SRI Research Streams

College of Science faculty are engaged in research across disciplines. SRI scholars will have the opportunity to interact with faculty and determine which research stream best meets their interests starting in the spring semester of SRI participation. Research can be performed for credit depending on a student's academic program, and scholarship opportunities are available.

Click on a tile to learn more about the stream.


CS Cancer Systems Biology
Cancer Systems Biology

Stream Leader: Dr. Fred Adler

Our team will collaborate to use our collective strengths in evaluating the biological literature, analysis and graphical presentation of data sets, mathematical modeling and simulation.

What is cancer?

  • A failure of the body’s control systems
  • Cells escape the systems evolved to regulate numbers
  • Tissues fail to stop cells that escape homeostatic control
  • The immune system fails to stop vagrant cellsCancer is an ecological and evolutionary process

What is systems biology?

  • A way to address multiscale phenomena
  • Link what happens within cells to cell populations
  • Link short-term changes to long-term outcomes
  • Uses a wide range of quantitative methods

Developed Skills Include: Data analysis; mathematical modeling; computer simulation

Find more about Dr. Adler and their research at  

SC Surface Chemistry and Catalysis
Surface Chemistry and Catalysis

Stream Leader: Dr. Scott Anderson

Reactions occurring on surfaces are critical in many technology areas, including industrial chemical production, pollution remediation, semiconductor fabrication, and high tech materials production and applications. Catalysis is another type of surface chemistry, where the surface facilitates reactions of molecules that stick to it, but is not changed in the process.

One type of surface reaction this group studies is reactions of materials at high temperatures, which often determine the material performance. We are able study reactions on individual nanoparticles (NPs) over a temperature range up to ~3000 K – well above the range other methods can reach. The experiments are done in a custom-made instrument and there will be opportunities to learn about instrumentation, as well as the science of the surface reactions. We will be measuring chemical reactivity of different forms of carbon (diamond, graphite, nano-onions, etc) and of ultra-high temperature ceramics like HfC and ZrB2.

Students on this project will learn to work with the instrumentation, the physical principles behind the method, nanoparticle properties, and high temperature chemistry such as etching, oxidation, and sublimation.

Find more about Dr. Anderson and their research at 

MB Making and Breaking Bonds
Making and Breaking Bonds

Stream Leader: Dr. Peter Armentrout

This group is focused on measuring thermodynamic information although we obtain kinetic and often dynamic information about chemical reactions as well. Using an instrument called a guided ion beam tandem mass spectrometer (GIBMS), we examine how reactions of cations and molecules change as a function of the available kinetic (sometimes electronic) energy. When the reaction is endothermic (requiring extra energy), we can measure a threshold for the process, which directly provides the thermodynamic information of interest. We have applied this technique to a range of systems, simple atom + diatom reactions (most recently of lanthanide and actinide elements), hydration of metal ions, up to fragmentation of small biomolecules.

Recent experimental studies performed in this group include:

  1. Reactions of actinides (both uranium and thorium
  2. Reactions of lanthanides (of atmospheric interest to the US Air Force
  3. Measurement of hydration energies of transition metal dications (solvation energies)
  4. Fragmentation energies of peptides, useful information for sequencing proteins in analytical mass spectrometry

Find more about Dr. Armentrout and their research at

MS Molecular Systematics of Mushroom Species
Molecular Systematics of Mushroom Species

Stream Leaders: Dr. Bryn Dentinger/Kendra Autumn

This research program will give students the opportunity to work in the Mycology Genetics laboratory at the Natural History Museum of Utah. The data generated from this research will contribute to a project aimed at constructing the first complete molecular-based phylogeny of a newly described genus of fungi (Lanmaoa) in the mushroom forming family Boletaceae, thereby providing a baseline understanding of species diversity. Additionally, the results of this work will allow us to more precisely delineate species-level differences in a poorly studied group of economically important edible and putatively poisonous mushrooms.

Developed Skills Include: DNA extraction; DNA sequencing; PCR

Find more about Dr. Detinger and their research at

FA Flagellum Assembly in Bacteria
Flagellum Assembly in Bacteria

Stream Leader: Dr. David Blair

The Blair lab SRI project concerns an important molecular recognition process in which a protein at the base of the bacterial flagellum, called FlhB, specifically recognizes only certain proteins in the cell and directs them to be transported through the flagellum itself, so that they can be incorporated into the growing flagellar structureThe rules that govern the recognition of appropriate cargo molecules are not understood, in spite of decades of study. Our aim is to characterize the interactions between FlhB and the various exported cargo proteins using biochemical and spectroscopic approaches.

Developed Skills Include: protein expression and purification; analysis of protein-protein interactions; NMR spectroscopy to characterize interactions in molecular detail

Find more about Dr. Blair and their research at

SP Spintronics

Stream Leader: Dr. Christoph Bohme

Find more about Dr. Bohme and their research at

PM Pollination Metagenomics
Pollination Metagenomics

Stream Leaders: Dr. Heather Briggs, Dr. Joshua Steffen

Utah is home to an astonishing diversity of native bee species. Recent estimates suggest that over 900 bee species call Utah home including more than 100 at Red Butte Garden alone. Compared with honey bees, relatively little is known about the vast majority of these native bee species. To support native bees, and the plant species they pollinate, we need to gain a better understanding of their basic biology

Our research group will be employing a molecular approach called DNA metabarcoding to assay foraging behavior. DNA metabarcoding has the potential to reveal all the species in an environmental sample based upon the DNA sequences that are present in that sample. By gaining a nuanced understanding of foraging behavior we will be able to better inform practices used to support the health and diversity of plants and pollinators in native ecosystems.

Over the course of the next year undergraduates working with on this project will test molecular protocols, collect native pollinators in the field, and use bioinformatic tools to provide accurate descriptions of the foraging behavior nativepollinators. Students will have the opportunity to learn basic molecular, microbiology, and field ecology research techniques.

Find more about Dr. Briggs and Dr. Steffen at

BD Big Data for Climate Science
Big Data for Climate Science

Stream Leader: Dr. Tim Collins, Dr. Sara Grineski

Climate change is producing more severe heat waves, storms and floods. People’s access to protective resources, such as clean water and greenspace, is critically important in the context of climate change. Our team’s environmental justice (EJ) research has found disparities in the risks of climate change-related hazards/disasters and people’s access to protective resources, with communities of color, lower economic standing, and other socially disadvantaged statuses experiencing the greatest risks and the most limited access to resources at local, national, and international levels. Unfortunately, nearly all EJ studies rely on publicly accessible data about people, which are only available in aggregate or for coarse-scale geographic units.In this SRI stream, students will examine climate justice issues at an unprecedentedly fine scale and generate novel insights as part of our project team.

The project integrates big spatial data on climate change-related phenomena (e.g., heat, flood risk, air pollution, greenspace) with restricted-access “microdata” on the entire U.S. population, including individual people’s precise residential locations. We are conducting the project through the Wasatch Front Federal Statistical Research Data Center (WFRDC), located in the U’s Gardner Commons. Through the project, students will learn about environmental and climate justice research; master tools and techniques for integrating and analyzing spatial data from disparate sources on people and environmental conditions; acquire Special Sworn Status (SSS) to analyze the restricted-access microdata through the U.S. Census Bureau in the WFRDC; and contribute to advancing knowledge about climate justice issues. Students most likely to thrive in this stream will be interested in quantitative data analyses.

Find more about Dr. Collins / Dr. Grineski and their research at and

CM Computation Methods for Hot Nuclear Matter
Computation Methods for Hot Nuclear Matter

Stream Leader: Dr. David Clarke

Atomic nuclei are made of nucleons, i.e. protons and neutrons. When a collection of nucleons gets extremely hot and/or dense, the nucleons melt into a plasma, the so-called quark-gluon plasma. Physicists have to research this plasma in detail in order to understand some of the hottest and densest systems in nature. Some characteristics of quark-gluon plasma can only be calculated using computational techniques. The computational technique our group employs is called lattice field theory. Lattice calculations generate random snapshots of these hot and dense systems, then perform statistical analyses on these snapshots. Generating these snapshots is highly computationally demanding, utilizing a significant fraction of the resources of the most powerful supercomputers in the world. Therefore we must always consider how to make our code more efficient.

Undergraduates working in this Stream will learn basic statistical analysis, learn how to write rudimentary scripts to analyze data, see basic ways to assess performance, and gain modest familiarity with concepts in modern physics. If they like, students will also have the opportunity to get familiar with Linux operating systems and object-oriented programming and to manage simulations on supercomputers.

Find more about Dr. Clarke and their research at

SB Social Belonging in STEM Classes
Social Belonging in STEM Classes

Stream Leaders: Dr. Gina Frey

Students in introductory STEM courses often have concerns about whether they will be academically successful in large university courses, but many have an additional concern that maybe “people like me don’t belong in this course.” This concern is called belonging uncertainty and is related to the insecurity someone feels because of their identities.In our group, we are studying the effect that course-level student belonging has on student performance and retention in that course. We have found at two different institutions, course-level belonging affects student performance in large general chemistry and introductory physics courses. Expanding upon these studies, we are interested in understanding the mechanism of how social belonging affects course performance and retention. One step in determining the mechanism is to explore the characteristics of the course that students use when describing their sense of belonging and belonging uncertainty. Our goal is to help instructors create course environments that support and encourage all students to reach their potential and continue to pursue careers in STEM or healthcare.

Undergraduates will be studying open-ended responses from the belonging surveys to determine characteristics students use to describe their course-level belonging in STEM courses. They will be developing themes or ideas from the student quotes. Qualitative research is collaborative, hence the student, while having their own project component, will be part of a qualitative-research team. You will learn about social psychology, inclusivity and equity, and qualitative-research methods.

Find more about Dr. Frey and their research at

HW Human Wildlife Coexistence
Human Wildlife Coexistence

Stream Leader: Dr. Austin Green

Wild animals are under continuous pressure to adapt to new environments as more land surrounding protected areas is converted for human use and populations continue to grow. This highlights the importance of research that promotes human-wildlife coexistence on functional landscapes that combine both human use and conservationIt is critical that we understand how mammals occupy and navigate these functional landscapes, as they commonly function as ‘umbrella’or ‘flagship’ species because their natural rarity and large area requirements tend to place them under threat of extinction, and their use of multiple habitats makes it possible to protect other species. One way in which mammals may occupy urbanized landscapes and avoid the human ‘super-predator’ is by altering their behavior. Specifically, mammals may adapt how they use both space and time; adjust how they interact with other species; and change where and when they feed, sleep, and reproduce. In this stream, we will investigate how human influence alters mammalian behavior and space use in an effort to inform on-the-ground conservation initiatives.

In this stream, we will design and implement projects leveraging remote sensing trail cameras and large-scale fieldwork in both natural and urbanized landscapes, perform data analytics with Program R, develop ways to identify wildlife in photographs using artificial intelligence, and promote citizen science education and engagementThese techniques will help us answer questions with direct conservation implications, such as: How does varying levels of human disturbance affect wild mammal distribution, behavior, and community composition? What natural history and behavioral traits make species more or less susceptible to the effects of human disturbance? At what levels of human disturbance do wild mammal species begin showing behavioral responses, and how does this response vary by species? 
Find more about Dr. Green and their research at or by checking out Wasatch Wildlife Watch 
AR Hallar Aerosol Research Team (HART)
Hallar Aerosol Research Team (HART)

Stream Leader: Dr. Gannet Hallar

This research group makes measurements of gases and particles in the atmosphere. We then look at the chemical & physical make up of those particles and gases, which helps us understand the source location and impacts. We make these measurements at the University of Utah, where we are continuously understanding our urban environment and a mountain-top Lab in Steamboat Springs, Colorado  & in the town of Alta, which help us understand the remote environment.  

Over the course of the next year undergraduates working with on this project will gain hands-on experience with aerosol instrumentation through work with a variety of instruments in the aerosol monitoring lab on the 8th floor of the William Browning Building. Students who are interested will also have opportunities to gain field work experience through set-up and maintenance of aerosol monitoring equipment, often deployed along mountain regions. Specifically, students will study wildfire smoke, dust storms, and calibrate aerosol instrumentation.  

Find more about Dr. Hallar and their research at 

VS Viral Suppressors of RNAi
Viral Suppressors of RNAi

Stream Leader: Dr. Sarah Hansen

The Bass Lab studies Dicer, an enzyme that cleaves double-stranded RNA and is important for normal cellular function. It also plays a role in defense against viruses that we don’t fully understand. In this project we are studying viral  suppressors of RNAi (VSRs) which are a group of proteins that inhibit Dicer function and can be found in many viruses (e.g., ebola, influenza A, SARS-CoV-2, and Zika virus). The questions we want to answer include:1. How do these VSRs inhibit Dicer?2. Are they inhibiting the same Dicer function or do VSRs from different viruses act with different mechanisms?3. Are other pathways in the human innate immune response effected (e.g., RIG-I, MDA5)?These questions are explored through biochemistry and cell-based experiments. It is a great project for students who want to learn the fundamentals of biochemistry research and learn more about a university lab environment.

Undergraduate students working on this project will prepare and test one VSR of their choosing from a list of proteins/viruses we want to study. They will have the opportunity to learn basic molecular biology and biochemistry techniques. Future directions of this project include work in human cells and I am willing to teach these techniques to an interested student.

Find more about Dr. Hansen and their research at

CB Cancer Biology
Cancer Biology

Stream Leader: Dr. Sheri Holmen

Melanoma is the most deadly form of skin cancer resulting from abnormal growth of melanocytes, the pigment-producing cells of the skin. Multiple screening efforts have led to the discovery of new genes that may be responsible for the initiation or progression of melanoma. However, these genes need to be functionally tested before we are able to truly understand their impact on this disease. Our research will employ molecular cloning methods to study these novel genes and their impact on cellular signaling pathways.

Over the course of a semester, undergraduates will use SnapGene software to simulate molecular cloning. Then, they will learn to design and synthesize a target gene, construct an expression vector, transfect cells, and characterize gene expression at the protein level by western blotting. These genes will then be tested functionally using various in-vitroassays to gain an understanding of the gene’s effect on melanoma cell proliferation, invasion, and migration. By achieving a better understanding of the role of target genes and their contribution to melanoma, we will be able to identify therapeutic targets that may advance the outcome of melanoma therapies.

Find more about Dr. Holmen and their research at

CF Higher-Dimensional Chip Firing
Higher-Dimensional Chip Firing

Stream Leader: Dr. Selvi Kara

In this research stream, we will investigate unsolved mathematics problems in higher-dimensional chip firing games. These games are dynamical systems as they exhibit change over time. We will analyze their dynamics using tools from several mathematical fields such as combinatorics, linear algebra, and algebraic topology. We will start our investigation by studying various configurations of the chip-firing game and learn how to establish our findings rigorously using mathematical proofsOur goal is to prove new theorems that explain how these games behave over time. This research stream also offers opportunities to use programming languages such as Python.

Find more about Dr. Kara and their research at or

VB Vector Biology, Surveillance, and Management
Vector Biology, Surveillance, and Management

Stream Leader: SLC Mosquito Abatement 

Salt Lake City Mosquito Abatement District (SLCMAD) serves a 180 square mile region of Salt Lake City proper and the western rural expanse that approaches the Great Salt Lake. We use a complex blend of custom engineering, aviation technology, droplet physics, physiology, molecular biology, ecology, and integrated environmental sciences to serve our area. Research in mosquito control is whimsical and complex, spanning topics in community ecology, population genetics, pathology, epidemiology, and fundamental principles like mosquito behavior. As a result, we are a learning agency that tries to develop modern, environmentally conscientious, and effective means of protecting public health. Our research is balanced with routine tasks, such as field population monitoring, molecular assay of virus, and mosquito rearing for study. We use our regular program elements to gain a nuanced understanding of mosquito population dynamics and habitat exploitation and in turn fuel an everchanging portfolio of research intended to both safeguard public health and inform practices used across the nation.

Over the course of the next year undergraduates working with SLCMAD will be involved in molecular protocols, collect mosquitoes in the field, and use mosquitoes in a variety of tasks, such as pesticide sensitivity tests, virus detection, mosquito identification, and research bioassays. Undergraduates will have the opportunity to learn basic molecular, toxicology, and field ecology techniques.

Find more about SLCMAD and their research at

SO Synthetic Organic Electrochemistry
Synthetic Organic Electrochemistry

Stream Leader: Dr. Shelley Minteer, Dr. Henry White

Mission: To make synthetic organic electrochemistry mainstream through the invention of enabling, green, safe and economic new reactions, the demystification of fundamental electrochemical reactivity, vibrant partnerships with industry,education of a diverse set of scientists and engineers, and by engaging in community-wide education and outreach

Our stream will work on fundamental studies of electrocatalytic systems for synthetic organic chemistry reactions where we will utilize electricity instead of dangerous and expensive reagents for important chemical reactions.

  • Undergraduate researchers perform hands-on research in electroorganicsynthesis.
  • Participation in the entirescientific process (literature searches, experiment design, laboratory work, analysis, and dissemination of results)
  • Students rated the top benefits of this SRI stream as: learning laboratory skills, critical thinking, teamwork, and communication skills, which reflects the unique interdisciplinary and cooperative nature of the CSOE program.

Find more about Dr. Minteer / Dr. White and their research at and

PC Investigating Potassium Channels
Investigating Potassium Channels

Stream Leader: Dr. Shrinivasan "Cheenu" Raghuraman, Dr. Baldomero "Toto" Olivera 

Ion channels are proteins that are found in the cell membrane and allow the movement of ions across the membrane. They shape the physiological properties of different cell types. For example, they control the release of cytokines by immune cells, control the bioelectrical signals in neurons and cardiomyocytes which are important for cellular communication and proper functioning of the brain and the heart. All ion channels are made of multimeric subunits that assemble together to form a pore.  One of the largest and most diverse family of ion channels is the voltage-gated potassium-channel. Although there are limited number of subunits (encoded by ~70 genes), each subunit can combine in different combinations, resulting in an enormous array of homomeric and heteromeric subytpes. An example of different K-channel subtypes formed by two subunits is shown in the figure below. The function of different K-channel heteromers have remained elusive due to the lack of selective pharmacology to discriminate between the heteromers. Our lab discovered and developed conotoxins as pharmacological tools to study the properties of different K-channels. Conotoxins are used by cone snails for predatory purposes- they paralyze their prey by targeting various ion channels and receptors. In our lab, we have extracted and purified conopeptides from the venom of different cone snail species. In this project, we will use conopeptides and other marine bioactive compounds to study the properties and functions of different voltage gated K-channels. We will use a technique called two-electrode voltage clamp to study the properties of K-channels. Students will gain an understanding of different concepts from molecular biology, bioelectricity and biophysics.

(collaborative project With Wayne Potts lab) The global COVID19 pandemic has uncovered the need to understand and address the roles of immune cells in combating pathogenic attacks. While initial inflammation is essential to control invading pathogens, prolonged inflammation results in “cytokine storms” with unintended consequences and pulmonary complications. Current anti-inflammatory drugs are non-selective and are often contraindicated in patients with comorbities, highlighting the need to develop drug leads that are selective and superior to current anti-inflammatory drugs. We recently developed an in vitro drug screening platform to identify marine natural products with immunomodulatory properties and identified a library of conotoxins that modulate cytokine release. In the next phase of this project, our goal is to test these drug leads in animal models of respiratory distress. Using mice infected with influenza virus (H3N2 strain) as a model system, we will test the library of conotoxins in modulating cytokine levels. Students will be exposed to animal handling techniques, dissection skills, immunostaining and ELISA assays. In addition, students  will gain experience in testing drug leads using in vitro and in vivo assays that are essential for conducting pre-clinical trials.  

Find more about Dr. Raghuraman / Dr. Olivera and their research at and

NN Neural Networks
Neural Networks

Stream Leader: Dr. Braxton Osting

The abundance of data created in science, engineering, business, and everyday human activity is simply staggering. This data is often complex and high-dimensional, taking the form of video or time-dependent sensor data. Machine learning methods allow us to understand such data, automatically identifying patterns and making important data-driven decisions without human intervention. Machine learning methods have found a wide variety of applications, including providing new scientific insights and the development of self-driving cars.

One machine learning method in particular, neural networks, has emerged as the preeminent tool for the supervised learning tasks of regression and classification. Loosely modeled after the human brain and the basis for deep learning, neural networks use composition to develop complex representations of data. In recent years, researchers using Neural Networks have made tremendous breakthroughs in topics as varied as image processing, natural language processing, and playing board games such as Go.

Undergraduate students participating in this SRI stream will be introduced to machine learning and learn how machine learning tools are used in practice. Students will learn about the mathematics that forms the basis for neural networks and the optimization methods used to train them. They'll learn how to program in python and use packages such as scikit-learn and pytorch to analyze data. Working in teams, students will use neural networks to solve real-world classification problems like object recognition in images, detecting falsified financial transactions, and controlling for manufacturing defects. They'll also learn to effectively communicate and visualize results. 

Find more about Dr. Osting and their research at

FV Functional Validation of Potential Cancer Targets
Functional Validation of Potential Cancer Targets

Stream Leader: Dr. Gennie Parkman

This SRI Research Stream aims to understand more about the genetics of cancer, specifically melanoma, beginning with the effects of certain genes that are up or downregulated in BRAF mutant melanoma on proliferation, invasion, and migration in vitro. Through collaboration with the Huntsman Cancer Institute, this in vitrowork has tremendous potential to be translated into pre-clinical testing in in vivomodels.

In this research stream, we will conduct literature review and data analysis using publicly available data sets, such as the Broad Institute’s Project Achilles database, to ask “What genes may be important in melanoma?” We will then learn fundamental steps of molecular cloning in order to generate target genes and clone them into an expression vector. Then, we will produce cell lines expressing these genes and test them! Students will learn cell culture, as well as many molecular biology methods, such as mRNA and protein expression analyses, proliferation assays, etc., to functionally validate gene targets. If the results of our analyses are promising, these genes may be tested in established mouse models through collaborators at HCI.

Find more about Dr. Parkman and their research at

DB DNA Barcoding
DNA Barcoding

Stream Leader: Dr. Rodolfo Probst

In this stream, we will test molecular protocols for barcoding species involved in symbioses (I am an expert on mutualisms between ants & plants, groups that we have many new species to discover and several unanswered questions about their interaction) but eventually apply our protocols to any groups of interest. While participating in this stream, you will learn molecular techniques (different DNA extractions, PCR, cutting-edge genetics, bioinformatics), evolutionary thinking, and biodiversity monitoring and on top of that, learn about symbioses! These techniques and analyses will help us recognize and catalog new species, know how they are genetically related and how their communities change over time. Plus, we will be able to understand how symbiotic organisms interact across areas (for example, Central America) and eventually conduct real-time barcoding in the field.

Find more about Dr. Probst and their research at

AM Ant Mutualism
Ant Mutualism

Stream Leader: Dr. Joshua Scholl

In this stream we will study the Aspen sunflower, Helianthellaquinquenervisand its ant bodyguards (shown above). We’ll ask questions like, which ant species is the best bodyguard? Do the ants increase the plant’s reproductive success (more seeds)? Do the ants stay on the plant all day/season or just during certain parts of the day/season?

As part of this project, you will get outside and learn about the wonderful world of species interactions and capture ants using our state-of-the-art ant aspirator. You will also be introduced to basic plant identification and anatomy and experimental design. In the Wasatch Mountains we’ll apply these skills to conduct ant exclusion experiments and use a variety of ecological analysis tools to evaluate hypotheses. Important transferable skills that you can gain by participating in this project include competency in the popular R software (data wrangling and visualization), public speaking, writing, wilderness safety skills, and creative problem solving.

Find more about Dr. Scholl and their research at or

SE Seed Ecology
Seed Ecology

Stream Leader: Dr. Joshua Scholl

Our goal in this stream is to explore the environmental factors (e.g climate, elevation, urbanization, etc.) that drive seed ratios in seed heteromorphic species. For example, how does increased drought, a consequence of climate change, affect seed ratios? How do changes in seed ratios affect plant population growth? Seed heteromorphic species allow us to ask very exciting questions about germination ecology which in turn help us to understand and ultimately predict plant population dynamics in changing environments.

To answer these questions students will design and implement projects collecting plant species across environmental gradients (e.g. from SLC west to the Nevada border or from downtown SLC up into the mountains). We may also conduct germination and growth trials of the seeds we collect in a greenhouse. As part of this project, students will learn basic plant identification skills, plant anatomy, collect plants in the field, have the opportunity to conduct greenhouse and growth chamber experiments, and learn to use a variety of ecological analysis tools to quantitatively evaluate hypotheses. Important transferable skills that students can gain in this project include competency in the popular R software (data wrangling and data visualization), public speaking, writing, wilderness safety skills, and creative problem solving.

Find more about Dr. Scholl and their research at or

CS Complex Systems
Complex Systems

Stream Leader: Dr. Mikhael Semaan

From the intricate highway system of human vasculature, to the large-scale geological formation of mountains, to the individual motions of atoms and molecules, and so much in between... Can we detect and describe emergent pattern and structure? How do real-world systems process information? How do they absorb and dissipate energy to function? What do they have in common? All “complex systems!”

In this stream, you will develop and apply tools to understand a “candidate system” most interesting to you, tailored to your field. You will learn and build the rest of the skills needed as part of the stream.

Topic Outline

  • Nonlinear dynamics and chaos: How does simple complex?
  • Simulating and visualizing: Hidden order in chaos!
  • Symbolic dynamics and measurement: Producing noisy data
  • Modeling stochastic processes: From data model
  • Information theory and energy: How does the system function?
  • Project outcome: apply tools to student-chosen example system (molecular motors, neuron channels, information engines, disease dynamics...)

Skills Developed Include:

  • Programming literacy
  • Scientific computing (Python)
  • Model simulation and data genesis
  • Data science / visualization and statistics
  • Nonlinear dynamics and information theory

Find more about Dr. Semaan and their research at

MA Underexplored Molecular Architectures
Underexplored Molecular Architectures

Stream Leader: Dr. Ryan Stolley

This SRI stream will uncover new chemical reactions to build never-before seen arrangements of atoms and use a variety of chemical, analytical and computational tools to uncover how these new groups of atoms behave; and to expand on this capability to build ever more complex molecules. In our lab students will learn the principles of organic chemistry and chemical experimentation and the instrumental tools for us to ascertain structure and function of organic molecules.

Skills Developed Include:

  • Rules of the physical world
  • Basics of reaction chemistry
  • Broadly applicable analysis methods
  • Navigating a busy lab environment
  • Project management

Find more about Dr. Stolley and their research at

BN Biogeography of Nematodes
Biogeography of Nematodes

Stream Leader: Dr. Werner

This Research Stream will sample nematodes from pedestrian locations on campus to exotic locations across Utah, including deserts, mountains, and the Great Salt Lake. After field collections, we will process soil samples in the laboratory, and perform molecular genotyping to identify species abundance and diversity. Then, we will use statistical and computational methods to analyze their relatedness. By studying the biogeography of nematodes in Utah, we will better understand the diversity, evolutionary history, and limits of this remarkable taxa.

Undergraduates will have the opportunity to gain experience in field work, and learn methods in molecular biology and phylogenetics. There may even be the opportunity to describe and name new species. We anticipate that student results will eventually be published in a scientific journal.

Find more about Dr. Werner and their research at

UE Urban CO2 Emissions
Urban CO2 Emissions

Stream Leader: Dr. Kai Wilmot

To investigate relationships between urban CO2 emissions, population density, and a number of socioeconomic variables, we are combining satellite observations of CO2 with atmospheric modeling techniques for 113 major urban centers around the world. Ideally, our results will improve understanding of the role of cities in addressing climate change and point to possible development strategies that may be relevant to policymakers.

Over the course of the Spring 2023 and Fall 2023 semesters, undergraduates working with this project will consider and help analyze observed COdata and atmospheric transport modeling outputs for cities around the globe. Students will have the opportunity to learn basic techniques/approaches in atmospheric modeling and observation, will identify, read, and share literature related to climate change, emissions, and urbanization, and will develop preliminary skills in programing/coding.

Find more about Dr. Wilmot and their research at

PL Plant Light Sensing and Greening
Plant Light Sensing and Greening

Stream Leader: Dr. Chan Yul Yoo

Undergraduates joining our SRI research stream will grow various plant species under varying light conditions using LED light (red, far-red, blue, white light, and dark) and under various stressed conditions (drought, salinity, etc.) to understand the mechanisms by which chloroplast biogenesis is affected at the molecular and cellular levels.

Participants will learn a variety of basic molecular biology and cell biology techniques such as DNA/RNA/protein extraction, PCR, quantitative RT-PCR, DNA/protein gel electrophoresis, western blotting, and fluorescence microscopy. In addition, undergraduates will learn how to access various bioinformatics resources to search and analyze genes of interest from various organism.

Find more about Dr. Chan Yul Yoo and their research at

PI Plant Immunity and Amino Acid Metabolism
Plant Immunity and Amino Acid Metabolism

Stream Leader: Dr. Heejin Yoo

This research team will try to elucidate the effect of individual amino acid for plant immunity especially during PCD. Additionally, we will try to do amino acid profiling using HPLC after exogenous application of specific amino acid to analyze amino acid dynamics. Combined outcomes will enhance scientific understanding of the role of amino acids for plant immunity and provide foundational knowledge to improve disease resistance of economically important crop species.

Undergraduates who register for this project will first learn basic mechanisms for plant immunity; Then, students will test the effect of exogenous application of individual amino acid for programmed cell death and elucidate underlying mechanisms using basic molecular biology technique and metabolic analysis.

Find more about Dr. Heejin Yoo and their research at or