Browsing by Subject "kinetics"
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Item A Study of Formation and Dissociation of Gas Hydrate(2012-07-16) Badakhshan Raz, SadeghThe estimation of gas hydrate volume in closed systems such as pipelines during shut-in time has a great industrial importance. A method is presented to estimate the volume of formed or decomposed gas hydrate in closed systems. The method was used to estimate the volume of formed gas hydrate in a gas hydrate crystallizer under different subcoolings of 0.2, 0.3, 0.6 and 4.6 degrees C, and initial pressures of 2000 and 2500 psi. The rate of gas hydrate formation increased with increases in subcooling and initial pressure. The aim of the second part of the study was the evaluation of the formation of gas hydrate and ice phases in a super-cooled methane-water system under the cooling rates of 0.45 and 0.6 degrees C/min, and the initial pressures of 1500, 2000 and 2500 psi, in pure and standard sea water-methane gas systems. The high cooling rate conditions are likely to be present in pipelines or around a wellbore producing from gas hydrate reservoir. Results showed that the initial pressure and the chemical composition of the water had little effect on the ice and gas hydrate formation temperatures, which were in the range of -8 +/- 0.2 degrees C in all the tests using the cooling rate of 0.45 degrees C/min. In contrast, the increase in the cooling rate from 0.45 to 0.6 degrees C/min decreased the ice and gas hydrate formation temperatures from -8 degrees C to -9 degrees C. In all tests, ice formed immediately after the formation of gas hydrate with a time lag less than 2 seconds. Finally, an analytical solution was derived for estimating induced radial and tangential stresses around a wellbore in a gas hydrate reservoir during gas production. Gas production rates between 0.04 to 0.12 Kg of gas per second and production times between 0.33 to 8 years were considered. Increases in production time and production rate induced greater radial and tangential stresses around the wellbore.Item Adsorption and desorption of atrazine on a melamine-based soil amendment(Texas A&M University, 2004-09-30) Neitsch, Susan LynnAdsorption kinetics and adsorption-desorption of atrazine on organoclay composites prepared with the surfactant 6-piperazin-1-yl-N,N'-bis-(1,1,3,3-tetramethyl-butyl)-(1,3,5)triazine-2,4-diamine and Houston Black clay were studied using the indirect batch equilibration procedure. The organoclay composites sorbed significantly more atrazine than the Houston Black clay. Adsorption equilibrium was reached after 72 h for the organoclay composites. Atrazine adsorption isotherms were described by linear partitioning. The Koc values ranged from 605 to 5271 L kg-1 for the organoclay composites compared to a value of 41 L kg-1 for the Houston Black clay. The organoclay composite containing 20% surfactant on a total weight basis provided the most efficient adsorption of atrazine, although organoclay composites containing much lower amounts of surfactant also adsorbed significant amounts of atrazine. An average of 11% of sorbed atrazine was released during desorption. Characterization of desorption products showed only atrazine molecules being released from the organoclay composites.Item Adsorption of As(V), As(III) and methyl arsenic by calcite and the impact of some groundwater species(2009-05-15) Jones, Robert GarretThe objective of this research was to investigate the retention of arsenate (iAsV), arsenite (iAsIII), monomethyl arsenate (MMAsV) and dimethyl arsenate (DMAsV) by calcite and assess the impact of dissolved Ca2+, Mg2+, phosphate and sulfate on arsenic solubility, adsorption and precipitation phenomena. Adsorption kinetics of iAsV, evaluated at a low and high concentration, was a relatively rapid process, with a fast initial reaction rate within the first few minutes and a subsequent slower reaction rate as equilibrium was approached. The relative adsorption of arsenicals decreased in the following order: iAsV > iAsIII > DMAV > MMAV. In no case was a clear adsorption maximum observed with increasing dissolved arsenic concentration. Dissolved 0.01 M Ca2+ resulted in an increase in iAsV adsorption; however, in the presence of 0.1 M Ca2+ adsorption of iAsV was decreased. The presence of Mg2+ as 0.01 M Mg(NO3)2 resulted in decreased iAsV adsorption probably the result of a lower iAsV affinity for adsorbed Mg2+ as compared to Ca2+. Phosphate and sulfate were highly competitive with iAsV in adsorption to calcite and both resulted in decreased iAsV adsorption. The total prevention of iAsV adsorption at initial equimolar arsenic/phosphate concentrations > 88 ?M each could be from the consumption of available calcite surface sites by the specific adsorption of phosphate. Equilibrium modeling, using the geochemical and mineral speciation of equilibrium model (MINTEQA2), indicated that at low concentrations of arsenate or phosphate solid-phase precipitation was not likely and adsorption processes likely controlled solubility. At high concentrations of arsenate Ca3(AsO4)2 ? 3 2/3 H2O and Ca3(AsO4)2 ? 4 1/4 H2O solid phases could be controlling arsenate solubility. This study indicates that arsenic adsorption response by calcite was different than that of phosphate suggesting that arsenic may not be specifically adsorbed to calcium at the calcite surface. Reduction and biomethylation of arsenic decreased adsorption, suggesting that processes which could affect the speciation of arsenic in the environment, could increase arsenic mobility in environmental systems where calcite and dissolved aqueous calcium play a predominant role in controlling arsenic solubility. Dissolved aqueous concentrations of magnesium, phosphate and sulfate generally reduced the ability of arsenic to be adsorbed to calcite.Item Advances in Synthesis of Co- and Ter- Polycarbonates and Polyesters from Non-Petroleum Feedstocks and Kinetic Studies of Ligand Substitution from Manganese Half-Sandwich Complexes(2012-07-16) Poland, Ross RiversThis dissertation is written in two parts. The first pertains to polycarbonate and polyester synthesis using relatively benign processes. The synthesis of polycarbonates from the coupling of CO2 and epoxides catalyzed by transition metal catalysts has long been studied in the DJD group. The benefits of this process are that it utilizes comparatively benign reagents, can be performed using no extraneous solvent, and is 100% atom efficient. A method potentially useful for achieving more desirable polycarbonate properties is to produce an epoxide A/epoxide B/CO2 terpolymer, thus allowing more fine "tuning" of properties to what one may desire while simultaneously influencing relative epoxide reactivity to potentially increase catalytic turnovers. Specifically, the coupling of propylene oxide and cyclohexene oxide with CO2 to yield a random copolymer with tunable properties has been studied via a Fineman-Ross analysis. Propylene oxide was found to be incorporated into the resultant polymer chain with anywhere from 4-10 times the preference of cylcohexene oxide. Although it has been reported as early as 1969, the copolymerization of epoxides and cyclic anhydrides catalyzed by transition metal complexes to yield polyesters via a chain-growth mechanism has recently gained much attention. This robust method of polyester synthesis can utilize rather inexpensive reagents to synthesize an array of polyester products which have a wide range of Tg values (-30 degrees C ? 90 degreesC), achievable through simple monomer selection. The second part of this dissertation deals with the kinetic study of ligand substitution from manganese carbonyl metal fragments. Some time ago it was postulated that complexes of the (Cp)M(CO)2L variety undergo ligand substitution via a associative mechanism allowed by a haptotropic eta5-eta3 shift in the eta5 ligand. Through kinetic studies and theoretical modeling, an approximate activation energy barrier of ~34 kJ/mol has been calculated for the ring slip of (2,5-dimethylpyrrole)Mn to occur. Additionally, further kinetic studies were performed in which Tp, a ligand electronically similar to Cp, was compared to MnCp complexes.Item Applications of hydrogenation and dehydrogenation on noble metal catalysts(2009-05-15) Wang, BoHydrogenation and dehydrogenation on Pd- and Pt- catalysts are encountered in many industrial hydrocarbon processes. The present work considers the development of catalysts and their kinetic modeling along a general and rigorous approach. The first part deals with the kinetics of selective hydrogenation, more particularly of the C3 cut of a thermal cracking unit for olefins production. The kinetics of the gas phase selective hydrogenation of methyl-acetylene (MA) and propadiene (PD) over a Pd/?-alumina catalyst were investigated in a fixed bed tubular reactor at temperatures 60 - 80 oC and a pressure of 20 bara. Hougen-Watson type kinetic equations were derived. The formation of higher oligomers slowly deactivated the catalyst. The effect of the deactivating agent on the rates of the main reactions as well as on the deactivating agent formation itself was expressed in terms of a deactivation function multiplying the corresponding rates at zero deactivation. Then, the kinetic model was plugged into the reactor model to simulate an industrial adiabatic reactor. In the second part the production of hydrogen from hydrocarbons was investigated. In both cyclohexane and decalin dehydrogenations, conversions higher than 98% could be obtained over Pt/?-alumina catalyst at temperature of 320 and 340 oC, respectively, with no apparent deactivation for 30 h and with co-feed of H2 in the feed. Except for H2 and trace amounts of side cracking products, less than 0.01%, benzene was the only dehydrogenated product in cyclohexane dehydrogenation. In the case of decalin dehydrogenation, partially dehydrogenated product, tetralin, was also formed with selectivity lower than 5%, depending on operating conditions. A rigorous Hougen-Watson type kinetic model was derived, which accounted for both the dehydrogenation of cis- and trans- decalin in the feed and also the isomerization of the two isomers. Jet A is the logic fuel in the battlefields. The dehydrogenation of Jet A can produce H2 for military fuel cell application. Although the H2 production is lower than that of steam/autothermal reforming, it eliminates the needs of high temperature and product separation operation.Item Biodegradation of Estrogenic Steroidal Hormones(2011-10-21) Kim, Sang HyunNatural and synthetic estrogens are some of the most potent hormones detected in the environment. Agriculture fields often release higher concentrations of natural estrogens to the environment, but wastewater treatment plants (WWTPs) commonly release higher concentrations of synthetic estrogens. Estrogens can disrupt endocrine functions in wildlife and humans. Less attention has been paid to the fate and occurrence of estrogens in agricultural operations than WWTPs. Their fate is influenced by major mechanisms such as sorption and biodegradation. Sorption typically accounts for less than 10 percent of estrogen removal in WWTPs. However, biodegradation is a primary method for estrogen loss at high ammonia concentration in the agricultural and municipal operation. Less attention has been paid to the biodegradation kinetics of estrogens in the field application. Therefore, this dissertation focused on the occurrence of estrogens in agricultural fields and their biodegradation by a mixed culture and a pure culture. The estrogens in turkey litter amended fields might be biodegraded to some degree by turkey litter borne bacteria. The estrogen biodegradation by a mixed culture showed different mechanisms for each estrogen. E1 and E2 were easily degraded as a carbon source of the mixed culture. E3 and EE2 were favorable for cometabolic degradation by AOB. EE2 was not readily biodegraded by the mixed culture due to a steric hindrance of enzyme expression and EE2 metabolism in the ethynylgroup of EE2. The cometabolic kinetics of individual estrogen was evaluated by using a pure culture. The cometabolism of estrogen was demonstrated by a reductant model. This model appropriately estimated the cometabolic kinetics of individual estrogens. In addition, the effect of antibiotics on the hormone degradation was investigated in Sequencing Batch Reactors (SBRs). No significant difference was detected for the removal efficiency of target compounds in the SBRs in presence or absence of antibiotics (oxytetracycline and chlortetracycline) during long sludge retention time (SRT). However, the effluent organic matter (EfOM) was less decomposed with the presence of antibiotics, especially causing less degradation of the humic-like substances in EfOM. The results indicated the flux of antibiotics to WWTPs did not affect hormone degradation, but reduced the decomposition of humic-like substance. Finally, the findings from the research provide insight into how biodegradation influences estrogen removal in agricultural fields and municipal WWTPs. The models developed in this research yielded valuable predictive values for engineered systems.Item Calcite dissolution kinetics and solubility in Na-Ca-Mg-Cl brines of geologically relevant composition at 0.1 to 1 bar pCO2 and 25 to 80??C(Texas A&M University, 2006-08-16) Gledhill, Dwight KuehlSedimentary basins can contain close to 20% by volume pore fluids that are commonly classified as brines. These fluids can become undersaturated with respect to calcite as a result of processes such as migration, dispersive mixing, or anthropogenic injection of CO2. This study measured calcite solubility and dissolution rates in geologically relevant Na-Ca-Mg-Cl synthetic brines (35 to 200 g L-1 TDS). In brines < 50 g L-1 TDS, the EQPITZER calculated calcium carbonate ion activity product (IAP) at steady-state was in reasonable agreement (??10%) with the thermodynamic solubility constant for calcite (Kc). However, the IAP systematically exceeded Kc in more concentrated brines. The deviation was strongly correlated with calcium concentration and also was observed in magnesium-free solutions. This is interpreted as an uncertainty in the carbonate ion activity coefficient, and minor adjustment in stoichiometric association constants (K*M2+CO30) for the CaCO30 or MgCo30 ion pairs would correct for the error. The dissolution rate dependency on brine composition, pCO2 (0.1 to 1 bar), and temperature (25.0 to 82.5 ??C) was modeled using the empirical rate equation ()nkRΩ−=1 where R is the rate, k and n are empirical fitting terms, and Ω the degree of disequilibrium with respect to calcite. When Ω was defined relative to an apparent kinetic solubility, n could be assumed first-order over the range of Ω investigated (Ω = 0.2 to 1.0). Rates increased with increasing pCO2 as did the sensitivity to brine concentration. At 0.1 bar, rates were nearly independent of concentration (k = 13.0 ??2.0 x 10-3 moles m-1 hr-1). However, at higher CO2 partial pressures rates became composition dependent and the rate constant, k, was shown to be a function of temperature, pCO2, ionic strength, and calcium and magnesium activity. The rate constant (k) can be estimated from a multiple regression (MR) model of the form k = B0 + B1(T) + B2(pCo2) + B4(aCa2+) + B5(aMg2+). A relatively high activation energy (Ea = 20 kJ mol-1) was measured, along with a stirring rate independence suggesting the dissolution is dominated by surface controlled processes at saturation states Ω > 0.2 in these calcium-rich brines. These findings offer important implications to reaction-transport models in carbonate-bearing saline reservoirs.Item Clot Kinetics in the Progression of Cerebral Vasospasm(2011-02-22) Hackney, Erin KathleenCerebral vasospasm following subarachnoid hemorrhage has high morbidity and mortality. Mathematical modeling of the progression of the condition provides insight to improve clinical treatment of patients post subarachnoid hemorrhage. An existing model of the clotting cascade is expanded to include the theoretical conditions of cerebral vasospasm. We consider clotting factor XIIIa, which has been implicated as a primary cause of the entrenchment of the smaller diameter. Solutions for clotting are used as boundary conditions to solve the concentration of diffusible clotting factors in the vessel wall and cerebrospinal fluid (CSF). Each domain (clot, vessel wall, CSF) is described by a separate initial-boundary value problem, requiring unique conditions, reaction-diffusion equations, and diffusion coefficients. Additionally, the results from the first domain (the clot) provide a subset of the boundary conditions for the second and third domains (arterial wall and CSF, respectively). Although this approach captures many detailed components of the clotting process, a simpler method for investigating the formation and dissolution of a clot post subarachnoid hemorrhage is to neglect the bulk of the clot cascade to focus on the most salient features, namely, the formation of cross-linked fibrin and the degradation of fibrin by plasmin. By assuming first order kinetics in the initial hours following hemorrhage, we find a simplified expression with kinetic rates that may be adjusted depending on experimental conditions.Item Dynamic and kinetic investigations of SEM-5/SOS peptide interactions(2009-04-01) li chieh Chen; Jose M. Barral; Vincent J. Hilser; Juniji IwaharaThe dynamics of SEM-5 SH3 domain protein can provide an important insight into how structural dynamics contribute to protein function. This is important because solving the structure of protein alone only provides the detail on the population weight average of native ensembles. NMR (Nuclear Magnetic Resonance) is one of the best techniques that can be used to elucidate the conformational fluctuation of SH3 domain under native condition, The hypothesis of this study is that the protein during ligand-free ¬form is undergoing an equilibrium between binding-competent (BC) and binding-incompetent (BI) states(1). In order to test this hypothesis, we apply a Glycine mutation in a solvent exposed and highly dynamic region within RT loop of SH3 domain protein. Through this mutation, we aim to manipulate the dynamics of the protein but preserve the protein-ligand interface. Several NMR methodologies including order parameter and line-shape analysis are applied to observe the correlation of protein dynamics with its function, taking into consideration several thermodynamic and kinetic aspects of the structural changes involved.\r\n\r\nItem Evaluation of kinetic controls on sulfate reduction in a contaminated wetland-aquifer system(2009-05-15) Kneeshaw, Tara AnnOur ability to understand and predict the fate and transport of contaminants in natural systems is vital if we are to be successful in protecting our water resources. One important aspect of understanding chemical fate and transport in natural systems is identifying key kinetic controls on important redox reactions such as sulfate reduction. Anaerobic microbial activities like sulfate reduction are of particular interest because of the important role they play in the degradation of contaminants in the subsurface. However, current rate estimates for sulfate reduction have a wide range in the literature making it difficult to determine representative rates for a given system. These differences in rate data may be explained by varying kinetic controls on reactions. Push-pull tests were used to evaluate sulfate reduction rates at the wetland-aquifer interface. Anaerobic aquifer water containing abundant sulfate was injected into sulfate-depleted wetland porewater. The injected water was subsequently withdrawn and analyzed for geochemical indicators of sulfate reduction. Complexities in rate data, such as presence of a lag phase, changing rate order and spatial variability, were observed and are hypothesized to be linked to activities of the native microbial population. Subsequent experiments explored the response of native microorganisms to geochemical perturbations using a novel approach to measure directly the effects of a geochemical perturbation on an in situ microbial population and measure rates of resulting reactions. In situ experiments involved colonization of a substrate by microorganisms native to the wetland sediments followed by introductions of native water amended with sulfate and tracer. Experimental results showed that higher sulfate concentrations and warmer seasonal temperatures result in faster sulfate reduction rates and corresponding increases in sulfate reducing bacteria. Findings from this research provide quantitative evidence of how geochemical and microbiological processes are linked in a system not at equilibrium.Item Kinetics and dynamics study on the allosteric pathway of phosphofructokinase from Escherichia coli(Texas A&M University, 2008-10-10) Tie, CuijuanPhosphofructokinase from Escherichia coli (EcPFK) is allosterically regulated by MgADP and phosphoenolpyruvate (PEP), which act to activate or inhibit, respectively, by changing the substrate (Fru-6-P) affinity of the enzyme. Both ligands bind to the same allosteric site in EcPFK. Therefore, the questions we want to address are how these two molecules regulate EcPFK and how the allosteric signal is propagated throughout the enzyme. EcPFK has 28 potential site-site interactions. These interactions in turn derive from multiple copies of 6 potentially unique homotropic interactions and 4 potentially unique heterotropic interactions. Making hybrid tetramer of EcPFK is used to isolate a single heterotropic interaction. To improve the yield of the 1:3 hybrid, the in vivo hybrid formation method was developed. Four heterotropic interactions were isolated by this manner and re-evaluated. The same kinetics characteristics were obtained for each 1:3 hybrid from both the in vivo and in vitro method. To address the question of how the allosteric signal is transmitted throughout EcPFK, we identified residues (G184, Asp59 and S157) that are important for the allosteric regulation for both PEP inhibition and MgADP activation. The impact of each mutation on individual interaction is unique and also suggests that the structural basis for PEP inhibition is different from that for MgADP activation. Most importantly, since the sum of each heterotropic interaction with a modification in only one subunit is equal to the total heterotropic interaction with a modification in all four subunits, this result indicates that the heterotropic allosteric signal transmission is realized in a single subunit. The 23? heterotropic interaction, which contributes the most to the PEP inhibition, was chosen to study the dynamic properties. Fluorescence was used to study the dynamic perturbations of the 23? interaction upon ligand binding. Taking advantage of the hybrid formation strategy and the tryptophan-shift mutagenesis method, a tryptophan residue can be placed at different individual locations throughout the native subunit containing the 23? heterotropic interaction. The steady-state anisotropy and lifetime measurement at each tryptophan position indicate that the 23? allosteric interaction involves the perturbation of side-chain dynamics both near and quite far away from the respective ligand binding sites.Item Kinetics of acrylamide formation in potato chips(Texas A&M University, 2006-08-16) Granda, Claudia EsthelaAcrylamide is considered a carcinogen in animals and a possible carcinogen in humans. It has been found in starch rich foods cooked at high temperatures. Vacuum frying (10 Torr) was studied as a possible alternative to reduce acrylamide formation in potato chips. Seven potato cultivars were analyzed to determine their influence on acrylamide formation during traditional and vacuum frying. The White Rose cultivar produced the highest level of acrylamide during both traditional and vacuum frying. Vacuum frying (10 Torr, 118oC, 8 min) produced chips with lower acrylamide content than those produced under traditional frying (165oC, 4 min) for all cultivars. The cultivar Atlantic was used to determine the kinetics of acrylamide formation during traditional and vacuum frying at different temperatures because it is a good chipping cultivar and it was the most abundant in the lab. Acrylamide accumulation under vacuum frying was modeled using first-order kinetics, and during traditional frying it was modeled using the logistic kinetic model. The behavior of the kinetics of acrylamide content in potato chips fried under the two processes was different mainly due to the different temperatures used. During traditional frying, higher temperatures areused (150oC to 180oC) and acrylamide after some time is produced but also starts degrading, producing a constant level of acrylamide content at longer times. During vacuum frying (10 Torr), acrylamide increased exponentially (but at lower levels) for all frying times. The effect of potato components was studied by infusing leached potato slices with predetermined amounts of glucose and asparagine. Increasing glucose and asparagine content in the slices increased the acrylamide content in the potato chips. Color could not be used as an indication of acrylamide content, since potato chips with similar color had very different acrylamide concentrations.Item Nanofabrication, Plasmon Enhanced Fluorescence and Photo-oxidation Kinetics of CdSe Nanoparticles(2011-08-08) Chen, JixinUnconventional nanofabrication techniques; both those which have been newly developed and those under development, had brought inexpensive, facile, yet high quality means to fabricate nanostructures that have feature sizes of less than 100 nm in industry and academia. This dissertation focuses on developing unconventional fabrication techniques, building studying platforms, and studying the mechanisms behind them. The studies are divided into two main facets and four chapters. The first facet, in Chapter II and Chapter III, deals with the research and development of different nanofabrication techniques and nanostructures. These techniques include litho-synthesis, colloidal lithography, and photolithography. The nanostructures that were fabricated by these techniques include the metal nanoparticle arrays, and the self-assembled CdSe nanoring arrays. At the same time, the dissertation provides mechanisms and models to describe the physical and chemical nature of these techniques. The second area of this study, in Chapter III to Chapter V, presents the applications of these nanostructures in fundamental studies, i.e. the mechanisms of plasmon enhanced fluorescence and photo-oxidation kinetics of CdSe quantum dots, and applications such as molecular sensing and material fabrication. More specifically, these applications include tuning the optical properties of CdSe quantum dots, biomodification of CdSe quantum dots, and copper ion detection using plasmon and photo enhanced CdSe quantum dots. We have successfully accomplished our research goals in this dissertation. Firstly, we were able to tune the emission wavelength of quantum dots, blue-shifted for up to 45 nm, and their surface functionalization with photo-oxidation. A kinetic model to calculate the photo-oxidation rates was established. Secondly, we established a simple mathematical model to explain the mechanism of plasmon enhanced fluoresce of quantum dots. Our calculation and experimental data support the fluorescence resonance energy transfer (FRET) mechanism between quantum dots and the metal nanoparticles. Thirdly, we successfully pattered the CdSe quantum dots (diameter ~4 nm) into nanorings with tunable diameters and annular sizes on different substrates. We also established a physical model to quantitatively explain the mechanism with the forces that involved in the formation of the nanorings.Item Remediation of chromium(VI) in the vadose zone: stoichiometry and kinetics of chromium(VI) reduction by sulfur dioxide(Texas A&M University, 2004-11-15) Ahn, MinImmobilization and detoxification of chromium in the vadose zone is made possible by the existence of an effective reductant, SO2, that exists in a gaseous form at room temperature. Experimental studies were designed to characterize stoichiometry and kinetics of chromium reduction both in aqueous solutions at pH values near neutrality and in soil. First, batch experiments and elemental analyses were conducted to characterize the stoichiometry and kinetics of Cr(VI) reduction in water. The stoichiometric ratio of S(IV) removed to Cr(VI) removed ranged between 1.6 and 1.8. The overall reaction is believed to be the result of a linear combination of two reactions in which dithionate is an intermediate and sulfate is the stable oxidized product. The reaction was also rapid, with the half-time of about 45 minutes at pH 6 and about 16 hours at pH 7. A two-step kinetic model was developed to describe changes in concentrations of Cr(VI), S(IV), and S(V). Nonlinear regression was applied to obtain the kinetic parameters. The rate of reaction was assumed to be second-order with respect to [Cr(VI)] and first-order with respect to [S(IV)], and [S(V)]. The values for the rate coefficient for the first reaction (k1) were found to be 4.5 (?10%), 0.25 (?9.4%) (mM-2h-1) at pH 6 and 7, respectively. The values of the rate coefficient for the second reaction (k2) were 25 (?29%), 1.1 (? 30%) (mM-2h-1) at pH 6 and 7, respectively. The reaction rate decreased as pH increased. Experiments showed that the rate at pH 7 was lower than that at pH 6 by one order of magnitude. Second, batch experiments and elemental analyses were conducted to characterize the stoichiometry and kinetics of Cr(VI) reduction in soil. The stoichiometric ratio of S(IV) removed to Cr(VI) removed was almost 2, which is slightly higher than that for the reaction in water. This higher value may be due to S(IV) oxidation by soil-derived Fe(III). The reaction was rapid, with the half-time less than 2 minutes, which is faster than in water. The rate coefficients, k1 and k2, were 22 (?41%) and 13 (?77%) (M-2h-1), respectively.Item Study of Adsorption of Methanol in an Activated Carbon and Carbon Nanotube Matrix for Use in a Solar Based Refrigeration Cycle(2012-07-16) Sambath, SrivathsThis thesis seeks to investigate the adsorption capabilities of activated carbon and carbon nanotubes. The adsorption of methanol on both of these substances was tested for their application in a solar based refrigeration cycle. Research on carbon nanotubes and their growth has been carried out for applications in the semiconductor industry. Enough focus has not been given to the use of nanotubes for refrigeration purposes. Adsorption refrigerators have been designed with the energy source being solar energy. Various adsorbent/adsorbate pairs have been tested in literature. The present work focuses on carbon nanotubes because theoretically, nanotubes should be able to adsorb better than activated carbon due to their high surface to volume ratios and hence a higher number of adsorption sites available for methanol to adsorb. The amount of adsorption of methanol on nanotubes depends on whether the end caps of the nanotubes are open or closed and also on the hydrophilic nature of the nanotubes. Nanotubes with ends closed are supposed to adsorb less than the nanotubes with their ends opened. The ends of carbon nanotubes can be blocked because of iron and other impurities. In this project, nanotubes are annealed under high vacuum to open the end caps. The hydrophobic nature of the nanotubes is corrected by treating them with concentrated nitric acid. The hydrophobic nature of the nanotubes is corrected by treating them with concentrated nitric acid. The acid treated nanotubes are used to obtain adsorption data at different temperatures. The adsorption of methanol on activated carbon, pristine and treated carbon nanotubes is measured at different temperatures. Electron microscopy is used to validate that annealing the nanotubes at high temperature under vacuum opens the end caps of the nanotubes. Finally, a matrix of nanotubes and carbon powder is prepared with different concentrations. The mixture is tested for adsorption of methanol. It is observed that the carbon nanotubes, pristine or treated, do not perform better than activated carbon. However, performance seems to increase when mixtures of activated carbon and carbon nanotubes are used as adsorbent. Also, it is found that mixtures containing annealed nanotubes perform better than mixtures with pristine nanotubes. Kinetics of the adsorption process is calculated for the different adsorbents used, which is used to explain the increase in the amount of methanol adsorbed for the activated carbon-carbon nanotube mixture.Item Study of pure-silica Zeolite Nucleation and Growth from Solution(2011-10-21) Li, XiangZeolites are microporous crystalline materials, which are widely used in catalysis, adsorption, and ion-exchange processes. However, in most cases, the synthesis of novel zeolites as functional materials still relies on trial-and-error methods, which are time consuming and expensive. Therefore, the motivation for this thesis work is to understand the zeolite synthesis mechanismand further develop knowledge for manipulating zeolite properties and ultimately the rational design of porous materials. This work focused on formation of silicalite-1 (pure-silica ZSM-5) from basic aqueous solutions containing tetraorthosilicate (TEOS) as silica source, and tetrapropylammonium (TPA) cations as the organic structure-directing agent. The presence of silica precursor particles with size of 2-5 nm in these mixtures prior to and during hydrothermal treatments have been observed through dynamic light scattering (DLS), small-angle X-ray (SAXS) and transmission electron microscopy (TEM). However, to quantify composition and the molecular structure transformation of these silica precursor particles during zeolite synthesis is still a technical challenge. Another important yet unresolved question is how organocations interact with these nanoparticles and direct zeolite nuclei. Unlike many studies performed analyzing the inorganic phase (silica) present in synthesis mixtures, this study quantified the organocation-silica particle interaction and its ultimate effect on zeolite growth mainly through probing the behavior of the organocations. Pulsed-field gradient (PFG) NMR was used to capture the mobility change of organocations, and was complemented with scattering measurements (DLS, SAXS) on the silica nanoparticles. On the basis of the measurement results, the thermodynamic and kinetic properties of the organic-inorganic interaction were derived. Upon aging at room temperature, this interaction manifested as binding of TPA onto the silica particles due to electrostatic interactions, and such binding behavior can be well described by the Langmuir adsorption model. Upon hydrothermal treatment, a fraction of TPA adsorbed at room temperature dissociates from the growing silica nanoparticles and the corresponding desorption profiles were fitted well by the pseudo-second order kinetic model. The addition of tetramethylammonium (TMA) as "competitors" promoted TPA desorption kinetics and hindered silica nanoparticle growth due to stronger association of TMA with particles than that of TPA. Finally, the TPA adsorption strength increased via addition of monovalent salts with increasing ionic size whereas that of TMA shows an opposite trend. This suggests one potential route for tuning the organic-silica precursor particle interactions and thus possibly affecting some kinetics steps in the synthesis.Item Techniques for modeling and analyzing RNA and protein folding energy landscapes(2009-05-15) Tang, XinyuRNA and protein molecules undergo a dynamic folding process that is important to their function. Computational methods are critical for studying this folding pro- cess because it is difficult to observe experimentally. In this work, we introduce new computational techniques to study RNA and protein energy landscapes, includ- ing a method to approximate an RNA energy landscape with a coarse graph (map) and new tools for analyzing graph-based approximations of RNA and protein energy landscapes. These analysis techniques can be used to study RNA and protein fold- ing kinetics such as population kinetics, folding rates, and the folding of particular subsequences. In particular, a map-based Master Equation (MME) method can be used to analyze the population kinetics of the maps, while another map analysis tool, map-based Monte Carlo (MMC) simulation, can extract stochastic folding pathways from the map. To validate the results, I compared our methods with other computational meth- ods and with experimental studies of RNA and protein. I first compared our MMC and MME methods for RNA with other computational methods working on the com- plete energy landscape and show that the approximate map captures the major fea- tures of a much larger (e.g., by orders of magnitude) complete energy landscape. Moreover, I show that the methods scale well to large molecules, e.g., RNA with 200+ nucleotides. Then, I correlate the computational results with experimental findings. I present comparisons with two experimental cases to show how I can pre- dict kinetics-based functional rates of ColE1 RNAII and MS2 phage RNA and their mutants using our MME and MMC tools respectively. I also show that the MME and MMC tools can be applied to map-based approximations of protein energy energy landscapes and present kinetics analysis results for several proteins.Item The chemical mechanisms of flavin-dependent amine oxidases and the plasticity of the two-his one-carboxylate facial triad in tyrosine hydroxylase(2009-05-15) Ralph, Erik C.Despite a number of kinetic and spectroscopic studies, the chemical mechanisms of amine oxidation by flavoenzymes remain widely debated. The mechanisms of by Nmethyltryptophan oxidase (MTOX) and tryptophan 2-monooxygenase (TMO) were probed using a combination of pH and primary deuterium, solvent, and 15N kinetic isotope effects. Slow substrates were chosen for these studies; MTOX was characterized with N-methylglycine and TMO was characterized with L-alanine. Primary deuterium kinetic isotope effects of 7.2 and 5.3 were observed for sarcosine oxidation by MTOX and for alanine oxidation by TMO, respectively, independent of the substrate concentration and pH. Monitoring the reduction of flavin spectroscopically revealed no intermediate flavin species with both enzyme-substrate systems. Furthermore, the magnitudes of the 15N kinetic isotope effects observed with both systems suggest that nitrogen rehybridization and C-H bond cleavage are concerted. These results are consistent with both enzymes utilizing a hydride transfer mechanism for amine oxidation. The role of the iron ligands of tyrosine hydroxylase (TyrH) was also investigated. TyrH contains one iron per monomer, which is held by three conserved amino acid residues, two histidines and a glutamate. As a probe of the plasticity of the metal binding site, each of the metal ligands in TyrH was substituted with glutamine, glutamate, or histidine. The resulting proteins were characterized for metal content, catalytic activity, and dopamine binding. The H336E and H336Q enzymes retain substantial catalytic activity. In contrast, the E376Q enzyme retains about 0.4% of the wild-type catalytic activity, and the E376H enzyme has no significant activity. The H331E enzyme oxidizes tetrahydropterin in a tyrosine-independent manner. The position of the charge-transfer absorbance band for the H336E and H336Q enzyme-inhibitor complexes is shifted relative to that of the wild-type enzyme, consistent with the change in the metal ligand. In contrast, the E376H and E376Q enzymes catalyze dopamine oxidation. These results provide a reference point for further structural studies of TyrH and the other aromatic amino acid hydroxylases, and for similar studies of other enzymes containing this ironbinding motif.