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Applying Bayesian Machine Learning Methods To Theoretical Surface Science, Shane Carr

McKelvey School of Engineering Theses & Dissertations

Machine learning is a rapidly evolving field in computer science with increasingly many applications to other domains. In this thesis, I present a Bayesian machine learning approach to solving a problem in theoretical surface science: calculating the preferred active site on a catalyst surface for a given adsorbate molecule. I formulate the problem as a low-dimensional objective function. I show how the objective function can be approximated into a certain confidence interval using just one iteration of the self-consistent field (SCF) loop in density functional theory (DFT). I then use Bayesian optimization to perform a global search for the solution. …

Manipulating Electron Transfer Reactions From Micro- To Preparative Scale, Matthew Duane Graaf

Arts & Sciences Electronic Theses and Dissertations

The utilization of electron transfer reactions has allowed the transformation of a variety of substrates from polymer surfaces to highly functionalized organic molecules. The intricacies of these electron transfer reactions have been utilized to develop a new platform for building and studying addressable molecular libraries as they interact with biological targets. As a low cost, reusable alternative to other methods of these studying binding interactions, microelectrode arrays are beginning to gain traction with the scientific community as we continually push the limits of their potential. Additionally, the electron transfer techniques used to build the molecular libraries can be expanded to …

Solid-State Nmr Studies Of Carbon Capture And Carbon Mineralization Reactions, Jeremy Moore

Arts & Sciences Electronic Theses and Dissertations

This dissertation presents research on the chemistry of carbon dioxide capture and mineralization which has been accomplished with a variety of solid-state nuclear magnetic resonance (NMR) spectroscopy techniques. Materials used for carbon capture interact with CO2 through different adsorption mechanisms, physisorption and chemisorption. The physisorption systems studied have shown that adsorbed CO2 undergoes a hopping mechanism within the material. The studies of chemisorption systems indicate a mixture of adsorption products forms during the adsorption interaction. Carbon mineralization reactions have been studied to better understand the reactions that can occur at underground carbon sequestrations sites that are used for storing CO2. …

Structural And Functional Analysis Of The Reaction Center Complexes From The Photosynthetic Green Sulfur Bacteria, Guannan He

Arts & Sciences Electronic Theses and Dissertations

The reaction center (RC) complex of the green sulfur bacterium Chlorobaculum tepidum is composed of the Fenna-Matthews-Olson (FMO) antenna protein and the reaction center core (RCC) complex. The RCC complex has four subunits: PscA, PscB, PscC, and PscD. The structure of the intact and functional FMO-RCC complex was studied by chemically cross-linking the purified sample followed by biochemical and spectroscopic analysis. The interaction sites of the cross-linked complex were also studied using LC-MS/MS. A structural model is proposed based on those results. In addition, the RCC complexes were purified, both the PscA-PscC complex from the Chlorobaculum tepidum and the PscA-PscB …

Structure And Function Of Cytochrome Containing Electron Transport Chain Proteins From Anoxygenic Photosynthetic Bacteria, Erica Lois-Wunderlich Majumder

Arts & Sciences Electronic Theses and Dissertations

This dissertation examines the structure and function of photosynthetic proteins that contain c-type heme cofactors that function in the electron transport chains of anaerobic phototrophic bacteria. The diversity and range of these cytochromes proteins was explored. Then, individual proteins were studied in detail. The diheme cytochrome c from Heliobacteria modesticaldum was studied using hydrogen deuterium exchange mass spectrometry and homology modeling. A structural model of the protein and a mechanism for the cytochrome bc complex was proposed. Next, the monoheme cytochrome c subunit from the Alternative Complex III from the Filamentous Anoxygenic Phototrophs was studied using biochemistry and found to …

Mass Spectrometry-Based Strategies For Biomolecular Structure Analysis: Steroid Metabolites Structures And Protein-Protein Interactions, Yuetian Yan

Arts & Sciences Electronic Theses and Dissertations

Mass spectrometry is an important method for studying the structure of both small molecules and large biomolecules (e.g., proteins). The majority of the applications prior to 1970 were focused on small molecules, owing to the limited ionization methods which posed difficulties in producing gas-phase ions for large biomolecules then. Beginning in the 1980's, with the introduction of new ionization methods (ESI and MALDI), the applications have gradually switched to biological science measuring large bioorganic molecules. Today, with the developing interest in metabolomics and proteomics, and ongoing improvement in MS-based techniques, mass spectrometry is extensively applied in the study of both …

Light-Harvesting, Redox Control, And Biomimicry Of The Photosynthetic Antennas Of Green Sulfur Bacteria, Gregory Scott Orf

Arts & Sciences Electronic Theses and Dissertations

The green sulfur bacteria (class Chlorobea) are obligately anaerobic photoautotrophic prokaryotes. Members of this bacterial class are found in anoxic, sulfur- or iron-rich environments such as hydrothermal vents and hot springs. These bacteria are champions of lowlight adaptation, with some species being able to thrive photosynthetically on less than eight photons hr-1 per pigment. We have studied the two photosynthetic antenna complexes from these organisms that are responsible for light capture: the chlorosome and the Fenna-Matthews-Olson (FMO) protein.

In regards to the chlorosome, we studied, using steady-state and time-resolved spectroscopic methods, the effect of incorporation of an expected, but as-yet-undiscovered-in-nature, …

Development And Application Of Mass Spectrometry-Based Biophysical Approaches, Ying Zhang

Arts & Sciences Electronic Theses and Dissertations

Mass spectrometry (MS)-based biophysical approaches are new "tools" for protein characterization owing to its capability to analyze proteins and protein complexes that range in molecular weight from kDa to MDa. Protein characterization requires more than identifying the primary structure. More importantly, protein high order structures (i.e., secondary, tertiary and quaternary structures) are needed for biological studies. MS has become the major tool in studies of protein primary structure and post translational modifications (PTMs) over the past two decades. Because MS has high sensitivity and fast turnaround, more and more biophysical approaches rely on MS to generate information for protein higher …

Synthesis, Structure, Spectroscopy, And Reactivity Of Azapentadienyl-Ruthenium-Phosphine Complexes, Meghan Leigh Stouffer

Arts & Sciences Electronic Theses and Dissertations

This dissertation focuses on the systematic synthesis of ¬bis-azapentadienyl-ruthenium-phosphine complexes. The synthetic approach involves the treatment of Cl2Ru(PPh3)3 with potassium tert-butylazapentadienide reagent. The reactivity of this parent compound with other 2e- donor ligands is investigated. These resultant complexes' reactivity with triflic acid is also studied.

Treatment of Cl2Ru(PPh3)3 with potassium tert-butylazapentadienide produces [(1,2,3-η3)-5-tert-butylazapentadienyl]2Ru(PPh3)2 (1). Compound 1 undergoes single substitution of one of the triphenylphosphines when treated with PMe3, dmpe, P(OMe)3, CNCMe3, CO, and PEt3 at room temperature, resulting in [(1,2,3-η3)-5-tert-butylazapentadienyl]2Ru(PPh3)(L) (2, L = PMe3; 3, L= dmpe; 4, L = P(OMe)3; 5, L = CNCMe3; 6, L = CO; 7, …

Kinetic Analysis And Inhibition Studies Of Iron-Dependent Histone Demethylases, Barbara Gordon Cascella

Arts & Sciences Electronic Theses and Dissertations

The research presented herein focuses on the kinetics and inhibition of the KDM4 subfamily of Jumonji C (JmjC) domain-containing histone demethylases (HDMs). Belonging to the larger class of alpha-ketoglutarate (alpha-KG)-dependent, non-heme iron monooxygenases, the JmjC-HDMs remove methyl groups from mono-, di-, and tri-methylated histone lysine residues through an Fe(IV)-oxo-catalyzed hydroxylation reaction. JmjC-HDMs have been found to play integral roles in the maintenance of genomic integrity as well as in the regulation of transcription. Three KDM4 members were studied: the mixed H3K9/H3K36 demethylases KDM4A and KDM4C, and the pure H3K9 demethylase KDM4E. KDM4C is a hypoxia-inducible factor 1 (HIF-1) target gene …

Isotope Harvesting At Heavy-Ion Fragmentation Facilities, Tara Elise Mastren

Arts & Sciences Electronic Theses and Dissertations

Isotope harvesting from heavy-ion fragmentation facilities is a potential source of isotopes of interest for applications research. With the upgrade of the National Superconducting Cyclotron Laboratory (NSCL) to the Facility for Rare Isotope Beams (FRIB) usable quantities of many isotopes of interest will be produced and available for harvest from an aqueous beam dump. If available, these isotopes would be of interest to a broad range of applications such as medicine, geology, and stockpile stewardship. Preliminary experiments were performed at the NSCL in order to determine the feasibility of isotope harvesting at (FRIB).

A water target station that consisted of …

Synthesis And Characterization Of Pbs Quantum Sheets Through Lamellar Assembly, And Updates To The Cdse Quantum Wire Synthesis, Paul James Morrison

Arts & Sciences Electronic Theses and Dissertations

This dissertation reports the novel synthesis of PbS quantum plates (QPs) via a reaction executed at low temperatures. The PbS QPs are grown in a template-assisted mechanism, with the first excitonic peak observed in the visible region of light at ~620 nm (2.0 eV), at an energy radically different than the band gap of bulk PbS (~3000 nm, 0.42eV). The large energy shift is due to the extremely thin dimension of these nanoplates, which is determined to be ~1 nm in thickness. Thickness measurements are made in a powder X-ray diffractometer (XRD) at low angles (between 2-15º 2θ). These measurements …

Study Of Ii-Vi Colloidal Semiconductor Magic-Size Nanoclusters And Crystalline Quantum Platelets, Yuanyuan Wang

Arts & Sciences Electronic Theses and Dissertations

The main objective of this project is to prepare and isolate the smallest, discrete, magic-size nanoclusters of cadmium selenide (CdSe) and to grow crystalline, wurtzite CdSe quantum platelets (QPs) at room temperature. The achievement of these goals enables us to provide a general synthesis of II-VI semiconductor magic-size nanoclusters and low-temperature routes to well-passivated nanocrystals having a range of compositions and morphologies.

The magic-size nanocluster (CdSe)13 is grown in a lamellar-bilayer soft template at room temperature. The results described in this thesis strongly suggest that [(CdSe)13(n-octylamine)13] is the most thermodynamically stable nanocluster and serves as a key intermediate in the …

Polyol Synthesis Of Silver Nanowires By Heterogeneous Nucleation And Mechanistic Aspects Influencing Its Length And Diameter, Waynie M. Schuette

Arts & Sciences Electronic Theses and Dissertations

Various additives are employed in the polyol synthesis of silver nanowires (Ag NWs), which are typically halide salts such as NaCl. A variety of mechanistic roles have been suggested for these additives. My research showed that the early addition of NaCl in the polyol synthesis of Ag NWs from AgNO3 in ethylene glycol results in the rapid formation of AgCl nanocubes, which induce the heterogeneous nucleation of metallic Ag upon their surfaces. Ag NWs subsequently grow from these nucleation sites. The conclusions are supported by studies using ex-situ generated AgCl nanocubes.

Additionally, the final mean silver nanowire diameter is found …

High Valent Palladium Complexes And Their Role In C-C And C-X Bond Formation Chemistry., Fengrui Qu

All Theses and Dissertations (ETDs)

Energy is the currency of the universe. Without energy everything will come to a stall. According to the Energy Information Administration, in 2007 over 80 % of energy came from fossil fuel. When the fossil fuel will eventually run out at the current consumption rate, then what can we use for energy? While finding alternative energy sources is our ultimate goal, our research focus on the basic study of the role metal ions play in the catalysis of energy related process. Namely, the water oxidation catalysis and methane oligomerization process.

Water oxidation is a multi-electron process, which requires multiple single …

Mri Characterization Of Radiation Necrosis In An Animal Model: Time To Onset, Progression, And Therapeutic Response, Xiaoyu Jiang

All Theses and Dissertations (ETDs)

Radiation necrosis is a severe, but late occurring type of injury to normal tissue, within and surrounding a radiation treatment field, which can lead to significant complications for neurooncology patients. Radiation necrosis is difficult to distinguish from recurrent tumor by either neurologic examination or clinical imaging protocols. Concerns for the development of radiation necrosis often limit therapeutic radiation doses. Current treatment options for radiation necrosis are limited. The development of solutions to these clinical challenges has been hampered by an appropriate animal model of radiation necrosis.

With a novel mouse model of radiation necrosis developed in our lab employing a …

Photoelectron Imaging Of Iodide Centered Alkyl Halide Cluster Anions, Joshua S. Lasinski

All Theses and Dissertations (ETDs)

This dissertation presents results from cluster anion photodetachment experiments of the solvated iodide anion as a means of investigating electron molecule interaction. Due to the localization of the excess charge on the iodine atom, these experiments proceed analogously to electron scattering experiments, in that exposure to sufficient photon energy detaches the electron, which may or may not interact with the target molecule before being detected. Such interactions are related to temporary electron capture into the σ* orbital of the target molecule.

This dissertation begins with an analysis of the previously published I−·CH3X: X = I, Br, Cl) photodetachment results. These …

Structural And Functional Study Of The Diheme Cytochrome C Subunit Of The Cytochrome Bc Complex In Heliobacterium Modesticaldum, Hair Yue

Arts & Sciences Electronic Theses and Dissertations

This dissertation is focused on the structural and functional study of the unique diheme cytochrome c subunit of the cytochrome bc complex in H. modesticaldum, and its application in determining the stoichiometry between H. modesticaldum's cytochrome bc complex and its reaction center. Heliobacterium modesticaldum is a gram positive, anaerobic, anoxygenic photoheterotrophic bacterium. Its cytochrome bc complex (Rieske/cyt b complex) has some similarities to cytochrome b6f complexes from cyanobacteria and chloroplasts, and also shares some characteristics of typical bacterial cytochrome bc1 complexes. One of the unique features of the heliobacterial cytochrome bc complex is the presence of a diheme cytochrome c …

Photosynthetic Chromophore Analogs And Biohybrid Antenna For Light Harvesting, Joseph William Springer

Arts & Sciences Electronic Theses and Dissertations

Photosynthetic chromophore analogs are studied, starting with simplified structures and systematically building complexity to elucidate overarching design principles. The general goals are to achieve an artificial light-harvesting system that exhibits broad spectral coverage, including extension well into the photon rich red and near-infrared portions of the solar spectrum. For example, the spectral properties of chlorophylls are primarily a consequence of the 13¹-oxophorbine base macrocycle, with further tuning provided by the dramatic difference in auxochromic effects of a given substituent at the 7- versus 3-position, consistent with Gouterman's four-orbital model.

While light-harvesting antennas in photosynthetic bacteria generally have near-quantitative …

A Study On The Structure And Photodetachment Dynamics Of Copper Based Molecular Anions Using Photoelectron Spectroscopy, Nicholas Stephen Holtgrewe

Arts & Sciences Electronic Theses and Dissertations

This dissertation represents a study of the effects of electron molecule interactions in the detachment and dissociation dynamics of copper based molecular anions. Results are presented on the photodetachment of small copper oxide CuO_n⁻ (n = 1, 2) and copper fluoride CuF _n⁻ (n = 1, 2) molecular anions. Effects of different resonances are explored using the photoelectron angular distributions (PADs) and the relative intensity variations in vibrational channel cross sections. The specific resonances studied include dipole bound resonances, in which the electric dipole moment of the neutral molecule captures the outgoing electron, and electronic Feshbach resonances, …

Assessing Optic Neuritis In A Mouse Model Of Multiple Sclerosis With Diffusion Mr Imaging, Chia-Wen Chiang

Arts & Sciences Electronic Theses and Dissertations

Optic neuritis (ON) is an early manifestation in patients of multiple sclerosis (MS), typically resulting in visual dysfunction. The inflammatory demyelination of the optic nerve in ON closely resembles pathologies of the rest of central nervous system (CNS) white matter in MS. Since accumulated axonal degeneration in MS was considered as the potential cause leading to permanent disability, correlating optic nerve pathology and visual function in ON could be a model system to investigate the relationship between functional outcome and neuropathology. It may also present a new way to reflect the disease progression in MS. Various MR techniques have been …

Molecular Design And Photophysical Characterization Of Synthetic Bacteriochlorins For Solar Energy Conversion And Photodynamic Therapy, Eunkyung Yang

All Theses and Dissertations (ETDs)

The design, photophysical characteristics and some potential applications of synthetic bacteriochlorins are discussed. Bacteriochlorins: e.g., bacteriochlorophylls) are tetrapyrrole macrocycles with two reduced pyrrole rings, whereas chlorins: e.g., chlorophylls) and porphyrins: e.g., hemes) have one and zero reduced pyrrole rings. Molecular design characteristics are revealed by understanding the effects of substituent types and patterns and the central metal ion on the photophysical properties and electronic structure. These effects are elucidated via studies of the optical absorption and emission spectra and excited-state decay pathways, and analysis of the molecular-orbital characteristics within the four-orbital model. The studies also encompass analysis of the properties …

Energetics And Dynamics In Quantum Confined Semiconductor Nanostructures, Jessica Hoy

All Theses and Dissertations (ETDs)

The ability to tune the band-gap energies of semiconductor quantum dots, nanoplatelets, and quantum wires, their significant absorption cross sections, and high photoluminescence quantum yields make these nanostructures promising moieties for use in optoelectronic devices, solar concentrators, chemical sensors, and biological labels. The variable dynamics of the electron-hole pairs that occur within semiconductor nanostructures, however, can complicate the utility of these devices. The variability of the dynamics is born from the different paths accessible for the charge carriers to undergo. In this work, three pathways are proposed to be of primary consequence, namely, electronic intraband relaxation, coupling to surface-mediated processes, …

Rapid, Efficient And Versatile Strategies For Functionally Sophisticated Polymers And Nanoparticles: Degradable Polyphosphoesters And Anisotropic Distribution Of Chemical Functionalities, Shiyi Zhang

All Theses and Dissertations (ETDs)

The overall emphasis of this dissertation research included two kinds of asymmetrically-functionalized nanoparticles with anisotropic distributions of chemical functionalities, three degradable polymers synthesized by organocatalyzed ring-opening polymerizations, and two polyphosphoester-based nanoparticle systems for various biomedical applications.

Inspired by the many hierarchical assembly processes that afford complex materials in Nature, the construction of asymmetrically-functionalized nanoparticles with efficient surface chemistries and the directional organization of those building blocks into complex structures have attracted much attention. The first method generated a Janus-faced polymer nanoparticle that presented two orthogonally click-reactive surface chemistries, thiol and azido. This robust method involved reactive functional group transfer by …

Use Of Self-Assembled Monolayers To Tailor Surface Properties: From Lubrication To Neuronal Development, Natalie Ann Lafranzo

All Theses and Dissertations (ETDs)

The subsequent work describes advances in modifying the chemical properties of various substrates to tailor the surface properties for specific applications. This is achieved by making use of a molecular assembly known as self-assembled monolayers, or SAMs. SAMs are composed of tightly packed organic molecules that form a well-ordered structure on a substrate. Typically, the head group of the monomer is covalently anchored to the substrate, and monolayer order and self-assembly is achieved through van der Waals interactions between the long alkyl chains of the monomer's tail group. Monolayers containing head groups consisting of thiols, siloxanes, and phosphonates have been …

Functional, Degradable Polyester Materials Synthesized From Poly(Epsilon-Caprolactone-Co-2-Oxepane-1,5-Dione): An Investigation Into The Derivatization, Self Assembly, And Degradation Behavior Of Poly(Epsilon-Caprolactone)-Based Materials, Rhiannon K. Iha

Arts & Sciences Electronic Theses and Dissertations

Biocompatible, degradable polymers possessing a high degree of complexity are an extremely desirable target for many applications. In order to further develop the range and utility of materials made from aliphatic polyesters, poly(epsilon-caprolactone-co-2-oxepane-1,5-dione) (P(CL-co-OPD)) was used as a polymeric precursor for the construction of a series of functional polyester-based materials. By taking advantage of the electrophilic ketone moieties characteristic of the OPD repeat unit, small molecule and polymer grafts were attached to the PCL backbone through the formation of both hydrazone and ketoxime ether linkages. This work has focused on both the synthesis and characterization of functional, degradable polyesters, including …

Discovery And Identification Of New Dna Photoproducts And Investigation Of The Redox Mechanism Of Human Apurinic/Apyrimidinic Endonuclease 1 (Hape1) Protein, Dian Su

All Theses and Dissertations (ETDs)

Exposure of cells to ultraviolet light results in the formation of DNA photoproducts, many of which have been linked to skin cancer. The majority of these photoproducts arise from a photoreaction between two pyrimidines. Irradiation of double stranded B form DNA under physiological conditions mainly produces adjacent dimers. Nonadjacent photodimers of both intrastrand and interstrand types are much rarer. Intrastrand-type nonadjacent dimers form when one or more nucleotides between two pyrimidines become extrahelical owing to the formation of single strand DNA or a slipped structure. This allows the two pyrimidines to photodimerize in a colinear arrangement, as if the intervening …