Digital Commons Network^™

Ai Is A Viable Alternative To High Throughput Screening: A 318-Target Study, Izhar Wallach, Denzil Bernard, Kong Nguyen, Gregory Ho, Adrian Morrison, Adrian Stecula, Andreana Rosnik, Ann Marie O'Sullivan, Aram Davtyan, Ben Samudio, Bill Thomas, Brad Worley, Brittany Butler, Christian Laggner

Chemistry Faculty Research & Creative Works

High throughput screening (HTS) is routinely used to identify bioactive small molecules. This requires physical compounds, which limits coverage of accessible chemical space. Computational approaches combined with vast on-demand chemical libraries can access far greater chemical space, provided that the predictive accuracy is sufficient to identify useful molecules. Through the largest and most diverse virtual HTS campaign reported to date, comprising 318 individual projects, we demonstrate that our AtomNet® convolutional neural network successfully finds novel hits across every major therapeutic area and protein class. We address historical limitations of computational screening by demonstrating success for target proteins without known binders, …

Psychology Graduate Student Experiences, Social Support, And Mental Health, Kathryn Lang

Theses and Dissertations

Graduate school is a highly stressful experience for many psychology students. Accordingly, graduate psychology programs need to identify and minimize unnecessary sources of stress on their students. Despite the importance of this topic, there is little research on factors that increase psychology graduate students’ stress. The present study determined how a student’s financial difficulties, quality of their social support, quality of their faculty support, number of adverse experiences they had in their program, the impact of a student’s negative experience in their program; and the population size of the location of their program affect a student’s mental health, perceived progress …

Developing Inclusive Practices Through Peer Coaching In College Science Teaching, Briana Miller

Theses and Dissertations

Historically underrepresented students pursuing STEM majors encounter systemic barriers. Students are more likely to experience success when faculty implement inclusive practices. Faculty often lack the pedagogical training necessary to adopt inclusive practices, further perpetuating inequities. To eliminate barriers and offer equitable opportunities for success in STEM majors, this case study explores the implementation of peer coaching and Culturally Relevant Science Teaching (CRST) in college level science teaching, focusing on the experiences of three participating faculty. Through a year-long professional development (PD) cycle, three science faculty members from a small liberal arts college engaged in reflective practices aimed at improving their …

Causes Of The Morphological Distinctiveness Of Ahuna Mons And Differences In Cryovolcanic Styles On Ceres And The Inner Uranian Satellites Miranda And Ariel, Caleb Strom

Theses and Dissertations

Ahuna Mons is one of the most distinctive features on the dwarf planet (1) Ceres and shows evidence of cryovolcanic activity on a main belt object in the geologically recent past. Ahuna Mons is unusual, however, in that it has a higher aspect ratio and sharper features than other candidate domes on Ceres. It also stands apart from cryovolcanic features identified on other suspected cryovolcanic worlds like Miranda and Ariel, where cryovolcanism is associated with double ridges and potential plume activity. In this work, dome age, based on crater counting, and aspect ratio are compared through correlative analysis to investigate …

Innovations In Full-Stack Web Development: Front-End To Back-End, Yassine Chahid, Patrick Slattery

Publications and Research

This research explores emerging technologies within full-stack web development and their potential impact on current front-end and back-end solutions. Both areas employ crucial technologies that determine how end-users access information and navigate web services. Front-end solutions include HTML, JavaScript, and CSS which shape user interaction on websites. Back-end solutions use technologies such as SQL and PHP for the foundation of data processing, retrieval, and storage. The research method involves examining official documentation for these technologies to better understand their key components and to understand how their use in cyberspace has changed. The research will observe several high-traffic websites and domains …

Investigation Of Gas Injection Eor In Conventional And Unconventional Reservoirs Based On Laboratory Experiments And Field Pilot Tests, Jin Zhao

Theses and Dissertations

Currently, fossil fuels (including oil, natural gas, and coal) are still the dominant energy sources in the United States. However, their extraction and utilization generate a significant volume of carbon dioxide (CO2) and associated gases, such as methane (CH4), ethane (C2H6), propane (C3H8), etc. Injecting these gases back into deep oil reservoirs offers a practical means to enhance oil recovery while reducing air pollution. The target formations are usually characterized by good porosity and permeability to ensure sufficient injectivity and storage capacity. However, recent unconventional reservoir development indicated that tight formations could also be potential targets for enhanced oil recovery …

Mobilizing Memory Diasporas, Transnational Sectarianism, And The Memory Of Violence, Mirna M. Wasef

Kroc IPJ Research and Resources

Memory has power. Memory and narratives of violence—beyond the acts themselves—shape identity and subjectivity. The significance of narrative lies not just in the story told, but in the political, social, and nationalist contexts surrounding it. When is memory invoked and why? How are acts of violence contextualized, narrativized, and mythicized? What galvanizes, or not, around the memory of the violence? Furthermore, how does violence expose the significant underpinnings of power inequalities and societal fissures that contribute to conditions conducive to its occurrence? The connection between memory and violence is crucial in understanding how memory is used to bolster, challenge, and …

Author Correction: Dual Nature Of Magnetism Driven By Momentum Dependent F-D Kondo Hybridization (Communications Physics, (2024), 7, 1, (186), 10.1038/S42005-024-01631-8), Byungkyun Kang, Yongbin Lee, Liqin Ke, Hyunsoo Kim, Myoung Hwan Kim, Chul Hong Park

Physics Faculty Research & Creative Works

Correction to: Communications Physicshttps://doi.org/10.1038/s42005-024-01631-8, published online 12 June 2024 In this article the grant number DE-AC02-07CH11358 relating to Ames National Laboratory was omitted. The original article has been corrected.

Comparative Analysis Of Multi-Criteria Techniques In Neutrosophic Environment And Their Applications To Economic Condition Assessment, Asmaa Elsayed, Mai Mohamed

Neutrosophic Systems with Applications

In economic decision-making, the challenge of evaluating multiple, often conflicting criteria necessitates advanced Multi-Criteria Decision-Making (MCDM) techniques. Traditional methods can struggle with the inherent uncertainty, ambiguity, and imprecision of real-world data. This paper addresses these challenges by investigating the effectiveness of various MCDM techniques within neutrosophic environments, with a particular focus on the Criteria-wise Alternatives Ranking and Correlation Analysis for Composite Scoring (CARCACS) method. Neutrosophic sets, which incorporate truth, falsity, and indeterminacy, provide a robust framework for addressing the vagueness and inconsistencies found in economic indicators such as GDP growth, employment levels, inflation rates, trade balances, investment activity, and government …

Soil Organic Matter Processes From The Treetops To The Clay Particle: The Role Of Climate, Minerals, And Organic Matter Chemistry In Soil Carbon Accumulation And Stability, Jessica G. Murray

All Graduate Theses and Dissertations, Fall 2023 to Present

Soils store more carbon than plants and the atmosphere, yet release ten times more carbon dioxide (CO₂) to the atmosphere than human activities each year. Small shifts in the balance of soil carbon storage and soil carbon emissions could make climate change less severe, by acting as a sink for the carbon plants pull from the atmosphere, or make climate change worse, by releasing even more planet-warming greenhouse gases. The processes governing whether soils store or release carbon depend on tiny soil microorganisms which convert plant carbon to soil organic matter, releasing CO₂ in the process. In …

Interpreting Neural Networks For Particle Tracing In Fluid Simulation Ensembles: An Interactive Visualization Framework, Maanav Choubey

All Graduate Theses and Dissertations, Fall 2023 to Present

Understanding the internal mechanisms of neural networks, particularly Multi-Layer Perceptrons (MLP), is essential for their effective application in a variety of scientific domains. In particular, in the scientific visualization domain their adoption has recently shown to be a promising tool to predict particle trajectories in fluid dynamics simulation and aid the interactive visualization of flows. This research addresses the critical challenge of interpretability of such models.

While interpretability has been extensively explored in fields like computer vision and natural language processing, its application to time series data, particularly for particle tracing (or prediction of trajectories), has not garnered sufficient attention. …

Finite-Time Control Strategies For Rendezvous And Proximity Operations, John Tamotsu Akagi

All Graduate Theses and Dissertations, Fall 2023 to Present

One common metric to use when designing a controller is the time that the system will take to reach the desired state. Unfortunately, many approaches to developing controllers only guarantee that the system will approach, but not exactly reach, the desired state. This can become a limitation in time-sensitive situations where rapid and complete convergence is necessary. One group of control methods, known as finite-time control, does guarantee both faster convergence and that the desired state will be reached, but often fails to define exactly what time that will occur, how much control will be used to get there, and …

Optimizing Mobility On Demand Systems: Multiagent Reinforcement Learning Approaches To Order Assignment And Vehicle Guidance, Jiyao Li

All Graduate Theses and Dissertations, Fall 2023 to Present

This dissertation explores ways to improve Mobility on Demand (MoD) systems, which are services like ride-sharing and autonomous taxi systems. The main goal is to make these services more efficient and reliable, benefiting both passengers and drivers by better matching the number of available vehicles with the number of people needing rides.

For ride-sharing services, a new method called T-Balance helps match riders with drivers and guides empty taxis to areas where more people need rides. This reduces wait times for passengers and increases earnings for drivers. Another method, called GRL-HM, looks at how riders and drivers behave to further …

Analysis Of A Gravity Wave Horizontal Blocking Event Using Hodograph Techniques Applied To Sodium Lidar Data, Neal R. Criddle

All Graduate Theses and Dissertations, Fall 2023 to Present

Atmospheric gravity waves are ubiquitous and important events in Earth’s atmosphere with impacts on space weather and associated technological effects. The population of gravity waves is determined by their formation mechanisms, and their interactions with the background atmosphere. These gravity waves transport energy and momentum into the near Earth space environment, and are responsible for movement of chemical species. Predicting the occurrence of space weather effects, then, is in part a process requiring the characterization of gravity waves. Case studies of unique and interesting gravity wave events are an important part of this process. These allow for the investigation of …

Immune Variation Across Different Contexts In Non-Model Systems, Kwanho Claudia Ki

All Graduate Theses and Dissertations, Fall 2023 to Present

The immune system is important to an animal’s survival against disease-causing agents and physical injuries. Accordingly, many resources are required to maintain and activate the immune system (such as energy). However, as these resources also need to be shared with other important systems of the body, the portion of resources that can be allotted to the immune system is variable. Thus, many different factors may alter how well the immune system operates. My dissertation sought to understand what sorts of factors can lead to changes in the immune system. Reptiles are known to have a very robust immune system. Therefore, …

From Pasture To Plate: Striking An Omega Balance Between Grass-Fed And Grain-Fed Beef Ribeyes - Fatty Acid Composition, Minerals, Soil, And Forage Analysis, Travis Earl Statham

All Graduate Theses and Dissertations, Fall 2023 to Present

Most beef cattle in the US are feedlot-finished where intensive feeding of grains is used to increase weight and yield; however, a minority are raised in grass-fed operations that use exclusive pasture, rangeland, and hay for feeding, possibly leading to benefits for the land, soil, ecosystems, forages, and the meat itself. These operations use a variety of methods, and the goal of this was to recognize differences in the soil and forage metrics to help understand the resulting meat fatty acid composition and mineral content. We collected these samples from 78 sets of farmers while testing 25 sets of grain-fed …

Feature Selection In Multivariate Time Series Data For Enhanced Solar Flare Classification, Yagnashree Velanki

All Graduate Theses and Dissertations, Fall 2023 to Present

Solar flares are powerful eruptions of energy from the Sun that can cause disruptions to technology here on Earth, like communication systems, GPS, and power grids. To help manage these risks, it’s important to accurately identify and classify these solar flares before they cause problems. In our research, we focused on improving how we classify solar flares by looking at large sets of complex data collected over time. We used several techniques to find the most important factors that help us tell different types of solar flares apart. Each method has its strengths, so instead of relying on just one, …

Mathematical And Statistical Methods To Harness Limited Data In Models For Ecological Space Use Under Global Change, Sarah C. Bogen

All Graduate Theses and Dissertations, Fall 2023 to Present

The dynamics of how plants and animals use space in their habitats has important implications for the fields of ecology and conservation. However, understanding and responding to these spatial and temporal dynamics is often limited by data availability, financial resources and biases. As average global temperatures increase, suitable habitats shift poleward and require local populations to move with suitable habitat, adapt to the changing environment, or risk extinction. Capacity to persist without movement may be estimated by considering changes to a combination of habitat characteristics. Capacity to track suitable habitat may be modeled through synthesizing information on species demographic mechanisms …

Supervised Generative Adversarial Networks For Time Series Generation In Embedding Space, Mohammadreza Eskandarinasab

All Graduate Theses and Dissertations, Fall 2023 to Present

Time series data, such as weather forecasts, stock market trends, or heart rate monitors, plays a vital role in many areas of our lives. However, creating realistic synthetic time series data for research and testing purposes has been a significant challenge due to limitations in existing methods, which often struggle with accuracy and consistency. In this study, we developed two new approaches to generate high-quality time series data more effectively. The first method introduces a dual-feedback system that helps the model learn and replicate real data patterns more accurately by providing guidance at different stages of the learning process. The …

Environmental Dna Identifies Coastal Plant Community Shift 1,000 Years Ago In Torrens Island, South Australia, Nicole R. Foster, Alice R. Jones, Oscar Serrano, Anna Lafratta, Paul S. Lavery, Kor-Jent Van Dijk, Ed Biffin, Bronwyn M. Gillanders, Jennifer Young, Pere Masque, Patricia S. Gadd, Geraldine E. Jacobsen, Atun Zawadzki, Andria Greene, Michelle Waycott

Research outputs 2022 to 2026

Anthropogenic activities are causing detrimental changes to coastal plants– namely seagrass, mangrove, and tidal marshes. Looking beyond recent times to past vegetation dynamics is critical to assess the response and resilience of an environment to change. Here, we develop a high-resolution multi-proxy approach, providing a new evidence base to decipher long-term change in coastal plant communities. Combining targeted environmental DNA analysis with chemical analysis of soils, we reconstructed 4,000 years of change at a temperate wetland on Torrens Island South Australia and identified an ecosystem shift that occurred ~ 1000 years ago. What was once a subtidal seagrass system shifted …

Lessons Learned From Establishing And Running A Mössbauer Laboratory In Industry, Paulo De Souza

Research outputs 2022 to 2026

Mössbauer spectroscopy offers unique capabilities for primary industry sectors such as mining, mineral processing, and steelmaking, as well as in environmental services and advanced manufacturing. However, there are three key limiting factors: the time required to record a single spectrum, the challenges of managing an additional radioactive source on company premises, and the lack of personnel skilled in analysing Mössbauer spectra and understanding its operation. More commonly used techniques such as XRD, SEM, or XRF have technical staff who can interpret data with support from standard libraries and user-friendly software packages. In contrast, Mössbauer spectroscopists, who often hold degrees in …

Genome-Wide Cross-Disease Analyses Highlight Causality And Shared Biological Pathways Of Type 2 Diabetes With Gastrointestinal Disorders, Emmanuel O. Adewuyi, Tenielle Porter, Eleanor K. O’Brien, Oladapo Olaniru, Giuseppe Verdile, Simon M. Laws

Research outputs 2022 to 2026

Studies suggest links between diabetes and gastrointestinal (GI) traits; however, their underlying biological mechanisms remain unclear. Here, we comprehensively assess the genetic relationship between type 2 diabetes (T2D) and GI disorders. Our study demonstrates a significant positive global genetic correlation of T2D with peptic ulcer disease (PUD), irritable bowel syndrome (IBS), gastritis-duodenitis, gastroesophageal reflux disease (GERD), and diverticular disease, but not inflammatory bowel disease (IBD). We identify several positive local genetic correlations (negative for T2D – IBD) contributing to T2D’s relationship with GI disorders. Univariable and multivariable Mendelian randomisation analyses suggest causal effects of T2D on PUD and gastritis-duodenitis and …

Engineered Microalgae Cultivations Systems: Conversion Of Wastewater Nutrients Into Biofuels And Bioplastics, Jacob Watkins

All Graduate Theses and Dissertations, Fall 2023 to Present

Dissolved Nitrogen and Phosphorus in wastewater can contribute to harmful algae blooms if released into the environment. One technology that can be used to recover dissolved nutrients from wastewater is the Rotating Algae Biofilm Reactor (RABR), which supports microalgae growth in an easily-harvested biofilm and produces nitrogenand phosphorus-rich biomass that can be used to produce slow-release fertilizers, biofuels, and compostable bioplastics. This thesis (1) examines the effects of several environmental factors on the biomass production rate and nutrient removal efficiency of RABRs treating municipal wastewater, (2) quantifies the composition and biofuel yields of microalgae biomass cultivated using a RABR at …

Analysis Of An Outdoor Pilot-Scale Rotating Algae Biofilm Reactor For Power Optimization, Ash-Enhanced Productivity, And Nutrient Uptake, Peter F. Jeppesen

All Graduate Theses and Dissertations, Fall 2023 to Present

Outdoor testing of a rotating algae biofilm reactor (RABR) was performed to see how well it could remove nutrients from water and produce algae. By adjusting the operation settings, we found the lowest power needed to remove nitrogen and phosphorus. The lowest power values needed were 1.36 kWh per kilogram of nitrogen and 20.1 kWh per kilogram of phosphorus. The algae production rate reached a maximum of 7.09 grams per square meter per day. Detailed analysis showed that the reactor worked like a continuous flow system, and the performance was influenced by factors including light and temperature. The results also …

Quantifying The Impact Of Rain-On-Snow Induced Flooding In The Western United States, Emma M. Watts

All Graduate Theses and Dissertations, Fall 2023 to Present

Serious flooding can happen when rain falls on snow, which we call a rain-on-snow (ROS) event. Increasing our understanding of the behavior of floods resulting from ROS events can help us design better systems to manage flood water and prevent it from causing damage. This thesis explores how ROS events affect streamflow in the Western United States by examining the weather conditions that precede a streamflow surge. We classify stream surges as ROS or non-ROS induced based on these weather conditions, which helps us separate floods caused by ROS events from those caused by other factors. By comparing these different …

Impact Of Snow Accumulation On Structural Integrity: Present And Future Perspectives, Kenneth K. Pomeyie

All Graduate Theses and Dissertations, Fall 2023 to Present

In the United States, accommodating the weight of accumulated snow on buildings is a crucial consideration in building design. Engineers are tasked with determining the design snow load, which is defined as the weight of accumulated snow that a structure should withstand to limit the risk of building collapse to an acceptably low level. Typically, this process involves analyzing historical data of the annual maximum snow accumulations for each snow season. However, accurately assessing these design snow loads entails navigating through a series of statistical challenges. This dissertation, composed of three papers, is dedicated to addressing these statistical hurdles in …

Testing For Patterns Of Deformation From The Yellowstone Hotspot Along The Gallatin River, Sw Montana, Jack Willard

All Graduate Theses and Dissertations, Fall 2023 to Present

Yellowstone has fascinated humans for thousands of years. Geologists have addressed many of the region’s mysteries, including the underlying mantle hotspot, the chain of calderas tracking the motion of the North American Plate over this hotspot, and the risks posed by the super volcano. However, the way that the hotspot impacts regional tectonics and topography remains under-studied. Influential previous work recognized the Yellowstone Crescent of High Terrain (YCHT), an arc of high topography around the Yellowstone Plateau with limbs extending to the west and south into central Idaho and northern Utah. The YCHT is also hypothesized to be the pattern …

Data-Driven Techno-Economic Analysis, Optimization, And Uncertainty Quantification Of Integrated Energy Systems In Deregulated Electricity Markets, Jacob A. Bryan

All Graduate Theses and Dissertations, Fall 2023 to Present

Electricity is a ubiquitous energy source in daily life, powering everything from stovetops and cellphones to vehicles and industrial processes. While wind and solar power have become increasingly common sources of electricity, the majority of electricity is still produced by burning fossil fuels, releasing greenhouse gases and propelling climate change. Wind and solar power cannot economically replace these fossil fuel energy sources on their own because they do not produce consistent power; the wind must be blowing, and the sun must be shining for them to make electricity. Nuclear power is a reliable source of energy that does not generate …

Constraining Decadal-Scale Erosion And Delivery Of Post-Wildfire Debris Flow Deposits, Casey Langstroth

All Graduate Theses and Dissertations, Fall 2023 to Present

Debris flows generated from wildfire pose significant risk to increased sedimentation to instream river networks, degradation of water quality, and accumulated sediment behind downstream reservoirs. Despite an abundance of research investigating the probability of debris flow generation, the constraints on deposit initial volume, and most recently the initial grain size distribution, there remains a significant knowledge gap in understanding the temporal scale at which debris flows supply sediment to river networks after deposition. To provide reliable estimates of sediment delivery from debris flow deposits over time, two important metrics must be constrained: 1) how does sediment delivery to river networks …

Interpretable And Robust Deep Anomaly Detection, He Cheng

All Graduate Theses and Dissertations, Fall 2023 to Present

Anomaly detection is crucial in fields like cybersecurity, healthcare, and finance, as it helps identify unusual or potentially harmful events in data. With the rise of deep learning, advanced models have been developed for anomaly detection, but they often operate as "black boxes" that lack transparency and can be susceptible to malicious attacks. My research addresses these issues by creating methods that make deep learning-based anomaly detection more understandable and by investigating how such models can be compromised by backdoor attacks.

To improve transparency, I propose three methods that explain how these models detect anomalies. The first method, called Anomalous …