Predicting the performance of wells in compartmentalized reservoirs can be quite challenging to most conventional reservoir engineering tools. The purpose of this research is to develop a Compartmentalized Gas Depletion Model that applies not only to conventional consolidated reservoirs (with constant formation compressibility) but also to unconsolidated reservoirs (with variable formation compressibility) by including geomechanics, permeability deterioration and compartmentalization to estimate the OGIP and performance characteristics of each compartment in such reservoirs given production data. A geomechanics model was developed using available correlation in the industry to estimate variable pore volume compressibility, reservoir compaction and permeability reduction. The geomechanics calculations were combined with gas material balance equation and pseudo-steady state equation and the model was used to predict well performance. Simulated production data from a conventional gas Simulator was used for consolidated reservoir cases while synthetic data (generated by the model using known parameters) was used for unconsolidated reservoir cases. In both cases, the Compartmentalized Depletion Model was used to analyze data, and estimate the OGIP and Jg of each compartment in a compartmentalized gas reservoir and predict the subsequent reservoir performance. The analysis was done by history-matching gas rate with the model using an optimization technique. The model gave satisfactory results with both consolidated and unconsolidated reservoirs for single and multiple reservoir layers. It was demonstrated that for unconsolidated reservoirs, reduction in permeability and reservoir compaction could be very significant especially for unconsolidated gas reservoirs with large pay thickness and large depletion pressure.

Predicting the performance of wells in compartmentalized reservoirs can be quite challenging to most conventional reservoir engineering tools. The purpose of this research is to develop a Compartmentalized Gas Depletion Model that applies not only to conventional consolidated reservoirs (with constant formation compressibility) but also to unconsolidated reservoirs (with variable formation compressibility) by including geomechanics, permeability deterioration and compartmentalization to estimate the OGIP and performance characteristics of each compartment in such reservoirs given production data. A geomechanics model was developed using available correlation in the industry to estimate variable pore volume compressibility, reservoir compaction and permeability reduction. The geomechanics calculations were combined with gas material balance equation and pseudo-steady state equation and the model was used to predict well performance. Simulated production data from a conventional gas Simulator was used for consolidated reservoir cases while synthetic data (generated by the model using known parameters) was used for unconsolidated reservoir cases. In both cases, the Compartmentalized Depletion Model was used to analyze data, and estimate the OGIP and Jg of each compartment in a compartmentalized gas reservoir and predict the subsequent reservoir performance. The analysis was done by history-matching gas rate with the model using an optimization technique. The model gave satisfactory results with both consolidated and unconsolidated reservoirs for single and multiple reservoir layers. It was demonstrated that for unconsolidated reservoirs, reduction in permeability and reservoir compaction could be very significant especially for unconsolidated gas reservoirs with large pay thickness and large depletion pressure.

No description available.

In this work, we seek to expand synthetic in vitro biological systems by using water-in-oil emulsions to provide an environment conducive to directed evolution. We approach this primarily by utilizing a model transcription system, the T7 RNA polymerase and promoter, which is orthogonal to both bacterial and eukaryotic transcription systems and is highly functional in vitro. First, we develop a method to identify functional promoter sequences completely in vitro. This method is tested using the T7 RNA polymerase-promoter model system. We then configure the T7 transcription system as an ‘autogene’ and investigate how this positive feedback circuit (whereby a T7 promoter expresses a T7 RNA polymerase gene) functions across various in vitro platforms, including while compartmentalized. The T7 autogene can be envisioned as a self-replicating system when compartmentalized, and its use for directed evolution is examined. Finally, we look towards future uses for these in vitro systems. One interesting application is to expand the utilization of unnatural base pairs within the context of a synthetic system. We investigate the ability of T7 RNA polymerase to recognize and utilize unnatural base pairs within the T7 promoter, complementing existing work on the utilization of unnatural base pairs for in vitro replication and transcription with an investigation of more complex protein-dependent regulatory function. We envision this work as a foundation for future in vitro synthetic biology efforts. / text

In vertebrate nervous system, formation of myelin sheaths around axons is essential for rapid nerve impulse conduction. However, the signals that regulate myelination in CNS remain largely unknown partially due to the lack of suitable in vitro models for studying localized cellular and molecular basis of axon-glia signals. We utilize microfabrication technologies to develop series of CNS neuron culture microsystems capable of providing localized physical and biochemical manipulation for studying neuron-glia interaction and neural progenitor development. First, a circular neuron-glia co-culture platform with one soma-compartment and one axon/glia compartment has been developed. The device allows physical and fluidic isolation of axons from neuronal somata for studying localized axon-glia interactions under tightly controlled biochemical environment. Oligodendrocyte (OL) progenitor cells co-cultured on isolated axons developed into mature-OLs, demonstrating the capability of the platform. The device has been further developed into higher-throughput devices that contain six or 24 axon/glia compartments while maintaining axon isolation. Increased number of compartments allowed multiple experimental conditions to be performed simultaneously on a single device. The six-compartment device was further developed to guide axonal growth. The guiding feature greatly facilitated the measurement of axon growth/lengths and enabled quantitative analyses of the effects of localized biomolecular treatment on axonal growth and/or regeneration. We found that laminin, collagen and Matri-gel promoted greater axonal growth when applied to somata than to the isolated axons. In contrast, chondroitin sulfate proteoglycan was found to negatively regulate axon growth only when it was applied to isolated axons. Second, a microsystem for culturing neural progenitor cell aggregates under spatially controlled three-dimensional environment was developed for studies into CNS neural development/myelination. Dense axonal layer was formed and differentiated OLs formed myelin sheaths around axons. To the best to our knowledge, this was the first time to have CNS myelin expressed inside a microfluidic device. In addition, promotion of myelin formation by retinoic acid treatment was confirmed using the device. In conclusion, we have developed series of neuron culture platforms capable of providing physical and biochemical manipulation. We expect they will serve as powerful tools for future mechanistic understanding of CNS axon-glia signaling as well as myelination.

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / The piggery for many years was characterized as a waste-generating activity of high polluter, but in recent decades many studies are responsible for changing this concept. The use of biodigester is well disseminated to lessen the impacts generated by this activity, gaining encouragement deployment in recent years, by encouraging the use of renewable energy. The biodigester is responsible for the production of biogas used as alternative energy on farms that have the digesters system. We observed few studies that investigate the geometry of the digesters and its effects on anaerobic digestion process. This work aimed to study the partitioning of the Canadian model digester anaerobic digestion of swine waste applied to evaluating the degradation (removal) of the physic-chemical parameters (temperature, pH, COD, BOD5, total nitrogen, total phosphorus, total solids, total fixed solids and total volatile solids), and determining a kinetic model describing the biogas produced in each of the compartments of the digesters. For the study were built three reactors in bench scale: the first with a partitioning which caused variation of the horizontal flow, the second with partitioning which flux change generated in the vertical and third, without fragmentation, to be used as a reactor testimony. The analyzes of the physicchemical parameters were made according to Standard Methods for the Examination of Water and Wastewater, since the determination of the kinetic model was done considering the existence of a plug flow (tubular reactor) to each of the reactors constructed and to qualification of biogas was use a gas chromatograph. On the analysis of physic-chemical was second reactor (flow variation vertically) that showed that showed a significant difference in the efficiency of COD removal and pH values, and this reactor also showed better removal of solids and BOD5. Already temperature, showed similar behavior in the three reactors, characterizing the anaerobic digestion occurred primarily in the mesophilic range. Considering the BOD5 as a substrate was obtained as rate constant 0.021 d-1, 0.025 d-1 and 0.024 d-1, respectively for the first, second and third reactor. However, considering the COD as a substrate was obtained 0.032 d-1, and 0.034 d-1, 0.027 d-1 for each of the reactors. Kinetic models had a higher correlation with the experimental data when considering the COD as substrate, and was the second reactor with the highest correlation (R2 = 0.599). In the evaluation of biogas the three reactors not showed difference between them. / A atividade suinícola por muitos anos foi caracterizada como uma atividade geradora de resíduos de alto índice poluidor, porém nas últimas décadas muitos são os estudos responsáveis por mudar esse conceito. O uso de biodigestor está bem disseminado para diminuir os impactos gerados por essa atividade, ganhando estímulo de implantação nos últimos anos, pelo incentivo ao uso de energia renovável. O biodigestor é responsável pela produção do biogás, usado como energia alternativa em propriedades rurais que possuem o sistema de biodigestores. Observam-se poucos trabalhos que pesquisam a geometria dos biodigestores e seus efeitos no processo de digestão anaeróbia. Esse trabalho objetivou o estudo da compartimentação do biodigestor modelo canadense no processo de digestão anaeróbia aplicada a resíduos da suinocultura, avaliando a degradação (remoção) dos parâmetros físico-químicos (temperatura, pH, DQO, DBO5, Nitrogênio total, Fósforo total, sólidos totais, sólidos fixos totais e sólidos voláteis totais), determinando um modelo cinético e qualificando o biogás produzido em cada um dos compartimentos dos biodigestores. Para o estudo foram construídos três reatores em escala de bancada: o primeiro com uma compartimentação que provocava variação de fluxo na horizontal, o segundo com uma compartimentação, a qual gerava variação de fluxo na vertical e o terceiro, sem compartimentação, para ser utilizado como um reator testemunho. As análises dos parâmetros físicoquímicos foram realizadas de acordo com o Standard Methods for Examination of Water and Wastewater, já a determinação do modelo cinético foi realizada considerando a existência de um fluxo pistão (reator tubular) para cada um dos reatores construídos e para a qualificação do biogás utilizou-se um cromatógrafo a gás. Quanto à avaliação dos parâmetros físico químicos, foi o segundo reator (variação de fluxo na vertical) que apresentou diferença significativa na eficiência de remoção de DQO e nos valores de pH, sendo que esse reator também apresentou melhor remoção de DBO5 e sólidos. A temperatura apresentou comportamento semelhante nos três reatores, caracterizando que a digestão anaeróbia ocorreu prioritariamente na faixa mesofílica. Considerando a DBO5 como substrato obteve-se como constante de velocidade 0,021 d-1; 0,025 d-1 e 0,024 d-1, respectivamente para o primeiro, segundo e terceiro reator. Todavia, considerando a DQO como substrato obteve-se 0,032 d-1; 0,034 d-1 e 0,027 d-1 para cada um dos reatores. Os modelos cinéticos apresentaram uma maior correlação com os dados experimentais quando considerada a DQO como substrato, sendo que foi o segundo reator que apresentou maior correlação (R2 = 0,599). Na avaliação do biogás os três reatores não apresentaram diferença entre si.

Nesta tese é abordado o problema da mochila compartimentada e o problema de corte de estoque unidimensional acoplado ao problema dimensionamento de lotes. Para o problema da mochila compartimentada é apresentada a versão unidimensional e proposta a versão bidimensional, denominados como problema da mochila compartimentada unidimensional e problema da mochila compartimentada bidimensional, respectivamente. Para o problema de corte de estoque acoplado ao dimensionamento de lotes são apresentadas três variações: uma máquina para produzir um tipo de objeto; uma máquina para produzir vários tipos de objetos; múltiplas máquinas para produzir vários tipos de objetos. Algumas formulações matemáticas de programação inteira e inteira-mista, decomposições dos problemas em problema mestre e subproblemas e heurísticas baseadas no método geração de colunas são propostas para os problemas da mochila compartimenta e o problema acoplado. Em específico, para o problema acoplado são aplicadas decomposições Dantzig-Wolfe, que podem ser por período, por máquina ou por período e máquina. Além disso, uma heurística baseada em grafo E/OU é proposta para o problema da mochila compartimentada bidimensional / In this thesis we present the constrained compartmentalized knapsack problem and the one dimensional cutting stock problem integrated with the capacitated lot sizing problem. For the constrained compartmentalized knapsack problem, the one dimensional version is presented and the two dimensional version is proposed, called one-dimensional compartmentalized knapsack problem and two-dimensional compartmentalized knapsack problem, respectively. For the cutting stock problem integrated with the capacitated lot sizing problem three variations are considered: one machine to produce one type of object; one machine to produce multiple types of objects; multiple machines to produce multiple types of objects. Some integer and mixed programming formulations, decompositions of the problems in master problem and subproblems and heuristics based on column generation method are proposed for the compartmentalized knapsack problem and the cutting stock problem integrated with the capacitated lot sizing problem. In particular, the period, the machine, and the period and machine Dantzig- Wolfe decompositions are applied for the integrated problem. Moreover, a heuristic based on the graph AND/OR is proposed for the two-dimensional compartmentalized knapsack problem. Computational results show that these mathematical formulations and methods provide good solutions

Isoelectric trapping (IET) has become an accepted preparative-scale electrophoretic separation technique. However, there are still a number of shortcomings that limit its utility. The performance of the current preparative-scale IET systems is limited by the serial arrangement of the separation compartments, the difficulties in the selection of the appropriate buffering membranes, the effect of Joule heating that may alter separation selectivity and a lack of methods for the determination of the true, operational pH value inside the buffering membranes. In order to bolster the current membrane pH determination methods which rely on the separation of complex ampholytic mixtures, a fluorescent carrier ampholyte mixture was synthesized. The use of a fluorescent mixture allows for a reduced load of carrier ampholytes, thereby reducing a possible source of error in the pH determinations. A mixture of carrier ampholytes tagged with an alkoxypyrenetrisulfonate fluorophore was shown to have suitable fluorescence and ampholytic properties and used to accurately determine the pH of high pH buffering membranes under actual IET conditions. In a more elegant solution to the difficulties associated with pH determinations, a method utilizing commercial UV-transparent carrier ampholytes as the ampholyte mixture to be separated was developed. By using commercial carrier ampholytes and eliminating the need to synthesize, purify, and blend fluorescently tagged ampholytes, the new method greatly simplified the determination of the operational pH value of the buffering membranes. In order to address the remaining limitations, a new system has been developed that relies on (i) parallel arrangement of the electrodes and the collection compartments, (ii) a directionally-controlled convection system for the delivery of analytes, (iii) short anode-to-cathode distances, (iv) short intermembrane distances, and (v) an external cooling system. This system has been tested in four operational modes and used for the separation of small molecule ampholytic mixtures, for the separation of protein isoforms, and direct purification of a target pI marker from a crude reaction mixture.

Evolución dirigida de proteínas: La evolución dirigida es una técnica que nos permite explorar funciones enzimáticas que no son requeridas en el ambiente natural. Esta técnica, simula procesos genéticos naturales y de selección. Esta estrategia se utiliza cuando un diseño racional es muy complicado. Consiste en una repetición de ciclos de diversificación y selección que llevan a la acumulación de mutaciones benéficas. Aquí se presenta dos ejemplos de evolución dirigida con los cuales se ha trabajado directamente: la ADN polimerasa del organismo  Thermus aquaticus usada comúnmente en PCR, y la proteína LacI que regula la expresión de genes usados para el metabolismo de lactosa en E. Coli. / Directed evolution allows us to explore protein functionalities not required in the natural environment. It mimics natural genetic processes and selective pressures. This approach is used when the molecular basis is not completely understood and rational design is a difficult task. This approach consists of serial cycles of consecutive diversification and selection which eventually lead to the accumulation of beneficial mutations. Here are presented two cases where directed evolution is used to modify two different proteins: Taq polymerase, enzyme used for DNA extension in PCR, and the LacI repressor protein which regulates gene expression on E.coli.

Made available in DSpace on 2015-05-14T13:21:51Z (GMT). No. of bitstreams: 1 arquivototal.pdf: 1010298 bytes, checksum: a5a24de3f4abc4b3987d2584b46eea8f (MD5) Previous issue date: 2009-07-27 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / The waste from fruit and vegetables and the discharge of domestic and industrial wastewaters in an unacceptable way cause serious problems for the majority of cities in Brazil and the rest of the world. The residues from fruit and vegetables and domestic and industrial wastewater could be treated jointly by the process of anaerobic digestion resulting in the production of energy and a reduction in negative environmental impacts. The principal objective of this work was to study the kinetics of the process of anaerobic biostabilization of vegetable residual solids (RSV), treated at different concentrations of total solids with the view to optimizing energy production and anaerobic biostabilization. To execute this study a completely mixed, compartmentalized anaerobic reactor comprising three compartments separated by glass plates with unit volumes of 25 litres, was designed, installed and monitored,. The resulting products from anaerobic biostabiliztion in the form of semi-solids were monitored weekly except for pH, total alkalinity and volatile fatty acids which jointly with biogas production were monitored twice weekly during a the total monitoring period of 294 days. The work was divided into two stages. In the first stage a substrate comprising twelve different types of vegetable solid waste with a total solids concentration equal to 75, 4 g/L was used. In the second stage the concentration of total solids applied to compartments C1, C2 and C3 were 40, 22.6 and 23.2 g/L respectively, with the with the level of humidity being adjusted by the addition of domestic sewage. The maximum percentage of methane in the biogas was 61.5% obtained in the first compartment (C1) of the reactor during the second experimental stage. The maximum kinetic constants for bioconversion (k) for COD total and soluble, TKN and sulphate during the first stage were respectively 3.86 x 10-2, 3.01 x 10-2, 4.75 x 10-2 and 2.13 x 10-2d-1. During the second stage of the study the values maximum obtained were 1.28 x 10-2, 1.90 x 10-2, 2.90 x 10-2 and 3.22 x 10-2d-1, for COD total and soluble, TKN and sulphate respectively. / O desperdício de frutas e verduras e o lançamento de águas residuárias domésticas ou industriais de forma inadequada representam sérios problemas para maioria das cidades do Brasil e do mundo. Os resíduos de frutas e verduras e as águas residuárias domésticas e industriais podem ser tratados de forma conjugada pelo processo de digestão anaeróbia, resultando no aproveitamento energético e na redução de impactos ao meio ambiente. O objetivo principal deste trabalho foi o estudo cinético do processo de bioestabilização anaeróbia de resíduos sólidos vegetais (RSV), tratados com diferentes concentrações de sólidos totais, visando o aproveitamento do potencial energético e consequentemente a bioestabilização anaeróbia do material orgânico. Para realização deste trabalho foi projetado, construído, instalado e monitorado um reator anaeróbio compartimentado de mistura completa, contendo três câmaras individuais de reação, construídas com placas de vidro, com volumes unitários de 25 litros. Os produtos resultantes do processo de bioestabilização anaeróbia que se encontravam na forma semi-sólida foram monitorados semanalmente, exceto pH, alcalinidade total e ácidos graxos voláteis que juntamente com o biogás foram monitorados duas vezes por semana; o período total de monitoração foi de 294 dias. O trabalho foi dividido em duas etapas. Na primeira etapa, o substrato constituído por doze diferentes tipos de (RSV) foi digerido a uma concentração de sólidos totais igual a 75,4 g/L. Para realização da segunda etapa, a concentração de sólidos totais aplicada às câmaras C1, C2 e C3 foram de 40; 22,8 e 23,2 g/L respectivamente, haja vista o teor de umidade do substrato preparado ter sido ajustado com adição esgoto doméstico. A porcentagem máxima de metano contido no biogás foi de 61,5%, obtida para primeira câmara de reação, no decorrer da segunda etapa. A produção máxima de biogás foi de 56 litros, também obtida na primeira câmara C1, ao longo da segunda etapa. Os valores máximos das constantes cinéticas de bioconversão (k) obtidos no decorrer da primeira etapa para DQOt, DQOs, NTK e sulfato foram respectivamente 3,86.10-2, 3,01.10-2, 4,75.10-2 e 2,13.10-2d-1. Durante a segunda etapa do trabalho os valores máximos obtidos foram de 1,28.10-2, 1,90.10-2, 2,90.10-2 e 3,22.10-2d-1 para DQOt, DQOs, NTK e sulfato, respectivamente.