Physical Sciences and Mathematics Commons^™

Dft Modeling Of Water-Assisted Hydrogen Peroxide Formation From A C(4a)-(Hydro)Peroxyflavin, Yilmaz Özkiliç

Turkish Journal of Chemistry

The cofactor of a class A monooxygenase is reduced at an external location of the enzyme and is subsequently pulled back into the active site after the reduction. This observation brings the question; is there any defense mechanism of the active site of a monooxygenase against the formation of the harmful hydrogen peroxide from the reactive C(4a)-(hydro)peroxide intermediate? In this study, the barrier energies of one to three water molecule-mediated uncoupling reaction mechanisms in water exposed reaction conditions were determined. These were found to be facile barriers. Secondly, uncoupling was modeled in the active site of kynurenine 3-monooxygenase complex which …

Design And Characterization Of Phosphonic Acid-Functionalized Grafted Sepiolite Nanohybrids And Their Adsorption Studies For Removal Of Copper Ions From Aqueous Solution, Mehwish Tahir, Asif Raza, Amara Nasir, Tariq Yasin, Shamila Imtiaz

Turkish Journal of Chemistry

In this study, we synthesized novel, economically efficient phosphonic acid-functionalized grafted sepiolite nanohybrids for selective elimination of copper ions from water. These nanohybrids were prepared by graft polymerization of glycidyl methacrylate onto sepiolite. We utilized free radical graft polymerization to graft glycidyl methacrylate (GMA) onto silanized sepiolite. The nanohybrids obtained exhibited a grafting percentage of 479% at 0.3 g of KPS initiator, 15% GMA monomer, and after 4 h of reaction. In pursuit of selectively removing metal ions from water, the nanohybrid with the highest grafting (PGE3) was chemically treated with phosphoric acid to introduce phosphonic acid groups on it. …

Fundamental Mechanisms Of Energy Exchanges In Autonomous Measurements Based On Dispersive Qubit-Light Interaction, Nicolò Piccione, Maria Maffei, Xiayu Linpeng, Andrew N. Jordan, Kater W. Murch, Alexia Auffèves

Mathematics, Physics, and Computer Science Faculty Articles and Research

Measuring an observable which does not commute with the Hamiltonian of a quantum system usually modifies the mean energy of this system. In an autonomous measurement scheme, coupling the system to a quantum meter, the system's energy change must be compensated by the meter's energy change. Here, we theoretically study such an autonomous meter-system dynamics: a qubit interacting dispersively with a light pulse propagating in a one-dimensional waveguide. The phase of the light pulse is shifted, conditioned to the qubit's state along the 𝑧 direction, while the orientation of the qubit Hamiltonian is arbitrary. As the interaction is dispersive, photon …

Scale-Dependent Effects Of Urban Canopy Cover, Canopy Volume, And Impervious Surfaces On Near Surface Air Temperature In Portland, Or, Carson Ralls

Geography Masters Research Papers

Cities are significantly warmer than their surrounding rural environments. Known as the ‘urban heat island effect’, it can affect the health of urban residents and lead to increased energy use. Although this effect is extensively researched, less is known about how landscape characteristics within cities affect local temperature variation. With a warming climate and the need for heat mitigation strategies becoming more urgent, having a finer detailed understanding of the effects on temperature is critical to guide proper management policies. This study examined how tree canopy cover, canopy volume, and impervious surface cover affect daytime near surface air temperature, and …

Mapping Mental Models Through An Improved Method For Identifying Causal Structures In Qualitative Data, Erin S. Kenzie, Wayne Wakeland, Antonie Jetter, Kristen Hassmiller Lich, Mellodie Seater, Melinda M. Davis

Complex Systems Faculty Publications and Presentations

Qualitative data are commonly used in the development of system dynamicsmodels, but methods for systematically identifying causal structures in qualita-tive data have not been widely established. This article presents a modifiedprocess for identifying causal structures (e.g., feedback loops) that are commu-nicated implicitly or explicitly and utilizes software to make coding, tracking,and model rendering more efficient. This approach draws from existingmethods, system dynamics best practice, and qualitative data analysis tech-niques. Steps of this method are presented along with a description of causalstructures for an audience new to system dynamics. The method is applied to aset of interviews describing mental models of …

Effect Of Quince Seed Gum (Qsg) On The Performance Of Injectable Hyaluronic Acid Hydrogels In Terms Of The Rheological, Morphological, And Mechanical Aspect, Serdar Kolay, Ni̇lhan Kayaman Apohan, Erdi̇nç Babuç, Gökay Gün

Turkish Journal of Chemistry

Injectable hydrogels play an important role in tissue engineering as a filling and repairing material. This study aimed to develop a new injectable hydrogel based on hyaluronic acid (HA) and quince seed gum (QSG) and investigate the effect of QSG on hydrogel performance. The amount of unreacted 1,4-Butanediol diglycidyl ether (BDDE) is maintained at an undetectable level for HA-QSG hydrogels. Amino acid analysis showed that the HA-QSG hydrogel had rich amino acid concentrations of leucine, arginine, and valine. After thermal sterilization, the elastic modulus of HA-QSG gels for dermal and intra-articular filler applications is 63 Pa and 92 Pa respectively. …

Theoretical Study On The Insertion Reaction Of The Stannylenoid H2snlif With X-H Bonds (X = N, O, F), Shuo Wu, Bingfei Yan, Shaoli Liu, Wenzuo Li

Turkish Journal of Chemistry

The insertion reactions of p-complex (RP) and three-membered ring configuration (RS) of stannylenoid H2SnLiF with NH3, H2O and HF have been studied theoretically by quantum chemical calculation. The structures of reactants, precursors, transition states, intermediates and products have been fully optimized at the M06-2X/def2-TZVP level. The single point energy of all fixed points were calculated using the QCISD method. The calculation results show that the three-membered ring configuration is easier to conduct the insertion reaction. Comparing the reaction energy barriers of RP, RS to NH3, H2O and HF, we found that the difficulty of the insertion reaction is NH3 > H2O …

Rapid Synthesis Of Azoindolizine Derivatives Via Aryldiazonium Salts, Ferruh Lafzi̇

Turkish Journal of Chemistry

A practical, rapid, and efficient method for the synthesis of azoindolizine derivatives via aryldiazonium salts with excellent yields was reported. Firstly, the corresponding aniline derivatives were synthesized via a simple and rapid method. Then, the optimal reaction conditions were investigated using a variety of protic and aprotic solvents that demonstrating the robustness of the approach. Finally, the applicability of this method to various sources of indolizine and phenyldiazonium tetrafluoroborate salts was expanded.

Modeling Exciton Delocalization And Transport In Pdbd-T-2f With The Line-Dipole Improvement For Coupling Calculation, Brian Dvorak

College of Science and Health Theses and Dissertations

A non-atomistic representation of the conjugated polymer PDBD-T-2F was constructed to model exciton delocalization and transport in the material. A Hamiltonian was built in the site basis to model the energy transfer, using excitation energies calculated using density functional theory and inter-site through-space coupling values calculated with either density functional theory or the newly integrated line-dipole approximation. The Hamiltonian allowed calculation of the excitation energies available for each system, prediction of the absorption spectrum, and simulation of the dynamics of exciton transport. For realistic crystal sizes at room temperature, the model predicts a band gap at 1.9 eV with decreasing …

Final Butte Priority Soils Operable Unit (Bpsou) Unreclaimed (Ur) Sites: Ur-35 Remedial Action Work Plan (Rawp), Pioneer Technical Services, Inc.

Silver Bow Creek/Butte Area Superfund Site

No abstract provided.

The Institutional Challenges Of A Quantified Self Study: An Attempt To Ascertain How Data Collected From A Mobile Device Can Be An Indicator Of Personal Mental Health Over Time, Julian Lazaras

University Honors Theses

The adoption of an application of new technology always comes with a bias, this is never more true for the case of human behavioral analytics within higher education. While movements such as the quantified self movement make strides to reinterpret the realm of data analytics, psychology, and computer science, there are inevitably limitations to the adoption and application of such approaches within the standard realm of research. Herein is presented a case where an effort to evaluate the prospect of use of mobile phone data as secondary indicators of personal mental health through the lens of data analysis was put …

Cards With Class: Formalizing A Simplified Collectible Card Game, Dan Ha

University Honors Theses

Collectible card games (CCGs) have been a wildly popular game genre since the release of Wizards of the Coast's Magic: The Gathering. These games revolve around their thousands of cards and the hundreds of thousands of interactions they can create with their many effects. For designers, it is an incredibly demanding task to ensure that every single card works properly and that each card's text unambiguously conveys its intended behavior in all cases. The task only grows more difficult over time as the number of cards in the game grows and card effects become more complex or experimental. If the …

Evaluating The Influence Of Perfluorooctane Sulfonic Acid Exposure On Blood Glucose Levels: A Comprehensive Multiple Regression Analysis Considering Confounding Factors, Henry Mensah

Theses and Dissertations

Perfluorooctane sulfonate (PFOS) are widely used for industrial and commercial purposes and have received increasing attention due to their adverse effects on health. This thesis investigates the relationship between PFOS exposure and blood glucose levels, considering potential confounding factors. Regression analysis was conducted on a dataset comprising demographic, lifestyle, and biomarker data from a diverse population sample. Sex exhibited a significant role, with females demonstrating an 11.77% increase in blood glucose levels in response to PFOS exposure compared to males, supported by a p-value of 1.04 × 109. Body mass index (BMI) also played a pivotal role, revealing a 2.17% …

Heterogeneous Resources In Infrastructures Of The Edge Network Paradigm: A Comprehensive Review, Qusay S. Alsaffar, Leila Ben Ayed

Karbala International Journal of Modern Science

The late 1990s saw the rise of the edge computing network paradigm, as well as an increase in the number of IoT de-vices. This concept is viewed as a link between cloud servers and end-devices, bringing processing and storage re-sources closer to clients. As a result of its low latency and high performance, researchers and developers have expressed interest in it. However, this paradigm confronts a number of obstacles and restrictions, including restricted and hetero-geneous resources at network edges. In this paper, we provide a detailed review of heterogeneous resources in edge network infrastructures using a three-dimensional method. These three …

Classification And Removal Of Hazy Images Based On A Transmission Fusion Strategy Using The Alexnet Network, Roa'a M. Al-Airaji, Haider Th. Salim Alrikabi, Rula Kamil

Karbala International Journal of Modern Science

Outdoor images are used in many domains, such as surveillance, geospatial mapping, and autonomous vehicles. The occurrence of noise in outdoor images is a widely observed phenomenon. They are primarily attributed to extreme natural and manufactured meteorological conditions, such as haze, smog, and fog. In autonomous vehicle navigation, recovering the ground truth image is essential, enabling the system to make more informed decisions. Accurate air-light and transmission map calculation is vital in recovering the ground truth image. An efficient approach for image dehazing that utilizes the mean channel prior (MCP) is presented in this paper to estimate the transmission map, …

Mathematical Modeling Of An Epidemic In Scale-Free Network With Imperfect Vaccination, Heba Hameed

Thesis/ Dissertation Defenses

In light of the recent COVID-19 pandemic, the mathematical epidemiological model has proven to be essential for understanding the disease dynamic and finding the best control tool to help contain the disease and minimize its impact. This thesis investigates the dynamics of an infectious disease spread with latent infection and vaccination. The aim is to study this model's dynamic in a network that reflects the heterogeneity of the environment where the disease spreads. The vaccination is assumed to be not perfect, which means that vaccinated persons are likely to be infected and that the vaccinated person could lose their immunity, …

Development Of Highly Efficient Hybrid-Functionalized Membranes For Sustainable Water Harvesting, Ahmed Abuibaid

Thesis/ Dissertation Defenses

Water scarcity has emerged as a critical global challenge. This problem catches the world interest by events such as the severe drought in Europe during the summer of 2022. While desalination plants offer a solution, their high energy consumption necessitates the exploration of alternative, sustainable water resources. Addressing the urgent need for alternative water resources in the face of increasing water scarcity. A viable option was presented by fog harvesting. Which is a method to collect water from atmospheric fog. This method was initially developed to meet the demands of varieties of sectors such as agricultural purposes, household used and …

The Product Of Distributions And Stochastic Differential Equations Arising From Powers Of Infinite Dimensional Brownian Motions, Un Cig Ji, Hui-Hsiung Kuo, Hara-Yuko Mimachi, Kimiaki Saitô

Journal of Stochastic Analysis

No abstract provided.

Role Of Hypogenesis In The Evolution Of Karst In The Taurus Mountains Range, Turkey, Serdar C. Bayari, Naciye Nur Özyurt, Lütfi Nazik, Koray A. Törk, Noyan İ. Güner, Emrah Pekkan, Pınar Avcı

International Journal of Speleology

Field observations and laboratory data collected from the Taurus Mountains Range, Turkey during the last two decades provided evidence for the link between the evolution of hypogene karst and the geodynamic history. Major evidence includes; carbonate-hosted secondary ore deposits that are converted from primarily hypogene minerals by epigene, oxygen-rich groundwater circulating at local to intermediate depths. Another piece of evidence of hypogene karst in the Tauride is the Kırkgöz springs’ huge submerged cave/conduit system, which formed the Antalya Travertine Plateau, which is the world’s largest deposit precipitated by cool karst groundwater. The obruks in central Tauride are giant collapse dolines …

Modified Method For Assessing The Required Expenditures And Estimated Time Of Hard Coal Mine Liquidation, Andrzej Chmiela, Małgorzata Wysocka, Adam Smoliński

Journal of Sustainable Mining

The restructuring of hard coal mining requires significant budgetary expenditures. A comprehensive scientific approach may facilitate the rationalisation and minimisation of mine closure costs. This study proposes a method for the preliminary estimation of the costs and time required for the potential liquidation of a hard coal mine. In addition to a literature review, a statistical analysis and a case study, personal interviews were conducted with individuals with direct management over the restructuring, reclamation and liquidation processes pertaining to mines undergoing closure.

The assessment method is based on an analysis of the mine liquidation costs, divided into successive years of …

Data Visualization, Licensing, And Other Generative Ai Initiatives At Minnesota State University Mankato, Evan Rusch, Nat Gustafson-Sundell

Library Services Publications

At Minnesota State University Mankato (MNSU), we’ve undertaken several experiments and initiatives focused on Generative Artificial Intelligence. At the start of the fall semester, we collaborated with university Information Technology Services to present a professional development session for returning faculty through the MNSU Center for Excellence in Teaching & Learning on “5 Tips for Teaching with AI.” We also presented to librarians across the regional consortium, Minitex, on “The Library & Generative AI.” This presentation included several demonstrations. It was offered as an introduction to Generative AI focused on topics most relevant to librarians, including information literacy, as well as …

Mechanical Calculations On Atomically Thin Membranes, Burak Aslan

Turkish Journal of Physics

No abstract provided.

Federated Learning Based Autoencoder Ensemble System For Malware Detection On Internet Of Things Devices, Steven Edward Arroyo

Theses and Dissertations

New technologies are being introduced at a rate faster than ever before and smaller in size. Due to the size of these devices, security is often difficult to implement. The existing solution is a firewall-segmented “IoT Network” that only limits the effect of these infected devices on other parts of the network. We propose a lightweight unsupervised hybrid-cloud ensemble anomaly detection system for malware detection. We perform transfer learning using a generalized model trained on multiple IoT device sources to learn network traffic on new devices with minimal computational resources. We further extend our proposed system to utilize federated learning …

Integrated Computational Approaches: Elucidating Molecular Mechanisms Of Pathogenic Proteins And Designing Novel Inhibitors Against Mycobacterium Tuberculosis And Sars-Cov-2, Justin David Carbone

Theses and Dissertations

Chapter 1 introduces computational strategies in computer aided drug design (CADD), focusing on physics-based methodologies to enhance drug discovery. This chapter also discusses the theoretical foundations and practical applications of molecular dynamics (MD) simulations including free energy and stochastic kinetic analysis. In Chapter 2, CADD methods lead to development of inhibitors targeting the RNA Dependent RNA Polymerase (RdRP) of SARS-CoV-2. Inspired by the nucleotide inhibitor Molnupiravir, we aim to design a combinatorial library of 72 novel inhibitors capable of impeding a dual threat inhibition mechanism inducing lethal mutations along with stalling viral replication with specific selectivity to RdRp over Human …

Incorporating Oxygen Isotopes Of Oxidized Reactive Nitrogen In The Regional Atmospheric Chemistry Mechanism, Version 2 (Icoin-Racm2), Wendell W. Walter, Masayuki Takeuchi, Nga L. Ng, Meredith G. Hastings

Faculty Publications

The oxygen isotope anomaly (Δ¹⁷O = δ¹⁷O − 0.52 × δ¹⁸O > 0) has proven to be a robust tool for probing photochemical cycling and atmospheric formation pathways of oxidized reactive nitrogen (NO_y). Several studies have developed modeling techniques to implicitly model Δ¹⁷O of NO_y molecules based on numerous assumptions that may not always be valid. Thus, these models may be oversimplified and limit our ability to compare model Δ¹⁷O values of NO_y with observations. In this work, we introduce a novel method for explicitly tracking Δ …

Methionine Sulfoxide Speciation In Mouse Hippocampus Revealed By Global Proteomics Exhibits Age- And Alzheimer’S Disease-Dependent Changes Targeted To Mitochondrial And Glycolytic Pathways, Filipa Blasco Tavares Pereira Lopes, Daniela Schlatzer, Mengzhen Li, Serhan Yılmaz, Rihua Wang, Xin Qi, Marzieh Ayati, Mehmet Koyutürk, Mark R. Chance

Computer Science Faculty Publications

Methionine oxidation to the sulfoxide form (MSox) is a poorly understood post-translational modification of proteins associated with non-specific chemical oxidation from reactive oxygen species (ROS), whose chemistries are linked to various disease pathologies, including neurodegeneration. Emerging evidence shows MSox site occupancy is, in some cases, under enzymatic regulatory control, mediating cellular signaling, including phosphorylation and/or calcium signaling, and raising questions as to the speciation and functional nature of MSox across the proteome. The 5XFAD lineage of the C57BL/6 mouse has well-defined Alzheimer’s and aging states. Using this model, we analyzed age-, sex-, and disease-dependent MSox speciation in the mouse hippocampus. …

High-Performance Computing In Next-Generation Sequencing Read Alignment, Minh H. Pham

USF Tampa Graduate Theses and Dissertations

Advancements in Next-Generation Sequencing (NGS) have dramatically reduced the cost and increased the speed of DNA sequencing. However, this rapid influx of data necessitates efficient and robust analysis tools, particularly for the complex task of aligning short NGS reads to reference genomes such as the human genome. We explore groundbreaking computational strategies and hardware acceleration to optimize this critical alignment process. This dissertation is structured around three innovative studies. First, we introduce a novel approach to dynamic memory allocation tailored for massively parallel systems, particularly Graphical Processing Units (GPUs), to support NGS alignment and other applications. Unlike traditional memory allocators …

Nanodysferlins Support Membrane Repair And Binding To Trim72/Mg53 But Do Not Localize To T-Tubules Or Stabilize Ca2+ Signaling, Joaquin Muriel, Valeriy Lukyanenko, Thomas A. Kwiatkowski, Yi Li, Sayak Bhattacharya, Kassidy K. Banford, Daniel Garman, Hannah R. Bulgart, Roger B. Sutton, Noah Weisleder, Robert J. Bloch

Chemistry Faculty Publications

Mutations in the DYSF gene, encoding the protein dysferlin, lead to several forms of muscular dystrophy. In healthy skeletal muscle, dysferlin concentrates in the transverse tubules and is involved in repairing the sarcolemma and stabilizing Ca2+ signaling after membrane disruption. The DYSF gene encodes 7-8 C2 domains, several Fer and Dysf domains, and a C-terminal transmembrane sequence. Because its coding sequence is too large to package in adeno-associated virus, the full-length sequence is not amenable to current gene delivery methods. Thus, we have examined smaller versions of dysferlin, termed "nanodysferlins," designed to eliminate several C2 domains, specifically C2 domains D, …

Methionine Sulfoxide Speciation In Mouse Hippocampus Revealed By Global Proteomics Exhibits Age- And Alzheimer’S Disease-Dependent Changes Targeted To Mitochondrial And Glycolytic Pathways, Filipa Blasco Tavares Pereira Lopes, Daniela Schlatzer, Mengzhen Li, Serhan Yılmaz, Rihua Wang, Xin Qi, Marzieh Ayati, Mehmet Koyutürk, Mark R. Chance

Computer Science Faculty Publications

Methionine oxidation to the sulfoxide form (MSox) is a poorly understood post-translational modification of proteins associated with non-specific chemical oxidation from reactive oxygen species (ROS), whose chemistries are linked to various disease pathologies, including neurodegeneration. Emerging evidence shows MSox site occupancy is, in some cases, under enzymatic regulatory control, mediating cellular signaling, including phosphorylation and/or calcium signaling, and raising questions as to the speciation and functional nature of MSox across the proteome. The 5XFAD lineage of the C57BL/6 mouse has well-defined Alzheimer’s and aging states. Using this model, we analyzed age-, sex-, and disease-dependent MSox speciation in the mouse hippocampus. …

Geometric Representation Of Classes Of Concave Functions And Duality, Elisabeth M. Werner

Faculty Scholarship

Using a natural representation of a 1/s-concave function on R ᵈ as a convex set in R ᵈ⁺¹, we derive a simple formula for the integral of its s-polar. This leads to convexity properties of the integral of the s-polar function with respect to the center of polarity. In particular, we prove that the reciprocal of the integral of the polar function of a log-concave function is log-concave as a function of the center of polarity. Also, we define the Santaló regions for s-concave and log-concave functions and generalize the Santaló inequality for them in the case the origin is …