Thesis (Ph. D.)--University of Washington, 2001. / Vita. Includes bibliographical references (pages 49-54).

No description available.

Current enzyme kinetic equations are inadequate for modelling enzymatic reactor systems because they fail to take into account the interactions between that various process parameters. They also are unable to predict reaction rates in complex solute systems. A quasi-native kinetic model was developed that predicts enzyme activity by examining the effect of solute addition on the overall protein structure. The theory was tested using the enzyme urease (urea aminohydrolase EC 3.5.1.5). / The quasi-native model was found to accurately predict both the activation and inhibition phenomena observed with urease and could also predict enzymatic activity in complex solute systems. The quasi-native isomerization constant was shown to be a function of hydrophobic effects characterized by the Sechenov theory and electrostatic effects characterized by the DeBye-Huckel theory. The Sechenov constant was found to be independent of temperature and pH. / The urease denaturation rate constant displayed a response to solute addition similar to that observed with the quasi-native isomerization equilibrium constant. However, the effect of pH on urease kinetics was a complex function of the ionization of active-site ligands and enzyme surface charge interactions.

No description available.

Pour faire face à l’épuisement des combustibles fossiles conventionnels et aux préoccupationsenvironnementales dont le réchauffement climatique, de nouveaux carburants issus de la biomasse sontutilisés purs ou comme co-carburants ; d’autres sont envisagés pour le futur. Une meilleure connaissance dela cinétique chimique d’oxydation des composés présents dans ces carburants alternatifs est indispensable.L’objectif de cette thèse est donc d’obtenir de nouvelles bases de données expérimentales et d’élaborer desmécanismes cinétiques d’oxydation des constituants de ces nouveaux carburants. Des molécules de deuxfamilles chimiques, à savoir les esters méthyliques et les alcools, ont été sélectionnées. L’oxydation de cescomposés purs ou en mélanges a été étudiée en réacteur auto-agité à haute pression (10 atm) et dans un largedomaine de températures (530-1250 K) et de richesses (ca. 0,3-4). Les profils de concentration des réactifs,produits et principaux intermédiaires stables ont été obtenus par spectroscopie d’absorption infrarouge àtransformée de Fourier (IRTF) et chromatographie en phase gazeuse (GC-FID-TCD-MS). Les résultatsobtenus ont permis de proposer des modèles cinétiques permettant de simuler avec un bon accord une grandepartie des résultats expérimentaux obtenus au cours de cette thèse. Les analyses cinétiques ont permis dedéterminer les principales voies de consommation de ces composés (principalement des mécanismes deperoxydation-isomérisation à basse température et de métathèse puis décomposition par β-scission à hautetempérature). Elles ont permis d’identifier les réactions les plus influentes (réactions de métathèse etréactions impliquant particulièrement les composés de la base C0-C2). / To overcome the problems of conventional fossil fuels depletion and environmental issues includingglobal warming, new fuels derived from biomass are used pure or in blends; others are proposed for thefuture. A good knowledge of the chemical kinetics of oxidation of components present in these alternativefuels is necessary. The aim of this work is to obtain a new experimental database and to build a chemicalkinetic reaction mechanism for the combustion of these new fuels. Molecules of two functional groups werechosen: methyl esters and alcohols. The kinetics of oxidation of these compounds were studied in a Jet-Stirred Reactor at high-pressure (10 atm), over the temperature range 530-1250 K, for several equivalencesratios (ca. 0.3-4) Concentration profiles of reactants, products and main stable intermediates were obtainedby probe sampling and FTIR (Fourier transform infrared spectroscopy) and GC-FID-TCD-MS analyses. Theresults allowed proposing detailed kinetics models that successfully simulate concentration profilesdetermined by Jet-Stirred Reactor method. The kinetic analyses allowed delineating the main oxidation pathsof consumption (peroxidation-isomerisation at low temperature and beyond, metathesis followed by betascissiondecomposition), and identifying the most influencing reactions for the oxidation rate of the fuels, i.e.metathesis reactions with C0-C2 species.

Esta tese apresenta a aplicação de biossorventes alternativos obtidos a partir da casca da noz pecã (Carya illinoensis) e da casca do pinhão (Araucaria angustifólia) na remoção de íons metálicos tóxicos presentes em soluções aquosas. O biossorvente de casca de nozes foi aplicado com sucesso na remoção dos íons metálicos: Cu(II), Mn(II), Pb(II), Cr(III), Fe(III) e Zn(II), enquanto que o biossorvente obtido a partir da casca de pinhão apresentou, também, excelente capacidade de adsorção de íons de Cr(VI) em soluções contaminadas pelo mesmo. Os biossorventes casca de nozes PNS (do inglês: pecan nutshell) e casca de pinhão PW (do inglês: Piñon Waste) foram caracterizados química e fisicamente através de: isotermas de adsorção e dessorção de N2, espectroscopia no infravermelho com transformada de Fourier, microscopia de varredura eletrônica, análise elementar, determinação da composição mineral e quantificação de grupos funcionais. A capacidade de adsorção desses biossorventes foi investigada utilizando procedimentos de biossorção em batelada. Os efeitos causados pela modificação de parâmetros experimentais como pH, dosagem de biossorvente e concentração inicial dos íons nos sistemas de adsorção também foram pesquisados. Testou-se a adequação de cinco modelos de cinética de adsorção aos dados experimentais obtidos com o biossorvente PNS, constatou-se que os modelos de ordem-fracionária e o de difusão intrapartícula apresentaram os melhores resultados. Já para adsorções de Cr(VI) em PW o melhor modelo cinético foi o de quimiossorção de Elovich, apresentando taxas de biossorção de 284,9, 396,9 e 461,5 mg g-¹ h-¹ para os níveis de concentração inicial de Cr(VI) de 500,0, 700,0 e 1000,0 mg l-¹ respectivamente. O estudo do equilíbrio de adsorção envolveu a aplicação dos modelos de isotermas de: Langmuir, Freundlich, Redlich-Peterson e Sips aos dados experimentais no intuito de verificar o modelo mais apropriado para descrever os sistemas de adsorção quando em equilíbrio. Avaliou-se, utilizando a função estatística de erro, que o modelo de Sips foi o que mais se adequou aos dados experimentais obtidos nos diversos sistemas pesquisados (biossorvente - ion metálico). A capacidade máxima de adsorção para íons de Cr(III), Fe(III), Zn(II), Cu(II), Mn(II) e Pb(II) em PNS foi de 93,0, 76,6, 108,0, 85,9, 98,0 e 195,9 mg g-¹, respectivamente, enquanto que a de Cr(VI) em PW foi de 240,0 mg g-¹. / This thesis reports the possibility of applying the alternative biosorbent pecan nutshell (PNS- Carya illinoensis) used to remove the followed metallic ions: Cu(II), Mn(II), Pb(II), Cr(III), Fe(III), Zn(II) from aqueous solutions. This thesis also shows the application of Brazilian-pine fruit coat, named piñon wastes (PW; Araucaria angustifolia) as biosorbent to remove Cr(VI) from aqueous solutions. The PNS and PW biosorbents were characterized by N2 adsorption-desorption isotherms, FTIR spectroscopy, scanning electron microscopy, elemental analysis, mineral composition determination, and functional groups detection. The biosorbents ability to remove the metallic ions was investigated by using batch biosorption procedure. The effects of changing experimental parameters such as, pH, biosorbent dosage and initial ion concentration on the biosorbents adsorption capacities were studied. Five kinetic models were tested, being the adsorption kinetics better fitted to fractionary-order kinetic model. Besides that, the kinetic data were also fitted to intra-particle diffusion model, presenting three linear regions, indicating that the kinetics of adsorption should follow multiple sorption rates. The equilibrium data were fitted to Langmuir, Freundlich, Sips and Redlich-Peterson isotherm models. Taking into account a statistical error function, most of PNS biosorption equilibrium data were best fitted to Sips isotherm model. The maximum biosorption capacity of PNS were 93.0, 76.6, 108.0, 85.9, 98.0 and 195.9 mg g-¹ for Cr(III), Fe(III), Zn(II), Cu(II), Mn(II) and Pb(II), respectively. The adsorption kinetics followed the Elovich chemisorption kinetic model, obtaining the following the initial adsorption rate, 284.9, 396.9 and 461.5 mg g-¹ h-¹ using a 500.0, 700.0 and 1000.0 mg L-¹ initial concentration of Cr(VI), respectively. The maximum adsorption capacity of PW was 240.0 mg g-¹ for Cr(VI), using Sips isotherm model. This high adsorption capacity of PW places this biosorbent as one of the best adsorbents for removal of Cr(VI) from aqueous effluents.

Esta tese apresenta a aplicação de biossorventes alternativos obtidos a partir da casca da noz pecã (Carya illinoensis) e da casca do pinhão (Araucaria angustifólia) na remoção de íons metálicos tóxicos presentes em soluções aquosas. O biossorvente de casca de nozes foi aplicado com sucesso na remoção dos íons metálicos: Cu(II), Mn(II), Pb(II), Cr(III), Fe(III) e Zn(II), enquanto que o biossorvente obtido a partir da casca de pinhão apresentou, também, excelente capacidade de adsorção de íons de Cr(VI) em soluções contaminadas pelo mesmo. Os biossorventes casca de nozes PNS (do inglês: pecan nutshell) e casca de pinhão PW (do inglês: Piñon Waste) foram caracterizados química e fisicamente através de: isotermas de adsorção e dessorção de N2, espectroscopia no infravermelho com transformada de Fourier, microscopia de varredura eletrônica, análise elementar, determinação da composição mineral e quantificação de grupos funcionais. A capacidade de adsorção desses biossorventes foi investigada utilizando procedimentos de biossorção em batelada. Os efeitos causados pela modificação de parâmetros experimentais como pH, dosagem de biossorvente e concentração inicial dos íons nos sistemas de adsorção também foram pesquisados. Testou-se a adequação de cinco modelos de cinética de adsorção aos dados experimentais obtidos com o biossorvente PNS, constatou-se que os modelos de ordem-fracionária e o de difusão intrapartícula apresentaram os melhores resultados. Já para adsorções de Cr(VI) em PW o melhor modelo cinético foi o de quimiossorção de Elovich, apresentando taxas de biossorção de 284,9, 396,9 e 461,5 mg g-¹ h-¹ para os níveis de concentração inicial de Cr(VI) de 500,0, 700,0 e 1000,0 mg l-¹ respectivamente. O estudo do equilíbrio de adsorção envolveu a aplicação dos modelos de isotermas de: Langmuir, Freundlich, Redlich-Peterson e Sips aos dados experimentais no intuito de verificar o modelo mais apropriado para descrever os sistemas de adsorção quando em equilíbrio. Avaliou-se, utilizando a função estatística de erro, que o modelo de Sips foi o que mais se adequou aos dados experimentais obtidos nos diversos sistemas pesquisados (biossorvente - ion metálico). A capacidade máxima de adsorção para íons de Cr(III), Fe(III), Zn(II), Cu(II), Mn(II) e Pb(II) em PNS foi de 93,0, 76,6, 108,0, 85,9, 98,0 e 195,9 mg g-¹, respectivamente, enquanto que a de Cr(VI) em PW foi de 240,0 mg g-¹. / This thesis reports the possibility of applying the alternative biosorbent pecan nutshell (PNS- Carya illinoensis) used to remove the followed metallic ions: Cu(II), Mn(II), Pb(II), Cr(III), Fe(III), Zn(II) from aqueous solutions. This thesis also shows the application of Brazilian-pine fruit coat, named piñon wastes (PW; Araucaria angustifolia) as biosorbent to remove Cr(VI) from aqueous solutions. The PNS and PW biosorbents were characterized by N2 adsorption-desorption isotherms, FTIR spectroscopy, scanning electron microscopy, elemental analysis, mineral composition determination, and functional groups detection. The biosorbents ability to remove the metallic ions was investigated by using batch biosorption procedure. The effects of changing experimental parameters such as, pH, biosorbent dosage and initial ion concentration on the biosorbents adsorption capacities were studied. Five kinetic models were tested, being the adsorption kinetics better fitted to fractionary-order kinetic model. Besides that, the kinetic data were also fitted to intra-particle diffusion model, presenting three linear regions, indicating that the kinetics of adsorption should follow multiple sorption rates. The equilibrium data were fitted to Langmuir, Freundlich, Sips and Redlich-Peterson isotherm models. Taking into account a statistical error function, most of PNS biosorption equilibrium data were best fitted to Sips isotherm model. The maximum biosorption capacity of PNS were 93.0, 76.6, 108.0, 85.9, 98.0 and 195.9 mg g-¹ for Cr(III), Fe(III), Zn(II), Cu(II), Mn(II) and Pb(II), respectively. The adsorption kinetics followed the Elovich chemisorption kinetic model, obtaining the following the initial adsorption rate, 284.9, 396.9 and 461.5 mg g-¹ h-¹ using a 500.0, 700.0 and 1000.0 mg L-¹ initial concentration of Cr(VI), respectively. The maximum adsorption capacity of PW was 240.0 mg g-¹ for Cr(VI), using Sips isotherm model. This high adsorption capacity of PW places this biosorbent as one of the best adsorbents for removal of Cr(VI) from aqueous effluents.

Esta tese apresenta a aplicação de biossorventes alternativos obtidos a partir da casca da noz pecã (Carya illinoensis) e da casca do pinhão (Araucaria angustifólia) na remoção de íons metálicos tóxicos presentes em soluções aquosas. O biossorvente de casca de nozes foi aplicado com sucesso na remoção dos íons metálicos: Cu(II), Mn(II), Pb(II), Cr(III), Fe(III) e Zn(II), enquanto que o biossorvente obtido a partir da casca de pinhão apresentou, também, excelente capacidade de adsorção de íons de Cr(VI) em soluções contaminadas pelo mesmo. Os biossorventes casca de nozes PNS (do inglês: pecan nutshell) e casca de pinhão PW (do inglês: Piñon Waste) foram caracterizados química e fisicamente através de: isotermas de adsorção e dessorção de N2, espectroscopia no infravermelho com transformada de Fourier, microscopia de varredura eletrônica, análise elementar, determinação da composição mineral e quantificação de grupos funcionais. A capacidade de adsorção desses biossorventes foi investigada utilizando procedimentos de biossorção em batelada. Os efeitos causados pela modificação de parâmetros experimentais como pH, dosagem de biossorvente e concentração inicial dos íons nos sistemas de adsorção também foram pesquisados. Testou-se a adequação de cinco modelos de cinética de adsorção aos dados experimentais obtidos com o biossorvente PNS, constatou-se que os modelos de ordem-fracionária e o de difusão intrapartícula apresentaram os melhores resultados. Já para adsorções de Cr(VI) em PW o melhor modelo cinético foi o de quimiossorção de Elovich, apresentando taxas de biossorção de 284,9, 396,9 e 461,5 mg g-¹ h-¹ para os níveis de concentração inicial de Cr(VI) de 500,0, 700,0 e 1000,0 mg l-¹ respectivamente. O estudo do equilíbrio de adsorção envolveu a aplicação dos modelos de isotermas de: Langmuir, Freundlich, Redlich-Peterson e Sips aos dados experimentais no intuito de verificar o modelo mais apropriado para descrever os sistemas de adsorção quando em equilíbrio. Avaliou-se, utilizando a função estatística de erro, que o modelo de Sips foi o que mais se adequou aos dados experimentais obtidos nos diversos sistemas pesquisados (biossorvente - ion metálico). A capacidade máxima de adsorção para íons de Cr(III), Fe(III), Zn(II), Cu(II), Mn(II) e Pb(II) em PNS foi de 93,0, 76,6, 108,0, 85,9, 98,0 e 195,9 mg g-¹, respectivamente, enquanto que a de Cr(VI) em PW foi de 240,0 mg g-¹. / This thesis reports the possibility of applying the alternative biosorbent pecan nutshell (PNS- Carya illinoensis) used to remove the followed metallic ions: Cu(II), Mn(II), Pb(II), Cr(III), Fe(III), Zn(II) from aqueous solutions. This thesis also shows the application of Brazilian-pine fruit coat, named piñon wastes (PW; Araucaria angustifolia) as biosorbent to remove Cr(VI) from aqueous solutions. The PNS and PW biosorbents were characterized by N2 adsorption-desorption isotherms, FTIR spectroscopy, scanning electron microscopy, elemental analysis, mineral composition determination, and functional groups detection. The biosorbents ability to remove the metallic ions was investigated by using batch biosorption procedure. The effects of changing experimental parameters such as, pH, biosorbent dosage and initial ion concentration on the biosorbents adsorption capacities were studied. Five kinetic models were tested, being the adsorption kinetics better fitted to fractionary-order kinetic model. Besides that, the kinetic data were also fitted to intra-particle diffusion model, presenting three linear regions, indicating that the kinetics of adsorption should follow multiple sorption rates. The equilibrium data were fitted to Langmuir, Freundlich, Sips and Redlich-Peterson isotherm models. Taking into account a statistical error function, most of PNS biosorption equilibrium data were best fitted to Sips isotherm model. The maximum biosorption capacity of PNS were 93.0, 76.6, 108.0, 85.9, 98.0 and 195.9 mg g-¹ for Cr(III), Fe(III), Zn(II), Cu(II), Mn(II) and Pb(II), respectively. The adsorption kinetics followed the Elovich chemisorption kinetic model, obtaining the following the initial adsorption rate, 284.9, 396.9 and 461.5 mg g-¹ h-¹ using a 500.0, 700.0 and 1000.0 mg L-¹ initial concentration of Cr(VI), respectively. The maximum adsorption capacity of PW was 240.0 mg g-¹ for Cr(VI), using Sips isotherm model. This high adsorption capacity of PW places this biosorbent as one of the best adsorbents for removal of Cr(VI) from aqueous effluents.

Chemical reactions involving small number of reacting molecules are noisy processes. They are simulated using stochastic simulation algorithms like the Gillespie SSA, which are valid when the reaction environment is well-mixed. This is not the case in reactions occuring on biological media like cell membranes, where alternative simulation methods have to be used to account for the crowded nature of the reacting environment. Ion channels, which are membrane proteins controlling the flow of ions into and out of the cell, offer excellent single molecule conditions to test stochastic simulation schemes in crowded biological media. Single molecule reactions are of great importance in determining the functions of biological molecules. Access to their experimental data have increased the scope of com-putational modeling of biological processes. Recently, single molecule experiments have revealed the non-Markovian nature of chemical reactions, due to a phenomenon called `dynamic disorder', which makes the rate constants a deterministic function of time or a random process. This happens when there are additional slow scale conformational transitions, giving the molecule a memory of its previous states. In a previous work, the hTREK1 two pore domain potassium channel was revealed to have long term memory in its kinetics, prompting alternate non-Markovian schemes to analyze its gating. Traditionally, ion channel gating is modeled as Markovian transitions between fixed states. In this work, we have used single channel data from hTREK1 ion channel and have provided a simple diffusion model for its gating. The main assumption of this model is that the ion channel diffuses through a continuum of states on its potential energy landscape, which is derived from the steady state probability distribution of ionic current recorded from patch clamp experiments. A stochastic differential equation (SDE) driven by Gaussian white noise is proposed to model this motion in an asymmetric double well potential. The method is computationally very simple and efficient and reproduces the amplitude histogram very well. For the case when ligands are added, leading to incorporation of long term memory in the kinetics, the SDE is modified to run on coloured noise. This has been done by introducing an auxiliary variable into the equation. It has been shown that increasing the noise correlation with ligand concentration improves the fits to the experimental data. This has been validated for several datasets. These methods are more advantageous for simulation than the Markovian models as they are true to the physical picture of gating and also computationally very efficient. Reproducing the whole raw data trace takes no more than a few seconds with our scheme, with the only input being the amplitude histogram and four parameters. Finally a quantitative model based on a modified version of the Chemical Langevin equation is given, which works on random rate parameters. This model is computationally simple to implement and reproduces the catalytic activity of the channel as a function of time. From the computational analysis undertaken in this work, we can infer that ion channel activity can be modeled using the framework of non-Markovian processes, lending credence to the recent understanding that single molecule reactions are basically processes with long-term memory. Since the ion channel is basically a protein, we can also hypothesize that the some of the properties that make proteins so vital to living organ-isms could be attributed to long-term memory in their folding kinetics, giving them the ability to sample specific regions of their conformation space, which are of interest to biological functions.