc to inform new library features and optimization efforts on emerging hardware.

8 Week Shadowing Period: During the 8-week period, the mentor will introduce the student to the governing equations of motion in fluid dynamics. The student will be introduced to spatial  and temporal discretization techniques of the equations of motion and to the mathematical libraries libCEED and PETSc. This will be achieved through regular meetings and hands-on activities.

16 Week Guided Research: The aim is to rely on the fundamental skills learned in the 8-week period, use them to solve real life problems in computational fluid dynamics (CFD). Guided by the mentor, the student will use libCEED and PETSc to solve engineering problems and perform verification and validation studies on test cases.

Skills and experience you will obtain: 

* Open source mathematical software libraries such as libCEED and PETSc
* High-performance computing skills and programming languages such as Python, Julia, C, and/or Rust
* Graphics libraries and visualization tools such as ParaView
* How to solve problems, communicate, and write for computational science and engineering

Civil, Environmental, & Architectural Engineering

Department: Civil, Environmental, & Architectural Engineering

Research group: Mansfeldt Lab

Project title: Down the Drain: Wastewater Infrastructure Inventory

Brief Project Overview​: Wastewater-based epidemiology has been demonstrated as a successful monitoring tool for SARS-CoV-2, other infectious agents, and emerging chemical contaminants of concern. But the wide diversity of wastewater pipe-materials, diameters, orientations, age, condition, and design potentially introduces variability into these monitoring campaigns. The main goals of this project are (1) to survey and catalog the wastewater infrastructure of collection systems within Colorado, (2) to expand this analysis to the United States of America, and (3) to detail the main components that vary and those materials that must be considered as influencing factors in developing sensitive monitoring systems. The successful outcome of these goals will inform future experiments that optimize the uncertainty of our monitoring campaigns and assist in the interpretation and utilization of surveillance data.

Department: Civil, Environmental, & Architectural Engineering, INSTAAR

Research group: Gooseff Lab

Project title: Down River and Up a Creek?  Water Quality Changes Along the Colorado River

Brief Project Overview​: The goal of our project is to determine where, how, and why water quality changes along the mainstem of the Colorado River and a few of it's tributaries (the Gunnison and Green Rivers).  40 million people in the US depend on the Colorado River as a source of water and power generation.  It also hosts many critical habitats for endangered fish and other animals.  As drought conditions persist in the southwestern US, our group is trying to determine how water quality is changing.  Next to quantity (amount), quality is of paramount importance.  Salty water, polluted water are not useful to plants, animals, or humans.  We have collected very high frequency water quality data along the Colorado, Gunnison, and Green Rivers over the past 4 summers.  We are seeking a student to help us work with these data and figure out what messages they hold.

Biomedical Engineering

Department: Biomedical Engineering

Research group: Ultrafast Photonics Research Group

2 Project Options (both projects are fully funded; you may list both as separate preferences)

Project title: AI-Enhanced Non-Invasive Medical Imaging

Brief Project Overview​: Medical imaging, industrial materials and chemical analysis, through-the-wall detection and miniaturized LIDAR all use 3D imagers that share common physics principles. They also suffer from image degradation based on the wavelengths used.  At short wavelengths, the images are high-resolution, but this resolution rapidly deteriorates below the surface because of absorption and scattering. Longer-wavelength imagers can scan far deeper in the material, but diffraction and coherence issues limit the usefulness of these scans. To break these constraints, we propose using AI for 3D image enhancement of the long-wavelength circular ranging optical coherence tomography (LW-CR-OCT) recently developed in my group. The generic deep learning algorithm can then be applied to a wide range of coherent imaging modalities that share similar principles.

Student will work with me and Jan Bartos (Graduate Student Assistant) not only on the AI algorithm but also on optimizing the performances of our unique LW-CR-OCT. Student thus will learn the modern medical imaging apparatus from the system point of view. We also have collaborations with faculties in Computer Engineering department who will interact with the student whenever needed.


Project title: Counter-propagating All Normal Dispersion (CANDi) femtosecond fiber laser

Brief Project Overview​: Our lab has invented a cost-effective high-energy ultrafast fiber laser that can simultaneously generate two fully correlated femtosecond pulses or frequency combs in one single compact fiber cavity. Our design significantly reduces the size, weight, power, and cost (SWaP-C) of ultrafast lasers and thus solves a main constraint in the ubiquitous ultrafast lasers’ adoption in the fields of high-grade LiDAR, advanced micromachining, and ultra-precise spectroscopy.

Our work on the Counter-propagating All-Normal Dispersion (CANDi) ultrafast fiber laser has been recently published in Optica (Optica 7, 961 (2020)), the top journal of the Optical Society of America. In addition, its patent disclosure (PCT/US2021/015887) has attracted much attention and praise from other companies in the ultrafast laser ecosystem including Toptica, Vescent Photonics, and LongPath Technologies.

In this project, students will work with two seasoned laser physicists to build two CANDi lasers for our collaborations with Colorado State University and Colorado School of Mines on pump-probe spectroscopy and THz imaging, respectively. Students will be involved in the laser design, layout, and packaging as well as the development of electronics, embedded system, and control software. In the long run, students will also be involved in the fundamental study that aims to answer the question of how to scale up the CANDi laser pulse energy so it becomes competitive for the micromachining industry.

INSTAAR & Geography

Department: Institute of Arctic & Alpine Research, Geography

Research group: Barnard Lab

Project title: Investigating the Mid-Elevation Snowpack Dynamics of the Colorado Front Range

Brief Project Overview​: Snowmelt from mountain watersheds is a vital to meeting societal water demands. Rapidly changing temperatures have the potential to decrease the total amount of snow, when it melts, and how quickly it melts. Topography also controls snow dynamics – especially at mid-elevations due to microclimates. The goal of this project is to assess how snow accumulation and melt differs on north- versus south-facing slopes in montane catchments in the Colorado Front Range. The student intern will use computer-aided image analysis tools to examine snowpack dynamics from historic snow photos. During the winter months, the student intern will have opportunities to directly measure snow dynamics at local research sites if their schedule allows for field site visits. The student intern will be a valued member of a team researchers focused on the hydrology and ecology of western watersheds and will be supported by a faculty mentor, graduate students, and professional research associates.

Molecular, Cellular, & Developmental Biology

Department: Molecular, Cellular, and Developmental Biology

Research group: Knight Lab

Project title: Understanding how metacognition and self regulation affect learning in Genetics

Brief Project Overview​: This project combines cognitive science and biology. The goal is to use student grade predictions and their reflections during Genetics to help understand the relationship between being reflective, and being able to improve one's performance in this course. The research involves interviewing students, learning how to ascribe "codes" to student behaviors and reflections, and learning how to analyze both this qualitative and additional quantitative data.

Department: Molecular, Cellular, and Developmental Biology

Research group: Copley Lab

Project title: Evolution of new enzymes and metabolic pathways

Brief Project Overview​: The Copley lab is interested in the evolution of new enzymes and metabolic pathways in bacteria. Projects available in the lab address 1) how new metabolic pathways are assembled by patching together promiscuous activities of enzymes that normally serve other functions; 2)  whether and how regulatory mechanisms compensate for very high copy numbers (up to 20) of genes that are accidentally co-amplified along with a gene encoding an inefficient enzyme; and 3) how different bacteria respond to the same environmental challenge that requires evolution of a new enzyme or metabolic pathway. These projects provide new insights into how microbial life originated and diversified on earth and how microbes may evolve in the future in response to antibiotics and environmental pollutants.

Department: Molecular, Cellular, & Developmental Biology, Biofrontiers

Research group: Chuong Lab

Project title: Regulation of the IFN Response

Brief Project Overview​: The goal of the project is to study how key immune-related genes are regulated in human cells. The student will help generate CRISPR’d cell lines to test the impact of different regulatory elements hypothesized to regulate human innate immunity.

Department: Molecular, Cellular, & Developmental Biology

Research group: Klymkowski Lab

Project title: Examining the effects of socratic feedback on student thinking

Brief Project Overview​: Our project aims to examine how socratic instructor feedback to student questions, and  students' reflections on and response to that feedback impacts students' disciplinary literacy and their sense of belonging within a discipline.  Our working hypothesis is that both depend upon providing students with practice in taking part in meaningful dialogs with instructors and peers, responding to challenging (socratic) feedback, in order to produce increasingly sophisticated responses – a process analogous to the preparation, review, and revision of a scientific manuscript.

Working with Mike Klymkowsky (and course learning assistants), the team will characterize i) the types of questions students ask, ii) the types of feedback they receive from the instructors (and fellow students), and iii) how that feedback impacts their thinking. These studies will be carried out in the context of Developmental Biology (DEVO), the final required course in the molecular, cellular, and developmental biology degree program, but students involved in the project do not need to have taken any MCDB courses. Text analyses will be based on rubrics to characterize specific features of questions, feedback, and revisions.

Department: Molecular, Cellular, & Developmental Biology

Research group: Brumbaugh Lab

Project title: Histone modifications in stem cell culture

Brief Project Overview​: Embryonic stem cells can be maintained as pluripotent in vastly different culture media. Notably, although cells in any media are capable of both self-renewal and differentiation any cell in the adult body, their molecular properties are different. This project seeks to clarify the importance of histone modifications in controlling those molecular properties. We will use two culture conditions (serum/LIF and 2i) to grow cells and profile chromatin marks. We will also perturb histone modifications using an established dominant negative histone mutant. Overall, we seek to understand the epigenetic basis for differences between pluripotent stem cells under different culture conditions.

Department: Molecular, Cellular, & Developmental Biology, JILA

Research group: Perkins Lab

Project title: Folding Pathways of Diverse Biomolecules

Brief Project Overview​: Single-molecule biophysics allows one to directly observe the folding and unfolding of individual biomolecules. In single molecule force spectroscopy, an atomic force microscopy cantilever—a micron-sized diving board—is used to pull on a molecule to mechanically unfold it. Our lab is broadly interested in the energetics and folding pathways of diverse biomolecules from membrane proteins and globular proteins to structured RNA. To accomplish this, we employ a combination of biochemical and physical techniques.


8 Week Shadowing Period: A graduate student in the lab has been working on setting up an assay to repeatedly pull on double stranded DNA and a RNA-pseudoknot positioned in the center of a DNA molecule. To do so, she covalently couples biotinylated DNA molecules to glass coverslips and streptavidin to the tip of AFM cantilever. You will be paired with this graduate student and learn about experimental protocols for cleaning glass coverslips and AFM tips, silanizing these surfaces, and then conjugating protein and DNA to these surfaces. You will observe her testing these surfaces in a state-of-the-art AFM. During this time, you will learn to set up and debug these assays as well as familiarize yourself with relevant literature from this subdiscipline.

16 Week Guided Research: After your 8-week shadowing period, you will prepare such surfaces on your own, with guidance from the graduate student and be trained on how to use the AFM, with the goal of preparing a single-molecule assay that allows an RNA-pseudoknot to be repeatedly unfolded and refolded. Once established, you will learn how to acquire quantitative data and perform analysis using data analysis software.


Department: Biochemistry

Research group: Taatjes Lab

Project title: Transcription regulation and molecular condensates

Brief Project Overview​: It has recently been discovered that the protein factors that control human gene expression, such as RNA polymerase II and the Mediator complex, undergo a process called liquid-liquid phase separation (LLPS), which alters the biochemical properties and activities of these factors in ways that are poorly understood.  This project will examine how human transcription/gene expression is controlled by LLPS.  The project will implement biochemical and fluorescence microscopy techniques, as well as cell-based methods.  The protein complexes that will be studied are broadly implicated in human development and disease, and the potential role of LLPS in disease pathogenesis will be explored.

Department: Biochemistry

Research group: Kasinath Lab

Project title: Functional Studies into Gene Regulatory Complexes



Brief Project Overview​:The project will involve a bottoms-up approach with comprehensive training in molecular biology, protein biochemistry, and electron microscopy. The student will be exposed to wide variety of ideas and techniques and will be trained and mentored in basic wet lab work, science communication (presentations), and science writing (scientific reports). The student will also be mentored in research planning and organization.

The scientific aspects of the project will involve designing molecular biology and biochemistry expression system to isolate protein complexes. Following which, the student will carry out functional assays to ascertain the molecular determinants of activity. Finally, time permitting, the student will be exposed to biophysical structural methods such as negative stain electron microscopy and cryo-electron microscopy.

The objective of this research plan is not to bombard the student with various research aspects but to build a strong core appreciation of how to plan a research study and how to go about solving challenging day-to-day biological problems.

Department: Biochemistry

Research group: Wuttke Lab

Project title: Human CTC1-STN1-TEN1 complex single-stranded DNA binding profile

Brief Project Overview​: Human CTC1-STN1-TEN1 (CST) is an essential heterotrimeric protein complex involved in genomic stability. CST binds to single-stranded DNA at telomeres, DNA replication forks and sites of DNA damage. Dysfunctional CST leads to the human diseases Coats Plus Syndrome and Dyskeratosis Congenita, which both result in death at an early age. CST has also been implicated as an important factor in cancer biology. In BRCA1-mutant cancers, a common mutation in breast cancers, CST is essential for the efficacy of a drug treatment called Poly-[ADP-Ribose] Polymerase-inhibitors. This project aims to understand the mechanisms by which CST interacts with DNA by using biochemical, structural, and biophysical methods.
CST binding to single-stranded DNA (ssDNA) is essential for proper biological function. The most well characterized substrate is the human telomere repeat sequence 5'-TTAGGG-3' with the optimal length being 18 nucleotides, or three repeats. A sequence specificity profile showed that while CST does prefer G-rich sequences, it is able to accommodate non-telomeric substrates, hence its function in DNA replication and the DNA damage response. This ability to accommodate varying sequences suggests that the DNA-binding interface of CST exhibits recognition plasticity, or that it can engage with ssDNA through multiple binding modes.

The project for an Uplift undergraduate researcher would include generating CST mutants that we hypothesize to be important for ssDNA binding. This will include mutagenesis cloning reactions, expression and purification of protein constructs, and fluorescence anisotropy assays to measure binding. Additionally, the student will perform data and statistical analysis to gain skills in quantification and reproducibility.

Department: Biochemistry

Research group: Aaron Whiteley Group

Project title: Uncovering the molecular dynamics of novel components of the bacterial immune system

Brief Project Overview​: In the Aaron Whiteley lab, we study the interactions between bacteria and the viruses that infect them, called bacteriophages (phages). When a phage invades its bacterial host, the host has a limited amount of time to mount a successful immune response before the virus degrades the host genome, hijacks cellular processes, replicates, lyses the host, and propagates to infect other bacteria. We are interested in the bacterial defense systems that stop phage in their tracks, particularly those that share an evolutionary history with components of the human immune system. In this way, we can gain new insight into how humans defend themselves against pathogens, as well as further understand the “arms race” between phage and bacteria.

Integrative Physiology

Department: Integrative Physiology

Research group: Ehringer Lab

Project title: Genetics of Substance Abuse

Brief Project Overview​: Drug addiction is a significant burden to society, and research has demonstrated that both genetic and environmental factors contribute to risk for addiction. It is important to recognize that hundreds of genes are involved the development of these complex disorders. Our laboratory uses behavioral genetic approaches to identify and study genes that are differentially expressed in response to drug exposure. Our projects hope to provide improved understanding of underlying biological mechanism, in order to develop improved prevention and treatments. Undergraduates working in our lab learn about relevant scientific literature, study design, specific lab protocols, data entry, followed by statistical analysis and interpretation of the results. Undergraduates are encouraged to attend weekly lab meetings, including the opportunity to present about their contributions to the project or a research article.

Department: Integrative Physiology

Research group: Reproductive Endocrinology Lab

Project title: Pharmacological intervention for the restoration of reproductive function

Brief Project Overview​: Successful reproduction ensures the survival of species for the last 3.5 billion years. Vertebrate animals, including humans, rely exclusively on a population of neurons in the brain to initiate the production of sperm and oocytes, hence reproduction. These neurons, called gonadotropin-releasing hormone (GnRH) neurons, can be compromised by multiple genetic mutations in humans and other animals. These mutations disrupt the development and function of GnRH neurons and result in the sterility of afflicted individuals. The overarching goal of my research program is to understand how GnRH neurons are affected by genetic mutations, and if compromised GnRH neurons can be rescued by pharmacological or environmental interventions. The student working on this project will use a genetically mutated mouse model to examine if a proprietary drug can restore the function of its GnRH neurons and eventually rescue its reproductive function.

Department: Integrative Physiology

Research group: Behavioral Neuroendocrinology Laboratory

4 Project Options (please list only one project from each lab you are interested in)

Project title: Investigating parasitology of Mycobacterium vaccae toward dendritic cells in vitro

Brief Project Overview​: Mycobacteria are considered intracellular parasites. The goal for this project is to record and image the process of immune cells interacting with Mycobacterium vaccae, a bacterium with anti-inflammatory, immunoregulatory, and stress resilience properties. Specifically, M. vaccae can reduce inflammation and reduce symptoms of allergies, anxiety, and depression. While it is known that M. vaccae can survive phagocytosis by dendritic cells and macrophages, little is known about the cellular and molecular processes through which this occurs. This project seeks to address the longevity of M. vaccae in dendritic cells and record the process using advanced microscopy tools.


Project title: Stress resilience effects of Mycobacterium vaccae on behavior and biological signatures of neuroinflammation in adult male rats

Brief Project Overview​: The hygiene or “old friends” hypothesis proposes that a lack of exposure to anti-inflammatory or immunoregulatory microorganisms, with which humans coevolved, is contributing to increases in inflammation and inflammatory diseases in modern urban societies. The “old friends” include organisms with which mammals coevolved, including: (i) the commensal microbiota, which have been altered by the Western lifestyle, including a diet that is commonly low in microbiota-accessible carbohydrates; (ii), pathogens associated with the “old infections” that were present throughout life in evolving human hunter-gatherer populations; and (iii) organisms from the natural environment with which humans were inevitably in daily contact with (and so had to be tolerated by the immune system). Immunization with one of these “old friends”, in the form of a heat-killed preparation of Mycobacterium vaccae NCTC 11659, a nonpathogenic, environmental saprophyte with anti-inflammatory and immunoregulatory properties, has been shown to increase stress resilience in rodents, as measured by prevention of stress-induced increases in anxiety-related defensive behavioral responses and neuroinflammation. This project will further explore the stress resilience effects of M. vaccae on anxiety-like behavior and biological signatures of neuroinflammation in adult male rats.


Project title: Stress resilience effects of Mycobacterium vaccae on the gut microbiome, host metabolome, and behavior in adult male rats

Brief Project Overview​: The hygiene or “old friends” hypothesis proposes that a lack of exposure to anti-inflammatory or immunoregulatory microorganisms, with which humans coevolved, is contributing to increases in inflammation and inflammatory diseases in modern urban societies. The “old friends” include organisms with which mammals coevolved, including: (i) the commensal microbiota, which have been altered by the Western lifestyle, including a diet that is commonly low in microbiota-accessible carbohydrates; (ii), pathogens associated with the “old infections” that were present throughout life in evolving human hunter-gatherer populations4; and (iii) organisms from the natural environment with which humans were inevitably in daily contact with (and so had to be tolerated by the immune system). Immunization with one of these “old friends”, in the form of a heat-killed preparation of Mycobacterium vaccae NCTC 11659, a nonpathogenic, environmental saprophyte with anti-inflammatory and immunoregulatory properties, has been shown to increase stress resilience in rodents, as measured by prevention of stress-induced increases in anxiety-related defensive behavioral responses and neuroinflammation. This project will further explore the stress resilience effects of M. vaccae by exploring the effects of M. vaccae on stress-induced changes in the gut microbiome, host plasma metabolome, and anxiety-like behavior in adult male Sprague Dawley rats.


Project title: Stress resilience effects of Mycobacterium vaccae ATCC 15483 in C57BL/6N mice exposed to high-fat diet and circadian disruption

Brief Project Overview​: Shift work has become a necessity in a thriving urban world that operates on 24-hour services. Unfortunately, shift work leads to numerous physiological and psychological consequences due to chronic disruption of the circadian rhythm. Health concerns include obesity, hypertension, and insulin resistance, as well as impairment of cognitive performance, emotional state, and alertness. Eating patterns are also disrupted along with an increase in fatigue, thus leading to shift workers substituting meals with industrial snacks, fast food, and sweets. Chronic disruption of rhythms (CDR) combined with a high-fat diet (HFD) induces systemic inflammation that may contribute to stress vulnerability and other pathologies. While time-restricted feeding is one therapeutic method to combat the effects of chronic disruption of rhythms, it may not be feasible to all shift workers. This study will be the first to investigate an alternative microbial therapeutic to prevent negative outcomes of high-fat diet and chronic circadian disruption. We hypothesize that immunization with the heat-killed Mycobacterium vaccae ATCC 15483 (M. vaccae), an environmental bacterium with immunoregulatory and anti-inflammatory properties, prevents the negative impacts of chronic disruption of rhythms and a high-fat diet on stress-induced changes in behavior and physiology in mice. The student will assist with conducting the experiment, analyzing anxiety-like defensive behavior, assisting with microbiome sequencing, and assisting with preparation of a manuscript.

ATLAS Institute

Department: ATLAS Institute

Research group: August Black Lab

Project title: Thumb-driven Radio

Brief Project Overview​: The "Thumb-Driven Radio" project aims to build a novel telematic service that allows multiple constituents to fluidly participate in broadcast-like scenarios through their mobile phone at the flick of their thumbs. It is simultaneously be hyper-local, border-crossing, and global-reaching. We have an active beta group with participants from multiple US institutions (UCSC, UMBC, Wave Farm), as well as from UK, Colombia, the Netherlands, and Australia.

While a lot has taken place since the first live mp3 streaming softwares existed 20+ years ago, much of it this last year during COVID, there is still little if anything available for real-time radio production or experimental sound telecasting.  "Thumb driven Radio" aims to build a next generation service for sound artists and radio activism.  Through software development, workshops with diverse communities, and experimentation among artists, it aims to catalyze new forms and genres of live interactive radio for the purpose of growing communities, making experimental acoustic and artistic situations, and enabling grassroots initiatives.

As a sizable portion of this application is already in beta phase, we are seeking students to build out specific isolated features for future versions. Depending on background and interest, an engineering student could choose to work on user Interface and Interaction, design, communication, real-time audio, networking, or some mixture thereof. We would teach students contemporary web development in typescript for frontend (React, tailwindcss, next.js) and backend (node.js, webRTC, docker).  As an example, a student might choose to work on integrating a real-time chat, an audio plugin api in webaudio for a VST like plugin system, server and container orchestration with docker, or adding MIDI hardware input, etc.

Department: ATLAS Institute

Research group: Zamore Lab

Project title: Craniate - Superpowered learning for underserved students

Brief Project Overview​: Craniate is a two-part informal STEM education tool that uses visual storytelling (comics) and project-based learning (experiment kits) to frame STEM concepts in a culturally relevant way. We are exploring if these tools, designed for low-income and BIPOC students, help improve competence, ability and attitudes toward STEM topics and careers. We are looking to develop 3 prototypes of both comics and kits along with surveys to measure how well these tools improve performance among students with minoritized identities. These prototypes should be created, tested and distributed by the summer of 2022. With this research, we can evaluate how these unique learning strategies (visual storytelling and project-based learning) influence feelings of inclusion and abilities when used alone or combined.
The undergraduate will be working alongside engineers, graphic designers, artists and scientists to create new prototypes to distribute to the Boulder K12 population and beyond. The Craniate Team is a diverse team of intersectional, visible and invisible minoritized identities; any new student interested should be mindful and respectful of all identities when working in such an environment.
This role requires a knowledge of material or electrical engineering, STEM education, and/or 3D graphic design. In the role, any training needed for new skills can be provided. The student will also have the opportunity to participate in the research aspect of production--anything from holding interviews with users to helping analyze and evaluate collected data. Finally, we aim to incorporate our personal experiences, creativity and passion into our work; we expect the same of any who look to join our fantastic team.

Department: ATLAS Institute, Institute of Cognitive Science

Research group: Sheppard Craft Technology Lab

2 Project Options (please list only one project from each lab you are interested in)

Project title: Designing software tools for debugging embedded systems

Brief Project Overview​: Debugging by Design is a research project to develop hardware and software tools for locating and fixing bugs in embedded systems.  The embedded systems in our project consist of a microcontroller and other components sewn into fabric-based objects.  For example, a series of LEDs sewn into a shirt might react to sounds in the surrounding environment.  This type of interplay between hardware and software can sometimes make it complicated to debug a project when it does not behave as expected.  In response to this, we are developing a web-based tool called Circuit Check which helps students understand and debug their embedded systems.

For more information about this lab and project:

8 Week Shadowing Period: As a first step, students will design a software dashboard to display data from a sensor (for example, something that detects light or sound).  While doing this, they will learn to design custom interfaces using a variety of web-based tools. Students will also participate in regular research group meetings and do background reading in technical as well as educational aspects of debugging.

16 Week Guided Research: Students will then apply these skills to design user interfaces to assist with debugging. They will follow a standard design process of working first with paper prototypes, progressing to an interactive prototype, and finishing with a functioning debugging component which may be incorporated into our existing toolset. The design process will include pilot tests with users, as well as regular reviews with the research team.


Project title: Sensory Extended Color Vision:  Exploration of Color Filters

Brief Project Overview​: This project involves creating real-world components to engage senses in relation to a PhET simulation about color vision:

For more information about the Craft Tech Lab:
For more information about the Sensory Extension project:

8 Week Shadowing Period: In the simulation Color Vision (PhET, 2020) learners can explore what colors are perceived while changing the amount of red, green, and blue light. A creative way to enable sensory extension with this sim is to use it as an input device for augmented color vision, through the use of a mobile phone and Google Cardboard as an augmented reality headset.  The student will design RGB controls in the sim to create a filter to change the color spectrum viewed through the headset. This would allow learners to explore the way that changing parameters in the sim impacts their own color vision and discuss their own experiences of color and how it relates to the perceived color displayed in the sim.  

During the shadow period, the student will do background reading and experimentation in sensory augmentation and embodied cognition, and will investigate development with Google Cardboard or a similar platform.

16 Week Guided Research: Expanding beyond the visual, three tangible devices could be created, each with unique haptic and auditory feedback to control the red, blue, and green values. This would allow learners to sense changes in color non-visually. These devices (Google Cardboard and tech-enhanced tangible devices) could be used together to enable multi-sensorial learning experiences where all learners have the ability to control the input and perceive a form of output from the displays.

Throughout this internship, students will participate in meetings with researchers from the PhET program as well as partners from other universities.  Students will test ideas with pilot participants and use the feedback to guide development of the devices.  At the end of this research period, the student will prepare a poster for submission to an academic conference.

Ecology & Evolutionary Biology

Department: Ecology & Evolutionary Biology

Research group: Li Lab

Project title: Population Genomics of the Blue Mud Shrimp (Upogebia pugettensis) in Alaska

Brief Project Overview​: In estuaries from southernmost California to southern Alaska, the blue mud shrimp Upogebia Pugettensis ​plays a significant role in nutrient cycling, landscape modification, and general health of its environment. However, with the arrival of the invasive isopod parasite (Orthione griffenis) ​during the 1980’s​, ​the blue mud shrimp populations ​have begun to rapidly collapse across nearly all of its natural range. Currently, the genetic diversity and biogeographic distribution patterns of the shrimp populations are unknown, which has made it difficult to move forward with any efforts to conserve the species. This study's main goal is to use genetic markers to assess the diversity and dispersal of the shrimp populations in Alaska. The student intern will be responsible for extracting DNA from ~200 shrimp specimens, examining DNA quality, submitting samples for Next-gen sequencing, and conducting population genetics analyses with the sequencing data. The student will also learn relevant information regarding marine ecology, conservation biology, and parasitology.

Department: Ecology & Evolutionary Biology

Research group: Kane Lab

Project title: Species distribution modeling of Lewis flax, a native wildflower

Brief Project Overview​: Climate change contributes to loss of biodiversity, making in critical to improve knowledge of how species will respond to climatic shifts in the coming decades and centuries. Species Distribution Models (SDMs) are powerful tools for making predictions about how climate change may cause species to undergo shifts in their geographical distributions. SDMs work by identifying climatic factors that best predict the geographical distribution of a species based on where it is currently known to occur. These models are also useful if the full extent or complexity of a particular species’ distribution is unknown. They can provide insight into where to search for unrepresented populations if conducting a study of intraspecific genetic diversity, which is an important but underappreciated component of global biodiversity.

The goal of this project is to have the undergraduate generate a novel SDM for a native, perennial wildflower, Lewis flax (Linum lewisii) This species is currently used for ecosystem restoration across western North America and is also a candidate for domestication as a new perennial oilseed crop. Lewis flax has broad seemingly patchy distribution across Western North America that has not been fully characterized. A SDM of Lewis flax will be a foundational tool for ongoing research into its ecology, population genetic diversity, evolutionary history, and agronomic potential.

The student will gather and curate Lewis flax occurrence data from publicly available, digitized herbarium records and verified observations on iNaturalist, a citizen-science databank. The student will then develop a SDM using geo-spatial software packages within the R programming language. This project is a unique opportunity to take ownership of a feasible yet critical question that will augment other research in the Kane lab.

Astrophysical & Planetary Sciences

Department: Astrophysical & Planetary Sciences

Research group: Malaspina Lab

Project title: Interstellar Dust in our own Backyard

Brief Project Overview​: Dust is an important constituent of the our solar system, capable of transporting significant mass, momentum, and energy through the system. However, full understanding of the sources, sinks, and transport of dust within the solar system, as well as the processes that couple dust populations to solar system plasmas like the solar wind has been limited by a scarcity of long duration in situ measurements of dust by spacecraft.

It was recently discovered that the electric field instrument on NASA’s Wind spacecraft has been detecting tiny dust grains of both interplanetary and interstellar origin near Earth for more than 25 years. These data span two full solar cycles in the near-Earth space environment, and present a unique opportunity to explore the interaction between the solar system and interstellar material, using measurements made in our own backyard.

The interested student will be the first to examine the full 25 year Wind dust data set, exploring how the variability of our Sun impacts the ability of interstellar material to reach deep into our solar system.

Department: Astrophysical & Planetary Sciences

Research group: Madigan Lab

Project title: Stars engulfing planets

Brief Project Overview​: Our Sun will end its life as a white dwarf, a densely packed star about the size of the Earth. Almost a third of white dwarfs that we observe in our Galaxy have metal lines in their spectra meaning that their surfaces contain heavy elements along with expected hydrogen and helium. The best explanation for these metals is that the white dwarf stars have recently swallowed planetary material.

This project will explore a dynamical explanation for the engulfment of planetary material by white dwarf stars. The undergraduate mentee will run gravitational N-body simulations of planetary systems around white dwarfs, inputting low velocity kicks to the central star to examine the effects on orbiting planets, asteroids and comets.

Department: Astrophysical & Planetary Sciences

Research group: Rast Lab

Project title: Solar brightness variations using models and observations

Brief Project Overview​: The Sun varies in brightness with time. This is called the solar irradiance variation. The observed variations are linked to the solar magnetic activity cycle. They have very small amplitude and must be measured using highly accurate radiometers in space. None-the-less, signatures of these variations are found in climate data.

While the total solar irradiance is well measured and calibrated, there are still fundamental disagreements over the sign of the variation in different spectral wavelength regions. It is important to understand the origin of the solar irradiance variations, the time scales over which they occur, and their spectral content, in order to assess the observed climate sensitivities and responses. To date, that understanding is based on the contribution of time varying magnetic fields on the solar surface. Images of the Sun are examined for small scale magnetic field structures. Each of these contributes a distinct spectrum to the solar output. The full spectrum is reconstructed by the summing over all the observed structures. As they come and go, the solar output is modulated. Such models have been very successful in reproducing the solar irradiance variation over recent times, but since they depend on high resolution images of the Sun, which have only been available in recent decades, it is difficult to use them in extrapolations to epochs of fundamentally different solar activity levels. Yet we know that there are such periods of fundamentally different behavior over long times.

This project will examine how the solar spectrum changes with magnetic activity using numerical models of the solar surface dynamics and magnetic fields. Such models allow careful sensitivity studies and manipulation of the solar conditions. The project will assess the validity of the conclusions drawn by making direct touchstone comparisons with observations of the Sun as possible. These comparisons will take advantage of the National Science Foundation's Daniel K. Inouye Solar Telescope, which will be the world’s largest solar telescope when it comes on line this winter. It will observe the Sun in exquisite detail and with very high precision, making the direct comparisons anticipated by the project possible for the first time.

Atmospheric & Oceanic Sciences

Department: Atmospheric & Oceanic Sciences, INSTAAR

Research group: Coastal Oceanography Modeling Lab

Project title: Analyzing changes in Alaskan lagoon circulation

Brief Project Overview​: Climate change is impacting Alaskan lagoons in many ways, including by increasing inputs of freshwater and nutrients from thawed permafrost into these coastal ecosystems. This can impact ocean circulation in the lagoon, as well as the extent to which nutrients are available for marine organisms such as phytoplankton.  Ocean models are being used to better understand and predict changes in these coastal lagoons.  The undergraduate mentee on this project will analyze results from an ocean model to better understand how environmental conditions, such as changes in river inputs, affect coastal hydrodynamics. We seek an undergraduate who is enthusiastic and willing to learn about coastal ocean processes and data analysis in python.