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 …

Data For Dopant-Induced Energetic Disorder In Conjugated Polymers: Determinant Roles Of Polymer-Dopant Distance And Composite Electronic Structures, Michael Lu Diaz, Muhamed Duhandzic, Simon Harrity, Subhayan Samanta, Zlatan Aksamija, Dhandapani Venkataraman

Data and Datasets

The data here is the raw data for Figures in the publication "Dopant-Induced Energetic Disorder in Conjugated Polymers: Determinant Roles of Polymer−Dopant Distance and Composite Electronic Structures" In the Journal of Physical Chemistry C. (https://doi.org/10.1021/acs.jpcc.3c07197)

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) …

Machine Learning Modeling Of Polymer Coating Formulations: Benchmark Of Feature Representation Schemes, Nelson I. Evbarunegbe

Masters Theses

Polymer coatings offer a wide range of benefits across various industries, playing a crucial role in product protection and extension of shelf life. However, formulating them can be a non-trivial task given the multitude of variables and factors involved in the production process, rendering it a complex, high-dimensional problem. To tackle this problem, machine learning (ML) has emerged as a promising tool, showing considerable potential in enhancing various polymer and chemistry-based applications, particularly those dealing with high dimensional complexities.

Our research aims to develop a physics-guided ML approach to facilitate the formulations of polymer coatings. As the first step, this …

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 …

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 …

Enabling An Equitable Energy Transition Through Inclusive Research, Michael Ash, Erin Baker, Mark Tuominen, Dhandapani Venkataraman, Matthew Burke, S. Castellanos, M. Cha, Gabe Chan, D. Djokic, J.C. Ford, Anna P. Goldstein, David Hsu, Matt Lacker, C. Miller, D. Nock, A.P. Ravikumar, Allison Bates, Anna Stefanopoulou, E Grubert, D.M Kammen, M. Pastor, S.Z, Attari, S. Carley, D.L Clark, D. Dean-Ryan, U. Kosar, Kerry Bowie, Tina Johnson

ETI Publications

Comprehensive and meaningful inclusion of marginalized communities within the research enterprise will be critical to ensuring an equitable, technology-informed, clean energy transition. We provide five key action items for government agencies and philanthropic institutions to operationalize the commitment to an equitable energy transition.

Vapor Deposition Strategies For Tuning Surface And Interface Chemistry For Optoelectronics And Biosensors, Kwang-Won Park

Doctoral Dissertations

Ordered assemblies of molecular semiconductors have been of particular interest for their integral role in organic optoelectronics, originating from interesting optical and charge transport properties. Compared with disordered films, organized nanostructured organic semiconductors display enhanced optoelectronic characteristics. However, past studies using template layer and self-assembly strategies are not applicable to molecular heterointerfaces and cannot be practically integrated into existing device fabrication routines to achieve large-area optoelectronic devices. This dissertation demonstrates unprecedented strategies to create one-dimensional (1D) nanostructures of molecular semiconductors using vapor deposition techniques. We begin this work by investigating how the interplay between dipole-dipole and van der Waals interactions …

Frontiers In The Self-Assembly Of Charged Macromolecules, Khatcher O. Margossian

Doctoral Dissertations

The self-assembly of charged macromolecules forms the basis of all life on earth. From the synthesis and replication of nucleic acids, to the association of DNA to chromatin, to the targeting of RNA to various cellular compartments, to the astonishingly consistent folding of proteins, all life depends on the physics of the organization and dynamics of charged polymers. In this dissertation, I address several of the newest challenges in the assembly of these types of materials. First, I describe the exciting new physics of the complexation between polyzwitterions and polyelectrolytes. These materials open new questions and possibilities within the context …

Intracellular Delivery Of Therapeutic Biomolecules Through Versatile Polymer Nanotechnology, David C. Luther

Doctoral Dissertations

Advancing pharmaceutical technology has made it possible to treat diseases once considered ‘undruggable.’ Access to these new pharmaceutical targets is possible thanks to the advent of protein and nucleic acid therapeutics. Responses to the COVID-19 pandemic, as well as cutting-edge treatments for cancer and multiple sclerosis have centered on these biologic therapies, promising even greater value in the future. However, their utility is limited at a cellular level by inability to cross the plasma membrane. Nanocarrier technologies encapsulate therapeutics and facilitate uptake into the cell but are often trapped and degraded in endosomes. Arginine-functionalized gold nanoparticles (Arg-NPs) provide efficient, direct …

Elucidating The Function Of Ions In Hybrid Perovskite Photovoltaics, Emily C. Smith

Doctoral Dissertations

Perovskite solar cells (PSCs) have risen to the forefront of versatile thin-film technologies with power conversion efficiencies rivaling traditional silicon and the potential to be fabricated at a fraction of the cost. However, one crucial drawback to PSCs is their instability to illumination, which is likely due in part to mobile ions during operation. It is difficult to predict the influences of ion dynamics in devices, and the exact nature and impact of these ions remain elusive. In this dissertation work, I have set out to unravel the complex interplay between ions and device operation in PSCs. Through the development …

Formation Of Doped Semiconductor Nanocrystals From Doped Molecular Clusters, Jillian E. Denhardt

Doctoral Dissertations

Transition metal doping of semiconductor nanomaterials, particularly magnetic dopant ions, is of great interest for the synthesis of diluted magnetic semiconductors (DMS) with spintronic-based applications. The incorporation of magnetic ions into quantum dots (QDs) would be particularly useful since the quantum confinement of these materials is theorized to enhance magneto-optical related properties. One major challenge in this field is the segregation of dopant ions towards the outer regions of the QD due to the exclusion of dopants during the nucleation process, thereby inhibiting the magneto-optical properties. In this dissertation, we address the dopant segregation challenge by exploring the underlying mechanisms …

Expanding The Polymer Zwitterion Library – Novel Phosphonium-Based Polymer Zwitterions And Analogous Structures, Marcel U. Brown

Doctoral Dissertations

This dissertation encompasses the synthesis, characterization and application of novel polymer zwitterions that significantly expand the library of available zwitterionic polymers. Their facile synthesis is facilitated by the preparation of a novel functional sultone precursor molecule, which can be ring-opened by commercially available phosphine, amine and sulfide nucleophiles, affording phosphonium, ammonium or sulfonium sulfonate monomers, respectively. Most notably, this work describes the invention of phosphonium-based polymer zwitterions, establishing a new class of zwitterionic polymer structures with unique solution and interfacial properties. Furthermore, the incorporation of these phosphonium sulfonates into block copolymer architectures with conventional polymer zwitterions, and the resulting switchable …

Enabling Nanoimprint Lithography Techniques Across Multiple Manufacturing Processes, Vincent Einck

Doctoral Dissertations

Advanced nanooptics in the areas of flat lenses, diffractive elements, and tunable emissivity require a route to high throughput manufacturing. Nanooptics are often demanding of high refractive index materials, nanometer precision and ease of fabrication. Nanoimprint lithography (NIL) is a low-cost, high throughput manufacturing technique beginning to be realized in commercial industry.^1,2 The NIL process is an ideal manufacturing candidate due to its ability to have a fast process time, efficient use of materials, repeatability and high precision while also having wide diversity of potential structures and material choices. Appling NIL techniques to other facets of manufacturing enable the …

Chromatographic Dynamic Chemisorption, Shreya Thakkar

Masters Theses

Reaction rates of catalytic cycles over supported metal catalysts are normalized by the exposed metal atoms on the catalyst surface, reported as site time yields which provide a rigorous standard to compare distinct metal surfaces. Defined as the fraction of exposed metal surface atoms to the total number of metal atoms, it is important to measure the dispersion of supported metal catalysts to report standardized rates for kinetic investigations. Multiple characterization techniques such as electron microscopy, spectroscopy and chemisorption are exploited for catalyst dispersion measurements. While effective, electron microscopy and spectroscopy are not readily accessible due to cost and maintenance …

Molecular Vibrations And Shape-Selectivity: A Computational Model Of Biofuel Precursors In Zeolites, Babgen Manookian

Doctoral Dissertations

We have used Density Functional Theory (DFT) to model acyclic and cyclic olefins in acidic zeolites. We have studied the impact of host-guest interactions between adsorbed molecules and zeolite frameworks through the lens of molecular vibrations and shape-selectivity. This work considered three zeolite frameworks with varying pore structures and environments: large pore zeolite HMOR and medium pore zeolites HZSM-5 and HZSM-22. A key finding is that for acyclic olefins in acidic zeolites there exists two regimes of host-guest interaction: a strong interaction leading to protonation and a weak interaction between charged guest and zeolite framework. We found that these interactions …

Designing Polymer-Protein Complexes For Intracellular Delivery, Hazel Davis

Doctoral Dissertations

Previous work in the Tew group has demonstrated polymer cell-penetrating peptide mimics (CPPMs) as effective transporters of biological agents, including proteins and antibodies. These synthetic polymers non-covalently bind to cargo, offering a mechanism to deliver proteins in a way that does not alter protein secondary structure. However, correlations of the protein binding-delivery relationship or the role of polymer-protein complexation on intracellular activity of protein cargo are understudied. The work presented herein connects a fundamental understanding of polymer-protein complexation with intracellular internalization and cargo activity. Characterization and quantification of polymer-protein binding relationships were established using fluorescence quenching assays. In particular, the …

Developing Injectable And Implantable Polymer Zwitterion Platforms For Glioblastoma Treatment, Sarah Ward

Doctoral Dissertations

This dissertation describes the synthesis, characterization, and application of novel polymer zwitterion-drug conjugates intended for treating glioblastoma, with a particular focus on phosphorylcholine (PC) and temozolomide (TMZ). Using versatile TMZ-containing monomers, injectable polymer prodrugs and implantable polymeric hydrogels were prepared over a broad range of drug incorporations with tunable properties, making them ideally suited for further in vivo and clinical evaluations. The work presented here greatly expands the knowledge base of TMZ formulations and gives rise to several routes which circumvent the challenges associated with its use. Chapter 2 describes the incorporation of a novel TMZ-methacrylate monomer into random and …

Deciphering Protein Higher-Order Structure And Interactions Via Diethylpyrocarbonate Labeling-Mass Spectrometry, Xiao Pan

Doctoral Dissertations

The study of protein higher-order structures is vital because it is closely related to the investigation of protein folding, aggregation, interaction and protein therapeutics. Consequently, numerous biochemical and biophysical tools have been developed to study protein higher-order structures in many different situations. The combination of covalent labeling (CL) and mass spectrometry (MS) has emerged as a powerful tool for studying protein structures and offers many advantages over other traditional techniques, such as better structural coverage, high throughput, high sensitivity, and the ability to study proteins in mixtures. This dissertation focuses on diethylpyrocarbonate (DEPC) as an effective CL reagent that can …

Synthesis, Fabrication, And Assembly Of Mesoscale Polymer Filaments, Dylan M. Barber

Doctoral Dissertations

Mesoscale materials, with feature sizes in the range of one hundred nanometers to tens of micrometers, are ubiquitous in Nature. In organisms, mesoscale building blocks connect the properties of underlying molecular and nanoscructures to those of macroscale, organism-scale materials through hierarchical assemblies of recurring structural motifs. The collective action of large numbers of mesoscale features can afford stunning features like the structural color of the morpho butterfly wing, calcium ion-mediated movement in muscle, and wood structures like xylem that can support enormous external compressive loads and negative internal pressure to transport nutrients throughout an organism. In synthetic systems, the design, …

The Thermoelectric, Thermoresistive, And Hygroresistive Properties And Applications Of Vapor Printed Pedot-Cl, Linden K. Allison

Doctoral Dissertations

Wearable electronics are a valuable tool to increase consumer access to real-time and long-term health care monitoring. The development of these technologies can also lead to major advancements in the field, such as self-charging systems that are completely removed from the electrical grid. However, much of the wearable technology available commercially contain rigid components, use unsustainable synthetic methods, or undesirable materials. The field has thus been moving towards wearables that mimic textiles or use textiles as a substrate. Herein, we discuss the use of oxidative chemical vapor deposition (oCVD) to produce textiles coated with poly(3,4-ethylenedioxythiophene) known as PEDOT-Cl. We evaluate …

Tailoring Interfaces And Composition For Stable And Efficient Perovskite Solar Cells, Hamza Javaid

Doctoral Dissertations

Metal halide perovskite solar cells (PSCs) have revolutionized the field of thin film photovoltaics. Within a decade, the power conversion efficiencies (PCEs) have increased at a phenomenal rate, rising from 3.8% to more than 25% in single-junction devices, moving them ahead of the current silicon-based technology. The high efficiencies of perovskite solar cells (PSCs) and their other unique properties arise from a combination of organic and inorganic components and electronic-ionic conduction, making them excellent candidates for a plethora of applications. However, PSCs face a significant—and ironic—roadblock to commercialization: these light-harvesting materials degrade under sunlight—the very condition they would need …