Browsing by Subject "Chemical engineering"
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Item Analysis of central metabolic pathways in cultured mammalian cells(2014-10) Yongky, AndrewRecombinant therapeutic proteins have transformed the field of medicine since their advent more than twenty years ago, providing treatments for various refractory illnesses. Mammalian cells are the preferred hosts for the production of these therapeutics. However, a lack of understanding of the behavior of the cells results in numerous issues that affect the performance of process cultures including inefficient glucose metabolism and improper post-translational modification of the product proteins. With the advances in the knowledge of regulation of metabolism of mammalian cells and the availability of genomics and transcriptomics resources, systems biology approach combining kinetic model and "-omics" tools can now be used to address such issues. The work presented in this thesis employs such systems biology approach to better understand the metabolic behavior of the cells and devise strategies to enhance their performance in culture. Cultured mammalian cells consume huge amount of glucose and convert most of it towards lactate. The accumulation of lactate in culture adversely affects cell growth and productivity. The reliance of these cells on anaerobic glycolysis is also observed in proliferating cells such as cancer cells and embryonic stem cells. In contrast, quiescent cells metabolize glucose at slower rate and glucose is mostly oxidized to carbon dioxide. In the first part of this thesis, we attempt to unravel the regulation of glucose metabolism in proliferating and non-proliferating cells using a mechanistic model of glycolysis. We show that multiple allosteric regulations of glycolysis enzymes can act in synergy to confer bistable behavior to glycolysis activity: at a given glucose concentration, glycolysis can operate at either a high flux state or a low flux state. In proliferating cells, the default state of the cells is to operate at high glycolysis flux. However, it is possible to modulate factors extrinsic and intrinsic to the cells in order to make them switch to low flux state.In the late stages of fed-batch culture, mammalian cells have been observed to shift their metabolism from lactate production to lactate consumption. While it has been correlated with higher productivity, such metabolic shift is not a consistent occurrence as some cultures continue to produce lactate. The metabolic model is used to explain the underlying mechanism behind the metabolic shift to lactate consumption in fed-batch culture. We show that the bistable behavior in glycolysis differs somewhat due to lactate inhibition and growth rate regulation on metabolism. As a result, the cells in culture may or may not shift their metabolism to consume lactate depending on the glucose, lactate and growth rate of the cells. In continuous culture, a similar metabolic behavior has been observed. With the same operating conditions of dilution rate and feed glucose concentration, some continuous cultures reach steady state with high glycolysis flux, while others reach steady state with low glycolysis. The two steady states are marked by distinct steady state cell concentrations. Using a multi-scale reactor model that combines the intracellular metabolism and macroscopic cell growth, we show that multiple steady states exist in continuous culture. At high flux steady state the vast majority of glucose is converted to lactate, whereas at low flux steady state most of the glucose consumed is converted to biomass. The two types of steady states thus have different metabolic efficiency, conferring different cell concentrations.In the final part of the thesis, RNA-seq and microarray are employed to survey the variability in CHO cell lines. We observe a wide range of transcript levels of glycolysis enzymes in CHO cell lines, potentially contributing to distinct metabolic characteristics in different cell lines. The extent of genetic variation in the protein coding regions of the growth signaling pathway genes in CHO cells are discussed.Item Cocontinuous polymer blends: controlling morphology via interfacial modification and rheology(2014-03) Hedegaard, Aaron ThomasCocontinuous polymer blends are formed by melt blending two or more immiscible polymers to form multiple continuous interpenetrated networks. These are non-equilibrium structures where the morphology is determined by a combination of processing conditions, interfacial properties, and rheology. Thermodynamic instability causes the morphology to coarsen during annealing. Furthermore, a thorough understanding of the conditions and mechanism of cocontinuity formation has not been developed, and predictive models are empirical and frequently contradictory. This thesis seeks to advance the field of immiscible polymer blends by providing insight to two critical questions. First, can a better understanding of the role of interfacial stabilization on cocontinuity be developed? Second, can morphological predictions based on rheology be improved? Concerning interfacial stabilization, this thesis approaches the problem via reactive blending and interfacially localized clay nanoparticles. The effectiveness of reactive blending was found to be heavily dependent on the molecular weight of the reactive polymers. Also, the formation of a copolymer brush at the interface was able to prevent coarsening due to a compression of that brush when interfacial area decreased. Nanoclays, when interfacially localized, were found to also prevent coarsening by jamming at the interface, and the combined compatibilization mechanism of reaction and clay was found to achieve the smallest phase sizes. As an application, these compatibilized blends were also tested as gas separation membranes. Concerning the predictions of cocontinuity, various models from the literature were tested against experimental data to determine the center of the compositions that resulted in cocontinuity. It was found that models based on droplet packing worked best, though they gave no information concerning the range of cocontinuous compositions. Various mechanisms and rules of thumb were developed from the present work to provide much-needed insight for predicting the relative size of these ranges. This study also investigated the role of extensional viscosity on cocontinuity by blending with long-chain branched polymers, where it was found that strain hardening branched polymers significantly broadened the range of cocontinuity. This demonstrated a shortcoming in the existing predictive models, which have only considered shear rheology when predicting cocontinuity.Item Construction, analysis, and modeling of complex reaction networks with RING(2013-08) Rangarajan, SrinivasComplex reaction networks are found in a variety of engineered and natural chemical systems ranging from petroleum processing to atmospheric chemistry and including biomass conversion, materials synthesis, metabolism, and biological degradation of chemicals. These systems comprise of several thousands of reactions and species inter-related through a highly interconnected network. This thesis presents methods, computational tools, and applications that demonstrate that: (a) any complex network can be constructed automatically from a small set of initial reactants and chemical transformation rules, and (b) a given network can be analyzed in terms of identifying topological information such as reaction pathways, determining thermodynamically feasible routes, evaluating the spectrum of plausible and synthetically feasible compounds, exploring dominant routes to form experimentally observed products, and formulating and solving a rigorous kinetic model. A new computational tool called Rule Input Network Generator, or RING, has been developed to construct and analyze complex reaction networks. Given initial reactants of a reaction system (e.g. the components of the feed to a reactor) and reaction rules that describe the possible chemical transformations that can occur, RING first constructs an exhaustive network of reactions and species consistent with the inputs. Inputs into RING are in the form an English-like domain specific language with syntax involving common chemistry parlance. The language compiler further catches erroneous chemistry rules, such as incorrect charge balance in a reaction rule, and heuristically optimizes user-specified instructions to improve the speed of execution. RING, further, accepts "post-processing" instructions that allow for: (i) lumping, or grouping together isomers to reduce the size of the reaction network, (ii) "querying" the network to extract information such as reaction pathways and mechanisms that describe how an initial reactant is transformed into a specific product, (iii) calculating thermochemical properties of species and reactions to evaluate thermochemical feasibility of reaction steps, and (iv) formulating and solving rigorous microkinetic models of complex reaction networks. RING, thus, provides a rule-based" framework to assemble and explore a complex reaction network. RING implements several algorithms, methods, and techniques from computer science, cheminformatics, and graph theory. The language has been developed using SILVER, a meta-language for specifying attribute grammars, and COPPER, a parser generator. The language is extensible in that independent additions can be incorporated to the original language to perform additional analysis without syntactical and semantic conflicts with the existing grammar. Algorithms from chemical graph theory and cheminformatics are adopted to (i) represent molecules as strings externally and as graphs internally, (ii) store reaction rules as graph transformation rules, (iii) identify fragments in molecules that can serve as reaction centers through pattern matching, (iv) determine molecular characteristics such as shape (linear, branched, cyclic, etc.) and aromaticity, and (v) identify isomeric lumps through a new molecular hashing technique. Graph traversal algorithms are further employed by the post-processing modules to identify pathways and mechanisms. This thesis presents several case studies of application of RING in elucidating complex networks of reactions. First, when chemistry alone is known about the system, RING can be used to identify plausible mechanisms for product formation consistent with experimental observations; it can further be used to postulate possible experiments to discriminate between the alternative mechanisms. This has been demonstrated with a case study of glycerol and acetone conversion on solid Bronsted acid catalysts. Second, if molecular properties can be evaluated quickly using semi-empirical methods for a large number of species and compounds, RING can be used to identify species in the network that have desired physical properties and thermochemically favorable synthesis routes to form them. A case study on identifying fatty alcohols, in a spectrum of more than 60,000 compounds, that can potentially be used to make nonionic surfactants with desirable properties and their synthesis routes from biomass-derived oxygenates presents an application of this method. It was found that lauryl alcohol, a fatty alcohol currently used to make surfactants, can be synthesized from biomass-oxygenates using a combination of metal, basic, and acid catalysts. It was also found that some of the intermediate synthesis steps could potentially be coupled to drive the overall reaction forward, or could benefit from using biphasic systems for immediate separation of products from reactants. Third, if activation barriers of each step in the reaction can be reliably predicted using semi-empirical methods, RING can be used to identify dominant reaction mechanisms for converting reactants to experimentally observed products. This was demonstrated by analyzing the energetically favorable mechanisms for glycerol conversion to syn gas or 1,2-propane diol on transition metal catalysts such as Platinum, Palladium, Rhodium, and Ruthenium. It was found that glycerol would decompose to syn gas on Platinum and Palladium, while a significant selectivity to the diol can be obtained on Rhodium and Ruthenium, thus offering insights for designing catalysts for complex biomass conversion systems. Finally, if kinetic parameters and thermochemistry can be estimated apriori, RING can be used to formulate and solve rigorous microkinetic models to get quantitative information such as yield and selectivity. This feature is demonstrated through a model developed for methanol conversion to hydrocarbons (MTH) on Bronsted acid catalyst HZSM-5. RING is generic in terms of chemistries it can handle and flexible in terms of the type of analysis that can be performed. This thesis posits that it can be used in conjunction with experimental and computational chemistry data to elucidate systems with complex reaction networks, especially in hydrocarbon processing and biomass conversion.Item Decoupling mechanical and ion transport properties in polymer electrolyte membranes(2014-08) McIntosh, LucasPolymer electrolytes are mixtures of a polar polymer and salt, in which the polymer replaces small molecule solvents and provides a dielectric medium so that ions can dissociate and migrate under the influence of an external electric field. Beginning in the 1970s, research in polymer electrolytes has been primarily motivated by their promise to advance electrochemical energy storage and conversion devices, such as lithium ion batteries, flexible organic solar cells, and anhydrous fuel cells. In particular, polymer electrolyte membranes (PEMs) can improve both safety and energy density by eliminating small molecule, volatile solvents and enabling an all-solid-state design of electrochemical cells. The outstanding challenge in the field of polymer electrolytes is to maximize ionic conductivity while simultaneously addressing orthogonal mechanical properties, such as modulus, fracture toughness, or high temperature creep resistance. The crux of the challenge is that flexible, polar polymers best-suited for polymer electrolytes (e.g., poly(ethylene oxide)) offer little in the way of mechanical robustness. Similarly, polymers typically associated with superior mechanical performance (e.g., poly(methyl methacrylate)) slow ion transport due to their glassy polymer matrix. The design strategy is therefore to employ structured electrolytes that exhibit distinct conducting and mechanically robust phases on length scales of tens of nanometers.This thesis reports a remarkably simple, yet versatile synthetic strategy---termed polymerization-induced phase separation, or PIPS---to prepare PEMs exhibiting an unprecedented combination of both high conductivity and high modulus. This performance is enabled by co-continuous, isotropic networks of poly(ethylene oxide)/ionic liquid and highly crosslinked polystyrene. A suite of in situ, time-resolved experiments were performed to investigate the mechanism by which this network morphology forms, and it appears to be tied to the disordered structure observed in diblock polymer melts near the order-disorder transition. In the resulting solid PEMs, the conductivity and modulus are both high, exceeding the 1 mS/cm and approaching the 1 GPa metrics, respectively, often cited for lithium-metal batteries. In the final chapter, an alternative synthetic route to generate nanostructured PEMs is presented. This strategy relies on the formation of a thermodynamically stable network morphology exhibited by a triblock terpolymer prepared with crosslinking moieties along the backbone. Although the mechanical properties of the resulting PEM are excellent, the conductivity is found to be somewhat limited by network defects that result from the solvent-casting procedure.Item Development and characterization of aptamer-amphiphiles against fractalkine for targeted drug delivery(2013-12) Waybrant, Brett M.A foundation of modern diagnostics and therapeutics is the ability to non-covalently bind to a molecule of interest. These affinity molecules are behind a broad array of products ranging from therapeutics to HIV tests. Currently, antibodies are used as the affinity molecule. Despite the success of antibodies, alternatives are needed due to high development and production costs, and issues with stability. Aptamers are an exciting alternative to antibodies. Aptamers are short sequences of single stranded DNA or RNA that bind molecular targets with high affinity and specificity. Aptamers are inexpensive to produce, are very stable, have long shelf lives, and could potentially replace antibodies in a number of applications. One potential application of aptamers is targeted drug delivery. The goal of targeted drug delivery is to selectively deliver a therapeutic payload to the site of action thereby increasing efficacy and decreasing side effects. Fractalkine is a cell surface protein expressed at sites of inflammation. It is expressed on several types of cancerous tissues and it is involved in the patheogenisis of arthritis, asthma, and atherosclerosis. This work describes the development and characterization of an aptamer that binds fractalkine with high affinity. The aptamer was modified with a hydrophobic tail, creating an aptamer-amphiphile, for use in a model drug delivery vesicle called a liposome. The aptamer-amphiphile was optimized for a high affinity interaction with fractalkine by adding a spacer molecule between the aptamer headgroup and the hydrophobic tail. The optimized amphiphile had high affinity for fractalkine and self-assembled into micelles and an interesting nanotape morphology. Finally, as a proof of concept, the optimized aptamer-amphiphile was incorporated into a liposome and targeted to fractalkine expressing cells. This work highlights the development of aptamers as affinity ligands, and demonstrates their use as potential drug delivery agents.Item Engineering Probiotic Bacteria for Use as Antibiotic Alternatives(2018-02) Forkus, Brittany AnneDecades of overuse of antibiotics has led to the emergence of resistant infections across the globe. Healthcare professionals are running out of viable options, as clinical isolates have begun resisting treatment to even last resort therapies. The emergence of these ‘superbugs’, coupled with the lack of new drugs in the discovery pipeline, has led to the possibility of a ‘post-antibiotic’ era. With the primary driving force for resistance development being the overuse of antibiotics, technologies are being sought to limit their injudicious application within the clinical and agricultural sectors. For decades, antimicrobial peptides (AMPs) have been proposed as a promising contender in the fight against microbial resistance. AMPs are small peptides that are produced natively from organisms across all domains of life as a first line of defense against microbial challenge. However, despite their therapeutic potential, AMPs have widely failed in translational success due to delivery and synthesis challenges. In this work, we propose engineering probiotic bacteria as AMP-delivery vehicles to overcome the inherent transport barriers of AMP-therapy. We focus on developing engineered probiotics to target resident pathogens of the gastrointestinal tract. The success of this technology could aid in the resistance crisis by unlocking the antibiotic power of many otherwise unusable peptide antibiotics. We have developed several derivatives of the probiotic strain, E.coli Nissle 1917 (EcN), which are capable of eliciting antibiotic activity against clinical and foodborne pathogens. The foundation of this work lays in the reorganization of AMP biosynthetic gene clusters for functional utility. We describe our development of the engineered probiotic, EcN(J25), which led to the first in vivo success of AMP-producing probiotics. Treatment with EcN(J25) was capable of reducing Salmonella carriage in pre-harvest poultry by 97% just 14-days post-treatment. In a similar workflow, we then focused on the development of EcN(C7) for use in decolonizing multidrug resistant E.coli in human carriers. Along the way we studied mechanisms of resistance, applied bioinformatics techniques, and developed novel synthetic biology tools for use in future engineered bacteria. The work within describes many of the challenges and potential of engineered probiotics, laying a foundation for future work in the field.Item Ionic liquid based polymer gel electrolytes(2012-11) Lee, Keun HyungIonic liquids have attracted significant interest in a wide variety of applications including electronic, electrochemical, and energy storage devices. This thesis investigates the use of ionic liquid-based polymer electrolytes (ion gels) as a gate insulator material for thin-film transistors. The first objective of thesis is to study the electrical properties of ion gels systematically to understand how the ion gels work as a capacitor to accumulate charge carriers in a semiconductor channel. Accordingly, electrical properties including specific capacitance, resistance and conductivity of ion gels were investigated as a function of film geometry (thickness and area) and temperature. This research also aims to develop new routes for incorporating an ion gel layer on a device to provide diversity and universality in ion gel processing. The first effort was devoted to prepare a smooth and uniform layer of ion gel by spin casting. Typical thicknesses of spin-coated ion gels were 1~20 m. Alternatively, transfer printing using an elastomeric stamp was utilized to prepare all-printed (semiconductor, ion gel dielectric, and gate electrode) thin-film transistors. For the last, mechanically free-standing ion gels that can be cut by hand and laminated on a layer of semiconductor using tweezers were developed for thin-film transistors. This `cut and stick' strategy facilitates convenient fabrication of transistors on a variety of semiconductor materials. Overall, these new processes provide reliable routes to employ ion gels on electrical and electrochemical devices.Item Modeling of transport processes during solution, melt and colloidal crystal growth.(2008-08) Gasperino, David Joseph.In this thesis, numerical models are developed and applied to study systems used for the growth of crystals from both solution and the melt. Additionally, numerical models are employed to study the convective self-assembly of microspheres within solution. Solution crystal growth can be visualized in real-time through the application of atomic force microscopy (AFM) within a fluid cell. We apply a three-dimensional finite element method on a parallel supercomputer to determine the continuum transport of momentum and mass in an AFM fluid cell during crystal growth, using data acquired from calcium oxalate monohydrate crystal growth measurements as a comparison. Simulations quantify mass transfer resistances to crystal growth inherent to the fluid cell geometry, and examine influences on growth via high-frequency cantilever oscillations. The melt growth of single crystal cadmium zinc telluride (CZT), a high-value crystal used in radiation detectors, has posed a serious challenge for crystal growers for over three decades. We employ a two-dimensional finite volume method to simulate CZT growth in a vertical Bridgman furnace used by our collaborators at Pacific Northwest National Laboratories. Models couple the continuum transport of mass, momentum and radiation, and track the interface shape between the melt and crystal. Results provide insight into the thermal behavior of two crucibles to be used for CZT growth by our collaborators. Three-dimensional computations of steady flows directed toward the (1 1 1) plane of a face-centered cubic (fcc) packing of microspheres are carried out to assess the convective steering hypothesis, which posits that solvent flow could play a role in the assembly of colloidal crystals. The computations clearly show the kinematics of flows into and through the packing and clarify the influences of fluid inertia and particle arrangement. Results from the computations accurately describe the outcome of macroscopic experiments.Item Modulation of BMP signaling during Dorsal-Ventral patterning in Drosophila melanogaster(2014-02) Brakken-Thal, ChristinaBone Morphogenic Protein (BMP) signaling is a conserved pathway used for development and homeostasis. In the model system Drosophila melanogaster patterning of the dorsal surface is controlled by Decapentapolegic (DPP), a BMP protein that robustly stimulates the BMP signaling pathway in a narrow domain of cells on the dorsal surface of the embryo. The levels of Dpp are estimated to be between 10-100 molecules / nucleus, which would predict a significant level of noise in Dpp signaling. However this is not observed, so there must be mechanisms that dampen noise in signaling pathways. I used molecular biology, genetics, and mathematical modeling to identify possible mechanisms for feedback control of BMP signaling and to elucidate mechanisms to dampen stochastic fluctuations in signaling molecules. I have identified a new novel allele of nejire with a stop codon in the 12th exon. This mutation truncates part of the glutamine rich domain at the end of the protein. This new allele has a highly variable phenotype with all embryos showing varying degrees of loss of Dpp signaling in the pre-cephalic furrow embryos, and half showing recovery just before and during gastrulation. I also studied the phenotype of Crossveinless-2 (Cv-2) during dorsal surface patterning. I found that cv-2 is a Dpp response gene that is a negative inhibitor of Dpp signaling during dorsal surface patterning. Cv-2 null embryos have a 20% wider area of Dpp signaling on the dorsal surface, and this change leads to a larger amnioserosa later in development. Interestingly loss of Cv-2 leads to a slight increase in noise in the width of pMad, the intracellular signaling of Dpp receptor activation. I followed up on this finding with a 3D stochastic model of Dpp for a single nuclear compartment which suggests that competition for BMP from the receptor could increase noise in signaling. In addition, the stochastic model suggests that endocytosis of Dpp bound receptors and nuclear accumulation of transcription factors may be mechanisms to decrease noise and increase robustness of Dpp signaling.Item A platform for next-generation cancer therapies: multi-targeted nonviral vectors for site-specific gene delivery and expression(2013-12) Adil, Maroof MohammadAdvances in genetics have empowered gene therapy as a cancer treatment, however there are many challenges to delivering genes specifically to target disease sites. Presented here is the development of a new non-viral gene delivery vehicle, consisting of branched polyethyleneimine (bPEI) condensed plasmid DNA polyplexes encapsulated within a PR_b functionalized stealth liposome, for the delivery of genes specifically to &alpha5&beta1 integrin overexpressing cancer cells. This new transfection agent mediated higher gene expression than non-targeted stealth liposomes and unencapsulated polyplexes in tissue culture. In a liver-metastatic colorectal cancer mouse model, PR_b functionalized stealth liposomes outperformed non-targeted stealth liposomes and was able to specifically transfect the tumor site while avoiding healthy tissues. In addition, a comparative investigation of the transfection mechanism of PR_b functionalized nanoparticles, DOTAP/DOPE lipoplexes, bPEI polyplexes and stealth liposomes was carried out in DLD-1 cells. Results demonstrated that PR_b functionalized nanoparticles were optimally balanced for the transfection of DLD-1 cells with high colloidal stability, fast integrin mediated internalization kinetics, caveolae mediated uptake and endosomal escape. To further increase the specificity of gene expression in cancer tissue, a new therapeutic plasmid DNA (pNF-&kappaB-DTA) was developed with expression of Diphtheria toxin fragment-A (DTA) gene regulated by the transcriptional activity of NF-&kappaB, which is a transcription factor upregulated in cancer. The multi-targeted gene delivery system formed by encapsulating pNF-&kappaB-DTA/bPEI polyplexes in PR_b functionalized stealth liposomes showed more specific gene expression in cancer cells versus healthy cells compared to either individually targeted system. Transfecting cancer cells using the multi-targeted gene delivery system resulted in a dose-dependent reduction of cellular protein expression and a dose-dependent increase in cytotoxicity. Our therapeutic delivery system specifically eradicated on average 70% of a variety of cancer cells while minimally affecting healthy cells. Moving forward, the modular nature of our non-viral delivery vehicle design can facilitate targeting novel pairs of extracellular receptors and upregulated transcription factors for applications beyond cancer gene therapy.Item Polymer stabilized nanosupensions via flash nanoprecipitation: particle formulation, strucyure and freeze drying.(2012-07) Pustulka, KevinAbstract summary not availableItem Sour Gas Sweetening and Ethane/Ethylene Separation(2018-05) Shah, Mansi SChemical separations are responsible for nearly half of the US industrial energy consumption. The next generation of separation processes will rely on smart materials to greatly relieve this energy expense. This thesis research focuses on two very energy-intensive and large-scale industrial separations: sour gas sweetening and ethane/ethylene separation. Traditionally, gas sweetening has been achieved through amine-based absorption processes to selectively remove H2S and CO2 from CH4. Ethane/ethylene is an even harder mixture since the two molecules have very similar sizes, shapes, and self-interaction strengths. Despite their low relative volatility (1.2-3.0), cryogenic distillation is the most commonly used technique for this separation. Compared to absorption and cryogenic distillation, adsorption allows for better performance control by choosing the right adsorbent. Crystalline materials such as zeolites, that have precisely defined pore structure, exhibit excellent molecular sieving properties. Performance is closely linked to structure; identifying top zeolites from a large pool of available structures (~300) is thus crucial for improving the separation. In this thesis research, molecular modeling is used to identify optimal materials for these two separations. Since the accuracy of predictive molecular simulations is governed by the underlying molecular models, the first objective of this thesis research was to develop improved molecular models for H2S, ethane, and ethylene. A wide variety of properties such as vapor-liquid and solid-vapor equilibria, critical and triple points, vapor pressures, mixture properties, relative permittivities, liquid structure, and diffusion coefficients were studied using molecular simulations to parameterize transferable molecular models for these molecules. These models are designed to strike a very good balance between accuracy of predictions and efficiency of simulations. For some of the zeolites for which experimental data existed in the literature, purely predictive adsorption isotherms agreed quantitatively with the available experiments. A computational screening was then performed for over 300 zeolite structures using tailored molecular simulation protocols and high-performance supercomputers. Optimal zeolites for each of the two applications were identified for a wide range of temperatures, pressures, and mixture compositions. Finally, a brief literature survey of the zeolites that have been synthesized in their all-silica form is presented and syntheses for two of the important target framework types is discussed.Item Supporting data for Polymeric medical sutures: An exploration of polymers and green chemistry(2018-01-17) Knutson, Cassandra M; Schneiderman, Deborah K; Yu, Ming; Javner, Cassidy H; Distefano, Mark D; Wissinger, Jane E; jwiss@umn.edu; Wissinger, Jane EThese files contain data along with associated output from instrumentation supporting all results reported in Knutson, C. M.; Schneiderman, D. K.; Yu, M.; Javner, C. H.; Distefano, M. D.; Wissinger, J. E. Polymeric medical sutures: An exploration of polymers and green chemistry. J. Chem. Educ. 2017, 94, 1761–1765. In Knutson, et. al. it was found that with new K–12 national science standards emerging, there is an increased need for experiments that integrate engineering into the context of society. Here we describe a chemistry experiment that combines science and engineering principles while introducing basic polymer and green chemistry concepts. Using medical sutures as a platform for investigating polymers, students explore the physical and mechanical properties of threads drawn from poly(ε-caprolactone) samples of different molecular masses and actual purchased absorbable and nonabsorbable medical sutures. An inquiry-based part of the experiment tasks students with designing their own experiment to probe the potential of melt blending poly(ε-caprolactone) with commercially available polylactide products in order to modify the properties of the “sutures” drawn. Through these lessons students gain an appreciation for the importance of plastics in our society and how scientists are working to develop more sustainable alternatives. Overall, this laboratory experiment provides a feasible, versatile, sophisticated laboratory experience that engages students in a relatable topic and meets many of the Next Generation Science Standards.Item The synthesis and characterization of thin film copper zinc tin sulfide for solar cell applications(2014-11) Johnson, Melissa C.Copper zinc tin sulfide (Cu2ZnSnS4 or CZTS) is a promising candidate as a sunlight absorbing layer in thin film solar cells. CZTS is comprised of earth abundant and non-toxic elements, and power conversion efficiencies in CZTS based solar cells have risen quickly. However, there is still a need to develop low-cost and scalable synthesis methods. Furthermore, the rapid rise in CZTS solar cell efficiencies is largely due to a trial-and-error approach to assembling devices, which has led to a knowledge gap in the fundamental material properties of CZTS, which this thesis aimed to help close. We first developed a low cost synthesis method by ex situ sulfidation of Cu-Zn-Sn thin metal films. The metal films are exposed to sulfur vapor at elevated temperatures to form CZTS. This takes place within an isothermal, sealed quartz ampoule. We found that phase pure CZTS films may be achieved at sulfidation temperatures of 600o C. With this method, we also found that the Sn content within the CZTS films was largely self regulating such that the Cu-to-Sn ratio always approached two. The mechanism behind this ultimately gave us strategies to carefully control stoichiometry. We also developed methods to control the film microstructure. Large grains are achieved by the introduction of Na and K. This occurs through diffusion from certain substrates, or via the vapor phase through NaOH and KOH coatings on the quartz ampoule. Finally, we examined how stoichiometry, grain size and Na content affect electronic properties of CZTS. The hole concentration decreases rapidly with small decreases in the Cu-to-Zn ratio. Increases in grain sizes led to gains in mobility, and the introduction of Na generated increases in hole concentrations. All films exhibited variable range hopping transport, however, Cu rich films had high levels of compensation making them unsuitable for solar cell devices.Item Synthesis, characterization, and applications of porous and hierarchically-porous silica nanostructures(2014-10) Swindlehurst, Garrett RichardSilicate nanostructures can be broadly defined as any material primarily composed of silicon dioxide and having one or more dimensions smaller than 100 nm. Silica is formed of SiO4 tetrahedra connected at their vertices, and the way in which these tetrahedra can be arranged leads to materials classified as amorphous or crystalline, depending on the degree of long-range order in the structure. Due to the complexity of tetrahedral connectivity that is possible, pores can be formed in silicas with length scales ranging from a few angstroms to tens of nanometers. Some microporous silicates exist in nature, but many other porous silicas of considerable importance to chemical engineering are synthetic. One important class of these synthetic porous silicates is the zeolites, which contain pores on the size of angstroms and therefore can act as molecular sieves. In this dissertation, methods for the synthesis and characterization of "zero-dimensional" silica nanoparticles, "two-dimensional" zeolite nanosheets, and "three-dimensional" mesoporous silicas and zeolites are presented. Applications for these materials in catalytic and adsorption processes are also explored. Many of these nanostructured silicates contain hierarchical pore structure with different characteristic pore sizes existing in the materials. One particularly studied material, the self-pillared pentasil (SPP) zeolite, contains both the microporosity of traditional zeolites and mesoporosity resulting from its crystal growth mechanism. Hierarchical pore networks can significantly improve intraparticle mass transfer for interacting chemical species, offering great performance gain in the considered applications.Item Synthesis, characterization, and applications of porous and hierarchically-porous silica nanostructures(2014-10) Swindlehurst, Garrett RichardSilicate nanostructures can be broadly defined as any material primarily composed of silicon dioxide and having one or more dimensions smaller than 100 nm. Silica is formed of SiO4 tetrahedra connected at their vertices, and the way in which these tetrahedra can be arranged leads to materials classified as amorphous or crystalline, depending on the degree of long-range order in the structure. Due to the complexity of tetrahedral connectivity that is possible, pores can be formed in silicas with length scales ranging from a few angstroms to tens of nanometers. Some microporous silicates exist in nature, but many other porous silicas of considerable importance to chemical engineering are synthetic. One important class of these synthetic porous silicates is the zeolites, which contain pores on the size of angstroms and therefore can act as molecular sieves. In this dissertation, methods for the synthesis and characterization of "zero-dimensional" silica nanoparticles, "two-dimensional" zeolite nanosheets, and "three-dimensional" mesoporous silicas and zeolites are presented. Applications for these materials in catalytic and adsorption processes are also explored. Many of these nanostructured silicates contain hierarchical pore structure with different characteristic pore sizes existing in the materials. One particularly studied material, the self-pillared pentasil (SPP) zeolite, contains both the microporosity of traditional zeolites and mesoporosity resulting from its crystal growth mechanism. Hierarchical pore networks can significantly improve intraparticle mass transfer for interacting chemical species, offering great performance gain in the considered applications.Item Synthesis, deposition, and microstructure development of thin films formed by sulfidation and selenization of copper zinc tin sulfide nanocrystals(2014-08) Chernomordik, Boris DavidSignificant reduction in greenhouse gas emission and pollution associated with the global power demand can be accomplished by supplying tens-of-terawatts of power with solar cell technologies. No one solar cell material currently on the market is poised to meet this challenge due to issues such as manufacturing cost, material shortage, or material toxicity. For this reason, there is increasing interest in efficient light-absorbing materials that are comprised of abundant and non-toxic elements for thin film solar cell. Among these materials are copper zinc tin sulfide (Cu2ZnSnS4, or CZTS), copper zinc tin selenide (Cu2ZnSnSe4, or CZTSe), and copper zinc tin sulfoselenide alloys [Cu2ZnSn(SxSe1-x)4, or CZTSSe]. Laboratory power conversion efficiencies of CZTSSe-based solar cells have risen to almost 13% in less than three decades of research. Meeting the terawatt challenge will also require low cost fabrication. CZTSSe thin films from annealed colloidal nanocrystal coatings is an example of solution-based methods that can reduce manufacturing costs through advantages such as high throughput, high material utilization, and low capital expenses. The film microstructure and grain size affects the solar cell performance. To realize low cost commercial production and high efficiencies of CZTSSe-based solar cells, it is necessary to understand the fundamental factors that affect crystal growth and microstructure evolution during CZTSSe annealing. Cu2ZnSnS4 (CZTS) nanocrystals were synthesized via thermolysis of single-source cation and sulfur precursors copper, zinc and tin diethyldithiocarbamates. The average nanocrystal size could be tuned between 2 nm and 40 nm, by varying the synthesis temperature between 150 °C and 340 °C. The synthesis is rapid and is completed in less than 10 minutes. Characterization by X-ray diffraction, Raman spectroscopy, transmission electron microscopy and energy dispersive X-ray spectroscopy confirm that the nanocrystals are nominally stoichiometric kesterite CZTS. The ~2 nm nanocrystals synthesized at 150 °C exhibit quantum confinement, with a band gap of 1.67 eV. Larger nanocrystals have the expected bulk CZTS band gap of 1.5 eV. Several micron thick films deposited by drop casting colloidal dispersions of ~40 nm CZTS nanocrystals were crack-free, while those cast using 5 nm nanocrystals had micron-scale cracks. We showed the applicability of these nanocrystal coatings for thin film solar cells by demonstrating a CZTS thin film solar cell using coatings annealed in a sulfur atmosphere. We conducted a systematic study of the factors controlling crystal growth and microstructure development during sulfidation annealing of films cast from colloidal dispersions of CZTS nanocrystals. The film microstructure is controlled by concurrent normal and abnormal grain growth. At 600 °C to 800 °C and low sulfur pressures (50 Torr), abnormal CZTS grains up to 10 µm in size grow on the surface of the CZTS nanocrystal film via transport of material from the nanocrystals to the abnormal grains. Meanwhile, the nanocrystals coarsen, sinter, and undergo normal grain growth. The driving force for abnormal grain growth is the reduction in total energy associated with the high surface area nanocrystals. The eventual coarsening of the CZTS nanocrystals reduces the driving force for abnormal crystal growth. Increasing the sulfur pressure by an order of magnitude to 500 Torr accelerates both normal and abnormal crystal growth though sufficient acceleration of the former eventually reduces the latter by reducing the driving force for abnormal grain growth. For example, at high temperatures (700-800 oC) and sulfur pressures (500 Torr) normal grains quickly grow to ~500 nm which significantly reduces abnormal grain growth. The use of soda lime glass as the substrate, instead of quartz, accelerates normal grain growth. Normal grains grow to ~500 nm at lower temperatures and sulfur pressures (i.e., 600 °C and 50 Torr) than those required to grow the same size grains on quartz (700 °C and 500 Torr). Moreover, carbon is removed by volatilization from films where normal crystal growth is fast. There are significant differences in the chemistry and in the thermodynamics involved during selenization and sulfidation of CZTS colloidal nanocrystal coatings to form CZTSSe or CZTS thin films, respectively. To understand these differences, the roles of vapor pressure, annealing temperature, and heating rate in the formation of different microstructures of CZTSSe films were investigated. Selenization produced a bi-layer microstructure where a large CZTSSe-crystal layer grew on top of a nanocrystalline carbon-rich bottom layer. Differences in the chemistry of carbon and selenium and that of carbon and sulfur account for this segregation of carbon during selenization. For example, CSe2 and CS2, both volatile species, may form as a result of chalcogen interactions with carbon during annealing. Unlike CS2, however, CSe2 may readily polymerize at room temperature and one atmosphere. Carbon segregation may be occurring only during selenization due to the formation of a Cu-Se polymer [i.e., (CSe2-x)] within the nanocrystal film. The (CSe2-x) inhibits sintering of nanocrystals in the bottom layer. Additionally, a fast heating rate results in temperature variations that lead to transient condensation of selenium on the film. This is observed only during selenization because the equilibrium vapor pressure of selenium is lower than that of sulfur. The presence of liquid selenium during sintering accelerates coarsening and densification of the normal crystal layer (no abnormal crystal layer) by liquid phase sintering. Carbon segregation does not occur where liquid selenium was present.Item Systems analysis of pheromone signaling and antibiotic resistance transfer in Enterococcus faecalis(2018-01) Bandyopadhyay, Arpan AnupAntibiotics have been an extremely important weapon in the fight against bacterial infections for over half a century. However, excessive use of antibiotics has led to increased frequencies of resistance among bacteria. Antibiotic resistance is an inevitable outcome of natural selection as organisms undergo random mutations to escape lethal selective pressure. Many of these resistant bacteria can also transfer their genetic material to other bacteria through direct cell-cell contact via conjugation, further facilitating the spread of resistance. The human gastrointestinal tract, replete with a high density of bacteria and often exposed to antibiotics, provides an ideal environment for antibiotic resistance genes to arise and propagate through bacterial populations. Enterococcus faecalis, a commensal bacterium of the human intestinal tract, has emerged as a major cause of healthcare-associated infections. Treatment of these infections has become increasingly difficult with the emergence of E. faecalis strains that are resistant to multiple major classes of antibiotics. The organism’s ability to acquire and transfer resistance genes and virulence determinants through conjugative plasmids poses a serious clinical concern. Here we present our study on conjugation of a tetracycline-resistance plasmid pCF10 which is regulated by intercellular communication using two antagonistic signaling peptides. An inducer peptide produced by the plasmid-free recipient cells functions as a “mate-sensing” signal and triggers the conjugative plasmid transfer in donors. The donors encode an inhibitor peptide on the plasmid which represses conjugation and functions as a "self-sensing" signal, reducing the response to the inducer in a density-dependent fashion. This form of dual signaling-controlled conjugation was also found to be prevalent across other pheromone-responsive plasmids, including pAD1 and pAM373. Though the donors calibrate their conjugation response in accordance with the relative abundance of donors and recipients, plasmid transfer can occur under otherwise unfavorable conditions, such as low inducing pheromone and high inhibitor concentrations. To better understand this apparent inconsistency, we formulated a stochastic mathematical model that integrates intracellular molecular regulation of conjugation and interactions between donors and recipients through the signaling peptides. Kinetic parameters for the model were estimated from literature and augmented by experimental RNA-Seq data and binding constant measurements. Simulations of the stochastic model and single-cell analysis using transcript quantification by HCR-FISH and GFP reporter fusions revealed distinct subpopulations of rapid responders under unfavorable conditions for plasmid transfer. We developed a series of fluorescent reporters to track the uninduced/induced donors, recipients, and uninduced/induced transconjugants in real-time using confocal microscopy and flow cytometry. We are further developing a microfluidic gut model which allow for co-culturing of human and bacteria cells in an in vivo-simulated microenvironment. This system will be used to model the in vivo biology of conjugation and gain a better mechanistic understanding of the community balance between the microbial inhabitants of the GI tract. A better understanding of the bacterial signaling mechanisms in vivo and the downstream effects on microbiome community balance may help us identify alternate strategies to prevent the spread of antibiotic resistance.Item A theoretical study of dopant atom detection and probe behavior in STEM(2013-12) Mittal, AnudhaVery detailed information about the atomic and electronic structure of materials can be obtained via atomic-scale resolution scanning transmission electron microscopy (STEM). These experiments reach the limits of current microscopes, which means that optimal experimental design is a key ingredient in success. The step following experiment, extraction of information from experimental data is also complex. Comprehension of experimental data depends on comparison with simulated data and on fundamental understanding of aspects of scattering behavior. The research projects discussed in this thesis are formulated within three large concepts.1. Usage of simulation to suggest experimental technique for observation of a particular structural feature. Two specific structural features are explored. One is the characterization of a substitutional dopant atom in a crystal. Annular dark field scanning transmission electron microscope (ADF-STEM) images allow detection of individual dopant atoms in a crystal based on contrast between intensities of doped and non-doped column in the image. The magnitude of the said contrast is heavily influenced by specimen and microscope parameters. Analysis of multislice-based simulations of ADF-STEM images of crystals doped with one substitutional dopant atom for a wide range of crystal thicknesses, types and locations of dopant atom inside the crystal, and crystals with different atoms revealed trends and non-intuitive behaviors in visibility of the dopant atom. The results provide practical guidelines for the optimal experimental setup regarding both the microscope and specimen conditions in order to characterize the presence and location of a dopant atom. Furthermore, the simulations help in recognizing the cases where detecting a single dopant atom via ADF-STEM imaging is not possible. The second is a more specific case of detecting intrinsic twist in MoS2 nanotubes. Objective molecular dynamics simulations coupled with a density functional-based tight-binding model revealed that a stress-free single-walled (14,6) MoS2 nanotube has a torsional deformation of 0.87 °/nm. Comparison between simulated electron diffraction patterns and atomic-resolution ADF-STEM images of nanotubes with and without the small twist suggested that these experimental techniques are viable routes for detecting presence of the torsional deformation. 2. Development of theory to cast light on aspects of scattering behavior that affect STEM data. STEM probe intensity oscillates as the probe transmits through a crystalline sample. The oscillatory behavior of the probe is extremely similar during transmission through 3-D crystals and the hypothetical structure of an isolated column of atoms, a 1-D crystal. This indicates that the physical origin of oscillation in intensity is not due to scattering of electrons away from one atomic column and subsequent scattering back from neighboring columns. It leaves in question what the physical origin or intensity oscillation is. This question was answered here by analysis of electron beam behavior in isolated atomic columns, examined via multislice-based simulations. Two physical origins, changes in angular distribution of the probe and phase shift between the angular components, were shown to cause oscillation in beam intensity. Sensitivity of frequency of oscillation to different probe and sample parameters was used to better understand the influence of the two physical origins on probe oscillation. 3. Acquisition of atomic-scale STEM data to answer specific questions about a material. Graphene, due to its 2-Dimensionality, and due to its thermal, optical, electrical, and mechanical properties, which are conducive to providing a unique material for incorporation in devices, has gained a lot of interest in the research world and even spurred start-ups. There are several feasible routes of graphene synthesis, among which chemical exfoliation of graphite is a promising method for mass-scale, low-cost production of graphene. Chemical exfoliation of graphite to produce graphene is a two-step process: oxidation to exfoliate the graphite layers, which results in graphene oxide, and reduction of graphene oxide, to produce graphene as a final product. Here, we examined the atomic and electronic structure of graphene oxide and of the reduced sheets. Two different methods of reduction, thermal reduction in vacuum and aqueous reduction in atmosphere, were compared. TEM-based techniques were used for nanoscale characterization. GO was synthesized using the modified Hummer's method and presence of single layer sheets was confirmed by electron diffraction (ED). Non-uniform distribution of oxygen in GO was observed using Z-contrast imaging in STEM. Presence of sp2 and sp3 hybridized carbon bonds in GO was confirmed by examining the fine structure of carbon K-edge in electron energy loss spectra (EELS). Changes in oxygen distribution and electronic structure of carbon were monitored using the same techniques in situ during thermal reduction of GO to graphene. Change in oxygen level and carbon hybridization was gradual with increasing temperature, with complete conversion to oxygen-absent, sp2 hybridized carbon sheet at 1000 ̊C. Gradual change confirmed the ability to fine-tune the level of oxygen on carbon sheets using thermal reduction in vacuum. Instantaneous heating from room temperature to 1000 ̊C showed formation of holes in the graphene product. A several-hour gradual heating process was suggested to decrease perforation in graphene sheets. The second reduction process, aqueous thermal reduction in ambient pressure, did not lead to completely sp2 hybridized carbon sheets, observed using EELS. Presence of oxygen was also observed via x-ray photoemission spectra (XPS). Yet, electrical resistance of the product was 5 orders of magnitude less than the starting GO sheets. This property was explained by examining the atomic structure of the reduced GO. High resolution conventional TEM (CTEM) images of nano-scale section of the reduced GO showed randomly shaped crystalline areas and amorphous areas, with crystalline area being above the 2-D percolation threshold and thus explaining the conductive property.Item Toughness in block copolymer modified epoxies(2014-09) Declet-Perez, CarmeloOne of the major shortcomings preventing the widespread use of epoxy resins in engineering applications is the inherent brittleness of these materials. The incorporation of small amounts of amphiphilic block copolymers into the formulation is one of the most promising strategies to toughen epoxies. These molecules are known to form nanostructures in the epoxy resin that can be preserved upon curing. This strategy is very attractive since significant enhancements in toughness can be obtained without detrimental effects on other properties of the matrix. Despite many examples of successful implementation, an in-depth understanding of the factors that lead to toughness in block copolymer modified epoxies is still elusive. The goal of this dissertation is to understand, first, the deformation mechanisms leading to toughness and, second, how different formulation parameters affect these processes.In this work we used two types of block copolymer modifiers, which produced nanostructures with different physical properties. These block copolymers self-assembled into well-dispersed spherical micelles with either rubbery or glassy cores in various epoxy formulations. Both of these modifiers toughened different epoxy formulations, although to different extents. The rubbery core micelles consistently outperformed the glassy core micelles by roughly a factor of two. While the toughening afforded by the rubbery core micelles was consistent with the current understanding of toughening, the results from the glassy core micelles could not be explained with the same reasoning.In order to understand the deformation mechanisms leading to different levels of toughness, we performed small-angle x-ray scattering experiments while simultaneously deforming our material. This combination of techniques, referred to as in-situ SAXS, allowed us to monitor changes in the structure of the block copolymer micelles as a result of the applied load. With this technique, we showed that the rubbery core micelles undergo a dilatational process while the glassy core micelles deform with constant volume. These results provide definitive evidence of cavitation in rubbery nanodomains, a result anticipated by theoretical calculations. The notion of cavitation is useful in understanding the toughness enhancement of the rubbery core micelles; however, it does not explain the toughening from the glassy core micelles. To explain the toughening afforded by the glassy core micelles we proposed the idea of network disruption in the region spanned by the corona block. We suggested that this mechanism is also capable of initiating plastic deformation of the matrix, although to a lesser extent than cavitation. Accordingly, the main toughening mechanism in block copolymer modified epoxies is plastic deformation of the matrix initiated by either cavitation of rubbery domains or by the zone of disrupted network depending on the properties of the micelle core. Having established that the matrix is responsible for dissipating the most amount of energy during fracture, we also investigated the effect of varying the crosslink density and flexibility of the network by means of in-situ SAXS. In networks formulated with different crosslink densities, but the same type of molecules, we found a correlation between different levels of toughness provided by either, rubbery or glassy core micelles, and differences in deformability of the epoxy network. In networks formulated with a different crosslinker, which incorporates flexible groups into the matrix, we found that the properties of the network strongly influence the type of deformation the block copolymer micelles undergo. In conclusion, this work has established a connection between different extents of toughening enhancement, the physical properties of the block copolymer micelles, and the properties of the epoxy network. Judicious selection of all of these formulation parameters is needed to obtain an optimal toughening effect.