Browsing by Subject "Kinetics"
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Item A Computational-based Approach for the Design of Trip Steels(2013-08-06) Li, Sheng-YenThe purpose of this work is to optimize the chemical composition as well as the heat treatment for improving the mechanical performance of the TRIP steel by employing the theoretical models. TRIP steel consists of the microstructure with ferrite, bainite, retained austenite and minor martensite. Austenite contributes directly to the TRIP effect as its transformation to martensite under the external stress. In order to stabilize austenite against the martensitic transformation through the heat treatment, the two-step heat treatment is broadly applied to enrich the carbon and stabilize the austenite. During the first step of the heat treatment, intercritical annealing (IA), a dual phase structure (ferrite+austenite) is achieved. The austenite can be initially stabilized because of the low carbon solubility of ferrite. The bainite isothermal treatment (BIT) leads to the further carbon enrichment of IA-austenite by the formation of carbon-free ferrite. Comparing to the experiments, the thermodynamic and kinetic models are the lower and upper bounds of the carbon content of retained austenite. The mechanical properties are predicted using the swift model based on the predicted microstructure. In this work, a theoretical approach is coupled to a Genetic Algorithm-based optimization procedure to design (1) the heat treated temperatures to maximize the volume fraction of retained austenite in a Fe-0.32C-1.42Mn-1.56Si alloy and the chemical composition of (2) Fe-C-Mn-Si and (3) Fe-C-Mn-Si-Al-Cr-Ni alloy. The results recommend the optimum conditions of chemical composition and the heat treatment for maximizing the TRIP effect. Comparing to the experimental results, this designing strategy can be utilized to explore the potential materials of the novel alloys.Item Characterization of HIV-1 Reverse Transcriptase substrate specificity by conformationally sensitive fluorescence(2010-12) Kellinger, Matthew William; Johnson, Kenneth Allen; Dalby, Kevin; Robertus, Jon; Russell, Rick; Zhang, Yan JessieWe have engineered a mutant of HIV Reverse Transcriptase that can be fluorescently labeled by covalent attachment of the environmentally sensitive fluorophore 7-diethylamino-3-((((2-maleimidyl)ethyl)amino)carbonyl)coumarin (MDCC). The result is a polymerase that is kinetically indistinguishable from the wild-type enzyme, but provides a signal to monitor changes in enzyme structure that result from conformational changes induced by substrate binding. Using this system, we have expanded the kinetic model governing nucleotide binding to include an enzymatic isomerization following initial nucleotide binding. In doing so, we define the role of induced-fit in nucleotide specificity and mismatch discrimination. Additionally, we have characterized the kinetics governing the specificity and discrimination of several widely administered Nucleotide Reverse Transcriptase Inhibitors (NRTI’s) used to combat HIV infection including 3TC (Lamivudine), FTC (Emtricitabine), and AZT (Zidovudine) for the wild-type polymerase and mutants with clinical resistance to these compounds. Our findings resolve the apparent tighter binding of these inhibitor compounds compared to the correct nucleotide by showing that the affinity for the correct nucleotide is stronger than the inhibitors. The apparent weaker binding of the correct nucleotide is a result of a incomplete interpretation of binding data that fails to account for the importance of the reverse rate of the conformational change. The apparent Kd (Kd,app) measurements for correct nucleotide estimates Km rather than Kd because nucleotide binding does not reach equilibrium. The conformationally sensitive enzyme has also been used to characterize the kinetics governing DNA association. We show that DNA binding is governed by a two-step process where a fast initial association is followed by a second, slow isomerization that is off the pathway for nucleotide binding and incorporation. Finally, we have implemented single molecule techniques using fluorophore labeled nucleotides to study the effects of AZT incorporation on the DNA translocation dynamics of the polymerase. We find that primer termination with AZT results in DNA that fails to translocate, therefore occluding the next nucleotide from binding. This shift in translocation equilibrium exposes the newly formed phosphodiester bond to ATP- or pyrophosphate-mediated AZT excision; thereby rescuing productive polymerization. This finding represents the first kinetic measurement of DNA translocation by a polymerase.Item Combustion characteristics of A1 nanoparticles and nanocomposite A1+MoO3 thermites(2005-05) Granier, John J.; Pantoya, Michelle; Seshaiyer, Padmanabhan; Oler, James W.; Levitas, Valery; Berg, Jordan M.Scientific advances in material synthesis such as exploding wire technology, plasma nucleation and wet precipitation have enabled industrial manufacturers to produce metal and metal oxide powders with nanometer-sized particles. These processes have enabled better overall quality control (i.e. more definitive particle size, smaller particle size distributions, oxide coating control and decreased contaminate concentration) and faster production rates. Much interest has been formed in the science and application of nano-sized aluminum (nm-Al) combustion. A thermite (or aluminothermic) reaction is an oxidation reaction between aluminum and a metal oxide with highly exothermic energy release. Thermite reactions of traditional Al powder (typically micron-sized particles) and Iron-oxide have been used for decades in welding and other intense heat applications. Nano-thermite reactions, have shown unique properties in ignition sensitivity and deflagration (flame propagation) speeds which have propelled thermites to new realms of applications. The decrease in required ignition stimuli of nano-thermites is an improvement for many payload critical applications, but the ignition sensitivity also creates various hazards during material handling and seems to be a factor in decreased reactivity of aged nano-thermites. Nano-thermites have displayed reaction rates near detonation speeds presenting applications as more efficient incendiary devices. The precise particle size control of nano-thermites is leading researchers to develop highly-tunable energy release mechanisms that can be applied as heat signature flare decoys. Studies have shown that the thermite reaction of nm-Al+MoO3 has a large theoretical energy density [19], increased ignition sensitivity [23][8], and near detonation flame propagation speeds [5][6] in comparison to traditional micron-particle thermites. This work will present macroscopic combustion behaviors (such as flame speed) along with experimental results focusing on the molecular reactions and thermal properties of nanocomposite Al+MoO3 thermite materials This work will outline the successes and precautions of several nm-Al+MoO3 powder mixing methods and several cold-pressing techniques used to form compressed solid samples. A general relationship of sample density as a function of pressing force and with a systematic methodology is presented to allow other researchers to produce similar samples for future comparison. Second, results from laser experiments performed to determine flame speeds of nano and micron-sized Al+MoO3 composites through a range of sample densities. Flame propagation speeds were measured using high-speed digital video. Samples were also tested to determine thermal conductivity, specific heat and thermal diffusivity as a function of compressed sample density. Theories are presented for the unique trends of the nano and micron-composite results. Third, experimental work is presented analyzing the effects of pre-heated compressed nm-Al+MoO3 samples. Sample pre-heating is achieved by volumetric heating using an isothermal oven and by varying the applied laser power to allow conductive heating. Both methods of preheating show unique behaviors and elevated flame propagation speeds compared to previous results. Results and discussion of this work also discuss the difficulties and critical time response of using bare-wire thermocouples to accurately measure nano-thermite reaction temperatures. Fourth, a series of DSC/TGA experiments were performed on the reaction of Al and gaseous oxygen to analyze the purest and ¡¥simplest¡¦ form of the Al oxidation (void of any reaction mechanisms dependent on the metal-oxide decomposition). Results are presented showing unique reaction onset temperatures, oxidation rates and activation energies for nano and micron-Al reacting in a gaseous oxygen environment. Fifth, a series of DSC/TGA experiments were performed on the reaction of Al and nano-MoO3. Results are presented for reaction onset temperatures, peak temperatures, heat of reaction values, and activation energies for Al+MoO3 composites with Al particles ranging from 50 nm to 20 ƒÝm. A final set of experiments was designed using the DSC/TGA to determine reaction duration and reaction self-propagation criteria for Al particle sizes ranging from 50 nm to 20 ƒÝm. Heating programs were manipulated for micron and nano-Al+MoO3 samples to determine the relationship between sample heating rate and reaction mechanisms. DSC tests were done using isothermal time intervals displaying that the nm-Al+MoO3 reactions are temperature dependent and not self-sustaining. Isothermal time intervals applied to ƒÝm-Al+MoO3 reactions displayed a delayed peak temperature. Finally, all of the results and experiments are combined as evidence in support of a single theory of the oxidation reaction of spherical Al particles. The presented results portray unique evidence in support of the nano and micron-sized Al reaction characteristics.Item Combustion characteristics of aluminum nanoparticles and nanocomposite aluminum+moly-trioxide thermites(Texas Tech University, 2005-05) Granier, John J.; Pantoya, Michelle; Seshaiyer, Padmanabhan; Oler, James W.; Levitas, Valery; Berg, Jordan M.Scientific advances in material synthesis such as exploding wire technology, plasma nucleation and wet precipitation have enabled industrial manufacturers to produce metal and metal oxide powders with nanometer-sized particles. These processes have enabled better overall quality control (i.e. more definitive particle size, smaller particle size distributions, oxide coating control and decreased contaminate concentration) and faster production rates. Much interest has been formed in the science and application of nano-sized aluminum (nm-Al) combustion. A thermite (or aluminothermic) reaction is an oxidation reaction between aluminum and a metal oxide with highly exothermic energy release. Thermite reactions of traditional Al powder (typically micron-sized particles) and Iron-oxide have been used for decades in welding and other intense heat applications. Nano-thermite reactions, have shown unique properties in ignition sensitivity and deflagration (flame propagation) speeds which have propelled thermites to new realms of applications. The decrease in required ignition stimuli of nano-thermites is an improvement for many payload critical applications, but the ignition sensitivity also creates various hazards during material handling and seems to be a factor in decreased reactivity of aged nano-thermites. Nano-thermites have displayed reaction rates near detonation speeds presenting applications as more efficient incendiary devices. The precise particle size control of nano-thermites is leading researchers to develop highly-tunable energy release mechanisms that can be applied as heat signature flare decoys. Studies have shown that the thermite reaction of nm-Al+MoO3 has a large theoretical energy density [19], increased ignition sensitivity [23][8], and near detonation flame propagation speeds [5][6] in comparison to traditional micron-particle thermites. This work will present macroscopic combustion behaviors (such as flame speed) along with experimental results focusing on the molecular reactions and thermal properties of nanocomposite Al+MoO3 thermite materials This work will outline the successes and precautions of several nm-Al+MoO3 powder mixing methods and several cold-pressing techniques used to form compressed solid samples. A general relationship of sample density as a function of pressing force and with a systematic methodology is presented to allow other researchers to produce similar samples for future comparison. Second, results from laser experiments performed to determine flame speeds of nano and micron-sized Al+MoO3 composites through a range of sample densities. Flame propagation speeds were measured using high-speed digital video. Samples were also tested to determine thermal conductivity, specific heat and thermal diffusivity as a function of compressed sample density. Theories are presented for the unique trends of the nano and micron-composite results. Third, experimental work is presented analyzing the effects of pre-heated compressed nm-Al+MoO3 samples. Sample pre-heating is achieved by volumetric heating using an isothermal oven and by varying the applied laser power to allow conductive heating. Both methods of preheating show unique behaviors and elevated flame propagation speeds compared to previous results. Results and discussion of this work also discuss the difficulties and critical time response of using bare-wire thermocouples to accurately measure nano-thermite reaction temperatures. Fourth, a series of DSC/TGA experiments were performed on the reaction of Al and gaseous oxygen to analyze the purest and ¡¥simplest¡¦ form of the Al oxidation (void of any reaction mechanisms dependent on the metal-oxide decomposition). Results are presented showing unique reaction onset temperatures, oxidation rates and activation energies for nano and micron-Al reacting in a gaseous oxygen environment. Fifth, a series of DSC/TGA experiments were performed on the reaction of Al and nano-MoO3. Results are presented for reaction onset temperatures, peak temperatures, heat of reaction values, and activation energies for Al+MoO3 composites with Al particles ranging from 50 nm to 20 ƒÝm. A final set of experiments was designed using the DSC/TGA to determine reaction duration and reaction self-propagation criteria for Al particle sizes ranging from 50 nm to 20 ƒÝm. Heating programs were manipulated for micron and nano-Al+MoO3 samples to determine the relationship between sample heating rate and reaction mechanisms. DSC tests were done using isothermal time intervals displaying that the nm-Al+MoO3 reactions are temperature dependent and not self-sustaining. Isothermal time intervals applied to ƒÝm-Al+MoO3 reactions displayed a delayed peak temperature. Finally, all of the results and experiments are combined as evidence in support of a single theory of the oxidation reaction of spherical Al particles. The presented results portray unique evidence in support of the nano and micron-sized Al reaction characteristics.Item Conformational dynamics plays a significant role in HIV reverse transcriptase resistance and substrate selection(2012-12) Nguyen, Virginia Myanh; Johnson, Kenneth AllenHuman immunodeficiency virus reverse transcriptase (HIV RT) is a virally encoded polymerase responsible for replicating the HIV genome. Most HIV treatments include nucleotide RT inhibitors (NRTIs) which inhibit HIV RT replication by serving as a substrate for the polymerase reaction but then blocks subsequent polymerization after incorporation. However, resistance to these NRTIs may occur through specific mutations in HIV RT that increase the discrimination of HIV RT for natural nucleotides over NRTIs. The role of enzyme conformational dynamics in specificity and substrate selection was studied using transient kinetic methods on HIV RT enzymes that have been site-specifically labeled with a conformationally sensitive fluorophore, to measure the rates of binding and catalysis. First, HIV RT with the mutation of lysine to arginine at the residue position 65 (K65R) was examined for its resistance against the NRTI tenofovir diphosphate (TFV), an acyclic deoxyadenosine triphosphate (dATP) analog. It was found that HIV RT K65R resistance to TFV was achieved through decreased rates of catalysis and increased rates of dissociation for TFV over dATP when compared with the kinetics of wild-type HIV RT. Moreover, global fitting analysis confirmed a mechanism where a large conformational change, after initial ground state binding of the substrate, contributed significantly to enzyme specificity. This led to our investigation of the molecular basis for enzyme specificity using HIV RT as a model system. Again, transient kinetic methods were applied with the addition of molecular dynamics simulations. The simulated results were substantiated by the corroborating experimental results. It was found that a substrate-induced conformational change in the transition of HIV RT from an open nucleotide-bound state to a closed nucleotide-bound state was the major determinant in enzyme specificity. The molecular basis for substrate selection resulted from the molecular alignments of the substrate in the active-site, which induced the conformational change. When the correct nucleotide was bound, optimal molecular interactions in the active-site yielded a stably closed complex, which promoted nucleotide incorporation. In contrast, when an incorrect nucleotide was bound, the molecular interactions at the active-site were not ideal, which yielded an unstable closed complex, which promoted substrate dissociation rather than incorporation.Item Effect of electron beam irradiation and sugar content on kinetics of microbial survival(Texas A&M University, 2006-10-30) Rodriguez Gonzalez, OscarThe killing effectiveness of electron beam irradiation has not been completely characterized. The type of microorganisms and the composition of food have a direct effect on the efficiency of this technology. The objectives of this study were to select a surrogate suitable for use in electron beam irradiation studies of fruits and to evaluate the effect of sugar content on the kinetics of microbial damage and recovery. A 2.0 MeV Van de Graaff linear accelerator was used to apply irradiation (up to 5.0 kGy), using different configurations, on gelatin-based systems with the addition of sugars. The systems were inoculated with pathogenic and non-pathogenic bacteria strains (surrogates). Initial studies showed that Escherichia coli K-12 MG1655 is a suitable surrogate that represents the damage induced to common fruit pathogens by irradiation. The reduction in bacteria population can be maintained by storing samples at 4????C. An increase in temperature up to 20????C was enough for the damaged population to recover in 48 hours. Gelatin-based systems proved to be a simple and inexpensive medium to evaluate the effects of irradiation (up to 5.0 kGy) on selected bacteria. Reduction of the system dimensions and their positioning related to the beam source were key factors in increasing the killing effectiveness of irradiation. The sugar levels (up to 8 %) used to mimic the maturity of cantaloupes had no effect on the radiation D10 values and the recovery of the surrogate population quantified as Generation Times. The resistance of the surrogate to irradiation was validated in an optimum configuration and in cantaloupes. Temperature and sugar content caused significantly higher changes to the physical structure of the gel-based systems than irradiation (1.0 kGy). Plate counts and light microscopy techniques demonstrated that the structure of the gelatin-based systems allow for motility of the bacteria in a 3-D array (length, width and depth). When little information was available about the effectiveness of using a low energy linear accelerator, the inoculation of gelatin-based systems proved to be a reliable method to select a suitable surrogate and to predict the effects of irradiation on bacteria as a function of sugar content.Item Effects of intermetallic compound formation on reliability of Pb-free Sn-based solders for flip chip and three-dimensional interconnects(2013-12) Wang, Yiwei; Ho, P. S.The effects of intermetallic compound (IMC) formation on reliability of Pb-free Sn-based solders for flip chip and three-dimensional (3D) interconnects were studied. The dissertation is organized into four parts. In the first part, the effect of Sn grain orientation on electromigration (EM) reliability of Pb-free Sn-based flip chip solder joints was studied. The Sn grain microstructure in flip chip solder joints was characterized using the electron backscatter diffraction (EBSD) technique, and wa found to be closely related to the EM failure mechanims. The approach to grain structure optimization for improved EM reliability was also explored. In addition to the experimental work, a kinetic analysis was formulated to investigate the early EM degradation mechanism in Sn-based solder joints with Ni under-bump metallization (UMB). The aforementioned kinetic analysis, the intrinsic diffusion coefficients were not readily available in the literature. In the second part of the work, a Monte Carlo method known as simulated annealing was applied to estimate the unknown diffusion coefficients using a multi-parameter optimization method by fitting to experimental measurements. The intrinsic diffusion coefficients of Ni and Sn in Ni₃Sn₄ between 150 and 200°C, and those of Cu and Sn in Cu₃Sn and Cu₆Sn₅ between 120 and 200°C were estimatd. The activation energies for these diffusion coefficients were also determined. Together, this provides the diffusivity parameters to predict the intermetallic growth as a function of temperature. The third objective focused on the EM reliability of Sn-based microbump joints in 3D interconnects with through-silicon vias (TSVs). No EM-induced bump failure was observed, showing a robust EM reliability in microbumps. High temperature thermal annealing test was also performed on microbumps with three different metallizations in an effort to explore structural and process optimization. Finally, interfacial reaction induced stress in IMC microbumps was investigated. A numerial analysis was formulated to study the concurrent diffusion, phase transformation, and deformation in the process of IMC formation. Stress generation due to unbalanced diffusion rates and volumetric change upon phase transformation was considered. The coupled analysis was applied to investigate Ni₃Sn₄ growth in the Ni-Sn microbumping system. A simulation approach based on finite difference method with moving boundaries was employed to numerically solve stress evolution in Ni₃Sn₄. The equilibrium stress was also investigated using a modified model with a finite thickness of solder. Simulation predictions were found to be in good qualitative agreement with experimental observations.Item Examining supercritical CO₂ dissolution kinetics during carbon sequestration through column experiments(2011-08) Kent, Molly Elizabeth; Bennett, Philip C. (Philip Charles), 1959-; Romanak, Katherine; Cardenas, Meinhard B.Carbon sequestration is a method of capturing and storing excess anthropogenic CO₂ in the subsurface. When CO₂ is injected, the temperature and pressure at depth turn it into a supercritical (SC) fluid, where density is that of a liquid, but viscosity and compressibility resemble a gas. Ultimately the SC CO₂ is trapped at depth either by low permeability sealing layers, by reactions with minerals, or by dissolving into fluids. The injected CO₂ is buoyant and initially exists as a non-aqueous hydrophobic layer floating on top of the subsurface brine, up against the upper sealing formation, but over time it will dissolve into the brine and potentially react with minerals. The details of that initial dissolution reaction, however, are only poorly understood, and I address three basic questions for this research: What is the fundamental kinetics of SC CO₂ dissolution into water? How fast does dissolved CO₂ diffuse away from the source point? And what geochemical conditions influence the dissolution rate? To answer these questions I employed a high pressure flow-through approach using a column packed with coarse quartz sand. The system was both pressure and temperature controlled to have either liquid or SC CO₂ present, and was typically run at 100 Bar, 0.5 to 2.5 mls/min, and 28-60°C. After establishing the hydraulic parameters for the column using two conservative tracers (Br, As), injections (5 and 20 [mu]l) were made either as aqueous solutions equilibrated to high pressure CO₂, or as pure liquid or SC CO₂ into 0.1 mmol NaOH. For all experiments the pH of the system was monitored, and [CO₂] over time was calculated from those data. For injections of brine with dissolved CO₂, transport was conservative and was nearly identical to the conservative tracers. The CO₂ quickly mixes in the column and does not react with the quartz. The liquid and SC CO₂ injections, however, do not act conservatively, and have a very long tailing breakthrough curve that extends to tens of pore volumes. I hypothesize that the SC CO₂ is becoming trapped as a droplet or many droplets in the pore spaces, and the long breakthrough tail is related either to the rate of dissolution into the aqueous phase, the diffusion of dissolved CO₂ away from the phase boundary, or the reaction with the NaOH, limited to the narrow contact zones in the pore throats. Because of the speed at which acid-base reactions occur (nanosecond kinetics), I infer that the rate limiting step is either surface dissolution or diffusion. From plots of ln[CO₂] v. time I obtained values for k, the specific rate of the dissolution reaction R=-k[CO₂]. No trend for k was seen with respect to changes in temperature, but k did show a trend with respect to changing flow rate. k increased from an average value of 3.05x10⁻³ at 0.5 ml/min to an average value of 3.38x10⁻³ at 1.6 ml/min, and then held constant at the higher flow rates, up to 2.5 ml/min. I interpret these data to show that at low flow rates, the reaction is diffusion limited; the fluid nearest the contact zone becomes saturated with dissolved CO₂. At higher flow rates, the fluid is moving fast enough that saturation cannot occur, and the kinetics of the dissolution reaction dominate. Simple geometric models indicate that the CO₂/water interface is shaped like a spherical cap, indicating that the snapped-off CO₂ is forming a meniscus in the pore throat, limiting the surface area across which dissolution can occur.Item Experimental Studies of Hydroxyl Radical Initiated Tropospheric Oxidation of Unsaturated Hydrocarbons(2011-10-21) Ghosh, BuddhadebThe tropospheric oxidation of unsaturated hydrocarbons is a central issue in atmospheric chemistry. These hydrocarbons are emitted into the atmosphere from both natural and anthropogenic sources, and their atmospheric oxidation leads to different atmospheric pollutants, including ground level ozone, photochemical smog and secondary organic aerosols. Isoprene and 1,3-butadiene represent a biogenic and an anthropogenic hydrocarbon, respectively, which primarily undergo electrophilic addition of OH radical, followed by chain propagating radical reactions. Their oxidation is the major source for ground level ozone formation in both rural and urban area and understanding their chemistry is essential for regional air quality modeling. Until recently, most of the studies of isoprene chemistry have been non-isomer specific, reflecting the reactivity of combined pathways and therefore were insensitive to specific details of the isomeric pathways. An isomeric selective approach to studying unsaturated hydrocarbon oxidation is described in this dissertation. A synthesized precursor, whose photolysis can provide a route to the formation of energy selected single isomer in the isoprene oxidation pathway, enables the study of important channels that are difficult to unravel in non isomer specific experiments. The major addition channel in OH isoprene oxidation has been studied following the isomeric selective approach and using Laser Photolysis-Laser Induced Fluorescence (LP-LIF) as the primary experimental technique. The study reveals important information about the oxidative chemistry of the ?-peroxy radicals, accounting for about 20 percent of missing carbon balance in isoprene oxidation, and isomeric specific rate constants. A similar approach was applied to study the oxidation of 1,3-butadiene, and the photolytic precursor for the dominant hydroxy alkyl isomer in the OH initiated oxidation of 1,3-butadiene was synthesized. The subsequent experiments and analysis revealed detailed information about the oxidative chemistry accounting for approximately 26 percent of the missing chemistry. Finally, non isomeric selective OH cycling experiments were carried out on the1,3-butadiene system. By analyzing the OH cycling data with the combined information obtained from the isomeric specific studies of the two isomeric channels of 1,3-butadiene oxidation, the relative branching between the two isomeric channels of OH-1,3-butadiene oxidation was determined.Item Investigation of oil adsorption capacity of granular organoclay media and the kinetics of oil removal from oil-in-water emulsions(Texas A&M University, 2007-04-25) Islam, SoniaProduced water, a byproduct of oil and gas production, includes almost 98% of all waste generated by oil and gas exploration and their production activities. This oil contaminated waste water has a great impact on our environment and is considered to be a high-cost liability. The Department of Energy??????s Oil and Gas Environmental Program is concerned with the development of new and affordable technology to clean this produced water. Organically modified clays are proposed as a good option for removal of oil from produced water. Organoclay, incorporated into a treatment process shows promise of being a cost effective method of treatment to remove crude oil from brine either as a final treatment prior to brine disposal at sea or as a precursor to desalination. Organoclay also pre-polishes the waste water before further treatment. This research studies the efficacy of using organoclay to remove oil by measuring its adsorption capacity to remove the oil from a SAE 30 (Golden West Superior) motor oil-water emulsion. A kinetic model was developed to examine the time dependent behavior of the oil adsorbing characteristics of the organoclay and to investigate how closely the experimentally obtained data matches the kinetic model. It was found that organoclay is effective in removing various percentages of oil depending on the concentrations of a SAE 30 (Golden West Superior) motor oil-water emulsion. Moreover, it was found that the experimental data closely follow the kinetic behavior of the organoclay as shown by the kinetic model. Since this research is specific to a particular type of oil, SAE 30, further research is required for verifying the adsorption capacity of organoclay in other types of oils. Moreover, it is also recommended that the adsorption capacity of the organoclay, together with conventional adsorbent such as GAC (Granular Activated Carbon), be investigated to determine if there is any further improvement in the adsorption capacity. Lastly, a detailed investigation using the actual produced water from the oil field should be conducted to determine the efficacy of the organoclay system in removing oil from water produced in the field.Item Investigation of the post-polyketide synthase (PKS) modifications during spinosyn A biosynthesis in Saccharopolyspora spinosa(2010-08) Kim, Hak Joong; Liu, Hung-wen, 1952-Diverse biological activities of polyketide natural products are often associated with specific structural motifs, biosynthetically introduced after construction of the polyketide core. Therefore, investigation of such "post-polykektide synthase (PKS)" modifications is important, and the accumulated knowledge on these processes can be applied for combinatorial biosynthesis to generate new polyketide derivatives with enhanced biological activities. In addition to the practical value, a lot of unprecedented chemical mechanisms can be found in the enzymes involved therein, which will significantly advance our understanding of enzyme catalysis. The works described in this dissertation focus on elucidating a number of post-PKS modifications involved in the biosynthesis of an insecticidal polyketide, spinosyn A, in Saccharopolyspora spinosa. First, three methyltransferases, SpnH, SpnI, and SpnK, responsible for the modification of the rhamnose moiety, have been investigated to verify their functions and to study how they are coordinated to achieve the desired level of methylation of rhamnose. In vitro assays using purified enzymes not only established that SpnH, SpnI, and SpnK are the respective rhamnose 4ʹ-, 2ʹ-, and 3ʹ-O-methyltransferase, but also validated their roles in the permethylation process of spinosyn A. Investigation of the order of the methylation events revealed that only one route catalyzed by SpnI, SpnK, and SpnH in sequence is productive for the permethylation of the rhamnose moiety, which is likely achieved by the proper control of the expression levels of the methyltransferase genes involved in vivo. The key structural feature of spinosyn A is the presence of the unique tetracyclic architecture likely derived from the monocyclic PKS product. To elucidate this "cross-bridging" process, which had been hypothesized to involve four enzymes, SpnF, SpnJ, SpnL, and SpnM, the presumed polyketide substrate was chemically synthesized using Julia-Kocienski olefination, Stille cross-coupling, and Yamaguchi macrolactonization as key reactions. Incubation of the synthesized substrate with SpnJ produced a new product where the 15-OH group of the substrate is oxidized to the ketone. Next, it was demonstrated that incubation of this ketone intermediate with SpnM produces a tricyclic compound, via a transient monocyclic intermediate with high degree of unsaturation. Whereas it was initially thought that SpnM catalyzes both dehydration and [4+2] cycloaddition in sequence, detailed kinetic analysis revealed that SpnM is only responsible for the dehydration step, and the [4+2] cycloaddition step is indeed catalyzed by SpnF. Finally, successful conversion of the tricyclic intermediate to the tetracyclic core was demonstrated using SpnL. Proposed chemical mechanisms of SpnF and SpnL, Diels-Alder and Rauhut-Currier reactions, respectively, are interesting because enzymes capable of catalyzing these reactions have yet to be characterized in vitro. This work not only establishes the biosynthetic pathway for constructing the spinosyn tetracyclic core, but also epitomizes the significance of the post-PKS modification as a rich source of new enzyme catalysis.Item Kinetic Modeling of the Hydrocracking of Fused-Ring Di-Aromatic Species(2015-01-16) Rojas, PedroThe derivation of kinetic models for the development and simulation of hydrocarbon processes require detailed information on the reaction network. In the present work, experiments on the hydrocracking of fused-ring species, specifically naphthalene and 1-methylnaphthalene were performed. The feed was diluted with n-heptane, and the experiments were conducted in a fixed bed catalytic reactor loaded with Pt/Pd HY zeolite catalyst in the temperature range 275 ?C to 350 ?C, at pressures between 28 and 35 bar, space times between 21 to 144 gcat h/mol of reactant and with hydrogen/hydrocarbon molar ratios ranging from 100 to 340. With naphthalene as the feed as many as 16 components were detected and identified in the reactor effluent, with 1-methylnaphthalene up to 42. The effect of catalyst deactivation on the rates of different reactions and elementary steps was studied, and the effects of temperature, pressure and space time on the product distribution in the absence of catalyst deactivation were observed. Following the rules of carbenium ion chemistry detailed networks in terms of elementary steps were generated for each feed species. The network for naphthalene contains a total of 16 reactions on the metal sites and 46 elementary steps on the acid sites, that for 1-methylnaphthalene 123 reactions on the metal sites and 258 elementary steps on the acid sites. Typical pathways to a given product include dehydrogenation/hydrogenation of ring structures on the metal sites and protonation/deprotonation, ring contraction/expansion, PCP branching of side chains, and endocyclic ?-scission on the acid sites. The presence of Pt in the catalyst also led to side chain and ring-opening hydrogenolysis. The single-event modeling approach aimed to reduce the number of independent parameters to be determined from the experimental data for the large number of reactions and elementary steps in the networks. The frequency factors on the acid sites were modeled using single-event kinetics and the activation energies using Evans-Polanyi relationship. On the metal sites the nature of the reacting species and the type of reaction determined the number of parameters. The kinetic model contains hundreds of parameters. Of those, there are only 25 independent parameters for steps on the acid sites, and 16 independent parameters for reactions on the metal sites. An optimization strategy was developed by the sequential use of three different optimization methods to fit the experimental data.Item Metal dependent structure, dynamics, and function in RNA measured by site-directed spin labeling and EPR spectroscopy(Texas A&M University, 2007-04-25) Kim, Nak-KyoonThe structure and function of RNA molecules are dependent on RNA-metal ion interactions in both diffusive and direct ways. Structural information for RNA has been obtained using various biophysical and biochemical methods. In this study, using site-directed spin labeling (SDSL) and EPR spectroscopy, distances in RNA duplexes, TAR RNA, and the hammerhead ribozyme have been measured to investigate RNA structures. Kinetic measurements have been performed in the extended hammerhead ribozyme to correlate the catalytic function with metal dependent ribozyme folding. As a basic model system for distance measurements, inter-spin distances in RNA duplexes with spin labels at various positions are measured using SDSL with continuous EPR and a Fourier deconvolution method. Divalent metal-ion dependent TAR RNA folding from bent to extended conformers is monitored by measuring inter-spin distances near the bulge region. In order to investigate a proposed loop-loop interaction in the extended hammerhead ribozyme which significantly enhances the ribozyme activity, distance measurements, dynamics studies, and kinetics measurements have been performed. We have introduced PELDOR long-distance measurements in order to investigate metal dependent folding of the hammerhead ribozyme. The dynamics of the spin labels attached to the hammerhead ribozyme with increasing mono- and divalent metal ion concentrations are monitored using CW EPR spectroscopy at room temperature. EPR data show that a loop-loop interaction occurs near the U1.6 nucleotide, and that in 0.1 M NaCl the docking occurs at submillimolar Mg2+ concentrations ([Mg2+]1/2, docking = ~ 0.7 mM). Kinetics measurements show that the hammerhead ribozyme requires high concentration of Mg2+ for the maximum cleavage activity ([Mg2+]1/2, cleavage = ~ 90 mM).Item On the reactions of trans-3-chloroacrylic acid dehalogenase and a cis-3-chloroacrylic acid dehalogenase homologue, Cg10062 : mechanistic and evolutionary implications(2015-05) Huddleston, Jamison Parker; Whitman, Christian P.; Johnson, Kenneth A; Kerwin, Sean M; Fast, Walter L; Hoffman, David WThe tautomerase superfamily (TSF) provides an excellent model system to study enzyme specificity, catalysis, and divergent evolution. trans-3-Cholroacrylic acid dehalogenase (CaaD), cis-3-chloroacrylic acid dehalogenase (cis-CaaD), and malonate semialdehyde decarboxylase (MSAD) are three TSF members that catalyze the final reactions in the degradation of the nematocide, 1,3-dichloropropene. All three enzymes have the TSF characteristic beta-alpha-beta fold and catalytic amino terminal proline (Pro-1). Both CaaD and cis-CaaD dehalogenate their respective isomers of 3-chloroacrylic acid yielding malonate semialdehyde. Subsequently, MSAD decarboxylates malonate semialdhyde resulting in acetaldehyde and CO2. Their catalytic and substrate specificities are exquisite considering they share three key and positionally conserved residues. As part of an effort to understand how such specificity evolved, a pre-steady-state kinetic analysis of CaaD was carried out. Alongside a similar study on cis-CaaD, a fluorescent mutant of CaaD was constructed that had minimal kinetic differences from the wild-type. The mutant was validated as an accurate fluorescent reporter of change in enzyme state that allowed for the reaction to be followed using stopped-flow methods. Stopped-flow fluorescence, rapid chemical quench data and ultraviolet spectroscopy were globally fit by computational simulation. The fit resulted in a kinetic mechanism for CaaD affording detailed information about the reaction, including measuring the rate of product release, the rate of chemistry, a previously unknown partially rate-limiting step associated with a conformational change, and the definition of binding constants for both products (MSA and Br-). In addition to the dehalogenation reaction, the reaction of the fluorescent mutant with a mechanism-based inhibitor, 3-bromopropiolate, was characterized. The values for the apparent rate of inhibition and potency were defined and estimates were determined for the values of the rate of chemistry and the release of bromide. The information gathered during these inhibition experiments was used to further refine the CaaD dehalogenation mechanism eliminating ambiguities present in the initial data set. Finally, the reactions of a cis-CaaD homologue, Cg10062 from Corynebacterium glutamicum were characterized. Cg10062 shares high sequence similarity (53%) and the same six critical active site residues as cis-CaaD, but Cg10062 has poor cis-CaaD activity. Moreover, Cg10062 dehalogenates both 3-chloroacrylic acid isomers. The reactions of Cg10062 with propiolate, 2-butynoate, and 2,3 butadienoate were investigated. Cg10062 functions as a hydratase/decarboxylase using propiolate generating malonate semialdehyde and acetaldehyde. Cg10062 catalyzes a hydration-dependent decarboxylation of propiolate as exogenously added malonate semialdehyde is not decarboxylated. With 2,3 butadienoate and 2-butynoate, Cg10062 functions as a hydratase and yields only acetoacetate. Mutations to the activating residues Glu114 and Tyr103 produced a range of results from a reduction in wild-type activity to a switch of activity. Possible intermediates for the hydration and decarboxylation products can be trapped as covalent adducts to Pro-1 when NaCNBH3 is incubated with certain combinations of substrate and mutant enzymes. Three mechanisms are presented to explain these findings along with the strengths and weaknesses of each mechanism in terms of being able to account for experimental observations.Item Ozonation of erythromycin and the effects of pH, carbonate and phosphate buffers, and initial ozone dose(2011-08) Huang, Ling, Ph. D.; Katz, Lynn Ellen; Lawler, Desmond F.The ubiquitous presence and chronic effect of pharmaceuticals is one of the emerging issues in environmental field. As a result of incomplete removal by sewage treatment plants, pharmaceuticals are released into the environment and drinking water sources. On the other hand, conventional drinking water treatment processes such as coagulation, filtration and sedimentation are reported to be ineffective at removing pharmaceuticals. Therefore, the potential presence of pharmaceuticals in finished drinking water poses a threat on public health. Antibiotics, as an important group of pharmaceuticals, are given special concerns because the potential development of bacteria-resistance. Ozonation and advanced oxidation processes are demonstrated to be quite effective at removing pharmaceuticals. The oxidation of pharmaceuticals is caused by ozone itself and hydroxyl radicals that are generated from ozone decomposition. Whether ozone or hydroxyl radicals are the primary oxidant depends on the specific pharmaceutical of interest and the background water matrix. In this research, erythromycin, a macrolide antibiotic, was chosen as the target compound because of its high detection frequency in the environment and its regulation status. The objective of this research was to investigate the removal performance of erythromycin by ozonation from the standpoint of kinetics. The effects of pH, carbonate and phosphate buffers, and initial ozone dose on ozonation of erythromycin were also studied. The second-order rate constant for the reaction between deprotonated erythromycin and ozone was determined to be 4.44x10⁹ M⁻¹·s⁻¹ while protonated erythromycin did not react with ozone. Ozone was determined to be the primary oxidant for erythromycin removal by ozonation. pH was found to have great positive impact on the degradation of erythromycin by ozonation due to the deprotonation of erythromycin at high pH. Carbonate and phosphate buffers were found to have negligible effects on the degradation of erythromycin by ozonation. Initial ozone dose showed a positive impact on the total erythromycin removal rate by ozonation.Item Preliminary studies of the influence of forces and kinetics on interfacial colloidal assembly(Texas A&M University, 2004-11-15) Fernandes, GregoryIn this research we illustrate how particle-particle and particle-substrate interactions affect structure in interfacial colloidal systems. A number of tools are used to quantify characteristics of deposited structures. These results help understand the effects of colloidal system interactions and deposition kinetics on the degree of ordering in interfacial colloidal structures. The first set of experiments involve 2.34 ?m silica colloids interacting with silica substrates in 0mM, 5mM, 10mM, and 100mM NaCl solutions. Only the 100mM NaCl solution resulted in rapid deposition driven by van der Waals attraction, while residual electrostatic repulsion produced levitation at lower ionic strengths. This allowed direct observation of the effects of varying magnitudes of attractive interactions on interfacial colloidal structures. Rapid deposition of positively charged 1?m latex colloids on negatively charged silica substrates driven by Coulombic and van der Waals attraction produced surface structures similar to those obtained with only van der Waals attraction. Experiments on 2.34 ?m silica colloids interacting with silica substrates in 10mM NaCl/pH 5.5 and 10mM NaCl/pH 10 conditions resulted in slower deposition rates. It was also found that slower deposition rates produced more compact structures displaying a higher degree of order. Another set of experiments was aimed at understanding interactions and structures formed in systems of polymerically levitated particles. Total internal reflection microscopy (TIRM) experiments revealed the influence of underlying substrate chemistry on interaction profiles in these systems. Basic experiments were also performed on the effects of varying amounts of specific ions on the dispersion stability in these systems. At conditions producing instability in polymeric systems, a similar degree of order was observed in comparison to experiments involving rapid deposition via salt addition in electrostatically stabilized systems. The results of this research clearly indicate that particle-particle and particle-substrate interactions are critical in determining structure formation by deposition. While the principal focus of this research is to study structures formed in various kinetic regimes, it also provides a basis for future studies aimed at tuning attractive interactions to produce equilibrium colloidal crystals on substrates.Item Quantitative Determination of Chemical Processes by Dynamic Nuclear Polarization Enhanced Nuclear Magnetic Resonance Spectroscopy(2012-07-16) Zeng, HaifengDissolution dynamic nuclear polarization (DNP) provides several orders of magnitude of NMR signal enhancement by converting the much larger electron spin polarization to nuclear spin polarization. Polarization occurs at low temperature (1.4K) and is followed by quickly dissolving the sample for room temperature NMR detection. DNP is generally applicable to almost any small molecules and can polarize various nuclei including 1H, 19F and 13C. The large signal from DNP enhancement reduces the limit of detection to micromolar or sub-micromolar concentration in a single scan. Since DNP enhancement often provides the only source for the observable signal, it enables tracking of the polarization flow. Therefore, DNP is ideal for studying chemical processes. Here, quantitative tools are developed to separate kinetics and spin relaxation, as well as to obtain structural information from these measurements. Techniques needed for analyzing DNP polarized sample are different from those used in conventional NMR because a large, yet non-renewable hyperpolarization is available. Using small flip angle pulse excitation, the hyperpolarization can still be divided into multiple scans. Based on this principle, a scheme is presented that allows reconstruction of indirect spectral dimensions similarly to conventional 2D NMR. Additionally, small flip angle pulses can be used to obtain a succession of scans separated in time. A model describing the combined effects of the evolution of a chemical process and of spin-lattice relaxation is shown. Applied to a Diels-Alder reaction, it permitted measuring kinetics along with the effects of auto- and cross-relaxation. DNP polarization of small molecules also shows significant promise for studying protein-ligand interaction. The binding of fluorinated ligands to the protease trypsin was studied through the observation of various NMR parameter changes, such as line width, signal intensity and chemical shift of the ligands. Intermolecular polarization transfer from hyperpolarized ligand to protein can further provide information about the binding pocket of the protein. As an alternative to direct observation of protein signal, a model is presented to describe a two-step intermolecular polarization transfer between competitively binding ligands mediated through the common binding pocket of the protein. The solutions of this model relate the evolution of signal intensities to the intermolecular cross relaxation rates, which depend on individual distances in the binding epitope. In summary, DNP provides incomparable sensitivity, speed and selectivity to NMR. Quantitative models such as those discussed here enable taking full advantage of these benefits for the study of chemical processes.Item Reaction of dimethyl trisulfide with hemoglobin(2016-11-17) Dong, XinmeiWhen samples of blood were spiked with the novel cyanide antidote dimethyl trisulfide (DMTS), the color of the blood was observed to darken. Additionally, recoveries of DMTS from spiked blood were low, and the loss of DMTS was more pronounced in 5-day old blood samples than in equivalently spiked 4-month old blood samples. It was hypothesized that DMTS oxidizes hemoglobin (Hb) in the red blood cells to yield methemoglobin (metHb), methanethiol (MeSH), methyl hydrogen disulfide (MeSSH), and hydrogen sulfide (H2S). The aim of this research was to determine the reactants, products, and chemical kinetics of the reactions of DMTS with Hb isolated from red blood cells, and with Hb in blood. The changes induced in the Hb absorption spectrum by the addition of DMTS were found to closely match those induced by the known metHb former sodium nitrite. These spectral shifts indicating the conversion of Hb to metHb were observed systematically when DMTS was added to red blood cell or Hb solutions. The formation of metHb was monitored as a function of time following the addition of a known amount of DMTS. The rate of the reaction of DMTS with Hb increased in the presence of the reducing agent dithionite (DT). H2S, MeSH, and MeSSH were expected as reaction products, but were not directly observed in headspace samples. 2,4-dithiapentane had not been predicted as a reaction product, but was observed in the headspace above reaction mixtures of DMTS and Hb. The 2,4-dithiapentane is hypothesized to be a reaction product of MeSH with formaldehyde-based polymers in the vial cap.Item The modeling of arsenic removal from contaminated water using coagulation and sorption(Texas A&M University, 2005-11-01) Kim, Jin-WookTo achieve predictive capability for complex environmental systems with coagulation and arsenic sorption, a unified improved coagulation model coupled with arsenic sorption was developed. A unified coagulation model coupled with arsenic sorption was achieved by the following steps: (1) an improved discretized population balance equation (PBE) was developed to obtain the exact solution of conventional coagulation, (2) the improved PBE was extended to an adjustable geometric size interval having higher numerical stability, accuracy, and computational efficiency than existing models for fractal aggregate coagulation that includes agglomeration and fragmentation, (3) a surface complexation equilibrium model and a sorption kinetic model was introduced to predict arsenic sorption behavior onto hydrous metal oxide surfaces, and (4) an improved discretized PBE was coupled with arsenic sorption kinetics and equilibrium models by aid of collision efficiency ?? depending on surface charge (potential) on the hydrous metal oxide particles, colliding particle size ratio, and fluid strain-rate in applied flow system. The collision efficiency ?? into the improved (r,r)ij(r,r)ijdiscretized coagulation model for fractal aggregate yielded a unified improved coagulation model coupled with arsenic sorption kinetics and the equilibrium model. Thus, an improved unified coagulation model could provide high statistical accuracy, numerical stability, and computational efficiency to enhance predictive capability for behavior of arsenic sorption and fractal colloid particle aggregation and break-up, simultaneously. From the investigation, it is anticipated that the unified coagulation model coupled with arsenic sorption kinetics and equilibrium will provide a more complete understanding of the arsenic removal mechanism and its application to water/wastewater treatment. Further, this coupled model can be applied to other water and wastewater treatment systems combined with sorption and filtration processes. These combined processes can be optimized by the coupled model that was developed in this study. By simulating the arsenic sorption and particle size distribution as a pretreatment before filtration (sand filtration or membrane filtration), the overall arsenic removal efficiency and operation cost can be estimated.Item Wrinkling of elastic thin films on compliant substrates(2009-05) Im, Se Hyuk; Huang, Rui, doctor of civil and environmental engineeringComplex wrinkle patterns have been observed in various thin film systems, typically with integrated hard and soft materials for various technological applications as well as in nature. The underlying mechanism of wrinkling has been generally understood as a stress-driven instability. On an elastic substrate, equilibrium and energetics set the critical condition and select the wrinkle wavelength and amplitude. On a viscous substrate, wrinkles grow over time and kinetics select the dominant wavelength. More generally, on a viscoelastic substrate, both energetics and kinetics play important roles in determining the critical condition, the growth rate, and wrinkle patterns. The dynamics of wrinkling, while analogous to other phase ordering phenomena, is rich and distinct under the effects of a variety of stress conditions and nonlocal film-substrate interactions. In this study, a new mathematical model is developed for wrinkling of isotropic and anisotropic elastic films on viscoelastic substrates. Analytic solutions are obtained by a linear perturbation analysis and a nonlinear energy minimization method, which predict the kinetics of wrinkle growth at the initial stage and the equilibrium states at the long-time limit, respectively. In between, a power-law coarsening of the wrinkle wavelength is predicted by a scaling analysis. Numerical simulations confirm the analytical predictions and show diverse wrinkle patterns under various stress conditions. For isotropic elastic films, a transition from parallel wrinkles to zigzag patterns is predicted under anisotropic biaxial stresses. For cubic crystal films, the anisotropic elastic property leads to formation of orthogonal wrinkle patterns under equi-biaxial stresses. In general, the competition between the stress anisotropy and the material anisotropy controls the evolution of wrinkle patterns. Based on the mathematical model, two potential applications of the wrinkling phenomenon are explored, one for surface patterning and the other for estimating viscoelastic properties of thin polymer films. The theoretical and numerical results from this study are compared with experimental observations that are available in literature and through collaborations with experimental groups. The last chapter of this dissertation considers ratcheting-induced wrinkling for an elastic film on an elastoplastic substrate under cyclic temperatures, demonstrating an analogy between plastic ratcheting and viscous creep.