Digital Commons Network^™

Advancing Simultaneous Extraction And Sequential Single-Particle Icp-Ms Analysis For Metallic Nanoparticle Mixtures In Plant Tissues, Lei Xu, Xingmao Ma, John Yang, Joel G. Burken, Paul Ki-Souk Nam, Honglan Shi, Hu Yang

Civil, Architectural and Environmental Engineering Faculty Research & Creative Works

Engineered Nanoparticles (ENPs) Have Been Increasingly Used in Agricultural Operations, leading to an Urgent Need for Robust Methods to Analyze Co-Occurring ENPs in Plant Tissues. in Response, This Study Advanced the Simultaneous Extraction of Coexisting Silver, Cerium Oxide, and Copper Oxide ENPs in Lettuce Shoots and Roots using Macerozyme R-10 and Analyzed Them by Single-Particle Inductively Coupled Plasma-Mass Spectrometry (ICP-MS). Additionally, the Standard Stock Suspensions of the ENPs Were Stabilized with Citrate, and the Long-Term Stability (Up to 5 Months) Was Examined for the First Time. the Method Performance Results Displayed Satisfactory Accuracies and Precisions and Achieved Low Particle Concentration …

“Use” As A Conscious Thought: Towards A Theory Of “Use” In Autonomous Things, Gohar Khan, A Karim Feroz

All Works

The way users perceive and use information systems artefacts has been mainly studied from the notion of behavioral beliefs, deliberate cognitive efforts, and physical actions performed by human actors to produce certain outcomes. The next generation of information systems, however, can sense, respond, and adapt to environments without necessitating similar cognitive efforts, physical contact, or explicit instructions to operate. Therefore, by leveraging theories of consciousness and technology use, this research aims to advance an alternative understanding of the "use" associated with the next generation of IS artefacts that do not require deliberate cognitive efforts, physical manipulation, or explicit instructions to …

Development Of An Experimentally Validated Computational Fluid Dynamics Model For A Pbi Membrane-Based Anhydrous Hcl Electrolyzer, Kris Likit-Anurak, Hunter R. Teel, Ishwor Karki, Ben I. Howard, Brian C. Benicewicz, Sirivatch Shimpalee, Benjamin H. Meekins

Faculty Publications

We report the development of an experimentally-validated computational fluid dynamics (CFD) model for simulation of an anhydrous HCl electrolyzer. The experimental data from 3 membrane variants was used to provide kinetic and membrane parameters for the model. The model not only accurately simulates overall electrolyzer performance, but it also provides key insights into the transport phenomena within the electrolyzer. The model allows simulation of experimental parameters like high HCl flowrates and increased cell pressure that pose a high safety risk to researchers. The model shows hotspots in the temperature distribution that will need to be addressed by flow field modification …

Tree Recovery By Dynamic Programming, Gustavo Alberto Gratacos

McKelvey School of Engineering Graduate Student Theses & Dissertations

Tree-like structures are common, naturally occurring objects that are of interest to many fields of study, such as plant science and biomedicine. Analysis of these structures is typically based on skeletons extracted from captured data, which often contain spurious segments or cycles that need to be removed. We propose a dynamic programming algorithm which seeks to recover directed trees from these noisy skeletons. Our method recovers trees by removing edges and duplicating nodes while adhering to edge-label constraints. Our algorithm proceeds by iteratively merging graph nodes, such that the solution on the original graph can be obtained from those on …

Impacts Of El Niño On The Florida Reef: A Case Study Of The 2016 El Niño Event, Evvie Yendra

Department of Environmental Studies: Undergraduate Student Theses

Coral reefs are vital ecosystems to coastal communities and the world’s oceans. They support other organisms, protect shorelines, and benefit coastal economies through fishing and recreation. Today, coral reefs face many threats, including ocean acidification, bleaching due to increased ocean temperatures, and disease. These threats are typically heightened during El Niño events across the globe. With a focus on the Florida Reef, these data encompass three key regions (Southeastern Florida, The Florida Keys, and Dry Tortugas) over the years 2014, 2016 (an El Niño event), and 2018. As 2024 is interpreted to be an El Niño year, this study predicts …

Strongly Stated And Loosely Held: Examining Stewart Brand's Role In The Ecomodernist Project, Liam J. Baker

Department of Environmental Studies: Undergraduate Student Theses

With the ecomodernist environmental perspective emerging in the wake of the 2015 publication of An Ecomodernist Manifesto, many researchers have sought to critique the ecomodernists and their theories of separating humanity from nature, intensifying agriculture, expanding energy production, and relying on technology to resolve the environmental challenges of the 21st century. In this paper, I add to these critiques by examining the history of Stewart Brand, one of the coauthors of An Ecomodernist Manifesto, to highlight connections between his personal environmental perspective, his material impacts, and the ecomodernist project as a whole. By analyzing the discourse produced by and about …

Analysis And Computation Of Constrained Sparse Coding On Emerging Non-Von Neumann Devices, Kyle Henke

Mathematics & Statistics ETDs

This dissertation seeks to understand how different formulations of the neurally inspired Locally Competitive Algorithm (LCA) represent and solve optimization problems. By studying these networks mathematically through the lens of dynamical and gradient systems, the goal is to discern how neural computations converge and link this knowledge to theoretical neuroscience and artificial intelligence (AI). Both classical computers and advanced emerging hardware are employed in this study. The contributions of this work include:

1. Theoretical Work: A comprehensive convergence analysis for networks using both generic Rectified Linear Unit (ReLU) and Rectified Sigmoid activation functions. Exploration of techniques to address the binary …

Sub-Stage Climatic Shifts During Mis 11 Refined From Diatom Assemblage Reconstruction In The Valles Caldera, New Mexico, Savannah Cutler

Earth and Planetary Sciences ETDs

Diatom assemblage reconstruction from the Valles Caldera sediment core (VC-3) was utilized to infer climatic and aquatic changes during a 50-thousand-year [ka] period in the Mid-Pleistocene (435-385 ka). This 50 ka interval spans most of Marine Isotope Stage 11 (MIS 11) – one of the most prominent interglacials of the past 500 ka – and is widely considered an analog for the Holocene and future climate regimes. Nearly all records from MIS 11 are either marine or ice-core based, making VC-3 unique among lacustrine sediment records as it captures insolation variations and climatic changes during the mid-Pleistocene. Analysis of the …

Building A Data Pipeline And Machine Learning Model For Insurance Data, Connor Weyers

Honors Program: Senior Projects (Public)

Insurance telematics is an emerging and exciting field. It combines the advancements in GPS tracking, computational analytics, data processing, and machine learning into a useful tool to help insurance companies make the best product for their consumers. This is why National Indemnity looked to implement a telematics portion to their business processes of underwriting insurance policies and sponsored a School of Computing Senior Design project. In this report, we will first review existing solutions that been used to solve problems and subproblems similar to that we are given in this project. We then propose designs for the data pipeline and …

Landscape Influences On Thermal Sensitivity And Predicted Spatial Variability Among Brook Trout Streams In The Southeastern Usa, George P. Valentine, Xinyi Lu, C. Andrew Dolloff, Craig N. Roghair, Jacob M. Rash, Mevin B. Hooten, Yoichiro Kanno

Mathematics and Statistics Faculty Publications

Warming water temperatures as a result of climate change pose a major threat to coldwater organisms. However, the rate of warming is not spatially uniform due to surface-ground-water interactions and stream and watershed characteristics. Coldwater habitats that are most resistant to warming serve as thermal refugia and identifying their locations is critical to regional aquatic conservation planning. We quantified the thermal sensitivity of 203 streams providing current and potential habitat for brook trout (Salvelinus fontinalis) across nearly 1000 linear km of their native range in the southern and central Appalachian Mountains region, USA, and characterized their spatial variability …

Assessing Reproducibility Of Brain-Behavior Associations Using Bootstrap Aggregation Methods, Zhetao Chen

Arts & Sciences Graduate Student Theses and Dissertations

在本论文中，随着越来越多地利用静息态功能连接 MRI (rs-fcMRI) 将神经活动与病理状况联系起来，我们面临着对此类数据可靠性的普遍担忧。我们的探索集中于提高人类连接组计划（HCP）数据集框架内大脑行为关联的可重复性。我们采用两种不同的引导聚合方法来研究功能连接可靠性的增强：使用循环块引导（CBB）的单独时间序列装袋和使用线性支持向量回归（LSVR）模型的主题级装袋。我们对 CBB 个体时间序列 bagging 的调查表明，这种方法并不能显着增强大脑行为关联的可重复性。这一发现指出了实现可靠的功能连接措施的复杂性以及某些聚合方法在克服这一挑战方面的局限性。相比之下，我们的学科水平考试 通过 LSVR 模型装袋呈现出更有希望的结果。这种方法显着增强了分析之间模型权重的可靠性，证明了其在提高数据稳健性和可重复性方面的功效。两种方法的这种不同影响强调了适当的分析策略在提高神经影像数据可靠性方面的关键作用。通过描述这两种方法的结果，本论文有助于对神经影像领域的数据可靠性进行更广泛的讨论。它强调了在不同数据集上持续进行方法创新和验证的必要性，以提高 rs-fcMRI 研究的可靠性和可解释性。

Thermal Physiology Of Sceloporus Olivaceus And Sceloporus Variabilis In South Texas, Ian Rockel

Masters Theses (Archived)

This study explores the thermal physiology of two sympatric lizard species, Sceloporus olivaceus (Texas spiny lizard) and Sceloporus variabilis (rose-bellied lizard), in South Texas. I document the metabolic rate and its temperature sensitivity, thermal limits, and performance at different temperatures to better understand the impact of rising temperatures and urbanization on these ectotherms, whose body temperature and, consequently, metabolic rate, activity level, and reproductive success depend on their thermal environment. We hypothesize that S. olivaceus will exhibit greater thermal resilience owing to its broader latitudinal range, variable habitat usage within Texas, and presumed more versatile thermoregulatory strategies. Scelorporus olivaceus's higher …

Avoiding Pitfalls In Molecular Simulation Of Vapor Sorption: Example Of Propane And Isobutane In Metal–Organic Frameworks For Adsorption Cooling Applications, Filip Formalik, Haoyuan Chen, Randall Q. Snurr

Physics & Astronomy Faculty Publications

This study introduces recommendations for conducting molecular simulations of vapor adsorption, with an emphasis on enhancing the accuracy, reproducibility, and comparability of results. The first aspect we address is consistency in the implementation of some details of typical molecular models, including tail corrections and cutoff distances, due to their significant influence on generated data. We highlight the importance of explicitly calculating the saturation pressures at relevant temperatures using methods such as Gibbs ensemble Monte Carlo simulations and illustrate some pitfalls in extrapolating saturation pressures using this method. For grand canonical Monte Carlo (GCMC) simulations, the input fugacity is usually calculated …

Burning Calories, Burning Ocean: Metabolic Rate In Bivalves As A Predictor Of Extinction Selectivity Through Time And During Rapid Global Warming, Siddharth Gavirneni

Theses - ALL

Organismal metabolic rate is linked to environmental temperature and oxygen consumption, and as such, may be a useful predictor of extinction risk during major climate- driven crises. However, metabolic attributes can be quantified in many ways, highlighting differing aspects of organisms’ ecology. Here, we estimate resting whole-body and mass-specific metabolic rates in post-Carboniferous bivalve taxa using body size and seawater paleotemperature to assess how metabolic rate determines survival both during and outside of intervals of rapid climate warming, or ‘hyperthermals’. Accounting for the effects of geographic range size, we find a pattern of preferential extinction of bivalves with lower total …

Stochastic Algorithms For Simulating Protein Assembly In Biological Cells, Advait Shukla

Theses - ALL

Understanding membrane protein assembly using computational methods is critical in developing drug delivery strategies for tight junction diseases such as Alzheimer’s and Crohn’s diseases. While experimental methods, such as freeze-fracture micrographs, provide microscopic details of the protein strand networks, they cannot offer molecular-level information, which is necessary for drug design. This work attempts to close the gap by computationally predicting strand networks of the claudin family of proteins that form tight junctions across neighboring cells in epithelial and endothelial tissues. Using claudin dimer data collected by the Protein AssociatioN Energy Landscape (PANEL) method coupled with some Markovian approximations, we built …

Development And Application Of Photoresponsive Small Molecule Probes To Modulate And Characterize Neuroreceptors, Spencer Kim

Dissertations - ALL

The field of neuroscience is rapidly evolving and so the development of novel tools that support innovative research is urgently needed. Two tools that have proven to be particularly impactful to the field of neuroscience are activity-based protein profiling (ABPP) and optogenetics, both of which have seen widespread application but with relatively limited advancement of the underlying technology. Limitations of ABPP and optogenetics have become increasingly apparent and research output is stalling due to lack of technological advancement. For example, few systems exist for targeting low-abundance and unstable proteins via ABPP and application of ABPP and optogenetic systems thus far …

Development And Progress Towards Functional Photoresponsive Systems, Jasmine Gomez

Dissertations - ALL

Chapter 2: Surface Functionalization of Thermally-Expandable Microspheres with Gold Nanoparticles The advancement of methods for controlling motion on a variety of scales is significant in order to develop finely tuned next-generation devices. Here, we’ve created a micron-scale actuator system triggered via photothermal activation and capable of powering macro-scale movement in an elastomer matrix. This system fundamentally relies on thermally-expandable microspheres (TEMs) – a core-shell complex containing a polymeric shell and liquid core that expands dramatically upon heating. To improve the ability of TEMs as soft-actuators controlled via light, we grafted a secondary silicate-silane copolymer shell to attach gold nanoparticles. The …

A Molecular Toolbox To Study Dopamine And Serotonin Receptors For The Development Of Improved Therapeutics, Emma Joanna Doukmak

Dissertations - ALL

Dopaminergic and serotonergic signaling pathways are involved in numerous biological processes including behavior, mood regulation, and cognition. Dysfunction in these pathways can lead to neurological and mental health disorders, which are often treated with drugs targeting the dopamine and serotonin receptors. However, many of these drugs, along with those targeting other G protein couple receptors (GPCRs), suffer a lack of target specificity, leading to nonspecific binding and therefore side effects. In recent years, new advances in chemical biological techniques, including affinity-based protein profiling (ABPP) and optogenetics, have further elucidated the structure and function of GPCRs, which can in turn aid …

Development And Application Of Small-Molecule Probes Targeting Ghrelin O-Acyltransferase, Jacob Moose

Dissertations - ALL

Ghrelin is a 28-amino acid peptide hormone that has wide-ranging physiological effects, including on metabolism, adipogenesis, insulin regulation, and addiction. Ghrelin offers an intriguing option for treatment of pathophysiologies related to these effects, as it requires a unique post-translational octanoyl modification to bind and activate its cognate receptor, growth hormone secretagogue 1a (GHSR). The enzyme responsible for this modification, ghrelin O-acyltransferase (GOAT) therefore offers the ability to modulate ghrelin signaling through inhibition of the maturation pathway. Due to a lack of structural or mechanistic information about GOAT, pharmaceutical development of molecules capable of GOAT inhibition has been desired, but few …

Agroecology And Soil Stewardship: Values And Techniques Of Smallholder Farmers In Bernalillo County, Stephanie Olivas

Geography ETDs

Agrarian movements around the world use agroecology to build sovereignty and steward dynamic ecosystems. Research has shown that agroecological farmers steward more resilient crops, more resilient soil biomes, and greater biodiversity than conventional agriculture. GIS and remote sensing offer many tools to detect the impacts of these farmers on the environment, but it is less clear how such technologies fit into agroecological goals. This study asks: what values, experiences and knowledge do smallholder producers in Bernalillo County embody in their soil stewardship practices? Also, what experience or knowledge do smallholder producers in Bernalillo County have about remote sensing, and would …

Molecular Dynamics Insights Into The Structural Behavior And Interactions Of Complex Biological Systems, Shenghan Song

Chemistry and Chemical Biology ETDs

All-atom molecular dynamics (MD) simulations are essential for examining the structural and dynamic aspects of proteins at high resolution, complementing experiments limited by resolution, size, and complexity. Advancements in algorithms and hardware have enhanced the role of computational tools in scientific research, allowing for more accurate simulations of proteins with standard residues. However, simulating real biological systems, which include non-standard residues such as lipid membranes, remains challenging despite the assistance of tools like CHARMM-GUI. My research initially focused on simulating the PICK1 BAR dimer using steered MD simulations to investigate its structure and dynamics. Simulation works expanded to include systems …

Directional Dopant Migration By ‘Atomic Trapping’ In Core/Multi-Shell Quantum Dots, Chun Chu

Dissertations - ALL

The study of transition metal ion-doped semiconductor nanocrystals (NCs) has attracted increasing attention due to their unique optical, electronic, and magnetic properties which sparked considerable interest towards a wide range of applications in material science, renewable energy and biological systems. Besides the size- and shape-dependent behavior, doped nanomaterials exhibit new and/or enhanced optical properties, which are sensitive to the dopant location or dopant distribution throughout the solid crystal lattice. Our work primarily focuses on understanding and elucidating the mechanism of dopant ion migration inside the NCs during post-synthetic treatments, such as shell passivation and high-temperature annealing. Mn(II) dopants migration behavior …

Defects And Deformation In Passive And Active Structural Glasses, Julia Ann Giannini

Dissertations - ALL

Glasses and disordered granular media represent a class of materials that are quite familiar to us, from the glass in windows and phone screens, to piles of fruits, grains, and sand. Further, living and active systems such as cellular tissues, collections of robots, and even human crowds behave as disordered solids when they are gathered at high enough densities. Despite their ubiquity, there are still many behaviors of these amorphous systems that lack a full understanding. Contrasting crystalline solids, the thermodynamic, vibrational, energetic, and mechanical properties of glasses are not well-characterized by solid state theory. In the case of active …

Comparison Of Various Theoretical Measures Of Aromaticity Within Monosubstituted Benzene, Caleb K. Swain, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

The effects of monosubstitution on the aromaticity of benzene are assessed using a number of different quantitative schemes. The ability of the mobile π-electrons to respond to an external magnetic field is evaluated using several variants of the NICS scheme which calculate the shielding of points along the axis perpendicular to the molecule. Another class of measures is related to the drive toward the uniformity of C-C bond lengths and strengths. Several energetic quantities are devised to approximate an aromatic stabilization energy and the tendency of the molecule to maintain planarity. There is a lack of consistency in that the …

Statistical Approaches For The Early Detection Of Colorectal Cancer Using Longitudinal Biomarkers, Emily Berry

Statistical Science Theses and Dissertations

Colorectal cancer (CRC) is the third leading cause of cancer-related death in the United States [45]. CRC is believed to advance from adenomatous polyps creating a unique opportunity for both early detection and cancer prevention [4, 23]. Like other diseases, CRC screening reduces mortality by detecting cancer at earlier, more treatable stages; however, it can also reduce incidence through the removal of precancerous lesions [4]. As a result, screening is recommended for average-risk adults ≥ 45 years of age and includes a variety of tests [4, 12]. Despite alternate screening options, colonoscopy capacity is often cited as a barrier to …

Paleoecology Of The Late Cretaceous Western Interior Seaway And Gulf Coastal Plain, Ceara Kathleen Quinn Purcell

Earth and Planetary Sciences ETDs

This dissertation presents research into the paleobiogeography and paleoecology of the Western Interior Seaway (WIS) and Gulf Coastal Plain (GCP) during the Late Cretaceous. The dataset utilized here includes an extensive record of marine invertebrates from over 200 years of fossil collecting and sedimentary data collated from over 45 different literature sources, representing approximately 17 million years of deposition. The high-resolution of this dataset, and its extensive geographic distribution and temporal duration, make it ideal for exploring various ecological questions. Using these data, I have attempted to reconstruct paleobiogeographic provinces as published in prior works, explore functional diversity patterns, and …

The Geology And Geochemistry Of The Western Iron Ore Group Greenstone Belt, Singhbhum Craton, Eastern India, Jordan Wright

Earth Sciences Theses and Dissertations

This thesis presents new data on the origin of the Western Iron Ore Group (W-IOG), a Paleoarchean succession deposited on sialic rocks of the Singhbhum Craton. U-Pb ages from zircons from a tuff overlying the Lower Shales just below a banded iron formation (BIF) pin the age of the section to 3.39 Ga. Unconformably overlying the whole IOG section is the Darjing Group, which contains the Birtola Sandstone (on the basis of this work, now estimated to be 2.35 Ga). The lack of penetrative deformation and low-grade metamorphism makes these rocks excellent subjects for combined radiogenic and stable isotope studies. …

Advancing Coupled Cluster Methods: Tensor Factorization And Analytic Gradient Implementation, Tingting Zhao

Chemistry Theses and Dissertations

With the rapid advancement of computing capabilities, computational chemistry has become increasingly indispensable in both experiment design and the interpretation of experimental outcomes. Wave-function-based quantum mechanistic methods are highly sought after for their ability to provide high-accuracy data and their potential for systematic improvement. However, to extend their applicability to larger molecules, it is essential to employ rank-reducing approximations to these methods. This dissertation dedicates Chapters Three and Four to the development of rank-reduced methodologies. Additionally, beyond single-point energies, molecular geometries and properties of molecule-excited states hold paramount importance across diverse fields of chemistry. Hence, Chapter Five presents the work …

Exploring The Complex Landscape Of Proteins: From Intrinsically Disordered Proteins To Peptidomimetics Through Computational Approaches, Tongtong Li

Chemistry and Chemical Biology ETDs

Protein function is closely related to their three-dimensional structures. However, some proteins lack a well-defined structure, so-called intrinsically disordered proteins (IDPs). They prefer to interconvert among different conformations in isolation and undergo a disorder-to-order transition upon binding to a partner. IDPs or proteins with intrinsically disordered regions (IDRs), constituting a large portion of the human proteome, are involved in many cellular activities and are therefore highly relevant to our health. In my dissertation, I used computational methods to systematically study systems including dynamic proteins, disordered proteins in complex with their targets, and synthetic peptidomimetics to reveal the unique physical properties …

Investigating The Effects Of Suspended Algal Content, Dissolved Oxygen, And Temperature On A High-Frequency Acoustic Attenuation System In A Controlled Laboratory Environment, Noah Watson

Honors Theses

The Single Frequency Acoustic Attenuation System (SFAAS) has been developed at the National Center for Physical Acoustics (NCPA). This system uses acoustic methods to monitor fine suspended sediment concentration in streams. Site-specific calibrations are necessary for this system, and previous research has indicated that algal concentration or dissolved oxygen concentration of water may affect collected data. Temperature, dissolved oxygen concentration, and fluorescence, used as a proxy for algal concentration, were monitored during this system’s use, and calibrations were derived to account for the effect of each of these variables on acoustic measurements. It has been shown that temperature has a …