Digital Commons Network^™

Predicting And Decoding Allosteric Binding Sites Using Protein Language Models And Structure-Based Machine Learning: An Energy Landscape-Guided Explainable Ai Framework, Kamila Riedlová, Vít Skrhák, William G. Gatlin, Max Ludwick, Lucas Turano, Marian Novotný, David Hoksza, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

Computational prediction of allosteric binding sites in protein structures remains a persistent challenge, as these regulatory pockets evade detection by both sequence-based and structure-based algorithms. Both computational and physical origins of this predictive asymmetry remain insufficiently understood. In this study, we systematically examine the determinants of binding site predictability using a dual framework that integrates a fine-tuned protein language model and the structure-based method P2Rank as complementary tools probing a diverse data set of 453 human kinases, together with a physics-based interpretability layer derived from energy landscape frustration analysis. Both predictors exhibit a sharp and reproducible dichotomy on protein kinases, …

A Remote Sensing Approach To Identifying Zones Of Instability In Mine Tailings Impoundments Using Multi-Sensor Satellite Data, Arden K. Pierce

Honors Theses

Mine tailings impoundments are structures built to contain the chemical and sedimentary byproducts generated by ore extraction activities. In this common method of mining waste storage, the tailings can be pumped into containment ponds and held behind earthen embankments to prevent the release of hazardous substances into the surrounding environment. Monitoring environmental factors that influence the structural integrity of these impoundments is essential for identifying areas vulnerable to instability and failure. Soil moisture is a factor that can affect the stability of mine tailings impoundment structures. This study evaluates the relationship between satellite-derived soil moisture and surface deformation at mine …

Not An Afterthought: Addressing The Academic And Social Challenges That Create Barriers To Belonging For Transfer Students, Brooke Jankowsky

Honors Theses

This thesis examines the academic and social barriers to belonging for transfer students at four-year institutions, with particular attention to the University of Mississippi. The goal is to bring attention to the issues that surround transfer student populations in general by identifying some of the most pressing structural and interpersonal challenges that shape their experiences. A qualitative approach was used, drawing on existing literature, prior unpublished research at the community college level, and reflective analysis to explore themes such as transfer shock, creating and maintaining social networks, and gaps in institutional support. Findings suggest that transfer students often face a …

Narratives Of Cultural Wealth: Understanding What Works For Underrepresented Minority Students In Stem, Grace Long

LMU Theses and Dissertations

This qualitative study examined the lived experiences of underrepresented minority alumni from Galileo STEM High School who are pursuing STEM degrees at four-year universities. Guided by Yosso’s (2005) Community Cultural Wealth (CCW) framework, the study focused on what worked for underrepresented minority groups (UMG) in STEM. In-depth semi-structured interviews were conducted to learn a) what factors contributed to their STEM development and identities, b) what forms of cultural wealth were leveraged in high school and in the first years of college to pursue and persist in STEM studies, and c) experiences from Galileo STEM High School that cultivated and affirmed …

Monitoring Groundwater Flow At Old Works Using Anisotropy, 3-D Electrical Geophysics, And Dem-Based Terrain Analysis, Yihaun Gao

Honors Theses

Groundwater flow in shallow heterogeneous environments is often difficult to characterize using a single geophysical method. This study applies an integrated approach combining azimuthal resistivity anisotropy, self-potential (SP) measurements, DEM-derived terrain indices, and three-dimensional electrical resistivity tomography (3-D ERT) to delineate preferential groundwater pathways at the Old Works Golf Course in Anaconda, Montana. Azimuthal anisotropy analysis from eighteen 2-D ERT profiles revealed a dominant directional dependence in electrical conductivity, indicating a structural or sedimentological control on subsurface flow. The anisotropy results indicate a preferred conductivity direction of approximately 200°–210° in azimuth (0° is north), suggesting that groundwater movement is guided …

Rf Properties Of Military Radio Enclosures, Ethan Messner

Honors Theses

Ghost radios are used in a MANET setup by the 11th Airborne Division during operations in Alaska, however, the Ghost radios are limited by battery life and extreme cold temperatures. This work investigates the effects of different enclosures on the propagation characteristics of the Ghost radio. A testing setup was created to measure the S-parameters of a 2-port network in an open field to quantify the impact the enclosures will have on antenna gain. A finite element model of the final enclosure design was created in ANSYS HFSS to determine the effectiveness of adding an attachment onto the enclosure to …

Asymmetric Synthesis Of Borylated Amines Via Rhodium Catalyzed Hydroboration Of Allylamine Derivatives: Surprising Role Of Counterions And Accelerators, Rukshani Wickrama Arachchilage

Dissertations and Doctoral Documents, University of Nebraska-Lincoln, 2023–

The Catalytic Asymmetric Hydroboration (CAHB) reaction is a valuable method for synthesizing chiral organoboron compounds. Nevertheless, key mechanistic details, including catalyst activation, ligand effects, and rate-determining steps, are difficult to generalize and remain not fully understood. Building on previous research from the Takacs group, this work explores acyclic N-acyl allylamines as substrates in rhodium-catalyzed hydroboration and investigates the formation of active catalysts from various rhodium precursors, the role of counterions (e.g. BF₄, BArF-), ligand-to-metal ratios, and the impact of external fluoride additives (e.g. TBAT). Hydroboration of acyclic N-acyl allylamines achieves up to 90% yield and 99 : 1 …

Toward Vehicle-Agnostic Driving Signatures For Cognitive Impairment Prediction From Naturalistic Driving Data, Aadarsha Gopala Reddy

McKelvey School of Engineering Graduate Student Theses & Dissertations

This thesis studies whether naturalistic driving data can help predict binary Clinical Dementia Rating (CDR) status while accounting for differences across vehicles. The final analytic dataset comprised 26,968 participant-weeks from 304 participants. Weekly driving features were derived from real-world telematics data and combined with four demographic covariates. Primary model comparisons used leave-one-participant-out (LOGO) cross-validation, with one individual held out at a time and pooled participant-level metrics used as the main reporting surface.

The main comparison includes six model families evaluated on the same dataset under a shared LOGO framework. Performance remained modest overall. GRU-DANN had the highest participant-level ROC AUC …

Improving Semantic Precision In Text-To-Image Diffusion Models Via Latent-Space Optimization And Semantically-Parsed Evaluation, Mohammad Rouie Miab

McKelvey School of Engineering Graduate Student Theses & Dissertations

Text-to-image diffusion models can produce visually impressive images from natural-language prompts, but they often fail to satisfy the detailed semantic constraints expressed in compositional prompts. Typical failure modes include omitted objects, merged entities, incorrect quantities, incorrect attribute binding, and leakage of one entity's attributes onto another. This thesis studies the problem of semantic precision in text-to-image generation: how faithfully a generated image satisfies the structured meaning of its prompt.   The thesis makes two linked contributions. First, it presents a training-free inference-time refinement method for diffusion-based image generation. The method operates directly in latent space during denoising and uses noun-phrase-aware cross-attention …

Interaction-Aware Safe Planning For Human-Robot And Multi-Robot Systems, Haoyi Wang

McKelvey School of Engineering Graduate Student Theses & Dissertations

Robots operating in shared environments must interact safely not only with static obstacles but also with other decision-making agents, including humans and other robots. In such settings, both safety and task completion depend on the ability to reason about interaction. Two major challenges arise. In human-robot interaction, future human behavior depends on latent internal factors, such as attentiveness and behavioral style, that are not directly observable to the robot. In multi-robot systems, decentralized reactive navigation can fail in cluttered environments when reciprocal interactions create deadlocks that prevent progress through narrow passages or bottlenecks. This thesis investigates these two challenges from …

Does Your Sleep Really Matter?, Kristy Riddle

Student Scholar Symposium Abstracts and Posters

In this project, I am tracking 10 of my daily statistics revolving around my routine. I am using an Oura Ring to help accomplish some of the statistics. These include: readiness score, sleep score, screen time on cell phone, time spent on social media, steps taken, stress levels, restorative time, pages read, homework time spent, and oz of water consumed. I will be utilizing Excel for my data and will have around 3 months worth of statistics. hope to learn more about my levels of efficient sleep and how I can better improve my motivation as a student. This project …

Interpreting American Sign Language: A Literature Review Of Assistive Technologies, Natalie Louise Paradiso, Emma Grace Kochenderfer

Student Scholar Symposium Abstracts and Posters

American Sign Language (ASL) is a visually elaborate, spatially oriented linguistic methodology that relies on combinations of hand movements, body positioning, facial expressions, and motion/spatial perception, aspects of which make interpretation difficult for automated machine recognition. Current assistive technology approaches to ASL interpretation are generally within the categories of computer vision models (including deep learning, multi-focus image fusion, and keypoint tracking) and wearable, multimodal/sensor-based approaches (such as smart glasses and inertial-sensor gloves). Within controlled environments, computer vision models perform well. However, when applied to conditions such as non-manual signs/features, signer variability, and rapid assimilation, they falter in processing all aspects …

Freshman 15? Freshman 50?? The Reality Of Daily Life Habits Of A First Year College Student, Gregorio R. Salgado

Student Scholar Symposium Abstracts and Posters

This project presents a personal data tracking study in which I collected daily self-reported metrics over the course of the Spring semester using Excel. The variables tracked include sleep duration, caloric intake, screen time, social media usage, phone checks per day, family communication, and personal spending. The goal of this project is to identify meaningful patterns and correlations between daily habits and personal well-being.

Data was collected through a combination of manual logging and smartphone-generated daily reports. This study explores potential relationships between variables such as sleep duration and social media usage, as well as the association between family communication …

Developing Narrative-Based Stem Learning Tool For K-6 Visually Impaired Students, Daniel Tsivkovski, Dylan Ravel, Jeffrey Kraskouskas, Brandon Foley, Maryam Etezad, Franceli Cibrian, Rajeev Joshi, Ariel Han

Student Scholar Symposium Abstracts and Posters

This research develops a free, accessible web application that enables K-6 students who are blind or visually impaired (BVI) to learn STEM concepts using refreshable braille displays. Currently, most online learning tools are not designed for BVI students, creating a significant educational barrier.

The application interfaces with commercial braille displays and uses narrative-based learning to make STEM content approachable and engaging. By presenting material as personalized interactive stories generated with the help of Artificial Intellligence (AI), students can connect with concepts while developing braille reading skills. The curriculum design prioritizes accessibility through the Accessible Rich Internet Applications (ARIA) standards and …

Kl Dra As A Benchmark Laboratory For Accretion-Disk Physics: Constraints From Tess And Ground-Based Surveys, Luis E. Salazar Manzano, Liliana E. Rivera Sandoval, Jean-Marie Hameury, Craig O. Heinke, Iwona Kotko, Thomas J. Maccarone, Manuel Pichardo Marcano

Physics & Astronomy Faculty Publications

We present the longest-term optical analysis of the AM CVn system KL Dra using ∼11 yr of monitoring from TESS and wide-field ground-based surveys. The continuous TESS coverage allows us to characterise its frequent outbursts with unprecedented detail, providing the first comprehensive study of an AM CVn during outbursts and enabling detailed modelling of these systems. The superoutbursts in KL Dra generally include a precursor and are followed by a series of rebrightenings after which a sequence of 3–4 large amplitude normal outbursts is observed. We fit parametric profiles to each superoutburst component (precursor, rise to plateau, plateau, and decay), …

Propasafe-Hybrid: A Text-Based Hybrid Propaganda Detection Tool, Thomas Kimmeth, Avijit Roy, Vivek Sharma

Publications and Research

Propagandistic content increasingly circulates through online news and social media, where readers often encounter it with limited scrutiny, highlighting the need for reliable and fine-grained detection. This paper introduces Propasafe-Hybrid, a sentence-level system that integrates a fine-tuned transformer classifier with LLM-based technique classification to identify, label, and explain specific propaganda strategies. The pipeline generates actionable outputs, including highlighted sentences, technique assignments, and concise rationales, so users can immediately understand why a sentence was flagged and how each label was determined. To control inference cost, Propasafe-Hybrid employs a cost-aware pre-filtering stage that forwards only high-likelihood sentences to LLMs, reducing token usage …

Genealogy-Based Trait Association With Locater Boosts Power At Loci With Allelic Heterogeneity, Xinxin Wang, Ryan Christ, Erica Young, Chul Joo Kang, Indraniel Das, Edward A Belter, Markku Laakso, Louis J M Aslett, David Steinsaltz, Nathan O Stitziel, Ira M Hall

2020-Current year OA Pubs

A key methodological challenge for genome-wide association studies is how to leverage haplotype diversity and allelic heterogeneity to improve trait association power, especially in noncoding regions where it is difficult to predict variant impacts and define functional units for variant aggregation. Genealogy-based association methods have the potential to bridge this gap by testing combinations of common and rare haplotypes based purely on their ancestral relationships. In parallel work, we have developed an efficient local ancestry inference engine and a novel statistical method (LOCATER) for combining signals present on different branches of a locus-specific haplotype tree. Here, we develop a genome-wide …

Coal Ash-Derived Aluminosilicate Precursors: A Chemical Engineering Approach To Geopolymer Characterization, Hafiz Abdul Basit, Abdullah Bashir, Abdur Raafey

World of Coal Ash Proceedings

The chemical and microstructural evaluation of coal-derived aluminosilicate precursors is critical for understanding their suitability in advanced construction material systems. In this study, a characterization of Class F fly ash, ground granulated blast furnace slag (GGBFS), and Silica Fumes (SF) was conducted to elucidate their morphological and elemental features. Scanning Electron Microscopy (SEM) was used to assess particle morphology and surface characteristics (porosity, particle diameter, particle geometry), and Energy-Dispersive X-ray Spectroscopy (EDS) to determine elemental composition and distribution. The analysis revealed distinct morphological and compositional differences among the precursors, including spherical fly ash particles, calcium-rich slag phases, and ultra-fine silica …

State Permitting Program Update, Jessica Reiss

World of Coal Ash Proceedings

State Permitting Program Update Jessica L. Reiss, Barnes & Thornburg LLP, 11 South Meridian Street, Indianapolis, IN 46204 KEYWORDS: states, permitting, permit program, rulemaking ABSTRACT At the end of 2016, the United States Congress authorized states to establish permit programs for coal combustion residuals (CCR) surface impoundments and landfills.[1] Since then, several states have established such programs, and the United States Environmental Protection Agency (U.S. EPA) has approved programs for Oklahoma,[2] Georgia,[3] Texas,[4] and North Dakota,[5] proposed approval for Wyoming,[6] and denied approval for Alabama.[7] Other states, such as Indiana,[8] are actively working through the state rulemaking process and plan …

Zero-Waste And High-Value Valorization Of Coal Combustion Residues Via Critical Minerals Recovery And Cementitious Materials Production, Hongyan Ma

World of Coal Ash Proceedings

Coal combustion residues (CCRs) pose significant environmental and disposal challenges, yet they also represent an untapped resource rich in aluminosilicates and critical minerals. This work presents a zero-waste, high-value valorization pathway that integrates critical mineral recovery with the production of cementitious materials. Advanced separation and extraction techniques are employed to recover strategically important elements such as gallium and rare earths, while the mineral-rich residues are simultaneously processed into supplementary cementitious materials (SCMs) for blended cements and concretes. This integrated approach not only offsets the environmental burden of CCR disposal but also supports domestic supply chains of critical minerals and reduces …

Revolutionizing Closure Systems: The Performance Advantages Of Structured Geomembranes, Scott Perugia

World of Coal Ash Proceedings

Coal combustion residual (CCR) containment facilities have traditionally been closed using methods that have changed little over several decades, but structured geomembranes are now reshaping closure design by improving slope stability, increasing interface friction, enhancing drainage, and providing long-term durability. Two systems are emerging as leading solutions: a structured geomembrane paired with a geotextile and vegetative cover, and a structured geomembrane paired with engineered turf. This presentation compares these approaches using field performance data, laboratory testing, and lessons learned, with emphasis on key factors such as infiltration control, drainage efficiency, slope stability, constructability, and regulatory compliance. The engineered turf system …

Developing Concentrated Brines / Salt Slurries For Disposal Of Coal Ash Wastewaters., Lance Edling

World of Coal Ash Proceedings

If coal ash wastewater is not fully concentrated to the greatest extent possible, then this results in greater disposal volumes and costs. However, concentrating a wastewater stream high in scaling compounds can be difficult. Membranes are prone to scale and Vacom thermal systems are higher in operating cost. This presentation will discuss the need to minimize disposal volumes by concentrating wastewater that is readily prone to scale and foul. The discussion will present past project examples of waste streams that were concentrated until salt crystals formed and the method used to minimize fouling and scaling during the concentration process. In …

Recinis™ Wet Beneficiation Process For Landfilled Coal Ash, Tim Sambrook

World of Coal Ash Proceedings

The decline of coal-fired power generation has reduced fresh “Run-of-Station” ash availability, increasing reliance on reclaimed ash from landfills to meet supplementary cementitious material (SCM) demand. This shift has lowered OPC replacement rates and raised concrete costs due to inconsistent ash quality. ReCinis™ offers a low-capex wet beneficiation solution for landfill-aged, saturated, and variable-quality coal ash. With over 5 billion tons of ash impounded in the U.S., this process enables long-term supply security where dry beneficiation is unsuitable. Combining proven mineral processing techniques with coal ash expertise, ReCinis™ can be deployed as a 150,000 tpa skid-mounted plant or scaled to …

Lessons Learned From A Full-Scale Discrete In-Situ Stabilization Project For Ccr Impoundment Closure, Tony Moran, Paul Jennings, Jacob Susser, Tim Silar

World of Coal Ash Proceedings

ENTACT, in collaboration with Silar Services, Inc., the patent holder of Discrete In-Situ Solidification (DISS) technology, has successfully performed a full-scale implementation of DISS in a Coal Combustion Residual (CCR) impoundment. DISS hydraulically isolates ash from surrounding groundwater by constructing a low-permeability barrier at the impoundment bottom to treat a layer of ash and tying into underlying natural soil layers. DISS enables targeted stabilization within a designated treatment zone, minimizing the disturbance of overburden compared to traditional excavation methods and reducing the use of costly cementitious reagents. The process starts with Reagentless Drilling of the overburden CCR utilizing a specialized …

From Clogs To Compliance: Overcoming Persistent Leachate Head Issues In Ccr Landfills, Breanne Kahnk, Zachary Bauman

World of Coal Ash Proceedings

State and federal regulations require that landfills, including coal combustion residual (CCR) landfills, be designed and operated to maintain leachate head levels of less than 30 centimeters (approximately 1 foot). While proper leachate collection system design and routine maintenance are critical for meeting this requirement, challenges such as clogging of drainage media, pipes, fittings and/or pipeline perforations, settlement of collection pipes, and breaks in the piping system can lead to elevated leachate levels, posing risks to compliance and long-term system performance. TRC will provide an overview of leachate collection system regulatory requirements along with design, operation, and maintenance strategies that …

Plasma Coal Ash Processing For Enhanced Recovery Of Rare Earth Elements & Precious Metals: Proven From R&D To Commercial Plants, George Paskalov, Victoria Campbell, Jason Honigberg

World of Coal Ash Proceedings

Our Radio-frequency Plasma System is an ash pretreatment before the application of extractive metallurgy and addresses current elemental, methodological, and technological limitations of complex and refractory coal ash. Our system data shows from 10-20% improved recovery, to 9x-100x. RFP can access all metals contained in coal ash. Our focus is not on the alteration of established methodologies, such as cyanidation for non-refractory ore, which has a proven return and capacity to achieve target revenue at-scale. Using the RFP systems, no waste is created, overburden can be more easily dealt with, and no metal content will be left behind. We assert …

Probing The Critical Element Chemistry Of Coal-Combustion Fly Ash: Electron Microbeam Investigations Of The Spent Ash From The Pilot-Scale Acid Extraction Of Rare Earth Elements From A Beneficiated Kentucky Fly Ash, James Hower

World of Coal Ash Proceedings

Fly ash derived from the combustion of an eastern Kentucky high volatile bituminous coal blend was beneficiated to yield a <75-μm product with a reduction in the carbon and spinels and reacted with a strong acid in a pilot-scale unit to extract rare earth elements. Electron microscopy showed a wide range of rare earth-bearing minerals. The acid-extracted fly ash had a rim that was depleted in REE and in most other elements except silicon.

Standardization Of Coal Ash Testing, Classification, And Harvesting, Benjamin Gallagher, Chris Frishcosy, Eric Hageman

World of Coal Ash Proceedings

Standards such as product specifications, test methods, practices and guides play a crucial role in supporting both commerce and science. Standardization helps build consistency and reliability whether it pertains to the performance of an ingredient in a product or in the measurement of a material characteristic. Coal combustion products, such as coal ash and synthetic gypsum, exhibit unique characteristics and many standard have been developed to characterize these materials and support their beneficial use. ASTM is a voluntary, consensus-based organization, and publishes many standards related to coal combustion products. Currently, there are seven ASTM standards related to chemical analysis of …

Leachate Quantification And Reduction – One Facility’S Path To Zld, Cedric Ruhl

World of Coal Ash Proceedings

The Environmental Protection Agency (EPA) promulgated Effluent Limitation Guidelines (ELG) that govern liquids discharged from energy production facilities. According to the ELG, energy production facilities that burn coal beyond December 31, 2034 must convert to a Zero Liquid Discharge (ZLD) system by December 31, 2029*. This presentation focuses on one coal-burning facility’s strategy to meet ZLD requirements. The predominant source of liquid that will be treated by the proposed ZLD system is leachate from an active coal combustion residual (CCR) landfill. Is the ZLD’s design capacity suitable for average leachate flow conditions? Is there enough leachate storage volume to manage …

Ai-Guided Upcycling Of Coal Combustion Residues In Blended Cement And Concrete, Hongyan Ma

World of Coal Ash Proceedings

Coal combustion residues (CCRs), including fly ash, bottom ash, desulfurization gypsum, etc., on specification or off-specification, remain an abundant yet underutilized byproduct of power generation. While these materials have long been considered as supplementary cementitious materials (SCMs), their variable chemical and physical characteristics limit broader adoption in blended cement and concrete. This study introduces an AI-guided framework to accelerate the upcycling of CCRs into high-performance construction materials. By integrating materials informatics, machine learning models, and experimental validation, the framework enables rapid property prediction and performance-based preprocessing recommendation or mix design optimization for diverse CCR sources. Preliminary results demonstrate the ability …