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31p Solution Nmr Investigation Of Abasic Dna, Clarissa R. Krimmel

Graduate Theses/Dissertations

Base excision repair (BER) mechanisms fix single base lesions in DNA, such as T:G mismatches. During the base excision repair mechanism, an abasic site (AP site) is formed as an intermediate. AP sites are unstable and highly mutagenic; they can stop DNA replication. This research investigates how the conformational properties of abasic sites in DNA affect the binding recognition of enzymes involved in DNA repair mechanisms, including BER. Three different abasic sequences are being analyzed for this research project. A second project looks at the effects of a naturally occurring purine derivative, hypoxanthine, on the DNA backbone. These hypoxanthine lesions …

Repeatability And Reproducibility Of Likelihood Ratio Estimation For Forensics Using Machine Learning: An Application To In-Silico Fire Debris Data, Cameron Ezazi

Graduate Studies Theses and Dissertations 2026

The importance of using statistical evidence to help inform the interpretation of forensic evidence has grown greater over time. This is especially evident in the field of forensic fire debris analysis, where the reliability and reproducibility of statistical results are crucial. This thesis investigates how the application of 5 different common machine learning methods on an in-silico fire debris dataset can be reduced to a univariate forensic score to create score-based likelihood ratios (SLRs), and how these ratios should be interpreted. These SLRs are crucial in supporting or rejecting a Prosecutor’s or Defense’s hypothesis, thus making the previously mentioned reliability …

Integrating Self-Organizing Maps And Explainable Artificial Intelligence To Unravel Surface Water-Groundwater Hydrochemical Evolution And Drinking-Water Suitability Controls In A Data-Limited Arid Basin, Hui Tong, Ruizhong Gao, Yinlong Wang, Xixi Wang, Limin Duan, Guoqiang Wang

Civil & Environmental Engineering Faculty Publications

Study region

The Dahei River Basin, located in the semi-arid northern region of China's Great Bend of the Yellow River.

Study focus

This study integrates hydrochemical characterization, stable hydrogen-oxygen isotopes, Self-Organizing Maps (SOM), the entropy-weighted water quality index (EWQI), and explainable ensemble learning (XGBoost-TreeSHAP) to investigate surface water-groundwater evolutionary patterns and identify key hydrochemical contributors to drinking-water suitability in the Dahei River Basin.

New hydrological insights for the region

Waters in the basin are predominantly weakly alkaline and are characterized by HCO₃^--Ca-Mg and HCO₃^--Na facies, indicating the combined effects of carbonate weathering and cation exchange, with …

Multi-Isotope Tracing Reveals Nitrate And Sulfate Sources And Fate Across Contrasting Activity Zones In A Semi-Arid Basin Of Northern China, Chang Yue, Ruizhong Gao, Limin Duan, Tianke Su, Xixi Wang, Tingxi Liu, Guoqiang Wang

Civil & Environmental Engineering Faculty Publications

In semi-arid surface water-groundwater systems, nitrate (NO₃^–) and sulfate (SO₄²^–) are jointly influenced by natural processes and anthropogenic activities, yet how their sources, transformations, and export vary across contrasting activity zones remains insufficiently understood. Integrating hydrochemistry, multiple stable isotopes, a Bayesian isotope mixing model, and representative-section flux analysis, this study investigated the source compositions, transformation processes, and export differences of NO₃^– and SO₄²^– in the Dahei River Basin.   New hydrological insights for the region: Results showed greater SO₄²^– enrichment in high-activity zones, whereas NO₃^– exceedance was more prominent in low-activity zones. In …

Absolute Quantification And Identification Of Rna From Rna-Lipid Nanoparticles Using High Resolution Mass Spectrometry, Jason C. Funderburk

Theses and Dissertations

RNA therapeutics are a rising drug category with potential use for a range of conditions encompassing infectious diseases to therapies for cancer, diseases, and genetic disorders. RNA-lipid nanoparticles (RNA-LNPs) are the prominent delivery method for these therapeutics approved products include mRNA vaccines and polyneuropathy treatments. The emergency use authorizations and orphan drug status of current RNA-LNP drugs has allowed approval without finalization of the regulatory analytical procedures for quality monitoring. The objective of the study was to develop an LC-MS assay to simultaneously measure identity and concentration of two therapeutically relevant intact RNA constructs extracted from RNA-LNPs to enhance quality …

Real-Space Imaging Of The Electron-Pair Density Hole In Molecular Auger-Meitner Decay, Mats Simmermacher, Nathan Goff, Andres Moreno Carrascosa, Elke Fasshauer, Thomas Northey, Lingyu Ma, Haiwang Yong, Brian Stankus, Asami Odate, Xuan Xu, Wenpeng Du, Kyle Acheson, Joseph C. Cooper, Daniel Ratner, Mengning Liang, Ruaridh Forbes, Michael P. Minitti, Adam Kirrander, Peter M. Weber

Physics Faculty Publications

Electrons in matter can rearrange extremely quickly under external perturbations, underpinning subsequent structural and chemical transformations. Coulomb interactions between neighbouring electrons often shape this response, giving rise to correlated motion and strongly affecting the distribution of electrons in the system. Here we show that non-resonant hard X-ray scattering can directly access changes in the radial electron-pair density during the rapid rearrangement of core and valence electrons. We do this by studying sulfur hexafluoride molecules undergoing Auger–Meitner decay. We exploit a second-order interaction between the X-ray photons and the molecules to trigger and probe the decay dynamics with a single pulse, …

Basis Design For Electronic Structure And Beyond, Weishi Wang

Dartmouth College Ph.D Dissertations

At the intersection of quantum physics, quantum chemistry, and materials science, electronic structure is the study of electrons in solid-state and molecular systems. Electronic-structure computation relies on discretizing the many-electron Hamiltonian with a finite single-particle basis set. However, basis-set construction is conventionally treated as an ad hoc preprocessing step. This thesis develops an expressive and flexible framework for active, system-oriented basis-set design and numerical modeling strategies that treat basis functions as tunable representations to encode electronic ground-state information.

We first introduce a multi-layered, differentiable basis-construction framework that embeds a set of primitive parameters into mixed-contracted Gaussian-type orbitals. We then develop …

Investigation Of Fine-Grain Cu And Cu Alloys For Low-Temperature Hybrid Bonding Applications, Sarabjot Singh

Electronic Theses & Dissertations (2024 - present)

Hybrid bonding has emerged as a key enabler for next-generation three-dimensional (3D) integration, offering fine-pitch interconnects and improved electrical performance. However, conventional Cu–Cu hybrid bonding typically requires elevated temperatures to achieve sufficient diffusion and interface quality, posing challenges for temperature-sensitive device integration and process compatibility. This work investigates materials engineering approaches to enable low-temperature Cu–Cu bonding through both microstructure design and alloying strategies.

This work begins by examining grain refinement in Cu as a pathway to enhance diffusion through increased grain boundary density, providing efficient atomic transport without introducing additional elements. Three Cu-based systems Cu–Co, Cu–Ag, and Cu–Al were systematically …

The Chemistry Of Red Lipstick: The Impact Red Lipstick Has On Society, Lilliana Weldeslassie

Electronic Theses & Dissertations (2024 - present)

Cosmetic chemistry is deeply embedded in everyday life, shaping the products people use from morning to night. Among these, red lipstick stands out as a formulation that blends complex chemistry with a cultural meaning. This thesis examines the scientific foundations of red lipstick through its chemical composition, pigment structure, toxicological history, analytical methods, and evolving sustainability practices. Historically, red lipsticks relied on high-risk ingredients such as lead, mercury, and other toxic metals, reflecting an era before chemical safety and regulatory oversight were incorporated.²¹ Modern formulations have established safer synthetic dyes, natural waxes, plant-based oils, and stabilizers created to optimize …

Development Of Photolabile Coumarin Linker For Rna Synthesis And Crisprcas9 Applications, Ian Mcclain

Electronic Theses & Dissertations (2024 - present)

The scope of RNA-based therapeutics continues to expand as more siRNA, mRNA, and CRISPR-based treatments are approved for various medical applications. Purification of synthetic RNA drugs is inherently challenging and requires considerable time and resources. New cost-effective and efficient purification strategies will expedite drug development process and will lower the drug costs. In this thesis I describe two generations of photolabile linkers for the non-chromatographic purification of therapeutic RNAs. In addition, the photolabile linker was utilized for regulation CRISPR-Cas9 gene editing. In the first part of the thesis, I describe the first generation of the photolabile coumarin-based linker for non-chromatographic …

Improving Modeling Of Corrosion Products In The Primary Circuit Of Light Water Reactors Through The Experimental Determination Of Crud Characteristics, Sri Saravana Konganapuram Narasimma Bharathi

Electronic Theses & Dissertations (2024 - present)

High-temperature water flowing through the coolant circuits in pressurized water reactors (PWRs) creates a harsh environment, deteriorating these materials. This corrosion results in the formation of oxide layer(s) primarily composed of nickel ferrites, iron oxides, nickel oxides, and other nickel-iron-chrome spinel oxides. Being exposed to fluid with high flow rates and pressure, these oxide layers can be eroded, resulting in particulate fouling due to the release of corrosion products (Chalk River Unidentified Deposits, CRUD) into the coolant circuit. When CRUD subsequently deposits on fuel surfaces, it negatively affects the fuel performance (heat transfer and fuel failure); in addition, the particles …

Bio-Orthogonal Chemistry-Based Strategy To Turn-On And Turn-Off Crispr-Cas9 Gene Editing In Solution And In Live Cells, Bhoomika Pandit

Electronic Theses & Dissertations (2024 - present)

The CRISPR–Cas9 system is a widely popular tool for genome engineering. There is a strong interest in developing tools for temporal control of CRISPR-Cas9 activity to address some of the challenges and to broaden the scope of potential applications. In this thesis I describe two biorthogonal based approaches to either Turn-ON and Turn-OFF CRISPR-Cas9 gene editing.

In first project work I describe a bio-orthogonal chemistry-based approach to Turn-ON Cas9 nuclease activity with temporal precision. We report a TCO-acylimidazole reagent that acylates 2′-OH groups of RNA. Poly-acylation (“cloaking”) of RNA was optimized in vitro using a model 18-nt oligonucleotide, as well …

A Geospatial Assessment Of Groundwater Salinization In A Multi-Aquifer System: Durango, Mexico, Juan Lopez-Sierra

Graduate Theses/Dissertations

Groundwater salinization poses a critical environmental concern for water resource sustainability in arid and semi-arid regions. This study evaluates spatial and temporal patterns of groundwater salinity across the state of Durango, Mexico, using total dissolved solids (TDS), sodium adsorption ratio (SAR), as salinity indicators and nitrate-nitrogen (NO₃–N) as an anthropogenic indicator. Groundwater quality data were obtained from (CONAGUA), a Mexican water agency. To assess salinity variations with respect to time, while minimizing interannual sampling bias, two multi-year sampling periods were selected: 2012-2013, and 2020-2021. Final datasets consisted of 122 wells for 2012–2013 and 131 wells for 2020–2021. The wells were …

Computational Design Of Nanoporous Materials For The Adsorption Of Per- And Polyfluoroalkyl Substances, Daniel D. Mottern

Dissertations

Per- and polyfluoroalkyl substances (PFAS) are a large family of chemicals that have seen wide usage due to their fluorinated carbon backbone. The presence of strong C-F bonds in the backbone lends PFAS molecules high thermal and chemical stability, as well as strong hydrophobicity and lipophobicity. This combination of properties has led to heavy use of PFAS as surfactants, non-stick coatings, and aqueous foam forming films and flame retardants. However, these properties bring their own consequences. The high chemical and thermal stability of PFAS renders them persistent, with the C-F bonds resisting naturally occurring forms of degradation. Existing forms of …

Data-Driven Analysis And Atomistic Simulations Of Next-Generation Materials For Energy Conversion And Storage, Yuliang Shi

Dissertations

Metal-organic frameworks (MOFs), with their modular architectures and tunable properties, represent an especially rich domain for accelerated material design and discovery for a range of diverse applications. Within this class of multifunctional materials, two-dimensional (2D) electrically conductive MOFs (EC MOFs) are of particular interest, as their 7r-stacked layered structures combine permanent porosity with electronic conductivity, enabling potential breakthroughs in energy storage, energy conversion, and quantum sensing. But the discovery and design of new EC MOFs based on expensive experimental screening is increasingly impractical due to the infinite chemical space. Furthermore, the practical implementation of EC MOFs for specific tasks depends …

Bio-Papcz: Corn Starch-Based Composite Bioplastic Reinforced With Pineapple Leaf Fiber (Palf), Zinc Oxide (Zno), And Polyvinyl Alcohol (Pva), Marvin C. Caya, Shervin Austin C. Huang, Jovar Khalel J. Maghari, Ruel M. Levida

Sinaya: A Philippine Journal for Senior High School Teachers and Students

Plastic pollution poses a serious global threat, as petroleum-based plastics persist for centuries, and their surging production of over 450 million tons overwhelms ecosystems (Ritchie et al., 2023). Using a quantitative experimental research design, the study examined the effects of varying concentrations of cornstarch-based bioplastic reinforced with pineapple leaf fiber (PALF), polyvinyl alcohol (PVA), and zinc oxide (ZnO) on the bioplastic’s tensile strength and soil degradability. Sample C2 (ZnO 3.0 %w/w; PVA 9.0 %w/w) demonstrated the optimal tensile properties with a tensile strength of 0.76 MPa and an elongation at break of 6.40%, which was attributed to the addition of …

Exploring The Metric Dimension Of The Graph Representing A Four-Ring Polycyclic Aromatic Hydrocarbon: Interstellar 1-Cyanopyrene, Andrei Matthew V. Robino, Sebastian Alex C. Traviña, Karl Benedict P. Narag, Mark Anthony B. Casao, Helix Raven C. Llanes, Azriel C. Alejo, Jonel C. Celamor

Sinaya: A Philippine Journal for Senior High School Teachers and Students

A graph's metric dimension is a parameter that denotes the minimum possible number of vertices in a subset that gives each vertex in the graph a unique representation. Despite extensive research on the metric dimension of polycyclic aromatic hydrocarbons (PAHs), there is currently no focused analysis on the metric basis and metric dimension of 1-cyanopyrene. In chemistry, graphs can be used to depict molecular structures. In this study, graph theory, specifically the concept of metric dimensions, is applied to the molecular structure of 1-cyanopyrene, which was detected in space for the first time in 2024. 1-cyanopyrene is a molecule made …

Integration Of Islamic Values In Mathematics Learning, Ai Mulya, Surya Faradiba

Jurnal Pendidikan Sains

This study aims to identify the integration of Islamic values in mathematics learning and its contribution to student character development. The method used is a systematic literature study by reviewing relevant accredited scientific articles. The results of the study indicate that the integration of Islamic values is carried out through the preparation of Islamic-context-based mathematics problems, linking concepts to verses of the Qur'an and hadith, the application of ethnomathematics with Islamic cultural nuances, and the introduction of Islamic economic concepts. The dominant values that emerge include honesty, responsibility, discipline, justice, and piety. These findings indicate that the integration of Islamic …

Understanding The Fidelity And Specificity Of Dna Polymerase I, Bill R. Miller Iii, Andrew V. Yeager, Jake A. Collins, Alexis Blake, Elise Tate, Carol A. Parish, Eugene Y. Wu

Chemistry Faculty Publications

High-fidelity DNA polymerases employ complex mechanisms to catalyze template-dependent DNA synthesis while quickly discarding mismatches. Atomic-level structural details about short-lived states during nucleotide discrimination are necessary to gain insight into the kinetic checkpoints that contribute to fidelity. We performed microsecond molecular dynamics simulations of DNA polymerase I, large fragment, from Bacillus stearothermophilus (Bacillus fragment, or BF) in complex with a template guanine and a mismatched thymidine triphosphate to observe the early events in the process of selection against a mismatch. Although the nucleobases formed a wobble base pair early, the mismatched pair was blocked from fully entering the active site …

Detection Of Ultra-Trace Levels Of Copper In Seawater Using A Bare Gold Microwire Electrode And A Portable Digital Voltammeter, Luke M. Brosnan, Wade Lonsdale, Paul Pringle, Paul Lewtas, Samantha Ridgway, Sebastien Allard, Magdalena Wajrak

Research outputs 2022 to 2026

The accumulation of biomass on ship hulls (biofouling) can greatly decrease their fuel efficiency. Many antifouling coatings contain copper as a biocidal agent, which can be released during hull cleanings and is of particular concern when cleaning the hulls in situ (i.e., without dry docking). Previously established voltammetric methods for the detection of copper in seawater using a gold microwire electrode have been modified and adapted to a portable on-site voltammetric technique. Notable differences from previous voltammetric methods include the use of linear sweep voltammetry, analysis under atmospheric conditions, alternating the potential during the deposition period and the use of …

Physicochemical, Pharmacognostic Standardisation And Phytochemical Analyses Of The Homoeopathic Drug Justicia Adhatoda, Bibaswan Biswas, Satish Patel, Digvijay Verma, Satyajit Maity, Shilpi Singh, Paulami Majumdar, Narasimha Kumar Gv

Indian Journal of Research in Homoeopathy

Background: Justicia adhatoda (J. adhatoda), also well known as Vasaka in India is a medicinal plant chiefly used to treat respiratory ailments in traditional and alternative medical systems. Objective: This study aimed to establish the physicochemical, pharmacognostic, and phytochemical standardisation parameters of the drug. The study involved the measurement of physicochemical parameters and chemical profiling of the raw drug. The chemical characteristics of the in-house mother tincture (prepared from in-house raw drug) and commercial mother tinctures available in India were also evaluated to assess the quality of commercially available mother tinctures. Materials and Methods: The present study …

Two Members Of The Editorial Board Of Journal Electrochemistry, Kai Wu Elected As An Academician Of The Chinese Academy Of Engineering And Yi Cui A Foreign Academician Of The Chinese Academy Of Sciences, Editorial Office Of J.Electrochem.

Journal of Electrochemistry

No abstract provided.

Electrochemical Characterization And Modulation Of Biological Processes, Yue-Qi Li, Wei-Hua Huang, De-Chen Jiang, Bao-Hong Liu, Bin Su, Yang Tian, Jing-Juan Xu, Ping Yu, Feng Zhao, Huang-Xian Ju, Jing-Hong Li

Journal of Electrochemistry

Electrochemical processes lie at the core of biological function, governing energy transduction, metabolic flux, and molecular signaling. Recent advances in electrochemical science now allow these processes to be probed and controlled with unprecedented spatial, temporal, and chemical resolution. In this review, we present an integrated framework that progresses from fundamental mechanisms to analytical technologies and functional modulation. We begin by outlining electron transfer pathways in mitochondrial respiration, microbial extracellular electron transfer, and DNA- and protein-based charge conduction, followed by the principles of photon-electron conversion in photosynthesis and the central role of redox equilibrium in coordinating cellular responses. We then highlight …

A Novel Electrolyte Pyridine Additive For Enhancing Cycle Life Of Lithium-Ion Batteries, Peng-Cheng Wang, Ding-Chang Li, Jun-Tao Li, Guang-Bo Lu, Shi-Wen Wang

Journal of Electrochemistry

Lithium-ion (Li-ion) battery using a graphite (Gr.) anode and a lithium iron phosphate (LiFePO₄, LFP) cathode (Gr.||LFP) has been widespread in energy storage. To match the warranty period of energy storage systems, the lifespan of this kind of Li-ion battery, not only under room temperature but also under relatively high temperature, is critical. Exploration of functional electrolyte additive provides an efficient approach to address this issue. This study reports the usage of pyridine (Py) as a new electrolyte functional additive for Gr.||LFP. In the first cycle, it was found that Py can be reduced before ethylene carbonate and …

Journal Of Electrochemistry Officially Indexed By Leading Oa Databases Oarl And Coaj, Editorial Office Of J.Electrochem.

Journal of Electrochemistry

No abstract provided.

Feature Column Of Journal Of Electrochemistry Nominated For 2025 Top 10 Famous Columns Of Fujian Provincial Newspapers And Periodicals, Editorial Office Of J.Electrochem.

Journal of Electrochemistry

No abstract provided.

Novel Spectrophotometric Method For The Determination Of Paclitaxel Through Complex Formation With Osmium, Basima A.A.Saleem, Salim A. Mohammed, Amer Th. Al-Taee

Turkish Journal of Chemistry

Paclitaxel (Pac) is an important anticancer bioactive compound, and the availability of an accurate and robust analytical method for its quantification is of utmost importance. In this investigation, a novel, direct, and reliable spectrophotometric method has been proposed for the estimation of Pac via a complex formation reaction with osmium (Os). The method was based on the reaction of Pac with Os tetroxide, which produced a yellowish-brown complex. The resulting complex is soluble in water and displays a maximum absorption peak at 482 nm. The reaction conditions, including reactant concentration, pH, temperature, and reaction time, were optimized to obtain the …

Synthesis, Characterization, Antimicrobial, Antioxidant, And Antiinflammatory Evaluation And Molecular Docking Studies Of N-((2-Hydroxy-3-(2-(Substitutedbenzylidene)Hydrazine-1-Carbonyl)Naphthalen-1-Yl)(3-Nitrophenyl/3,4-Dimethoxyphenyl)Methyl)Acetamide Derivatives, Shikha Kamboj, Alka Yadav, Samridhi Thakral, Rekha Tanwar, Sunil Kumar, Vikramjeet Singh

Turkish Journal of Chemistry

Hydrazone chemistry has become important and plays a key role in the development of organic compounds. Hydrazones can be useful pharmacophores for creating novel derivatives, owing to their broad range of activities. In this study, a series of N-((2-hydroxy-3-(2-(substitutedbenzylidene)hydrazine-1-carbonyl)naphthalen-1-yl)(3-nitro-phenyl/3,4-dimethoxyphenyl)methyl)acetamide derivatives were prepared, characterized by FTIR, 1H-NMR, 13C-NMR, and mass spectroscopy, and evaluated for their antimicrobial, antiinflammatory, and antioxidant activities along with in silico studies. The substituted derivatives were synthesized by the reaction of acetonitrile, chlorosulphonic acid, and substituted benzaldehyde with the hydrazones. The antimicrobial evaluation showed that compound 3i had more antimicrobial potential than the other tested molecules. Compound 3j …

Enhancing Analytical Performance Of Tyrosinase-Based Sensors With Nanoparticles For Detection Of Isoproterenol, Aysel Oktay, Sevi̇nç Kurbanoğlu, Gülsüm Gündoğdu, Cem Bülent Üstündağ, Frieder W. Scheller, Aysu Yarman

Turkish Journal of Chemistry

In this work, electrochemical biosensors utilizing tyrosinase (Tyr) for the detection of the nonselective beta-adrenergic agonist isoproterenol (ISO) are presented. Three different configurations for immobilizing Tyr on a graphite electrode (GE) are compared: (1) GE modified with poly(diallyldimethylammonium chloride) (PDADMAC), PDADMAC/Tyr/GE; (2) PDADMAC combined with iridium nanoparticles (IrNPs) in a stepwise preparation, resulting in PDADMAC/IrNPs/Tyr/GE; and (3) a composite of PDADMAC and IrNPs mixed with Tyr at a 1:1 (v:v), forming PDADMAC/(IrNPs-Tyr)/GE. Surface morphology was characterized using scanning electron microscopy (SEM). Cyclic voltammetry (CV) and amperometry were applied to characterize the biosensor’s performance. Within the linear range of 5 μM …

Synthesis, Characterization, And Theoretical Study Of New Cocrystals And Charge-Transfer Compounds, Zari̇fe Si̇bel Şahi̇n, Zeki̇ Kartal

Turkish Journal of Chemistry

This study used single-crystal X-ray diffraction, elemental analysis, infrared (IR) spectroscopy, theoretical nuclear magnetic resonance (NMR), and theoretical ultraviolet spectroscopy to characterize 3 newly synthesized crystalline compounds. Additionally, the nonlinear optical, highest occupied molecular orbital energies, lowest occupied molecular orbital energies, band gap, molecular electrostatic potential, and thermodynamic parameters of the 3 crystalline compounds were examined. The strong correlation between experimental IR spectra and theoretical NMR chemical shifts confirmed the accuracy of computational predictions. The molecular formulas of the 3 newly synthesized crystalline compounds, each containing different ligand molecules, were: C8H14O4·2(C6H4N2), C5H7N2·NCS, and Ni(CN)4·2(C5H7N2)·2(H2O) for compounds 1, 2, and 3, …