Physical Sciences and Mathematics Commons^™

Multi-Scale Simulations Of Dynamic Protein Structures And Interactions, Yumeng Zhang

Doctoral Dissertations

Intrinsically disordered proteins (IDPs) are functional proteins that lack stable tertiary structures in the unbound state. They frequently remain dynamic even within specific complexes and assemblies. IDPs are major components of cellular regulatory networks and have been associated with cancers, diabetes, neurodegenerative diseases, and other human diseases. Computer simulations are essential for deriving a molecular description of the disordered protein ensembles and dynamic interactions for mechanistic understanding of IDPs in biology, diseases, and therapeutics. However, accurate simulation of the heterogeneous ensembles and dynamic interactions of IDPs is extremely challenging because of both the prohibitive computational cost and demanding force field …

High Resolution Mass Spectrometry As A Platform For The Analysis Of Polyoxometalates, Their Solution Phase Dynamics, And Their Biological Interactions., Daniel T. Favre

Doctoral Dissertations

Polyoxometalates (POMs) are a class of inorganic molecule of increasing interest to the inorganic, bioinorganic and catalytic communities among many others. While their prevalence in research has increased, tools and methodologies for the analysis of their fundamental characteristics still need further development. Decavanadate (V10) specifically has been postulated to have several unique properties that have not been confirmed independently. Mass spectrometry (MS) and its ability to determine the composition of solution phase species by both mass and charge is uniquely well suited to the analysis of POMs. In this work we utilized high-resolution mass spectrometry to characterize V10 in aqueous …

Design, Synthesis, And Characterization Of Complex Chalcogenides For Energy Storage And Energy Conversion Applications, Srikanth Balijapelly

Doctoral Dissertations

"Through this investigation, complex chalcogenides with the combination of main group metals, transition metals, and rare earth metals have been synthesized using the building block approach and their structure-property relationships are evaluated. The main emphasis of research is on rationally designing new materials for applications in sodium and lithium ion conducting solid electrolytes, cathodes, thermoelectrics, and nonlinear optics. Along with the experimental studies, theoretical calculations are also employed to better understand the physicochemical properties of the synthesized compounds.

The first part of the research will discuss designing alkali ion containing complex chalcogenides using the building block approach. This investigation resulted …

Chirality Determination Using Three-Wave Mixing Microwave Spectroscopy, Nicole Taylor Moon

Doctoral Dissertations

"Rotational spectroscopy has established itself as a reliable gas-phase spectroscopic technique for the structural determination of molecules. This reliability has stemmed from both advancements in microwave technology and a willingness from the community to push the boundaries of the field. In this dissertation, the boundaries are tested in both how well the technique can determine the structure of molecules exhibiting large amplitude motion and through chirality determination. The first half of this dissertation explores the use of deep averaging to determine the structure of silicon containing molecules in collaboration with Dr. Guirgis from the College of Charleston. For each of …

Material Formulation And Process Optimization Towards Fabricating Robust 3d Printed Structures, Austin Riggins

Doctoral Dissertations

This dissertation focuses on understanding and addressing the fundamental physicochemical phenomena that lead to weak interfaces and structural warpage in material extrusion 3D printing. Polymeric feedstocks used for this manufacturing technique were manipulated through the incorporation of additives that alter the dynamics of the matrix during and after printing. In Chapter II, adhesion between layers of structures printed from PEEK was strengthened through a combination of low-molecular weight additive incorporation and post-printing thermal annealing. Chapter III reports a method for decreasing the irreversible thermal strain of structures printed from poly(lactic acid) by introducing nanographene and photoinitiator additives into the feedstock …

Integration Of Raman Spectroscopy And Python-Based Data Analysis For Advancing Neurobiological Research, Natalie E. Dunn

Doctoral Dissertations

The field of Raman spectroscopy continues to expand into biological applications due to its usefulness as a non-invasive technique that can be utilized qualitatively and quantitatively. However, the inherent weakness of Raman scattering leads to the need for each collected spectra to undergo a preprocessing step to remove noise, background drift, and cosmic rays. Biological research in particular needs large datasets due to the increased variability in samples. As datasets grow, the need to perform preprocessing on each individual spectra becomes daunting. Often, these steps are done by hand with the help of specialized software programs. Preprocessing can be accelerated …

Polymer-Based Nanotherapeutics To Combat Difficult-To-Treat Bacterial Infections, Jessa Marie V. Makabenta

Doctoral Dissertations

The continuous emergence and spread of antibiotic-resistant bacteria are a global health emergency, debilitating the capability to prevent and cure various infectious diseases that were once treatable. Antibiotic therapy is further rendered ineffective due to biofilm formation and the ability of bacteria to thrive and colonize inside mammalian cells. Given the diminishing efficacy of available antibiotics combined with the scarcity of new therapeutics entering the antibiotic pipeline, innovative treatment strategies are urgently in demand. Nanomaterial-based strategies offer ‘outside of the box’ approach for the treatment of antibiotic-resistant bacterial infections. Nanomaterials feature tunable physicochemical properties that can be carefully modified to …

Reactive Chemistries For Protein Labeling, Degradation, And Stimuli Responsive Delivery, Myrat Kurbanov

Doctoral Dissertations

Reactive chemistries for protein chemical modification play an instrumental role in chemical biology, proteomics, and therapeutics. Depending on the application, the selectivity of these modifications can range from precise modification of an amino acid sequence by genetic manipulation of protein expression machinery to a stochastic modification of lysine residues on the protein surface. Ligand-Directed (LD) chemistry is one of the few methods for targeted modification of endogenous proteins without genetic engineering. However, current LD strategies are limited by stringent amino acid selectivity. To bridge this gap, this thesis focuses on the development of highly reactive LD Triggerable Michael Acceptors (LD-TMAcs) …

Applying Density Functional Theory Simulations To Study The Charge Balancing And Structure Directing Roles Of Fluoride In Zeolite Synthesis, Tongkun Wang

Doctoral Dissertations

Zeolites represent a major cornerstone of today’s energy industry as the most-used petrochemical catalyst by weight in the world. Constituted by tetrahedra of T-atoms including Si, Al, Ge and Ti, zeolites form a huge family of nano-porous crystalline materials which also provide reliable candidates for novel, energy related applications such as efficient separations, hydrogen-purifying/storing and conversions from biomass to biofuel. However, the formation mechanism of zeolite is still not clear, as synthesis processes are complicated by requirements including structure directing agents (SDAs), hydroxide or fluoride medium, and experimental conditions like temperature. Attempts for designing new zeolite structures still fall in …

Atomistic Simulations Of Intrinsically Disordered Protein Folding And Dynamics, Xiping Gong

Doctoral Dissertations

Intrinsically disordered proteins (IDPs) are crucial in biology and human diseases, necessitating a comprehensive understanding of their structure, dynamics, and interactions. Atomistic simulations have emerged as a key tool for unraveling the molecular intricacies and establishing mechanistic insights into how these proteins facilitate diverse biological functions. However, achieving accurate simulations requires both an appropriate protein force field capable of describing the energy landscape of functionally relevant IDP conformations and sufficient conformational sampling to capture the free energy landscape of IDP dynamics. These factors are fundamental in comprehending potential IDP structures, dynamics, and interactions. I first conducted explicit solvent simulations to …

Dinitrogen Functionalization Using A Molybdenum Atom: Bridging The Gap Between Small And Coordination Complexes Via Quantum Mechanical Methods, Maria Virginia White

Doctoral Dissertations

Chemistry devotes a significant amount of its research to understanding small molecule activation from an electronic structure perspective to help with the investigation of the reaction pathways of catalytically active substances that can promote biomimetic catalysis. A large portion of the energy used annually in our planet is used for the artificial nitrogen fixation (Haber-Bosch process), which renders dinitrogen activation a subject of study. Molybdenum, a fourth row transitional metal, has demonstrated its effectiveness as an essential component of the dinitrogen reduction catalytic process. To better understand the multiple dinitrogen molybdenum binding modes, the work described herein combines wave function …

Theoretical Studies Of Adsorption And Reactivity At The Gas-Solid Interface, Carson J. Mize

Doctoral Dissertations

Catalytic transformations of small molecules is of great interest for both laboratory and industrial practices. Two specific transformations are ethylene to ethylene oxide and combinations of azides and alkenes into aziridine molecules. Ethylene oxide is an epoxide used as a feed-stock for many bulk reactions and commercial products such as antifreeze and various sterilization techniques, while molecules with the aziridine functional group are used for many ring opening and closing techniques as well as in pharmaceuticals and other drug treatments. For production of ethylene oxide, the combination of oxygen adsorbed onto a silver crystal is the known catalysts for thus …

Chirality, Symmetry-Breaking, And Chemical Substitution In Multiferroics, Kiman Park

Doctoral Dissertations

Multiferroic materials attract significant attention due to their potential utility in a broad range of device applications. The inclusion of heavy metal centers in these materials enhances their magnetoelectric properties, yielding fascinating physical phenomena such as the Dzyaloshinskii–Moriya interaction, nonreciprocal directional dichroism, enhancement of spin-phonon coupling, and spin-orbit-entangled ground states. This dissertation provides a comprehensive survey of magnetoelectric multiferroics containing heavy metal centers and explores spectroscopic techniques under extreme conditions. A microscopic examination of phase transitions, symmetry-breaking, and structure-property relationships enhances the fundamental understanding of coupling mechanisms.

In A2Mo3O8 (A = Fe, Zn, Ni, and Mn), we use optical spectroscopy …

Comprehensive Studies Of Magnetic Properties Of Metal-Organic Frameworks And Molecular Compounds, Pagnareach Tin

Doctoral Dissertations

Single-ion magnets (SIMs) are at the forefront of molecular electronic spin magnets with potential applications in magnetic memory storage devices. However, the magnetic properties of the SIMs are yet to be completely understood, especially the magnetic properties of large anisotropy systems. A part of this dissertation is to utilize optical and neutron spectroscopies such as far-IR magneto-spectroscopy (FIRMS) and inelastic neutron scattering (INS) to quantify the anisotropy and study the phonon properties of the SIMs as two-dimensional (2-D) metal-organic frameworks (MOFs) or coordination polymer (CP), and a molecular magnet. In addition, ab initio calculations are used to understand the origin …

Synthesizing, Purifying, And Characterizing Molten Chloride Salts, Phillip W. Halstenberg

Doctoral Dissertations

Molten chloride salts have vast potential as heat transfer fluids with both nuclear and concentrated solar power applications. For application in energy systems, the characteristics that govern these systems must be well understood. This work focuses on inorganic molten chloride salts with a special emphasis on the experimental aspect of chemical research. Chapter 2 covers the synthetic approaches for the formation of molten chloride mixtures. Many salts can be purchased from industrial suppliers, but most must be purified therefore, Chapter 3 evaluates various methodology developed for removal of impurities in salt mixtures. Once the salt of proper content and purity …

Mechanochemical Synthesis Of Task-Specific Conjugated Porous Networks Towards Enhanced Energy Storage, Juntian Fan

Doctoral Dissertations

Conjugated scaffolds with high electronic conductivity, high surface area, etc. are promising materials for diverse technological applications, especially in the electrochemical field. However, the current synthesis methods are still limited to the traditional solution-based method or the ionothermal method, which always require an inert atmosphere shield, large amounts of organic solvents, noble catalysts, long reaction time up to days, and high temperatures, etc. Therefore, there is a common goal of developing conjugated scaffolds through facile, green, straightforward pathways. Mechanochemistry, which is an efficient, sustainable, solvent-free methodology, could provide a unique reaction environment to synthesize this kind of functionalized materials, resulting …

Utilizing Ultra-Performance Chromatography High-Resolution Mass Spectrometry To Investigate Fatty Acid Mediated Antibiotic Tolerance, Brittni Woodall

Doctoral Dissertations

The lipid membrane is the first component necessary to sustain life. To maintain homeostasis, segregate cellular machinery, provide protection from the environment, and reproduce, an organism must establish a boundary in which the processes can occur. Throughout the last two decades, research has propelled our knowledge of lipid membranes much beyond original hypotheses. Once thought of to be static and uniform, the understanding of the lipid membrane has evolved to encompass a structure that is responsive, unique, and intricately constructed by the organism itself. By chance or by choice, organisms adapt the lipid membrane according to the environment for which …

The Novel Chlorination Of Zirconium Metal And Its Application To A Recycling Protocol For Zircaloy Cladding From Spent Nuclear Fuel Rods, Breanna K. Vestal

Doctoral Dissertations

A novel protocol has been developed for the chemical removal of zirconium alloy (Zircaloy) cladding from spent nuclear fuel rods and subsequent isolation and purification of nuclear-grade zirconium chloride derived therefrom. This protocol is based on the chemistry developed from two new scientific findings.

First, two new oxidative chlorination reactions have been discovered for zirconium metal. In both solvents, zirconium can be quantitatively chlorinated at temperatures less than 150°C, with the operative equations seen below. In sulfur monochloride, the reaction is completed in 2 – 4 hours via surface etching, exhibiting 0^th order kinetic behavior. The elemental sulfur byproduct …

Development Of Biomolecule Nanoparticle Conjugate For Targeted Delivery Of Therapeutics, Peidong Wu

Doctoral Dissertations

Delivery of therapeutics specifically to the disease site is the final goal for the field of drug discovery. Considerable efforts in understanding disease biology have contributed to identifying novel therapeutics such as small molecules, proteolysis targeting chimeras (PROTACs), peptides, proteins, and nucleic acids. However, improving their efficacy as well as minimizing their off-target toxicity remains challenging. Developing vectors that could not only efficiently encapsulate these therapeutics but also direct these therapeutics to the target site is a potential solution to address these challenges. In this dissertation, a block-copolymer-based nanoparticle platform has been developed optimized, and decorated with various kinds of …

Controlling Mechanical Properties Of Well-Defined Polymer Networks, Ipek Sacligil

Doctoral Dissertations

Polymer networks are one of the most versatile and highly studied material class that revolutionized many aspects of life. Connecting the final network properties to the molecular parameters of its building blocks remains a major research thrust. Recent advances in network synthesis techniques allowed for accurate predictions of elastic modulus in model networks. Tew Group has developed highly efficient, thiol-norbornene networks with controllable mechanical properties. Chapter 2 focuses on modifying the gel fracture energy predicted by Lake-Thomas theory by accounting for loop defects. This study allowed for a priori estimates of gel fracture energy by combining theory, experiments, and simulations. …

Determining Bond Strengths And Dissociation Dynamics Of Diatomic Metal-Containing Ions By Photofragment Imaging, Schuyler P. Lockwood

Doctoral Dissertations

Studies of simple metal ion – ligand complexes have primarily focused on understanding their roles in activating C-H and C-C bonds. However, data are often lacking on the fundamental properties of these species, which can have unusual bond orders and cluttered electronic structures with many states of multi-reference character, complicating their treatment in theoretical studies. Experimental work determining high-precision bond energies, ground state identities and excited state dynamics of a wider variety of metal-containing ions is needed to establish a robust set of well-characterized benchmark molecules. This work describes studies of the energetics and dynamics of several MX⁺ species, …

Scanning Probe And Spectroscopic Investigations Of Polarization-Driven Electronic Interactions At The Inorganic/Organic Interface Of 2d Materials, Nicholas Hight-Huf

Doctoral Dissertations

My thesis focuses on understanding the changes in electronic properties of two-dimensional materials produced by surface interactions not limited to charge exchange. Recent work from our group demonstrated that both small molecules and polymers can function as effective charge dopants for monolayered 2D materials such as MoS₂ and graphene, changing the Fermi energy by either donating or accepting electron density to/from the 2D material. Additionally, the underlying support material was found to play a significant role, where higher dielectric constant supports result in larger magnitude of Fermi energy shift of the 2D material because less of the dopant interaction …

Effect Of Chemical Identity And Morphology On Amphiphilic-Zwitterionic Block Copolymer Membranes, Ria Ghosh

Doctoral Dissertations

Amphiphilic block copolymers have gained a broad research interest attributed to their self-assembly properties over a range of pH, temperature, and ionic strength. Polyzwitterions have attracted special attention due to their hydrophilicity, charge sensitivity and coulombic attraction of the opposite charges over a range of environments making them a popular material of study in the field of stimuli responsive systems, for example in self-healing hydrogels, and water transport membranes. Combining the stimuli responsiveness and higher hydrophilicity of zwitterionic polymers with self-assembly behavior of amphiphilic block copolymers created an interest to study the effect of composition and identity of the zwitterionic …

Vapor Deposition Of Self-Wrinkling Polymer Films, Robert N. Enright

Doctoral Dissertations

Initiated chemical vapor deposition is used to grow polymer films on substrates of various three-dimensional shapes which exhibit wrinkling during film growth, termed self-wrinkling. Self-wrinkling avoids separate film growth and compression steps and more-closely mimics processes observed in nature. The self-wrinkling process is elucidated on flat elastic substrates, revealing control over the amount of compressive stress by changing deposition conditions. Next, a study of films grown on liquid substrates with interface profiles that either resemble cylinders or contain repeating concave cones, saddles, and bowls affirms the principle that the wrinkle roundness increases with interface curvature. The selection of high versus …

Electrodeposition Of Epitaxial Wide Bandgap P-Type Semiconductors And Copper Metal For Energy Conversion And Flexible Electronics, Bin Luo

Doctoral Dissertations

"Epitaxial electrodeposition is a simple, low-cost technology to produce highly ordered materials on single-crystal surfaces. This research focuses on the epitaxial electrodeposition of wide bandgap p-type semiconductors and epitaxial Cu thin films via a self-assembled monolayer for energy conversion and flexible electronics. Paper I introduces the epitaxial electrodeposition of hole conducting CuSCN nanorods onto Au (111) surface, and lift-off to produce flexible and transparent foils. Highly ordered CuSCN could serve as an inorganic transport layer in various opto-electronic devices such as perovskite solar cells, LEDs, and transistors. An ordered and transparent CuSCN foil was also produced by epitaxial lift-off following …

Fluorination Of Rubisco-Mimetic Co2 Capture Systems. Theoretical And Experimental Studies Of Ammonium Ion Acidity Depression And Carbamylation, Brian Michael Jameson

Doctoral Dissertations

"RuBisCO-inspired CO₂ capture and release (CCR) systems featuring amines have been developed for the purpose of reversable CO₂ capture from air. The enzyme active site consists of the tetrapeptide sequence Lys-Asp-Asp-Glu. The Lys sidechain amine undergoes carbamylation and an Mg²⁺ cation stabilizes the resulting carbamate. The N^a-acyl-lysinyl-aspratyl-aspartyl-glutamide (Lys-Asp-Asp-Glu, KDDE) peptide featured maximum capture at pH ≈ 10; a pH region too high for Mg²⁺ ions to remain in solution. This work aims to achieve pKa depression by introducing fluorine in the proximity of the lysine’s sidechain amine. A comparative analysis was made of butylamine, …

Elucidating The Importance Of Structure, Surfaces, And Interfaces In Polymer Nanoparticles And Nanocomposites, Jacob E. Fischer

Doctoral Dissertations

This dissertation details research conducted to elucidate the importance of structure, surfaces, and interfaces in both polymeric nanoparticles and polymer nanocomposites. The fundamental understanding that is garnered in these studies provides a foundation to rationally develop nanocomposites tailored for unique functionalities, performance and applications.

Soft polymeric nanoparticles, have shown to imbue non-traditional diffusive properties, the strength of which decreases with crosslinking density of the nanoparticle. The crosslinking dependent morphology of these nanoparticles is first characterized in a dilute solution of good solvent (Chapter 2). The scattering results revealed that the structure ranges from a swollen polymer in good solvent (0% …

Controlling Polymer Molecular Structure And Morphology: From Illumination Of Conjugated Polymers To Polymer Chain Depolymerization, Josh Moncada

Doctoral Dissertations

Polymers remain a prominent component of our lives, and finding methods to control their structure or morphology are needed to tune material properties. This dissertation reports methods to alter the conformation, morphology, or structure of polymeric materials. Chapter two describes the impact of exposure to white light during annealing of conjugated polymer blends on their morphology and optoelectronic performance. The observed changes in the morphology correlate strongly to the variation in photoluminescence (PL) with illumination, including that the PL varies less with illumination at higher Poly[2-methoxy-5-(2-ethylhexyloxy)-1,4-phenylenevinylene] loadings, offering foundational understanding to guide the structure and optoelectronic performance of conjugated polymer …

Intra-Skeletal Variation In Stable Isotopes Through Non-Destructive Approaches: Applications Of The Patterns Of Skeletal Remodeling To Biological Anthropology, Armando Anzellini

Doctoral Dissertations

Stable isotope analysis is a well-established method in biological anthropology used to deliver data on residence, diet, and life history. Samples for these analyses are often collected from the diaphyses of long bones with an assumption of an expected rate of turnover between five and ten years, depending on the skeletal element. However, the biological foundations of this assumption are still uncertain, especially concerning the intra-skeletal and intra-element variation of isotopic signatures that may relate to patterns of remodeling. Exploring these gaps in intra-element isotopic variation requires fine-grained work using multiple bones from multiple individuals, but such work is limited …

Light Matter Interactions: A Study Of Soft Materials Using Linear And Nonlinear Spectroscopy, Muhammad Redwan Hassan

Doctoral Dissertations

The adoption of complex fluids for various industrial applications is becoming normal. Complex fluids offer tunability, wide range solubility, and chemical and thermal stability which are the factors that conventional polar and non-polar solvents often lack. However, fundamental studies of these fluid systems are still lacking which is limiting the appropriate use of these complex fluids in many applications. The goal of this dissertation was to study and characterize complex fluids for application in electrolytes for redox flow batteries. Chapter 3 and chapter 4 feature the study of microemulsions and deep eutectic solvents (DES) by fluorescence techniques. Fluorescence studies of …