Student Name: Griffin Mahoney

Project Title: Computer simulation of parenting and the life history of the dinosaur Maiasaura

Project description: Maiasaura was a genus of dinosaur that lived in the Upper Cretaceous Period in North America. The discovery of Maiasaura was the first evidence of a dinosaur feeding its young, hence the name given to it, which means "good mother reptile." The number of fossil specimens of Maiasaura that have been obtained is extremely high and have led to a number of fairly low uncertainty estimates for life history statistics (e.g. age distributions, survival rates, etc.) making Maiasaura one of the best understood extinct vertebrates in the fossil record. In this project, we will take these empirically-obtained values and construct a computer simulation, specifically, an agent-based model (ABM), of the species to observe its population dynamics. ABMs are models where individuals (agents) are unique and autonomous and interact with each other and their environment locally. We will adjust survivorship rates simulating a trade-off between parenting and individual survival and see how these effects propagate to the population demographics. The goal of this project is to determine how impactful the role of parenting was in establishing a stable population.

Project Advisor: Alex Capaldi (Mathematics & Statistics)

Project Sponsored by REDI

Student Name: Summer Kantanen

Project Title: Localized pattern control in spatiotemporal patterns using reaction-diffusion equations 

Project description: Research into spatiotemporal self-organization and pattern formation in naturally evolving systems has garnered significant attention within the field of statistical mechanics over the past few decades. These patterns hold immense interest because of their remarkable similarity to crucial biological, chemical, and physical processes, such as DNA oligomers, skin pigment development, and oscillatory chemical reactions. 

While numerous Turing-like models have been proposed to mathematically describe reaction-diffusion systems, only a limited few exhibit the nonlinear and chaotic behaviors closely resembling those found in natural systems. The Gray-Scott model, serving as the primary model of study, uniquely possesses both of these behaviors and boasts a rich parameter space replete with a multitude of intriguing dynamical regimes. 

The Gray-Scott model is a cubic, autocatalytic reaction involving two chemical concentration densities, u and v. This research project centers on the exploration of emerging spatiotemporal patterns within the Gray-Scott model. This exploration involves systematic localized parameter adjustments and the incorporation of electric fields, providing a deeper understanding of the model's intricate behavior and its potential applications in various natural phenomena. 

Project Advisor: Jason Czak (Physics & Astronomy)

Project Sponsored by REDI

Student Name: Emily Euler 

Project Title: Computational investigation of butanol reactivity on gold-titania nanocatalysts  

Project description: When used as a biofuel for vehicles, butanol contributes to cleaner air by reducing unburned hydrocarbons in tailpipe exhaust. 1-butanol and 2-butanol are isomers, which means they have the same chemical formula (C4H9OH) but different structures. When they react on a gold-titania nanocatalyst surface 1-butanol and 2-butanol unexpectedly form different products. To understand why these two similar molecules follow different chemical reaction pathways this computational surface science project will use software based on quantum mechanics to predict the structure and energies of butanol molecules as they react on catalyst surfaces. Research will be conducted using high performance computing (HPC) resources available at JMU, UVA, and Argonne National Laboratory.  

Project Advisor: Kendra Letchworth Weaver (Physics & Astronomy)

Project Sponsored by REDI and Honors College

Student Name: Morgan Jones

Project Title: Discovering conserved genes in sister species of garter snakes

Project description: When vertebrates evolved from aquatic to terrestrial life, natural selection preserved a network of genes to synthesize lipids in the skin to prevent whole-body dehydration. Snakes are an ancient lineage of terrestrial vertebrates but have adapted to a variety of environments, including semi-aquatic habitats. Do closely-related species of garter snakes, despite their divergent habitats, all have and use the same genes for skin lipid synthesis? Recently, we identified some of these skin lipid synthesis genes in one species of garter snake, and these genes are seasonal and sex-specific in their activity. Next, we will extract RNA and make cDNA from skin samples from several other garter snake species and then use traditional and quantitative PCR to measure any differences in skin gene activity. Students involved in this project will read the primary literature and learn molecular biology techniques (RNA extraction, cDNA synthesis, PCR) to test hypotheses on the evolution of gene networks. If successful, and because this project is part of a larger collaborative study, the student will eventually co-author a manuscript that will be submitted for peer review. 

Project Advisor: Rocky Parker (Biology)

Project Sponsored by the College of Science & Mathematics

Student Name: Conor Bourke

Project Title: Evaluating the stability of supramolecular boronic acids gels for targeted drug delivery  

Project description: This project involves the study of peptides with boronic acid handles. Peptides are known to form hydrogels, materials that act like solids despite being predominantly water. The introduction of a boronic acid allows for recognition of drugs, such as L-DOPA. L-DOPA is a Parkinson’s drug that dramatically improves patients’ motor deficits. Despite its benefits, patients taking L-DOPA experience adverse gastrointestinal side effects, which primarily arise from drug breakdown. Transdermal L-DOPA administration with our hydrogel will minimize these side effects and improve drug efficacy. In this project, we will synthesize a library of boronic acid-peptides, use these molecules to form gels, and evaluate their stability under biological conditions. The enzymatic resistance of L-DOPA incorporated materials will also be investigated. 

Project Advisor: Gretchen Peters (Chemistry & Biochemistry)

Project Sponsored by REDI and Honors College

Student Name: Evelyn Page

Project Title: Molecular sponges: Using biopolymer metal-organic framework composites to remove ions from water

Project description: Is my water safe to drink? That’s a question we don’t have to ask at JMU because we have access to safe and reliable water sources. However, there are many places where water contains ions that we want to extract because we have a safety concern (lead) or because the ions are rare and are needed for other applications (gold). In this project, we will synthesize composite materials, or “molecular sponges,” to remove ions from water. These sponges consist of a biopolymer and a metal-organic framework (MOF). We are interested in exploring the biopolymer nanocellulose, nano-sized particles of cellulose, as a support to make molecular sponges that contain MOFs. MOFs are promising for isolating ions from water because MOFs can be modified to control how they interact with ions in solution. In this project, we will synthesize selective molecular sponges by controlling their materials properties and incorporating additives that can be used to selectively remove contaminants from solution.

Project Advisor: Barbara Reisner (Chemistry and Biochemistry)

Project Sponsored by REDI and Honors College

Student Name: Mckenna Witt

Project Title: Data and Disease: How do we use data to better model disease spread and intervention?

Project description: We will be investigating how to use data to study the spread of certain diseases as well as the efficacy of intervention strategies (such as quarantine, vaccination, treatment, etc.). Disease spread in a population will be modeled by using nonlinear dynamics models and/or discrete time models. We will then use statistical methods to approximate parameters from existing data sets. This work is interdisciplinary, touching on math, statistics, data sciences, biology, public health, and medicine.  

Project Advisor: Eva Strawbridge (Mathematics and Statistics)

Project Sponsored by REDI and Honors College

Student Name: Norah Squires

Project Title: Interactive Dimension Reduction for Microbiomes  

Project description: Math is great for combining variables and projecting observations into a 2D visualization space. Humans are great at finding patterns and groups among observations in 2D visualizations. If we let humans adjust the visualization, we can update the math to reflect the patterns the human found or imposed. Software for this human intervention is available in Python, which is great, but most people in the field are using R. So, we are translating code from Python to R and adding other useful features. We will test the code on both generic, publicly available data and on data generated in the biology lab where we study microbiomes - the community of bacteria, fungi, and other microbes living in or on an environment (i.e., in the human gut). While this project doesn't have a “wet” lab component, future projects could. Instead, this project focuses on a data science component, specifically visualization. Data science is one of the fastest growing and highest paying fields in the country right now and this project is a perfect introduction to the field and how it applies to biological data.  

Project Advisor: Laura Tipton (Mathematics & Statistics, and Biology)

Project Sponsored by Honors College

Student Name: Newton Elizabeth

Project Title: Use of JMU tree inventory data to estimate the carbon sequestration and building heating/cooling effect 

Project description: Determining the cooling impact of tree canopies relies significantly on carbon sequestration, wherein carbon dioxide stored in the carbon pool plays a crucial role. This becomes particularly vital in urban environments characterized by a high percentage of impervious surfaces, such as buildings. The Climate Change Resource Center of the U.S. Forest Service has introduced the Tree Carbon Calculator Tool (CTCC) to facilitate this assessment. This tool enables the estimation of carbon dioxide sequestration and energy savings associated with individual trees. Our approach involves employing the CTCC to compute the carbon sequestration of the trees within James Madison University. The essential parameters for the CTCC, derived from the JMU Tree Inventory (available as an ArcGIS Web App), encompass the climate zone, tree species name, tree size (precisely diameter at breast height), or the age of the tree species. Initially, we will estimate the carbon sequestration and cooling effects on a per-species basis. Subsequently, we will determine the overall or total sequestered carbon dioxide and cumulative cooling effect (annual energy savings in kWh in electricity) by aggregating the data from individual tree species. The final step involves leveraging ArcGIS Online to publish the final maps as a Web App or a story map.  

Project Advisor: Dhanuska Bandara Wijesinghe (Department of Geology and Environmental Science)

Project Sponsored by the College of Science & Mathematics

Student Name: Evan Poindexter 

Project Title: Monarch Butterflies and Milkweed species

Project description: Climate change is affecting pollinator species, such as the monarch butterfly. In experimental studies, we are determining monarch butterfly preference and caterpillar growth on eight species of native milkweed which may be increasing in toxicity due to increased levels of CO2. We will determine toxin levels in the plants as well as the caterpillars feeding on them. This may have an effect on the OE parasite that is infecting them. The student will cultivate milkweed species in the greenhouse in the early spring and plant the species in experimental plots in the late spring. The student will count eggs and measure caterpillars on milkweed species in garden plots during the fall semester if they continue in our lab.  Monarch butterflies are also captured to test for presence of the OE parasite. 

Project Advisor: Heather Griscom (Biology)

Project Sponsored by the College of Science & Mathematics

Student Name: Miah Leiva-Saba

Project Title: Exploring animal responses to climate change

Project description: My lab studies how animals interact with one another and their environment, and how those interactions might be shifting because of climate change. We do research in high mountain environments where climate change is happening very quickly. The FYRE student and I will work with existing data collected in the high Andes of Peru or the Rocky Mountains in Colorado to develop a research question and answer it. Example questions could be: Is there a seasonal pattern to animal activity in high elevation landscapes that have recently lost their glacier cover? Have the internal body temperatures of wild salamanders increased over the last 5 years? 

Project Advisor: Kelsey Reider (Biology)

Student Name: Nathan Koon

Project Title: Generation and molecular characterization of CRISPR/Cas9-induced mutations in immunity-associated genes in tomato

Project description: In this project, we will use a powerful gene-editing tool called CRISPR/Cas9 to study how tomatoes defend themselves against bacterial pathogens. Our goal is to modify or disrupt key genes involved in plant immunity and then examine how these changes affect tomato growth, development, and resistance to infection. Along the way, you will gain hands-on experience with modern lab techniques such as DNA cloning, bacterial transformation, DNA extraction, PCR, and sequencing, and learn how plant genomes can be modified through plant transformation and genome editing. You will also practice inoculating plants with bacterial strains and recording their responses to pathogen attack. The ultimate goal of this project is to discover how we can make tomatoes stronger and more resistant to disease - without sacrificing yield - knowledge that could improve agriculture and global food security. 

Project Advisor: Ning Zhang  (Biology)

Student Name: William Devlin

Project Title: Characterizing the zooplankton communities of the Belle Isle rock pools.

Project description: Zooplankton, small aquatic animals, play a critical role in the food web of many freshwater and marine systems. While small, zooplankton are very diverse and understanding what generates and maintains this diversity is critical to preserving this diversity and thus the functioning of freshwater ecosystems. This project is working to determine the environmental factors that are important in structuring the zooplankton communities in the Belle Isle rock pools in Richmond, VA. This system consists of hundreds of rock pools that vary in environmental factors such as temperature, depth, and flooding. We visit the rock pools four times a year to sample the zooplankton communities and track them across time. We then score these samples under a dissecting microscope, identifying and counting different types of zooplankton. The main groups of zooplankton we find include copepods, ostracods (seed shrimp), and cladocerans (water fleas). In addition to this phenotypic characterization, we are also working on developing ways to characterize these communities using genetics, which would allow for more high-throughput processing.

Project Advisor:  Karen Barnard-Kubow (Biology)

Student Name: Griffin Andrews

Project Title: Establishing pollinator plant species for Monarch Butterflies

Project description: Climate change and loss of habitat across migration routes is affecting pollinators, such as the monarch butterfly.  In a greenhouse study, we will determine the best methods for growing key plant species for monarchs depending on their phenology and nectar abundance.  Prior greenhouse studies in this lab have found that native milkweed species (the host plant for the monarch) are difficult to grow in the greenhouse and establish in the outside garden.  This season we will experiment with hardy, drought-tolerant, fast growing species, such as the Mexican sunflower (Tithonia) in addition to a few of the more successful milkweed species.  The student will learn how to cultivate ten plant species in the greenhouse in the early spring, prepare the pollinator garden bed, and plant the seedlings in the garden in the late spring.  The student will monitor monarch butterfly visits and caterpillars on the different plant species in the fall semester if they continue in our lab.  

Project Advisor:  Heather Griscom (Biology)

Student Name: Gabriela Koleva

Project Title: Investigating pigment evolution in Campion flowers

Project description: We are investigating the convergent evolution of red flower color in the genus Silene. Red is a rare color in this genus (1% of the genus!), and it seems that the few species that have red flower color use different pigments to achieve this hue. Changes in flower color has implications for floral evolution, plant-pollinator coevolution, and pollinator preference. We work on many aspects of floral color in the lab, from the chemistry, to genetics, to field assays with pollinators. The open position for a FYRE student would be to work with the pigments. We will be extracting and identifying which visible pigments are used for red and pink visual colors and which UV pigments (invisible to humans) are present in white, pink, and red colored flowers. We also use a photographic and spectrophotometric approach to measure petal reflectance to understand how different animals may perceive different colors. Knowing which pigments evolve where will help us to make predictions about the specific genetic changes that allowed red flower color to evolve. This project is at the interface of biochemistry and evolutionary biology. 

Project Advisor: Andrea Berardi (Biology)

Student Name: Wahid khan

Project Title: Investigating exotic forms of matter via electron-proton interactions in the ten gigaelectron-volt range

Project description: While most of the hadronic matter in the visible Universe is made out of up and down quarks (proton: up, up, down; neutron: up, down, down), the Standard Model predicts, and experimental nuclear and particle physics results provide evidence, for the existence of four more quarks: strange, charm, bottom, and top.  Of these, the strange quark is of particular importance because it might have played a role in the first moments after the Big Bang and, as astronomical observations suggest, is essential in understanding the later stages in the lifecycle of certain stars.  
Studying the production of strange matter is extremely challenging given the ubiquity of regular hadronic matter. Typically only one out of 10k-100k high energy interactions produce a strange particle.  
As part of the larger Jefferson Lab open strangeness production program, in this project we study the production of excited states of the Lambda and Sigma0 hyperons (quark structure: uus) via proton-electron scattering. The data was acquired at Jefferson Lab using a high intensity 10.6 GeV electron beam, a liquid hydrogen target, and the HMS and SHMS electromagnetic spectrometers available in the experimental Hall C. 

Project Advisor:  Loana Niculescu (Physics and Astronomy)

Student Name: Zoie Wagner

Project Title: Uncovering student misconceptions in inorganic chemistry: exploring the f-block

Project description: One of the challenges of teaching and learning inorganic chemistry is the breadth of content covered in the course. When students do not connect their learning to core ideas, they can develop a fragmented understanding of chemical concepts. The goal of this project is to develop classroom activities that promote meaningful learning of chemistry by connecting new learning to prior knowledge and disciplinary core ideas. The first step in designing effective activities is to uncover student misconceptions that interfere with learning. We will explore student ideas about periodicity, bonding, or reactivity in the f-block elements; how these elements compare to the rest of the periodic table; and connections between macroscopic, submicroscopic, and symbolic levels of chemistry. As part of this project, you will use qualitative analysis to examine participant responses to a written question and interview data. 

Project Advisor: Gina MacDonald (Chemistry and Biochemistry)

Student Name: Callie Maupin

Project Title: Perspectives on Objectives: Developing science communication learning objectives for STEM undergraduates

Project description: There is often a disconnect between science and society, where people within the community think about science differently than scientists themselves. STEM undergraduates often talk to people within their communities about science. In this way, they are boundary spanners, they are reaching between this divide and sharing scientific information. However, students often use ineffective communication strategies when they talk about science. This can include presenting themselves as the authority and/or shaming those who disagree with them, or with the broader scientific consensus. It is important for undergraduates to learn how to communicate about scientific topics effectively because they can reach audiences that are frequently inaccessible to scientific researchers. While science communication is recognized by educators as an important competency, many scientists and science instructors have never been trained to communicate with non-scientists. Instructors who have limited experience in science communication struggle to teach effective science communication skills. The goal of this project is to develop learning objectives (LOs) that can be used to train undergraduate students in science communication. It will involve working with a team of researchers across the U.S. to find, collate, and develop new LOs, and to test them by surveying and interviewing science communication experts. 

Project Advisor: Rosario Marroquin Flores (Biology)

Student Name: Coyt Walsh

Project Title: Application of Drone Based Imagery (Thermal and NIR) to Enhance Recreational Fishing in the Shenandoah Valley Region of VA. 

Project description: Recreational fishing is a popular practice in the Shenandoah Valley (SV) region of Virginia. The region consists of hundreds of miles of productive waterways. One challenge for anglers is determining the best time to start fishing. This is due to the streams' variety of cold and warm water habitats, which change across locations and seasons. Unmanned Aerial Vehicles (UAVs) have been used for aerial surveys of fishery activities, though their potential remains underexplored. The proposed study will utilize drone-based thermal (IR) and near-infrared (NIR) imagery to detect water temperature and thermal anomalies, as well as to observe land cover changes in the vegetation along 2-3 spring-fed streams in the SV region. Drone imagery will be collected monthly from January to April 2026. High-resolution IR imagery will aid in mapping thermal anomalies, while NIR will be used to analyze changes in vegetation. This is important because vegetation impacts water clarity and temperature by affecting the stream microclimate. Mapping thermal anomalies and vegetation changes will help us understand how spring temperatures relate to the best fishing times, both spatially and temporally. Moreover, many fish species are cold-blooded and thus are very sensitive to variations in water temperature. Identification of thermal anomalies helps locate fish species, as these anomalies create variations in oxygen concentrations that impact the abundance of the fish species. 

Project Advisor:  Dhanuska Wijesinghe (Geology and Environmental Science)

Student Name: Sophia Benard

Project Title: Statics and Dynamics of Granulated Systems

Project description: From snow, to seeds, and asteroid belts, granulated systems are present all around us. Despite our familiarity with them, fundamental aspects of their behavior, such as how they flow or jam, are poorly known. In this experimental project, we aim to better understand what makes granulated systems clog, unclog and flow. We probe the local interactions using imaging techniques seeking to uncover how these interactions impact the global flow behavior. Unveiling the interplay between microscopic and macroscopic behavior will provide a framework to improve critical industrial processes and understand natural phenomena such as avalanches, landslides and earthquakes. 

Project Advisor:  Klebert Feitosa (Physics and Astronomy)

Student Name: Bhargav Kuniki

Project Title: Computational investigation of silver/copper nanocatalysts for selective ethylene epoxidation 

Project description: Epoxidation, or the transformation of ethylene into ethylene oxide, is an industrial chemical reaction which is valued at billions of dollars on the global market. It is critical that reactions occurring on this scale have high selectivity to mitigate greenhouse gas emission, like the formation of carbon dioxide (CO2). Experimental measurements demonstrate that adding dissociated water to silver-copper catalysts causes reactions with ethylene which selectively produce more ethylene oxide and less CO2. To understand why ethylene follows different chemical reaction pathways in the presence of dissociated water, this computational surface science project will use software based on quantum mechanics to predict the structure and energies of ethylene molecules as they react on silver-copper catalyst surfaces. This Department of Energy funded research project will be conducted using high performance computing (HPC) resources available at JMU and DOE National Laboratories. 

Project Advisor:  Kendra Letchworth-Weaver  (Physics and Astronomy)

Student Name: Joshua Wowk

Project Title: Magnetic and Structural Perturbations in YCrO₃ 

Project description: Yttrium orthochromite (YCrO₃) is a member of the rare-earth orthochromite family (RCrO₃, R = rare earth), which crystallizes in the orthorhombically distorted perovskite structure with space group Pbnm and is known for its rich interplay between structure and magnetism.  YCrO₃ is particularly interesting because it is reported to exhibit multiferroicity. (Coexistence of magnetic and ferroelectric behavior). In YCrO3, chromium ions order antiferromagnetically around 140 K, with a weak ferromagnetic component. In this project, we will investigate the rare-earth-doped Yttrium orthochromite Y₁₋ₓRₓCrO₃ by doping YCrO₃ with small amounts of other rare-earth elements on the Yttrium site. We will explore how the size and magnetic moment of these rare-earth ions influence the crystal structure and magnetism.  
In this project, the student will synthesize materials with varying doping levels of several rare earth elements (Lu, Yb, Nd, etc.) using high-temperature furnaces and investigate their crystal structures using an X-ray diffractometer. After students synthesize high-quality samples, we will measure the magnetic properties of these materials using a PPMS Vibrating Sample Magnetometer at low temperatures/high magnetic fields, and study how structure influences magnetism. Ultimately, we will extend this approach to more complex multi-cation or high-entropy versions of this system.  

Project Advisor:  Sachith Dissanayake  (Physics and Astronomy)