Physical Sciences and Mathematics Commons^™

Aspects Of Stochastic Geometric Mechanics In Molecular Biophysics, David Frost

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In confocal single-molecule FRET experiments, the joint distribution of FRET efficiency and donor lifetime distribution can reveal underlying molecular conformational dynamics via deviation from their theoretical Forster relationship. This shift is referred to as a dynamic shift. In this study, we investigate the influence of the free energy landscape in protein conformational dynamics on the dynamic shift by simulation of the associated continuum reaction coordinate Langevin dynamics, yielding a deeper understanding of the dynamic and structural information in the joint FRET efficiency and donor lifetime distribution. We develop novel Langevin models for the dye linker dynamics, including rotational dynamics, based …

Hydrothermal Synthesis Of First-Row Transition Metal Polyanions Towards The Design Of Frustrated Magnetic Materials, Megan Smart

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Novel modern materials are constantly being discovered as humanity seeks constantly better improvement to the optics and electronics around us, from lasers used in medical therapies to the magnets and supercomputing chips in our phones. Inorganic oxides commonly draw inspiration from naturally occurring minerals to template new discoveries through substitution of similarly behaving elements with the goal of inducing certain desired properties, such as ferroelectricity or creating the elusive quantum spin liquid. While many minerals are silicates, its periodic table neighbor germanium(IV) has a rich and under-explored crystal chemistry that could contain many new structures and magnetic materials. Another common …

Studies On Electrochemical Hydrogen Isotope Separation, Liyanage Mayura Sankalpa Silva

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Graphene-integrated Proton Exchange Membrane (PEM) electrochemical cells have emerged as a novel area of scientific investigation in the realm of hydrogen isotope separation. Chemical Vapor Deposited (CVD) graphene has been especially useful due to its large-scale production capability for scaling-up purposes. The research described in this dissertation explores the role that inadvertent introduction of cations, notably ammonium and copper, during the CVD graphene transfer onto PEM substrates, such as Nafion, might play in affecting hydrogen ion transport and isotope separation in PEM electrochemical cells. An extensive review of existing literature exposed a gap concerning unintentional cation introductions during graphene transfer, …

Understanding The Interaction Of Environmental Contaminants With Polystyrene Nanoparticles And Dna Using Nuclear Magnetic Resonance Spectroscopy And Density Functional Theory, Saduni Arachchi

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The objective of the thesis is to study the effect of environmental pollutants on polystyrene nanoparticles and biomolecules. This is done in two different techniques, particularly NMR and density functional theory. In this thesis, we use a combination of 1H NMR, Saturation-Transfer Difference (STD) NMR and relaxation experiments to study the interactions, kinetics and dynamics of antibiotics with polystyrene nanoparticles. (PS NPs) Density functional theory (DFT) is used to study the binding of commonly used non-oxidative hair dyes to biomolecules (DNA and amino acids) and PS particles.

Computationally-Driven Insights Into The Ligand Environments Of Materials For Catalysis And Separations, Stephen Vicchio

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Designing new catalytic and sorption materials is necessary to limit global temperature rise below 1.5 ◦C by 2050, while also meeting global energy demands. Climate change and energy production are not mutually exclusive; global population growth has direct impacts on global energy demands and climate. In both catalysis and adsorption applications, new technologies are needed to address these challenges. Catalysis can provide alternate, low-energy routes for converting low-value gases into higher-value chemical commodities, thus altering our current energy production. Likewise, new sorption materials can capture previously emitted CO₂ from decades of energy production from fossil fuels, thus helping to …

Expansion Of The Diazacyclobutene Motif For Antiparasitic Evaluation, Brock Alexander Miller

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Molecules containing N-heterocycles are prevalent in pharmaceutical settings. The ability to generate highly functionalized molecules containing N-heterocycles in very few synthetic operations is valuable for drug discovery. Our group has developed a two-step synthesis to access a rarely studied diazacyclobutene scaffold via a formal [2+2] cycloaddition between 4-phenyl-1,2,4-triazolinedione and electron-rich thioalkynes. Our interest in this scaffold increased exponentially from promising preliminary biological evaluations against a protozoan parasite, Trypanosoma brucei. While we were able to double the number of historical examples of this scaffold, there were significant limitations in our methodology. The most notable limitations were the lack …

Atom Economical Reactions Of Terpenoids And Post-Consumer Plastics With Sulfur, Charini Maladeniya

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The production of Ordinary Portland Cement (OPC) and its uses have a complicated environmental impact, which is influenced by infrastructure development and building operations as well as CO₂ emissions, which account for 7% of all worldwide CO₂ emissions. Due to the increasing population, production is still ongoing. The search for cement and construction materials produced with zero to low CO₂ emissions is therefore continuous. Finding recyclable, CO₂ gas-free biocomposites with high sulfur content that can rival the mechanical properties of popular building supplies like Portland cement is the primary objective of the research discussed in this …

Composite And Polymer Formulation Employing Sulfur And Bio-Olefin Feedstocks, Claudia V. Lopez

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Environmental sustainability represents a challenge for society since industrial growth has a direct impact on natural resources and waste production. New technologies that effectively incorporate waste into renewable resources are critical to the development of a sustainable and circular economy. The manufacturing of structural materials like Portland cement (OPC) is responsible for >8% of the global anthropogenic emissions of carbon dioxide, with ~ 1 kg of CO₂ released to the atmosphere for every kilogram of OPC produced. For instance, the development of sustainable structural materials is a key factor to reduce the greenhouse emissions and to attenuate the climate …

Electron-Transfer Mediated Photo-Switching In Nanoparticles, Liaoran Cao

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Previous publications from our lab demonstrated viable approaches to design a photo-switching nanoparticle with arguably superior brightness and photostability resulting in an improved resolution in localization-based microscopy, as compared to other photo-switching dyes or particles. As a follow-up, this dissertation is focused on two major tasks: first, developing nanoparticles with better photo-switching properties for super-resolution imaging; second, trying to achieve a better physical picture of the mechanisms involved in photo-switching, including polaron dynamics, charge transfer, and energy transfer. A new class of photo-switchable nanoparticles was developed by blending conjugated polymer semiconductor with fullerene-based electron acceptors, and further blending with polystyrene …

The Influence Of Allostery Governing The Changes In Protein Dynamics Upon Substitution, Joseph Hess

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The focus of this research is to investigate the effects of allostery on the function/activity of an enzyme, human immunodeficiency virus type 1 (HIV-1) protease, using well-defined statistical analyses of the dynamic changes of the protein and variants with unique single point substitutions ¹. The experimental data¹ evaluated here only characterized HIV-1 protease with one of its potential target substrates. Probing the dynamic interactions of the residues of an enzyme and its variants can offer insight of the developmental importance for allosteric signaling and their connection to a protein’s function. The realignment of the secondary structure elements can …

Hydrothermal Synthesis Of Frustrated Lanthanide Pyrochlores And Transition Metal Double Perovskites And Germanates, Matthew S. Powell

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Magnetically frustrated materials hold promise of unique behavior allowing for the novel study of quantum phenomena. Such materials are poised to become an integral foundation for technological advancement in the post-Silicon Age. Crystalline materials are given special focus where the rigid lattice allows more detailed study of these quantized effects and frustration behavior. As opposed to polycrystalline powders, large single crystals can be preferentially aligned enabling the study of anisotropic behavior. Two cubic structure types have garnered significant interest due to their 3-D tetrahedral arrangement of symmetry-related metal centers with the potential for magnetic frustration: pyrochlores and perovskites.

The supercritical …

Elucidation Of Active Site And Mechanism Of Metal Catalysts Supported In Nu-1000, Hafeera Shabbir

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Advances in extraction of shale oil and gas has increased the production of geographically stranded natural gas (primarily consisting of methane (C1) and ethane (C2)) that is burned on site. A potential utilization strategy for shale gas is to convert it into fuel range hydrocarbons by catalytic dehydrogenation followed by oligomerization by direct efficient catalysts. This work focuses on understanding metal cation catalysts supported on metal-organic framework (MOF) NU-1000 that will actively and selectively do this transformation under mild reaction conditions, while remaining stable to deactivation (via metal agglomeration or sintering). I built computational models validated by experimental methods to …

Computational And Experimental Investigations Of Alkali Cation Interactions At The Rutile – Water Interface, Isaac Johnston

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Overall, the objective of this dissertation was to investigate the degree of sorption for the alkali cations on rutile to ascertain the impact of different cation properties, such as ion size and charge density, on sorption mechanics as well as probe how the ion may alter the surface – aqueous interface. Initial molecular dynamic simulations and batch experiments showed minimal surface sorption for any alkali cation at relatively low concentrations while simultaneously suggesting the enthalpy of deprotonation shifts slightly in the presence of the alkali cations at different ionic strengths. The cations are likely causing small reorientations of the near-surface …

Isolation And Characterization Of Extracellular Vesicles From Various Biological Matrices Using Capillary-Channeled Polymer (C-Cp) Fiber Solid-Phase Extraction Spin-Down Tips, Kaylan Jackson

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A number of recent works have emphasized the need to isolate nanometer-scale analytes, like extracellular vesicles (EVs), from various biologically-relevant fluids. Exosomes are a subset of small EVs that range from 30-200 nm in diameter that serve as biomolecular snapshots of their cell of origin containing mother cell-specific DNA, miRNA, mRNA, and proteins. As critical components of intercellular communication, exosomes and other EVs play significant roles in many physiological and pathological processes. Diverse populations of these vesicles can be collected from biofluids, including blood, saliva, and urine, from cell culture conditioned media and primary cells, and even from plant …

Development Of Plasmonic And X-Ray Luminescence Nanoparticles For Bioimaging And Sensing Applications, Meenakshi Ranasinghe

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This dissertation discusses the development of plasmonic and X-ray luminescence nanoparticles (~100 nm) to use in bioimaging and sensing applications. The nanoparticles have interesting optical properties compared to their atomic levels and bulk materials. The optical properties of nanomaterials can be controlled by changing size, shape, crystal structure, etc. Also, they have a large surface area that can be functionalized with biomolecules. Therefore, the optical properties and biofunctionalized nanomaterials are useful in biomedical applications such as targeted drug delivery, bioimaging, and sensing. The overall theme is to use nanoparticles with interesting optical properties compared to their atomic levels and bulk …

Understanding Dynamics Of Polymers Under Confinement: A Molecular Dynamics And Neutron Scattering Study, Supun Samindra Kamkanam Mohottalalage

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The current study probes the structure, dynamics, and rheological behavior of associating polymers including ionomers in melts and solutions as well as conjugated polymers confined into nanoparticles, using molecular dynamics (MD) simulations and neutron scattering techniques. The study focuses on two families of associative polymers, ion containing macromolecules and conjugated polymers.

Polymers that consist of ionizable groups along their backbone found uses in a broad range of applications. Examples include light weight energy storage and generation systems, and biomedical applications, where the polymers act as ion exchange membranes, and actuators. The ionic groups tend to form clusters that are in …

Radioluminescence Based Biochemical Sensing And Imaging Strategies To Measure Local Drug Release And Ph, Gretchen B. Schober

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In this dissertation we describe methods for measuring infection relevant biochemical analytes using radioluminescent and ultrasound luminescent materials. Films and nanoparticles fabricated with europium doped gadolinium oxysulfide (Gd₂O₂S:Eu³⁺) are used to quantitatively measure radiolabeled pharmaceutical concentration, specifically tritium labeled vancomycin (³H-vancomycin). Europium and dysprosium doped strontium aluminate is used to fabricate an ultrasound modulated, pH sensing film. These methods are indicated for theranostic evaluation of implant associated infection. Bacterial biofilms are inherently resistant to traditional antibiotic treatment and can coat biomedical implants. These biofilm related infections are difficult or impossible to eradicate …

Competition Between Halogen And Chalcogen Bonding And Their Role In Probing Organic Transformations, Andrew Peloquin

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Halogen bonding, the attractive interaction of an electrophilic region on a halogen atom with a nucleophilic region on another atom or molecule, provides a highly directional tool in forming solid-state motifs. This interaction, along with the related chalcogen bonding interactions, forms powerful synthons, which, when combined with other typical intermolecular attractions such as hydrogen bonding, allow for the design of supramolecular structures and inputs to crystal engineering. This dissertation research serves two primary purposes: (1) to catalog halogen and chalcogen bonding interactions with various donor molecules and (2) to utilize these interactions to probe interesting organic transformations.

In order to …

Synthesis Of Fluorinated Monomers And Polymers For Various Applications, Cassandra J. Hager

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The world of industry utilizes a variety of polymers for various applications in many prominent fields. From electronics to food storage, the versatility of this class of chemistry has been widely proven. The Thrasher research group undertook a program dedicated towards the development of a library of fluorinated materials that focused on the synthesis and characterization of perfluoroalkoxy (PFA) copolymers of tetrafluoroethylene (TFE) and perfluoroalkyl trifluorovinyl ethers. One aim of the project was to improve upon the mechanical strength and wearability of commercial PFA resins by incorporating bulkier perfluoroalkoxy trifluorovinyl ether monomers into these copolymers. In addition to focusing on …

Valorization Of Biopolymers And Biomass To Produce Materials For A More Circular Economy, Moira Lauer

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With a globally increasing population and largely unchecked consumption of raw materials, human society is on track for devastating consequences. Two industries responsible for utilizing massive amounts of raw materials and generating equally gargantuan quantities of waste are the packaging and infrastructure sectors. In 2017 in Europe, for example, packaging reached a record 173 kg of packaging waste per capita. One of the largest packaging consumers is the food industry, in which 40% of packaging is made of petroleum-derived single-use plastic, leading to a massive carbon imbalance. “The Built Environment,” on the other hand, is responsible for about 50% of …

Extractive Membranes For The Detection And Screening Of Waterborne Plutonium, James Foster

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The development of rapid screening tools for special nuclear materials remains a crucial focus for nonproliferation efforts. Traditional approaches for the analysis of trace-level Pu isotopes in water requires tedious and time-consuming sample preparation steps that do not lend well to expeditious screening. Therefore, a novel analytical method that combines both Pu concentration and source preparation into a single detection system would make for an invaluable tool for nuclear security applications. Extractive membranes absorbers can help to fulfill this role as they are capable of concentrating Pu to detectable limits while subsequently serving as alpha spectrometry sample sources. In Chapter …

Automated Parallel Optimization Of Simulation Parameters Using Modified Nelder-Mead Simplex Algorithm, Erina Mills

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Computational simulations used in many fields have parameters that define models that are used to evaluate simulated properties. When developing these models, the goal is to choose the parameters that best replicate a set of desired properties. Mathematical optimization methods can be used to optimize the simulation parameters by defining a function that uses simulation parameters as input and outputs a value describing how well a set of experimental properties are reproduced.

Because simulated properties are often calculated using stochastic sampling methods, this optimization involves an objective function that is noisy and expensive to evaluate. Also, optimization of the simulation …

Synthesis And Molecular Processes Governing Self-Healing Polymeric Materials, Siyang Wang

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Self-healing polymers capable of recovering from physical damages are promising materials for advanced technologies. In these studies, we developed routes to achieve self-healable properties in acrylic-based copolymers that rely on non-covalent dipolar interactions present in essentially all polymeric materials. Using a combination of spectroscopic tools, thermo-mechanical analysis, and molecular dynamic (MD) simulations, these studies have shown that dipolar interactions lead to conformational changes of macromolecular segments which, in turn, result in self-healing without external intervention. This dissertation also describes the development of novel self-healable acrylic-based covalent adaptable networks (CANs) that combine reprocessing and self-healing properties. The utilization of dipolar interactions …

Light Harvesting And Electrically Conducting Metal-Organic Frameworks, Monica Gordillo Varela

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Composed of metal clusters nodes and organic linkers, metal-organic frameworks (MOFs) have emerged as versatile platforms with unparalleled chemical and structural tunability, synthetic facility, permanent porosity, and size-selective guest encapsulation capability. These features make them potential candidates for a variety of applications such as gas storage,drug delivery, catalysis,and sensing. In recent years, the introduction of redox- and photoactive components have yielded stimuli-responsive electronic and photonic MOFs and expanded their utility in molecular electronics and energy storage devices/technologies.

Chapter one describes the light-harvesting ability of a porphyrin-based MOF. Herein, we have demonstrated spontaneous solvothermal growth of [100]-oriented uniform pillared-porphyrin framework-11 (PPF-11) …

Synthesis Of Nanoparticles In A Silicate Matrix, Tatiana Alexandra Estrada-Mendoza

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Nanoparticle synthesis is the driving force behind research and development in nanotechnology. The development of more tailored nanoparticles for different uses is increasing the need for more efficient and cleaner synthetic methods. The use of sodium silicate matrix for the synthesis of various nanoparticles is a novel strategy requiring minimum laboratory set up. Exploratory studies that are presented and discussed here highlight the robust nature, versatility, and multifaceted role this matrix plays in the synthesis of nanoparticles. This dissertation focuses on the synthesis and properties of plasmonic hybrid nanoparticles and metal sulfide nanoparticles. The introductory chapter highlights the importance of …

Development Of Capillary-Channeled Polymer (C-Cp) Fiber As Stationary Phase For Biological Sample Application, Lei Wang

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Capillary-channeled polymer (C-CP) fibers as an alternative support/stationary phase for biomacromolecule separations on analytical and preparative scales have been developed by Marcus research group. The combination of the fiber micro- and macro-structures and in-column orientation allows operation at comparably high linear velocities (~100 mm s-1) without excessive system backpressure. The ability to move fluid efficiently through the structure is complemented by the fact that the fiber physical structure is effectively nonporous with respect to the size of proteins, therefor there is no significant intrafiber diffusion. Ultimately, these factors combine for protein separations that are devoid of appreciable van Deemter C-term …

Nano-Scintillators As Next Generation Tools For Optogenetics, Ashley Dickey

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Optogenetics is a technique that is used to study neural pathways and has the ability to activate or silence synaptic behavior using visible light. Currently, the visible light sources used for optogenetics are surgically implanted into the brain tissue, but this harmful and invasive technique may be avoided if suitable scintillating nanoparticles can be inserted via injection. The proposed nano-scintillator particles must adhere to rigorous parameters including being under 100 nm, uniform, nontoxic, and dispersible to be successful in this biological system. The phase, crystallinity, and dopant concentration must be optimized to absorb X-ray radiation and emit photons of the …

X-Panding Halogen Bonding Interactions: Hybrid Cocrystals Composed Of Ionic Halides, Iodine And Organoiodines, Khadijatul Kobra

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Halogen bonding referred to as an attractive, noncovalent interaction between an electrophilic region of a halogen atom X (acts as Lewis acid) and a nucleophilic region of a molecule Y (acts as Lewis base). Such interactions and the resulting polymeric networks play an important role in many fields related to crystal engineering, including for example, the fabrication of liquid crystals and novel drug design. The application of halogen bonding has particular promise in biological systems by increasing the lipophilicity of drugs to improve penetration through lipid membranes and tissues, enabling better intracellular delivery.

Based on this concept, my research at …

Nanomaterials-Based Electrodes For Lithium-Ion Batteries And Alcohol Fuel Cells, Lakshman K. Ventrapragada

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This dissertation describes my research on surfactant-free synthesis of nanomaterials with applications for alcohol fuel-cell electrodes, and design and fabrication of nanomaterials-based current collectors that improve the performance of lithium-ion batteries (LIBs) by replacing existing current collectors.

Chapter 1 provides a background on the electroanalytical tools used in this research, and an introduction to fuel cells and LIBs.

Chapter 2 describes a novel synthesis method for fabricating gold-graphene composites by laser ablation of a gold strip in water. A well-known limitation in the fabrication of a metal-graphene composite is the use of surfactants that strongly adsorb on the metal surface …

A Targeted Drug Delivery Strategy For Trypanosomiasis Towards A Diastereoselective Boronate Ester Mediated Intramolecular Diels-Alder Cycloaddition, Heeren Manoj Gordhan

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Human African trypanosomiasis (HAT), commonly called African sleeping sickness, is caused by bloodstream form Trypanosoma brucei and has the potential to affect millions of people in sub-Saharan Africa. Treatments have existed for the past fifty years, but are characterized by severe adverse side-effects and poor efficacy. Trypanosomes generate ATP through glycolysis, or the metabolism of glucose, which is catalyzed by enzymes called hexokinases (TbHK1 and TbHK2) in trypanosomes. Through high-throughput screenings (HTS) and structure-activity relationships (SAR), both hexokinases could be targeted with small molecules to inhibit the first step in the glycolytic pathway of trypanosomes. Of the two hexokinases, TbHK1 …