Digital Commons Network^™

Advanced Multiscale Molecular Dynamics Simulations Of Amorphous Polymers, Sahar Zenoozi

USF Tampa Graduate Theses and Dissertations

Polymers are in a wide range of material forms with various resources, including natural to synthetic processes. Polymers consist of covalently bonded monomers to each other. The chain length of polymers varies from a few monomers to thousands of monomers. This wide range of chain length enables polymers with attractive capabilities of chemical and physical properties. Thus, polymers are highly attractive in different scientific and industrial applications such as drug delivery, optical coatings, catalysts, semiconductors and organic photovoltaics. This work has combined updated accurate methods for accurate initial conformations, and modified force field parameters to produce a generalized method for …

Faculty Senate Monthly Packet November 2023, Portland State University Faculty Senate

Faculty Senate Monthly Packets

The November 6, 2023 monthly packet includes the November agenda, appendices, and the Faculty Senate minutes and attachments from the meeting held November 6, 2023.

The Geologic History Of Primary Productivity, Peter W. Crockford, Yinon M. Bar On, Luce M. Ward, Ron Milo, Itay Halevy

Geosciences: Faculty Publications

The rate of primary productivity is a keystone variable in driving biogeochemical cycles today and has been throughout Earth’s past.¹ For example, it plays a critical role in determining nutrient stoichiometry in the oceans,² the amount of global biomass,³ and the composition of Earth’s atmosphere.⁴ Modern estimates suggest that terrestrial and marine realms contribute near-equal amounts to global gross primary productivity (GPP).⁵ However, this productivity balance has shifted significantly in both recent times⁶ and through deep time.^7,8 Combining the marine and terrestrial components, modern GPP fixes ≈250 billion tonnes of carbon …

The Influence Of A Supplemental Mathematics Course To 9th Grade Algebra 1 Students In A Medium Suburban K-12 School District In New Jersey, Jacob Cavins

Seton Hall University Dissertations and Theses (ETDs)

Math performance became an increasing concern in the United States after the launch of Sputnik in 1957. This concern began with attempts to prescribe mathematical standards in the United States to improve student mathematics preparation. When the COVID pandemic began in 2020, policies on quarantining and remote learning were implemented, resulting in increased education gaps. The most contemporary NAEP report shows the first decline in math scores in the United States since the inception of the NAEP. Districts are looking for solutions. Districts are exploring intervention options, including Multi-Tiered Support Systems and Response to Intervention initiatives. They hope to reduce …

System-Level Noise Performance Of Coherent Imaging Systems, Derek J. Burrell, Joshua H. Follansbee, Mark F. Spencer, Ronald G. Driggers

Faculty Publications

We provide an in-depth analysis of noise considerations in coherent imaging, accounting for speckle and scintillation in addition to “conventional” image noise. Specifically, we formulate closed-form expressions for total effective noise in the presence of speckle only, scintillation only, and speckle combined with scintillation. We find analytically that photon shot noise is uncorrelated with both speckle and weak-to-moderate scintillation, despite their shared dependence on the mean signal. Furthermore, unmitigated speckle and scintillation noise tends to dominate coherent-imaging performance due to a squared mean-signal dependence. Strong coupling occurs between speckle and scintillation when both are present, and we characterize this behavior …

A Definition Of Reliable Water Supply For Public Water Systems, Easton Hopkins

Theses and Dissertations

"Reliable water supply" does not have a universal definition in Utah, or the Western United States, where water resources are limited and such a definition would be especially useful. Utah's three water agencies and 500 public water systems have no consistent method to define, evaluate, and report it, potentially leading to an inability to meet regulatory water demands. We propose a unified definition of reliable water supply for Utah's public water suppliers that can also be used elsewhere. The qualitative definition we propose is necessary to precede quantitative evaluations, set policy, and provide consistency to water resources management in Utah. …

The Age Of Synthetic Realities: Challenges And Opportunities, João Phillipe Cardenuto, Jing Yang, Rafael Padilha, Renjie Wan, Daniel Moreira, Haoliang Li, Shiqi Wang, Fernanda Andaló, Sébastien Marcel, Anderson Rocha

Computer Science: Faculty Publications and Other Works

Synthetic realities are digital creations or augmentations that are contextually generated through the use of Artificial Intelligence (AI) methods, leveraging extensive amounts of data to construct new narratives or realities, regardless of the intent to deceive. In this paper, we delve into the concept of synthetic realities and their implications for Digital Forensics and society at large within the rapidly advancing field of AI. We highlight the crucial need for the development of forensic techniques capable of identifying harmful synthetic creations and distinguishing them from reality. This is especially important in scenarios involving the creation and dissemination of fake news, …

An Ontology Design Pattern For Representing Causality, Utkarshani Jaimini, Cory Henson, Amit Sheth

Publications

The causal pattern is a proposed ontology design pattern for representing the structure of causal relations in a knowledge graph. This pattern is grounded in the concepts defined and used by the CausalAI community i.e., Causal Bayesian Networks and do-calculus. Specifically, the pattern models three primary concepts: (1) causal relations, (2) causal event roles, and (3) causal effect weights. Two use cases involving a sprinkler system and asthma patients are provided along with their relevant competency questions.

Oregon State Rank Assessment For Leopard Dace (Rhinichthys Falcatus), Misty Nelson

Institute for Natural Resources Publications

Oregon state conservation status assessment for leopard dace (Rhinichthys falcatus) using NatureServe methodology, 2023.

Trace Metal Cycling During Phytoplankton Growth In The Southern Ocean, North Pacific, And Tampa Bay, Shannon Michelle Burns

USF Tampa Graduate Theses and Dissertations

The trace metals iron (Fe), manganese (Mn), cobalt (Co), nickel (Ni), copper (Cu), zinc (Zn), and cadmium (Cd) are essential to primary production in the oceans. They act as micronutrients, used in intracellular enzymes for macronutrient acquisition, light harvesting, and mediation of reactive oxygen species. In some cases, they can also substitute for each other when a primary trace metal micronutrient is depleted. Characterizing the interplay amongst trace metals, macronutrients, and phytoplankton growth is vital for understanding the biogeochemical underpinnings of primary production, and for modelers who develop biological pump frameworks for global carbon cycling.

In Chapter two, I investigated …

Integrating Embeddings From Multiple Protein Language Models To Improve Protein O-Glcnac Site Prediction, Suresh Pokharel, Pawel Pratyush, Hamid D. Ismail, Junfeng Ma, Dukka Kc

Michigan Tech Publications

O-linked β-N-acetylglucosamine (O-GlcNAc) is a distinct monosaccharide modification of serine (S) or threonine (T) residues of nucleocytoplasmic and mitochondrial proteins. O-GlcNAc modification (i.e., O-GlcNAcylation) is involved in the regulation of diverse cellular processes, including transcription, epigenetic modifications, and cell signaling. Despite the great progress in experimentally mapping O-GlcNAc sites, there is an unmet need to develop robust prediction tools that can effectively locate the presence of O-GlcNAc sites in protein sequences of interest. In this work, we performed a comprehensive evaluation of a framework for prediction of protein O-GlcNAc sites using embeddings from pre-trained protein language models. In particular, we …

Investigating Mobility In The Northern Balkans During The Fifth Millenium Bc Through Strontium Analysis Of Human Tooth Enamel, Aurélien Tafani

USF Tampa Graduate Theses and Dissertations

This research investigates how individual mobility among ancient populations in Romania during the Eneolithic, between 5000 and 4000 BC, may be related to the spread of the material culture known as Kodjadermen-Gumelniţa-Karonovo VI (KGK VI) that extended over most of southern Romania and Bulgaria. This work seeks to combine results on individual mobility with other lines of archaeological evidence to provide a better understanding of the social context and kinship relationships that were in place when these events took place.

Strontium isotopic analyses were performed on 130 individuals from two sites located in the southern Romania: 49 from Sultana and …

Wind Farm Optimization And Analysis Of Complex Wake Structures, Rubel Chandra Das

Mechanical Engineering ETDs

A high-fidelity computational solver was developed with direct numerical simulation (DNS), large eddy simulation (LES), and Concurrent Precursor Method (CPM) capabilities. Extensive validation ensured the solver's accuracy in modeling fluid dynamics, including the wake characteristics of both utility and miniature-scale wind turbines. Key performance statistics (e.g., velocity and turbulence intensity profiles) were compared against established theoretical, computational, and experimental results. The study examined the influence of ground clearance on turbine performance, comparing two scenarios with different hub heights. Results showed that larger ground clearance facilitates quicker wake recovery. Finally, the study uses a nine-turbine array model to explore wind farm …

Lessons Learned About Evaluating Fairness From A Data Challenge To Automatically Score Naep Reading Items, Maggie Beiting-Parrish, John Whitmer

Chinese/English Journal of Educational Measurement and Evaluation | 教育测量与评估双语期刊

Natural language processing (NLP) is widely used to predict human scores for open-ended student assessment responses in various content areas (Johnson et al., 2022). Ensuring algorithmic fairness based on student demographic background factors is crucial (Madnani et al., 2017). This study presents a fairness analysis of six top-performing entries from a data challenge involving 20 NAEP reading comprehension items that were initially analyzed for fairness based on race/ethnicity and gender. This study describes additional fairness evaluation including English Language Learner Status (ELLs), Individual Education Plans, and Free/Reduced-Price Lunch. Several items showed lower accuracy for predicted scores, particularly for ELLs. This …

Msis-Capaldi: Using Mathematical Models To Evaluate Strategies For Managing White-Nose Syndrome In Little Brown Bats, Julie Blackwood

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Long-Acting Cabotegravir And The Emergence Of Drug-Resistant Hiv, Katharine Gurski

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Utilizing Non-Negative Least Squares For Data-Driven Discovery Of Dynamics, Tracey G. Oellerich

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Modeling Student-Instructor Interactions To Predict Changes In Student Mindset, David Chan, Oyita Udiani, Rani Satyam, Miriah Dudley

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Effect Of Under-Reporting, Vaccine Efficiency And Social Behavior On Epidemic Progression, Samiran Ghosh, Samiran Ghosh

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Risk Management Meets Politics And The General Public: Is Risk Management Increasing Risk, Rodger Singley

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

An Integrated Pest Management Model Incorporating Prey Refuge And Movement Between Regions, Aashima Singh Sisodia, Timothy Comar

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Incorporating Adaptive Human Behavior Into Epidemiological Models Using Equation Learning, Austin Barton, Jordan Klein, Jonathan Greer, Kevin Flores, Patrick Haughey

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Computational Modeling Using A Novel Continuum Approach Coupled With Pathway-Informed Neural Networks To Optimize Dynein-Mediated Centrosome Positioning In Polarized Cells, Arkaprovo Ghosal, Padmanabhan Seshaiyar Dr., Adriana Dawes Dr., General Genomics Inc.

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

On Using The Information Index In Socio-Epidemiological Models, Bruno Buonomo

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

An Ode Model For Investigating The Sleep-Pain Relationship In Sickle Cell Disease, Quindel Jones, Angela Reynolds, Rebecca Segal, Reginald Mcgee

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Baa-Ttling Sore Mouth In Sheep With Mathematical Modeling, David C. Elzinga, W. Christopher Strickland

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Environmental, Ecological, And Epidemiological Applications: Introduction To Mathematical Modeling, Suzanne Sumner

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Understanding Impact Of Educational Awareness And Vaccines As Optimal Control Mechanisms For Changing Human Behavior In Disease Epidemics, Manal Badgaish, Dr. Padmanabhan Seshaiyer

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Parameter Estimation In Epidemiological And Climate Models Using Ensemble Smoothing With Multiple Data Assimilation, Emmanuel Fleurantin

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

A Multi-Model Approach To Understanding Growth, Reproduction, And Life History Strategies In Bromeliads, Erin N. Bodine

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.