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Biocomputing Approach to Modeling and Modulating Calcium Signaling
No full textBiocomputing is an emerging field that seeks to perform computational tasks using biological substrates and processes. Unlike conventional computing systems based on silicon hardware, biocomputing leverages the parallelism, energy efficiency, and complex dynamics of living systems. Among various cellular mechanisms, calcium (Ca2+) signaling stands out as a central regulator of diverse biological functions, offering a promising basis for programmable logic and control in living cells.
This thesis introduces a novel framework for modeling and modulating Ca2+ dynamics using biologically inspired Boolean logic circuits. Specifically, we propose the Ca2+ Boolean Logic (CaBL) model, in which Ca2+ fluxes and interactions are abstracted into logic gates constructed from the kinetic processes governing Ca2+ signaling. These logic gates—parameterized to reflect biochemical rates and reactions—are composed into sub-circuits, each representing a distinct physiological process such as membrane flux, buffering, and store release. Together, the sub-circuits form a digital circuit that replicates the behavior of a canonical Ca2+ signaling model.
To enable precise modulation of cytoplasmic Ca2+ concentration, we developed the Biosignal Modulation Engine (BME), an algorithmic framework that searches for gate configurations capable of generating a digital output corresponding to a desired Ca2+ level. Through circuit reconfiguration simulations, the BME identifies multiple configurations with suitable parameters that achieve the target behavior. Results show that its performance improves when the parameter search is limited to biologically realistic ranges.
A case study involving GPCR-mediated reduction of cytoplasmic Ca2+ concentration is also presented. By targeting a sub-circuit corresponding to Ca2+ channel activation, the BME identified a circuit configuration that achieves a reduction in the cytoplasmic Ca2+ level, thereby functionally replicating a downstream effect of GPCR-mediated signaling relevant to Ca2+ suppression for certain diseases.
Overall, this work contributes a logic-based abstraction of Ca2+ signaling that can be interpreted and manipulated within a digital framework. It establishes a foundation for programmable cellular systems, suggesting future applications in therapeutic biocomputing, synthetic biology, and the development of molecular-scale logic architectures.
Advisor: Sasitharan Balasubramania
Drift Dynamics of Early Life-stage Invasive Carps
No full textAsian carp species pose significant ecological threats to North American freshwater systems due to their invasive nature and prolific reproduction. Their semi buoyant eggs develop while drifting downstream with the river current. Understanding early life-stage transport is therefore critical for predicting recruitment potential and guiding management efforts. Existing fluvial egg drift models, including those relying on 1-D hydraulics and fully 3-D CFD-based models, are either inadequate for complex braided rivers or too computationally demanding for large-scale application. The Platte River in Nebraska, characterized by wide, shallow, multi-threaded channels, is dominated by two-dimensional flow conditions, making a depth-averaged 2-D modeling approach both appropriate and efficient.
In this study, a 12-mile reach of the Platte River, from Ashland to Louisville, Nebraska, was modeled using HEC-RAS 2D to generate depth and velocity fields under low (1,500 cfs), moderate (5,000 cfs), and high (10,000 cfs) flow conditions. The hydrodynamic model was calibrated and validated against water surface elevations from three 2022 flow events, showing good agreement with USGS gage observations. A three dimensional Lagrangian egg tracking framework was then developed by integrating the 2-D hydrodynamic outputs with empirical vertical velocity distributions, stochastic turbulent diffusion, and time-dependent egg growth functions to account for buoyancy and fall velocity. For each flow scenario, a total of 5,000 virtual silver carp eggs were tracked individually to assess egg dispersion.
Results demonstrated that egg transport and dispersion are highly sensitive to both flow magnitude and channel morphology. Under low-flow conditions, eggs remained largely confined in the upstream reach, reflecting high retention caused by shallow depths, low velocities, and the presence of multi-braided subchannels. Moderate and high flows promoted efficient downstream advection, reducing retention and enabling faster, more uniform downstream transport. Longitudinal dispersion increased with discharge, while lateral dispersion was dominated by morphology-driven pathways (e.g., sandbars and islands) at low flows and by turbulent diffusion at higher flows, with broader lateral spread observed under low-flow conditions. Sensitivity analyses showed that egg fall velocity had minimal influence on lateral dispersion but noticeably affected longitudinal transport by reducing travel times, highlighting the importance of vertical egg positioning in overall drift dynamics.
Advisor: David Admiraa
Feasibility of Using Recycled Waste Plastic in Concrete Pavements in Nebraska
No full textWaste plastic (WP) is a growing environmental concern due to its non-biodegradable nature, large-scale production, and harmful impact on natural resources. With nearly 75% of WP in the United States ending up in landfills, effective recycling strategies are urgently needed. In parallel, the limited availability of natural aggregates highlights the need for alternative materials in concrete construction. This study investigates the feasibility of using recycled waste plastic (RWP) in concrete mixtures, both as aggregates and fibers for rigid pavement applications in Nebraska. Concrete mixtures were prepared by partially replacing natural fine aggregates with recycled plastic aggregates (RPA) at replacement levels of 5%, 10%, and 15% by volume of the natural fine aggregates. Additionally, recycled plastic fibers (RPF) were incorporated into the mixtures at dosages of 0.5%, 1%, and 1.5% by total volume of the concrete. RWP materials underwent characterization tests to compare with traditional materials. A preliminary investigation evaluated fresh properties and compressive strength to assess suitability based on Nebraska Department of Transportation standards (NDOT), using the standard (47B) pavement mixture as a control. Mixtures meeting performance criteria were selected for further testing, including splitting tensile strength, flexural strength, and modulus of elasticity. Fracture behavior was assessed through semi-circular bending (SCB) tests. Also, durability was evaluated using the surface resistivity test, which assesses electrical resistivity as an indication of chloride ion penetration. Results showed that the inclusion of RWP aggregates can increase workability. Statistical analysis indicates that up to 10% RPA replacement does not significantly reduce compressive strength while satisfying the standard requirements set by the NDOT for paving applications. When RWP was used as fiber, a reduction in workability was observed. Nevertheless, the addition of RWP fibers had a positive influence on the flexural strength, ductility, and cracking resistance, with an optimum content of 1.5%. Surface resistivity confirmed acceptable durability performance with respect to NDOT requirements. Overall, incorporating RWP into concrete as aggregate or fibers offers a sustainable solution by reducing WP in landfills while maintaining or improving concrete performance for pavement applications.
Advisors: George Morcous and Jamilla E. Sudo Lutif Teixeir
Development and Implementation of a Vector-quantized Transformer Autoencoder for Monitoring Bicycle Road Conditions
No full textAdviser: Chun-Hsing Ho
The long-term, sustainable assessment of bicycle road conditions is essential for ensuring cyclist safety and promoting equitable infrastructure management. While traditional detection methods based on manual thresholds have demonstrated some effectiveness, they carry limitations due to the diversity of pavement materials, cyclist behaviors, and sensor platforms. Although recent advances in deep learning offer promising alternatives, established techniques are primarily applied to highway anomaly detection and are rarely adapted for bicycle roads. Furthermore, most related studies lack clear definitions for anomalies and transparent annotation procedures, resulting in a shortage of effective datasets and detection methods specifically for bicycle pavement.
To address these issues, this research puts forward a new model, the Vector Quantized Transformer Autoencoder (VQTransAE), which integrates self-attention mechanisms with discrete latent representations to monitor bicycle road conditions using smartphone sensor data. Field experiments conducted on various pavement types, including asphalt, concrete, and brick surfaces, demonstrate the model\u27s ability to accurately detect and locate anomalies such as cracks and potholes. Comprehensive testing using different smartphone platforms (Apple and Android devices) validates the method\u27s robustness across differing sensor characteristics. A systematic comparative analysis between traditional bicycles and electric bicycles (e-bikes) also reveals a noticeable spatial overlap in their detection results. In addition, this study defines a standardized data processing workflow and establishes a rigorous manual annotation protocol, producing a publicly available, high-quality labeled dataset for future research.
However, current limitations include an insufficient representation of data from extreme seasonal conditions and unvalidated threshold generalizability across diverse cyclist characteristics. Future research directions include leveraging crowdsourced data collection for long-term infrastructure monitoring, optimizing anomaly thresholds to accommodate different cyclist conditions, integrating e-bike data to increase model coverage, and creating a quantitative link between anomaly scores and the degree of pavement deterioration
Characterization of Undergraduate Biology Instructors’ Goals and Strategies for Implementing Quantitative Reasoning
No full textQuantitative reasoning (QR) is the application of mathematics and statistics to real-life and scientific contexts. It is essential for understanding complex biological phenomena and analyzing large datasets in both academic and professional settings. In response to the growing demand for QR skills, biology educators and researchers have engaged in curricular reforms and education research. This qualitative study explores how undergraduate biology instructors integrate QR into their teaching using a framework informed by pedagogical content knowledge (PCK) and QR. The study involved 21 biology faculty from various U.S. institutions who intentionally incorporated QR in their instruction. Data was collected through semi-structured interviews focused on participants’ instructional goals, strategies, and perceived challenges and supports. Findings reveal that instructors tailor QR instruction based on course level and student preparedness. In lower-division courses, they emphasized building foundational math skills, reducing student anxiety, and using scaffolding to build confidence. In upper-division courses, despite expecting greater fluency, instructors often encountered uneven student abilities and addressed misconceptions while deepening conceptual understanding of biology through math. Instructors’ personal and educational experiences, including their own struggles with math, influenced their empathetic and inclusive teaching approaches. Their research backgrounds shaped the integration of authentic data, statistical tools, and real-world applications into course content. Ongoing teaching experience contributed to improved lesson planning, pacing, and the use of active learning techniques. Despite these efforts, instructors faced barriers such as discomfort with teaching math, time constraints, student resistance, and institutional limitations. However, support like departmental encouragement, interdisciplinary collaboration, and curricular flexibility helped mitigate some of these challenges. This study highlights how instructors’ beliefs, experiences, and institutional contexts interact to shape QR instruction. The findings underscore the need for professional development that fosters reflective practice, interdisciplinary competence, and instructional strategies that effectively integrate biology and mathematics. Supporting biology instructors can enhance students’ development of QR skills and foster broader engagement in STEM through more inclusive, integrated teaching practices.
Advisors: Joseph T. Dauer and Brian A. Couc
“Tell Your papa”: Aesthetics of Confrontation and Visual Witnessing in Nigerian Protest Music
No full textThis study analyzes the music video “Tell Your Papa” (2025), a politically charged protest song by Nigerian artiste Eedris Abdulkareem, as an exemplary case of aesthetics of confrontation, here conceptualized as a multimodal strategy in which direct address, anti-spectacle visual style, literalism, and discomfort converge to confront political power. Focusing on the song’s explicit critique of President Bola Ahmed Tinubu, his son Seyi Tinubu, and other prominent political figures, the analysis demonstrates how Abdulkareem renders indistinct the line between music and political discourse through a visual-sonic language that is accusatory, documentary-stylized, and unflinchingly courageous. While building on the lineage of Nigerian resistance music, the study posits that “Tell Your Papa” functions not merely as a form of musical resistance but more critically as a visual and pedagogical archive of suffering, public anger, and national trauma, insisting that political art must witness, name, and disturb. Accordingly, this study makes a cross-disciplinary contribution to African popular music, protest movement, postcolonial, and pedagogical studies through the theorization of the aesthetics of confrontation as a framework that shows how sound, image, and performance converge to act as archive, pedagogy, and resistance. Importantly, the study further contends that, though grounded in the Nigerian context of the examined text, the framework establishes an adaptable conceptual tool for interpreting confrontational protest aesthetics across diverse postcolonial and global contexts, while simultaneously highlighting its pedagogical implications in educational discourses on media literacy, governance and resistance, and visual cultur
Fraggin’ The Superhero Genre: Parody And Carnival In DC’s Lobo
No full textThis essay examines the DC anti-hero Lobo as an ideal example of the constructive, creative power of parody and Bakhtinian carnival. Unlike Bakhtin’s assertion that carnival since the Renaissance has lost its spirit of play and become purely destructive, Lobo uses grotesque violence to create just as much as he destroys social norms. Ultimately, the mini-series under consideration provide a valuable tool for students to understand carnival, parody, and its power as criticism
Book Review of: Univision, Telemundo, and the Rise of Spanish-Language Television in the United States
No full textInsect Biodiversity of Prairie Land Based on Prescribed Fire Plans in Central Iowa
No full textIntroduction
Insects play a crucial role in the prairie ecosystems by helping to maintain a healthy balance in various aspects of human life. They play vital roles in assisting with pest control, waste decomposition, and the pollination of plants and crops (The Nature Conservancy, 2021). Additionally, they can serve as indicators of an environment\u27s health, such as nutrient cycling in water and soil formation in crop fields (The Nature Conservancy, 2021). Insect biodiversity is a crucial component in ensuring our environment is adequately cared for, and in turn, other aspects of life that rely on insect relationships.
In some states, such as Iowa, the majority of the region’s land is used for row crop farming, primarily for corn and soybeans (Edwards, 2024). According to the Iowa Environmental Council, the percentage of land used for agricultural production is 92% (Land Stewardship - Iowa Environmental Council, 2025). This puts a strain on insect populations as the plant diversity of different ecosystems is limited. Conservation efforts are essential in farming states to maintain the balance between plant diversity and insect populations. In Iowa, prescribed fires are a prominent means of preserving prairie land environments; however, they are not directly used to boost insect biodiversity. Prescribed fires are planned and manually controlled fires that are used for land management (U.S. Department of the Interior, 2025). At the local country conservation level, these fires are used to improve tree stand habitat, promote new plant growth, reduce hazardous fuels, and control invasive species (Polk County Iowa, 2025). However, this report will look at whether select planned prescribed fires have any impact on the diversity of insects in public prairie lands. Especially since selected prairies are among the few plots of land that insects can find habitat and native plant species in Iowa (Land Stewardship - Iowa Environmental Council, 2025)
Oregon Institute of Technology: Program Profile
No full textLocated in southern Oregon, the Oregon Institute of Technology (Oregon Tech) was founded in 1947 and is Oregon’s public polytechnic university. Its main residential campus is in Klamath Falls, OR; its other locations include an urban campus in Wilsonville, OR; an online campus; and additional sites in Salem, OR, and Seattle, WA. Oregon Tech’s mission is to provide professionally focused applied degrees. It offers forty-nine bachelor’s degrees, eight master’s degree programs, one doctoral program, and several certificates. As of fall 2023, 1,976 students were enrolled at the main campus in Klamath Falls: 51% were male, and 49% were female. Approximately 35% of students are minority students. Oregonians make up 70% of students who attend Oregon Tech. The university has an average class size of seventeen students, and about 36% live on campus in the Klamath Falls residence halls. Oregon Tech has a 14:1 student-to-faculty ratio, and 93.9% of faculty are full-time; 76.6% of full-time faculty are tenured or on a tenure track