Nos últimos anos grande número de modelos computacionais tem sido propostos com o intuito de descrever o movimento de solutos no perfil do solo, apesar disso, o que se observa é que existe grande dificuldade em se modelar esses fenômenos, para que o modelo possa predizer o processo de deslocamento e retenção dos solutos na natureza. Para tanto, o objetivo deste trabalho foi utilizar um modelo estatístico para descrever o transporte dos solutos no perfil do solo. Dessa forma, foi realizado um experimento em laboratório e observado os níveis de potássio e nitrato ao longo do perfil dos solos Latossolo Vermelho Amarelo e Nitossolo Vermelho. Para inferir sobre essas variáveis foram consideradas duas abordagens. Para a primeira abordagem foi utilizado um modelo de regressão não linear para cada uma das variáveis, cujos parâmetros do modelo apresentam uma interpretação prática, na área de solos. Para esse modelo foi realizado um esboço sobre a não linearidade do mesmo para verificar as propriedades assintóticas dos estimadores dos parâmetros. Para o método de estimação foi considerado, o método de mínimos quadrados e o método de bootstrap. Além disso, foi realizada uma análise de diagnóstico para verificar a adequação do modelo, bem como identificar pontos discrepantes. Por outro lado, para outra abordagem, foi utilizado um modelo multiresposta para analisar o comportamento das variáveis nitrato e potássio ao longo do perfil dos solos, conjuntamente. Para esse modelo foi utilizado o método da máxima verossimilhança para encontrar as estimativas dos parâmetros do modelo. Em ambas as situações, observou-se a adequação dos modelos para descrever o comportamento dos solutos nos solos, sendo uma alternativa para os pesquisadores que trabalham com estudo de solos. O modelo logístico com quatro parâmetros se destacou por apresentar melhores propriedades, como medidas de não linearidade e boa qualidade de ajuste. / In the last years, several computational models have been proposed to describe the movement of solutes in the soil profile, but what is observed is that there is great difficulty in model these phenomena, so that model can predict the displacement process and retention of solutes in nature. Thus, the aim of this study was to use a statistical model to describe the transport of solutes in the soil profile. Therefore, an experiment was conducted in the laboratory and observed levels of potassium and nitrate along the depth of soil Oxisol (Haplustox) and Hapludox,. To make inferences about these variables were considered two approaches. For the first approach was utilized a non-linear regression model for each variable and the model parameters have a practical interpretation on soil. For this model we performed a sketch on the nonlinearity of the model to check the asymptotic properties of parameter estimators. To estimate the parameters were considered the least squares method and the bootstrap method. In addition, we performed a diagnostic analysis to verify the adequacy of the model and identify outliers. In the second approach considered was using a multi-response model to analyze the behavior of the variables nitrate and potassium throughout the soil profile together. For this model we used the maximum likelihood method to estimate the model parameters. In both cases, we observed the suitability of the models to describe the behavior of solutes in soils, being an alternative for researchers working on the study of soils. The logistic model with four parameters stood out with better properties, such as non-linearity and good fit.

Submitted by Marlene Santos (marlene.bc.ufg@gmail.com) on 2016-06-15T20:13:15Z No. of bitstreams: 2 Tese - Fernando Ernesto Ucker - 2015.pdf: 2298051 bytes, checksum: d8ba74457fe737b3f2a05b9a4183e681 (MD5) license_rdf: 19874 bytes, checksum: 38cb62ef53e6f513db2fb7e337df6485 (MD5) / Approved for entry into archive by Luciana Ferreira (lucgeral@gmail.com) on 2016-06-28T12:27:51Z (GMT) No. of bitstreams: 2 Tese - Fernando Ernesto Ucker - 2015.pdf: 2298051 bytes, checksum: d8ba74457fe737b3f2a05b9a4183e681 (MD5) license_rdf: 19874 bytes, checksum: 38cb62ef53e6f513db2fb7e337df6485 (MD5) / Made available in DSpace on 2016-06-28T12:27:51Z (GMT). No. of bitstreams: 2 Tese - Fernando Ernesto Ucker - 2015.pdf: 2298051 bytes, checksum: d8ba74457fe737b3f2a05b9a4183e681 (MD5) license_rdf: 19874 bytes, checksum: 38cb62ef53e6f513db2fb7e337df6485 (MD5) Previous issue date: 2015-08-17 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / In the state of Goiás sugarcane cultivation has expanded into areas of sandy soil, known as fragile because of their high risk of degradation. Potassium is a vital nutrient used in the cultivation of sugarcane and has been applied to these cultivated soils. Little is known about the mobility of the potassium ion in such soils. This thesis set out to assess the vertical movement of potassium in Quartz-sand Neosols found in an area of the Araucária farm, in the municipality of Mineiros, Goiás, which is under two types of regime: sugarcane cultivation and Cerrado vegetation. The movement of this nutrient was studied on the basis of three experiments: 1st) a laboratory experiment with columns. Soil samples were sent to the Hydraulics Laboratory at the Pontifical Catholic University of Goiás where the experiment with columns was performed in triplicate for each type of soil management. Each 100 cm high column was sectioned into rings of 10 cm in height by 7.5 cm in diameter. A total of 105 mg of K2O, in the form of KCl, was applied to the surface layer. Over the next ten days, deionized water was applied to each column, the equivalent of 600 mm precipitation at the end. The leachate effluent was collected periodically and sent for potassium content analysis. At the end of the ten-day period, the columns were dismantled, and the soil in each ring was collected and sent for analysis of potassium, organic matter and pH levels. The mean values of potassium were submitted to descriptive analysis and a t test (α = 0.05); 2nd) a field experiment under two types of water regime, natural and controlled. In the natural water regime, rectangular metal troughs measuring 0.5 m2 were made. Three were installed in soil under sugarcane cultivation and another three in the same soil under Cerrado vegetation. Witness soil samples were collected in November 2013, before the onset of the rainy season in that region. After this initial collection, the equivalent of 120 kg ha-1 of K2O in the form of KCl was applied to the soil, and left for the full wet season, until the end of April of the following year. After that, soil samples were collected from the troughs at each level of 10 cm to a depth of 100 cm. The analysis of potassium movement under the controlled water regime took place in November 2013. The areas assessed were the same as those of the natural water regime. For this study concentric rings were used to delimit the area and ensure a vertical flow of the water applied. The equivalent of 600 mm of water was applied within the internal ring. After 24 hours the same amount of K+ as was applied in the natural regime and water equivalent to 600 mm of accumulated rain were applied. After 48 hours, soil sampling was carried out with a Dutch auger at levels of 10 cm to a depth of 100 cm. The soil samples collected in the field were sent for analysis in terms of total sand, silt, total clay, K+, pH and organic matter, and; 3rd) the field experiment with biennial evaluation of potassium movement. This experiment involved two parallel stretches of Quartz-sand Neosols along a slope, one with Cerrado vegetation and the other with sugarcane cultivation. In each of these stretches a transect with ten sampling points, each 30 m apart, was established and samples were collected at each point. Composite samples were collected in the two areas under study at depths of 0-20, 20-40, 40-60, 100-120 and 160-180 cm. After collection, the samples were bagged and appropriately identified, then forwarded for analysis to the Embrapa Soils Laboratory in Rio de Janeiro. The collections were made in November 2011 and 2012, the beginning of the rainy season in the region under study, and in April 2012 and 2013, the end of the rainy season, yielding a two-year evaluation period. In the laboratory, the samples were analyzed for cation exchange capacity, pH and organic matter, as well as for potassium. It was concluded from the first experiment that in the Quartz-sand Neosols there could be a significant loss of K+ after applying potassium to the soil. An increase of more than 1% in organic matter content could positively influence K+ retention in this type of soil. It was concluded from the second experiment that there was a significant movement of potassium levels to lower layers in the natural water regime after the accumulated rainfall of 1638 mm, both in the soil under cultivation and under Cerrado vegetation. From the third experiment it was concluded that the potassium ion behaved differently in the two soil regimes, sugarcane cultivation and Cerrado vegetation, and an increase in the nutrient was seen in layers of more than 100 cm in depth. / No Estado de Goiás o cultivo da cana-de-açúcar tem se expandido para áreas com solos arenosos, denominados frágeis por seus altos riscos a degradação. Potássio é um importante nutriente utilizado no cultivo da cana-de-açúcar e tem sido aplicado nesses solos sob cultivo. Pouco se conhece sobe a mobilidade do íon potássio em tais solos. Esta tese teve o objetivo de avaliar a movimentação vertical de potássio em Neossolo Quartzarênico encontrado em área da Fazenda Araucária, localizada na região do município de Mineiros-GO, que se encontra sob dois tipos de usos: sob o cultivo de cana-de-açúcar e sob vegetação de Cerrado. A movimentação deste nutriente foi estudada a partir de três experimentos: 1°) experimento laboratorial com colunas. Amostras de solo foram encaminhadas para o Laboratório de Hidráulica da Pontifícia Universidade Católica de Goiás onde o experimento com colunas foi realizado em triplicata para cada tipo de uso. Cada coluna possuía 100 cm de altura e foi seccionada em anéis de 10 cm de altura por 7,5 cm de diâmetro. Cada coluna recebeu acima da camada superficial, 105 mg de K+, na forma de KCl. Durante dez dias seguidos foi aplicada água deionizada em cada coluna, representando ao final uma precipitação de 600 mm. O efluente lixiviado foi coletado periodicamente e encaminhado para análise do teor de potássio. Ao final dos dez dias as colunas foram desmontadas e o solo foi coletado em cada anel e encaminhado para análise de teores de potássio, matéria orgânica e pH. As médias dos valores de potássio foram submetidas a análise descritiva e teste t (α = 0,05); 2°) experimento em campo sob dois tipos de regime hídrico, natural e controlado. No regime hídrico natural, calhas metálicas retangulares foram confeccionadas com área de 0,5 m2. Três calhas foram instaladas em solo sob cultivo com cana-de-açúcar e outras três calhas no mesmo solo sob Cerrado. Amostras de solo testemunhas foram coletadas em novembro de 2013, antes do início do período chuvoso na região. Após coleta inicial, foi aplicado sobre o solo o equivalente a 80 kg ha-1 de K+ na forma de KCl, e aguardou-se todo o período chuvoso, com fim em abril do ano seguinte. Após isto, amostras de solo foram coletadas no interior das calhas a cada 10 cm até a profundidade de 100 cm. A avaliação da movimentação de potássio sob regime hídrico controlado foi realizada em novembro de 2013 e as áreas avaliadas foram as mesmas do regime hídrico natural. Para esse estudo foram utilizados anéis concêntricos para delimitação da área e para garantir fluxo vertical da água aplicada. Aplicou-se no interior do anel interno o equivalente a 600 mm de água. Após 24 horas aplicou-se a mesma quantidade de K+ do regime natural e água equivalente a 600 mm de chuva acumulada. Após 48 horas procedeu-se a amostragem do solo a cada 10 cm até a profundidade de 100 cm com uso de trado holandês. As amostras de solo coletadas em campo foram encaminhadas para avaliação quanto aos teores de K+, pH e matéria orgânica e; 3º) experimento em campo com avaliação bianual da movimentação vertical do potássio. Nesse experimento foram considerados como tratamento duas faixas paralelas de um Neossolo Quartzarênico dispostas ao longo da vertente, sendo uma com vegetação de Cerrado e outra com cultivo de cana-de-açúcar. Em cada uma das faixas foi estabelecido um transecto com dez pontos de amostragem, espaçados de 30 m entre si, onde repetiu-se a coleta de amostras em cada ponto. Amostras compostas foram coletadas nas duas áreas estudadas nas profundidades de 0-20, 20-40, 40-60, 100-120 e 160-180 cm. Após a coleta, as amostras foram ensacadas e devidamente identificadas, sendo então encaminhadas ao Laboratório de Solos da Embrapa Solos – RJ para análise. As coletas ocorreram em novembro de 2011 e 2012, período que significa início da estação chuvosa na região de estudo e abril de 2012 e 2013, período correspondente ao final da estação chuvosa, totalizando dois anos de avaliação. Em laboratório, as amostras foram submetidas à análise da capacidade de troca catiônica, pH e matéria orgânica, além de potássio. Do primeiro experimento concluiu-se que em Neossolo Quartzarênico pode haver significativa perda de K+ após aplicação de potássio no solo. O aumento do teor de matéria orgânica acima de 1% pode influenciar positivamente a retenção de K+ neste tipo de solo. Do segundo experimento concluiu-se que houve movimento significativo dos teores de potássio para camadas inferiores em regime hídrico natural após precipitação acumulada de 1.638 mm, tanto no solo sob lavoura quanto no solo sob Cerrado. Já do terceiro experimento concluiu-se que o íon potássio teve comportamento distinto para o solo cultivado com cana-de-açúcar em relação ao solo sob Cerrado, e verificou-se acréscimo do nutriente em camadas superiores a 100 cm de profundidade.

A demanda alimentar vem aumentando de acordo com o crescimento populacional e com isso há uma necessidade de que as práticas agrícolas tornem-se cada vez mais intensas e tecnificadas, mediante o incremento, entre outros, da utilização de insumos químicos. Porém, uma vez aplicados de maneira desorganizada, sem a devida preocupação com os possíveis impactos aos recursos naturais, tais produtos podem vir a provocar danos ao solo, contaminação de águas subterrâneas (mediante sua lixiviação) e em alguns casos, podem ser responsáveis pelo aumento da salinidade em alguns solos da região do semiárido do nordeste brasileiro. Nesse sentido, devido ao fato de envolverem processos físicos na natureza, o estudo da dinâmica desses produtos químicos têm motivado diversos pesquisadores a aplicarem ferramentas matemáticas (modelos matemáticos) na área de engenharia de água e solo, buscando entender a correlação entre a dinâmica da água e o movimento de solutos no perfil do solo. Portanto, a presente pesquisa tem como objetivo a aplicação do modelo matemático HYDRUS-1D para a simulação do movimento da água e do íon potássio, em condições de laboratório, utilizando-se colunas preenchidas com dois tipos de material de solos salinos e não saturados: Argissolo Amarelo (S1) e Latossolo Vermelho Amarelo (S2). Além disso, buscou-se também avaliar tanto o desempenho do referido modelo, em condições salinas, quanto proceder a uma análise de sensibilidade. Para alcançar tais objetivos, foram conduzidas as seguintes etapas: 1) elaboração de curvas de distribuição de efluentes (Breakthrough Curves - BTC) para obtenção dos parâmetros de transporte do íon potássio, com a aplicação de soluções de 1000 ppm, 2000 ppm e 3000 ppm de concentração de potássio, nos dois tipos de solos salinos, 2) Aplicação dessas soluções de potássio na coluna preenchida com o mesmo material de solo salino não saturado, 3) Simulação dos perfis de água e potássio para os diferentes materiais de solo salino pelo modelo HYDRUS-1D e 4) Avaliação de desempenho e análise de sensibilidade do modelo HYDRUS-1D. A avaliação de desempenho foi feita levando-se em conta os seguintes índices estatísticos: erro máximo, erro absoluto médio, raiz quadrada do erro médio normalizado, coeficiente de massa residual, coeficiente de determinação, eficiência e índice de concordância de Willmott e a análise de sensibilidade foi feita mediante a determinação do erro padrão, por meio de variações positivas (+ 10%, + 20%, + 30%, + 40%, + 50%) e negativas (- 10%, - 20%, - 10%, - 40%, - 50%), dos valores de: umidade volumétrica do solo saturado, condutividade hidráulica e os parâmetros n e ? do modelo de van Genuchten (1980). Diante dos resultados obtidos, pôde-se perceber que os procedimentos experimentais (BTC\'s) para a estimativa dos parâmetros de transporte do íon potássio em condições de solo salino, foram suficientes para descrever a movimentação do íon potássio no solo, gerando informações de entrada precisas para os modelos de simulação. Em termos do modelo HYDRUS-1D, observou-se que o deslocamento do íon potássio acompanhou a frente de molhamento e que o modelo foi eficiente nas simulações de deslocamento do íon potássio e da água para ambos os solos, em condições salinas. A análise de sensibilidade evidenciou que o modelo apresentou-se sensível, às variações negativas dos dados de entrada: umidade volumétrica do solo saturado, condutividade hidráulica do solo saturado e parâmetros \"n\" e \"?\" do modelo de van Genuchten (1980). / The increased demand for food due to population growth requires that agricultural practices become increasingly intensive and very technical, including the increased use of agricultural chemicals (fertilizers). If improperly applied without considering possible impacts on natural resources, agricultural chemicals may lead to soil and groundwater contamination through their leaching from the soil root zone. They may be responsible also for increased salinity in some soils of semiarid regions in northeastern Brazil. Since many transient physical and chemical processes affect their transport in the subsurface, mathematical models have become popular tools in soil and water engineering and management in order to understand the correlation between water dynamics and solute movement in soils. Thus, this research aimed at using the HYDRUS-1D software package to simulate water and potassium movement, under laboratory conditions, in unsaturated saline soil columns filled with two soil types: an Ultisol (S1) and an Oxisol (S2). Comparisons were made with experimental data while also a sensitivity analysis was carried out to evaluate the effect of various parameters on solute transport under saline conditions. For this purpose the following studies were performed: 1) Measurement of solute breakthrough curves (BTCs) to estimate the transport parameters of the potassium ion by applying potassium solutions of 1,000 ppm, 2,000 ppm and 3,000 ppm to both soil types, 2) Application of similar potassium solutions to columns containing the same saline unsaturated soils, 3) Simulation of water and potassium distributions for different saline soil materials using HYDRUS-1D, and 4) Performance evaluation and sensitivity analyses of the HYDRUS-1D numerical model. The performance evaluation was conducted using the following statistical indices: maximum error, mean absolute error, normalized root mean square error, coefficient of residual mass, coefficient of determination, efficiency and Willmott\'s concordance index. The sensitivity analyses considered standard deviations resulting from positive and negative changes (+ 10% + 20% + 30% + 40% + 50%) (-10%, -20%, -10%, -40%, -50%) in the values of the saturated volumetric soil moisture content, the saturated hydraulic conductivity, and the parameters n and ? of van Genuchten\'s (1980) model for the unsaturated soil hydraulic functions. Results indicate that the experimental procedures (BTCs) for estimating the transport parameters of potassium for saline soil conditions were sufficient to describe potassium ion transport in the soils by generating the required input information for the simulation models. Relative to HYDRUS-1D model, the displacement of potassium was found to follow closely the wetting front, with the model providing a very efficient means for simulating the movement of both water and potassium in the two soils during saline conditions. The sensitivity analysis showed that the model was relatively sensitive to negative variations of the input data, notably the saturated water content, the saturated hydraulic conductivity, and the n and ? soil hydraulic parameters.

Com o avanço do poder computacional nas últimas décadas, a modelagem molecular de problemas em diversas áreas se tornou mais acessível, sendo hoje uma ferramenta fundamental para o entendimento de diversos processos. Em especial, simulações moleculares com campos de força clássicos vem sendo importante para a amostragem de propriedades termodinâmicas, para a determinação de estruturas e população de confôrmeros, e seleção de configurações para utilização com métodos que combinam mecânica quântica com mecânica molecular. Os principais métodos de simulação atualmente utilizados são a dinâmica molecular (MD, do inglês molecular dynamics) e o Monte Carlo (MC). Ambos os métodos são a princípio equivalentes quando o objetivo é a amostragem configuracional, tendo a MD a vantagem de permitir a análise da dinâmica e evolução temporal, e o MC a vantagem de poder gerar configurações de forma probabilística, sem a necessidade de seguir um caminho sobre a superfície de energia potencial, o que pode resultar em uma amostragem mais eficiente. Contudo, não há ainda uma metodologia de MC que possa ser considerada eficiente e bem estabelecida para a amostragem dos graus de liberdade internos de moléculas com complexidade arbitrária. Visando avançar no desenvolvimento de métodos que trabalham nesse sentido, neste trabalho o método apresentado por Shah e Maginn [1] foi implementado e aprimorado. No método, a molécula é fragmentada em partes menores, formadas de graus de liberdade rígidos, que não variam drasticamente durante a simulação. Esses fragmentos por sua vez são conectadas por graus de liberdade maleáveis, os diedros e termos não ligados da energia. Durante a simulação a molécula tem fragmentos apagados, e então é reconstruída utilizando um esquema de Configurational Bias Monte Carlo (CBMC). A contribuição deste trabalho para a metodologia consiste em generalizar os tipos de fragmentos possíveis dentro do método, a simplificação do critério de aceitação e extensões com vieses adicionais, como é o caso do viés no potencial eletrostático e no critério de aceitação da amostragem preferencial com o CBMC. A validade da implementação do método foi avaliada através de simulações em dois sistemas simples: o octano e o 1,2-dicloroetano. Comparando a amostragem e os resultados obtidos para as populações de confôrmeros com resultados de MD e experimentais ou obtidos com outros métodos de MC da literatura foi possível verificar que a implementação reproduz os resultados esperados. Além disso, o equilíbrio conformacional da molécula de óxido mesityl (MOx) que possui duas conformações: syn e anti, foi estudado. Graças a barreira de potencial entre as duas conformações de cerca de 10 kcal/mol, a MD não é capaz de realizar uma amostragem ergódica, enquanto o CBMC realiza a amostragem sem problemas. Na simulação CBMC, a inversão da população dominante em fase gasosa e em água foi observada. Simulações do MOx em acetonitrila e metanol mostraram que a população de confôrmeros anti de fato aumenta conforme a polaridade do solvente. Entretanto, devido ao estiramento da ligação C = O do MOx em metanol devido as ligações de hidrogênio, a contribuição conformacional à posição do máximo da banda de absorção não segue a tendência da polaridade, tendo um deslocamento para o azul maior na acetonitrila do que em metanol. O estiramento da ligação C = O só pode ser observado graças a introdução da amostragem de fragmentos com deslocamentos Cartesianos e algoritmo de Metropolis ao método CBMC original. Esse efeito devido ao estiramento é compensado pelo efeito solvente, de modo que a contribuição total à energia de transição segue a polaridade do solvente. De uma maneira geral, concluímos que o desempenho do método CBMC utilizado é excelente para os casos estudados, e é inclusive superior ao da MD em alguns casos. A implementação no software DICE deixa um legado importante para diversos grupos de pesquisa, não somente por introduzir o CBMC, mas também por melhorias gerais como paralelização, lista de vizinhos e modernização do código, que foram introduzidas ao decorrer do projeto. / With the increase of computational power in the last decades, the molecular modeling of problems in several areas has become more accessible, being today a fundamental tool used to understand several processes. In particular, molecular simulations with classical force fields have been important for the sampling of thermodynamic properties, for the determination of structures and population of conformers, and for the selection of configurations to be used with methods that combine quantum mechanics with molecular mechanics. The most common simulation methods used nowadays are molecular dynamics (MD) and Monte Carlo (MC). Both methods are in principle equivalent when the goal is configurational sampling, with MD having the advantage of allowing the analysis of the dynamics and temporal evolution, while MC has the advantage of generating the configurations in a probabilistic manner, not necessarily following a path in the potential energy surface, possibly resulting in a more efficient sampling. However, there is no MC methodology that can be considered efficient and established to sample the internal degrees of freedom of molecules with arbitrary complexity. In order to advance in the development of methods that want to achieve this goal, in this work the method presented by Shah e Maginn [1] has been implemented and improved. In the method, the molecule is fragmented into smaller parts, each one composed by the hard degrees of freedom, which do not vary dramatically during the simulation. Those fragments are then connected by soft degrees of freedom, the dihedral and non-bonded terms of the energy. During the simulation the molecule has some of its fragments deleted, and is reconstructed using a Configurational Bias Monte Carlo (CBMC) approach. The contribution of this work to the methodology is generalizing the fragment types within the method, the simplification of the acceptance criteria and some extensions with additional biases, such as electrostatic potential bias and the acceptance criterion of the preferential sampling with the CBMC. The implementation was evaluated through simulations in two simple systems: octane and 1,2-dichloroethane. Comparing the sampling and results obtained for the populations of conformers with MD results, experimental data or values obtained with different MC methods present in the literature, we verified that the implementation reproduces the expected results. Beyond that, the conformational equilibrium of the mesityl oxide (MOx) molecule which has two conformers: syn and anti, was investigated. Due to the potential energy barrier between the two conformers of about 10 kcal/mol, the MD does not perform an ergodic simulation, while the CBMC does the same sampling accordingly. In the CBMC simulation, the inversion of the dominant conformer in gas phase and water was observed. The MOx simulation in acetonitrile and methanol showed that the frequency of the anti conformer indeed increases with the solvent polarity. Nonetheless, due to the stretch of the C = O bond of MOx in methanol, attributed to the hydrogen bonds formed with the solvent, the conformational contribution to the maximum of the absorption band does not follow the polarity tendency, having a larger blue shift in acetonitrile than in methanol. The C = O bond stretch can only be seen because the Cartesian displacement sampling with the Metropolis method was introduced to the original CBMC method. This effect attributed to the stretch is compensated by the solvent, in a way that the total contribution to the transition energy follows the solvent polarity. In general, we conclude that the performance of the developed CBMC method is excellent to the studied cases, being even superior to MD in some cases. The implementation in DICE leaves an important legacy to several research groups, not only for introducing the CBMC method, but also due to general improvements such as parallelization, neighbor list and code modernization, which were introduced during the project.

Solute carriers (SLCs) constitute the largest family of membrane-bound transporter proteins in humans, and they convey transport of nutrients, ions, drugs and waste over cellular membranes via facilitative diffusion, co-transport or exchange. Several SLCs are associated with diseases and their location in membranes and specific substrate transport makes them excellent as drug targets. However, as 30 % of the 430 identified SLCs are still orphans, there are yet numerous opportunities to explain diseases and discover potential drug targets. Among the novel proteins are 29 atypical SLCs of major facilitator superfamily (MFS) type. These share evolutionary history with the remaining SLCs, but are orphans regarding expression, structure and/or function. They are not classified into any of the existing 52 SLC families. The overall aim in this thesis was to study the atypical SLCs with a focus on their phylogenetic clustering, evolutionary conservation, structure, protein expression in mouse brains and if and how their gene expressions were affected upon changed food intake. In Papers I-III, the focus was on specific proteins, MFSD5 and MFSD11 (Paper I), MFSD1 and MFSD3 (Paper II), and MFSD4A and MFSD9 (Paper III). They all shared neuronal expression, and their transcription levels were altered in several brain areas after subjecting mice to food deprivation or a high-fat diet. In Paper IV, the 29 atypical SLCs of MFS type were examined. They were divided into 15 families, based on phylogenetic analyses and sequence identities, to facilitate functional studies. Their sequence relationships with other SLCs were also established. Some of the proteins were found to be well conserved with orthologues down to nematodes and insects, whereas others emerged at first in vertebrates. The atypical SLCs of MFS type were predicted to have the common MFS structure, composed of 12 transmembrane segments. With single-cell RNA sequencing and in situ proximity ligation assay, co-expression of atypical SLCs was analysed to get a comprehensive understanding of how membrane-bound transporters interact.   In conclusion, the atypical SLCs of MFS type are suggested to be novel SLC transporters, involved in maintaining nutrient homeostasis through substrate transport.

Modéliser les phénomènes de transport de solutés organiques en milieux poreux colonisés par des populations bactériennes se développant sous forme de biofilms est un domaine de recherche important pour un certain nombre d’applications environnementales, comme par exemple pour les méthodes de bioremédiation des sols et des eaux contaminés par des polluants organiques (biosparging, bio-barrières …). Les biofilms, qui sont composés principalement de bactéries et de substances polymériques extracellulaires, peuvent se développer sur les parois de grains d’un milieu poreux. Le métabolisme bactérien dégrade les solutés organiques et contribue ainsi à la diminution de la contamination. Le transport bio-réactif de composés organiques dans un milieu poreux incluant un biofilm est un problème fortement multi-échelle (depuis l’échelle de la bactérie jusqu’à l’échelle de l’aquifère) et fortement couplé (avec des phénomènes hydrodynamiques, physico-chimiques et biochimiques). Le soluté organique est transporté par convection et diffusion dans la phase fluide et diffuse dans la phase biofilm, où il est dégradé par le métabolisme bactérien. Le but de ce travail est de développer des modèles de transport bio-réactif définis à l’échelle de Darcy à partir des données disponibles à l’échelle du pore, en adoptant la méthode de changement d’échelle dite de prise de moyenne volumique. Dans le cas général, une telle approche conduit à un modèle macroscopique de transport à deux équations couplées (une équation par phase de transport). En considérant les relations entre les concentrations moyennées dans chaque phase, plusieurs régimes de transport permettant de dégénérer ce modèle en modèle à une seule équation peuvent être identifiés. L’hypothèse d’équilibre de masse local conduit à un tel modèle simplifié. En condition de non-équilibre, deux cas limites permettent également de développer des modèles de transport à une équation : le cas où le taux de biodégradation est contrôlé par le transfert de masse externe et le cas ou il est contrôlé par la cinétique de réaction. L’utilisation de ces quatre modèles implique la résolution numérique de problèmes de fermeture, afin d’évaluer les paramètres macroscopiques de transports (tenseur de dispersion, taux de dégradation …). Des calculs de coefficients effectifs ont été effectués dans différentes conditions de transport afin d’étudier leur comportement. Les résultats de ces modèles ont été comparés avec ceux obtenus par simulations directe à l’échelle microscopique pour une géométrie de pore bidimensionnelle stratifiée. À partir de ces comparaisons, les domaines de validité de chaque modèle ont été identifiés en termes de conditions hydrodynamique et biochimique de transport. (i.e. le nombre de Péclet et le nombre de Damköhler). Le développement d’un modèle expérimental de transport en milieux poreux incluant un biofilm a également été entamé, afin d’une part d’effectuer une validation expérimentale des modèles numériques préalablement développés et d’autre part de fournir un outil supplémentaire pour l’étude des phénomènes considérés / Modeling transport in porous media of organic chemical solute in presence of a bacterial population growing as biofilms is an important area of research for environmental applications, for example for remediation of groundwater contaminated by organic pollutants (biosparging, bio-barriers …). Biofilms, which are composed of bacteria and extracellular organic substances, grow on the pore walls of the porous medium. Bacteria degrade the organic solute by their metabolism and thus may contribute to pollution decrease. Bio-reactive transport of an organic solute in a porous medium including a biofilm phase is a strongly multi-scale (from the bacteria scale to the heterogeneity scale of the aquifer) and coupled (involving hydrodynamic, physicochemical and biochemical phenomena) process. The organic solute is transported by convection and diffusion in the fluid phase and diffuses into the biofilm phase, where it is degraded by bacterial metabolism. The goal of this work is to develop macroscopic models of bio-reactive transport at the Darcy-scale through volume averaging based on the data available at pore-scale. In the general case, the macroscopic system obtained by averaging pore-scale equations is a two coupled equations system (one equation for each phase), called two-equation model. By considering the relation between averaged concentration in the fluid phase and averaged concentration in the biofilm phase, several regimes of transport can be found which allow simplifying this system into a one equation system. The local mass equilibrium assumption leads to such a simplified model. When an equilibrium relationship between phases cannot be considered, a one equation model may though be developed if the biodegration rate is limited by external mass transfer or by the kinetics of bacterial metabolism. The use of these models implies the numerical solving of closure problems, in order to set up the values of the macroscopic transport parameters (dispersion tensor, interfacial flux …). Computations of these effective coefficients have been performed in different situations of mass transport in porous medium in order to study their behaviour. The results of these models have then been compared with direct simulations performed on a simplified geometry representative of a two-dimensional porous medium including a biofilm phase. Based on these comparisons, the validity domain of this model has been identified in terms of hydrodynamic and biochemical conditions of transport (i.e. the Péclet number and the Damköhler number). The set up of an experimental model of transport in a porous media including a biofilm phase has also been started, in order to make experimental validations of the previously developed numerical models and to build up an additional tool to study the considered phenomena

Experimental mole fraction solubilities of several carboxylic acids (2-methoxybenzoic acid, 4-methoxybenzoic acid, 4-nitrobenzoic acid, 4-chloro-3-nitrobenzoic acid, 2-chloro-5-nitrobenzoic acid,2-methylbenzoic acid and ibuprofen) and 9-fluorenone, thianthrene and xanthene were measured in a wide range of solvents of varying polarity and hydrogen-bonding characteristics. Results of these measurements were used to calculate gas-to-organic solvent and water-to-organic solvent solubility ratios, which were then substituted into known Abraham process partitioning correlations. The molecular solute descriptors that were obtained as the result of these computations described the measured solubility data to within an average absolute deviation of 0.2 log units. The calculated solute descriptors also enable one to estimate many chemically, biologically and pharmaceutically important properties for the ten solutes studied using published mathematical correlations.

Nickel-base superalloys have been emerged as materials for gas turbines used for jet propulsion and electricity generation. The strength of the superalloys depends mainly from an ordered precipitates of L12 structure, so called gamma prime (γ’) dispersed within the disorder γ matrix. The Ni-base alloys investigated in this dissertation comprise both model alloy systems based on Ni-Al-Cr and Ni-Al-Co as well as the commercial alloy Rene N5. Classical nucleation and growth mechanism dominates the γ’ precipitation process in slowed-cooled Ni-Al-Cr alloys. The effect of Al and Cr additions on γ’ precipitate size distribution as well as morphological and compositional development of γ’ precipitates were characterized by coupling transmission electron microscopy (TEM) and 3D atom probe (3DAP) techniques. Rapid quenching Ni-Al-Cr alloy experiences a non-classical precipitation mechanism. Structural evolution of the γ’ precipitates formed and subsequent isothermal annealing at 600 °C were investigated by coupling TEM and synchrotron-based high-energy x-ray diffraction (XRD). Compositional evolution of the non-classically formed γ’ precipitates was determined by 3DAP and Langer, Bar-on and Miller (LBM) method. Besides homogeneous nucleation, the mechanism of heterogeneous γ’ precipitation involving a discontinuous precipitation mechanism, as a function of temperature, was the primary focus of study in case of the Ni-Al-Co alloy. This investigation coupled SEM, SEM-EBSD, TEM and 3DAP techniques. Lastly, solute partitioning and enrichment of minor refractory elements across/at the γ/ γ’ interfaces in the commercially used single crystal Rene N5 superalloy was investigated by using an advantage of nano-scale composition investigation of 3DAP technique.

RÉSUMÉ : Le but de cette thèse est d’étudier en ab initio l’influence des solutés hydrogène ou oxygène sur les défauts étendus dans le titane alpha. Les résultats sont divisés en trois parties. Dans la première partie le site interstitiel octaédrique du Ti-alpha est trouvé être le site énergétiquement le plus favorable pour un H ou un O. Les calculs avec différentes concentrations en H ou O montrent que la présence d’H augmente le volume tandis que O a un effet inverse. La présence d’H en soluté diminue légèrement les constantes élastiques, la présence d’O a un effet opposé. Deux nouvelles SF sont trouvées dans la deuxième partie : une faute 0,57·(c+a) dans le plan π2 et 0,215·[1-102] dans le plan π1. La deuxième est reliée à la faible énergie de formation de la macle {10-11}. Un mécanisme de dissociation triple du cœur de la dislocation vis c+a est proposé. Mais cette dissociation ne semble pas se produire spontanément à partir d'un cœur de dislocation initialement parfait. Puisque la ségrégation à la faute signifie une diminution de l’énergie de faute, nous déduisons de nos calculs de ségrégation que la présence d'O rend sans doute la formation des SF énergétiquement plus difficile, contrairement au cas d’H. H ségrége fortement au cœur d’une dislocation vis a, avec une énergie variant de 0,06 à 0,30 eV, tandis que O y segrége très difficilement. Positionnés dans les sites les plus internes du cœur d’une dissociation prismatique métastable, en glissement, H et O induisent une dissociation dans le plan π1 ou vers une configuration prisme-π1 mélangée. Les barrières d'énergie de Peierls mesurées avec H et O dans différents sites et avec différentes concentrations montrent que H rend le glissement de la dislocation plus difficile, augmentant ainsi sans doute la cission critique résolue dans le plan prismatique, ce qui est en accord avec les mesures expérimentales. Mais les effets de H ne sont pas assez grands pour induire un glissement dévié vers le plan π1 et la dislocation continuera à glisser dans un même plan prismatique. Avec un O, la barrière d'énergie de Peierls est extrêmement élevée, beaucoup plus que celle pour un glissement dans le plan π1 ou un glissement dans le plan prismatique le plus proche. Du glissement dévié devrait ainsi être induit. Finalement, trois méthodes différentes de déformations de macles sont utilisées. Les stabilités structurale des joints de macles dépendent de leurs caractères structuraux intrinsèques mais aussi des modes de déformation appliqués. La macle la plus observée, {10-12}, et la macle {11-22} ne résistent pas à une déformation de plus de 1% ou 2% selon l’axe c. La présence de H ou O ségrégés améliorent la stabilité des macles {10-12} et {11-22}. Un modèle de dipôle de dislocations de mâclage (TD) est proposé pour permettre de simuler une TD dans une super-cellule de petite taille. Pour {10-12} et sa TD, les énergies de ségrégation de H et O mesurées au niveau du joint permettent de valider ce modèle. H et O peuvent se distribuer de manière plus ou moins homogène au joint et niveau de la TD mais pas dans les sites interstitiels de la couche atomique liée à la TD. / ABSTRACT: The aim of this thesis is to study the influence of hydrogen or oxygen solutes on extended defects in alpha titanium by ab initio calculation. Results are divided into three parts. In a first part the octahedral interstitial site of alpha-Ti is found energetically more favorable for a H or an O atom. The presence of H increases the volume while O has the opposite effect. The presence of H slightly decreases the elastic constants of alpha-Ti while O has an opposite effect. In a second part two new SFs are found: 0.57·(c+a) on π2 and 0.215·[1-102] on π1 plane. The second one is related to the low formation energy of the {10-11} twin boundary. A c+a screw dislocation 3-part dissociation mechanism is proposed. However the c+a screw core tends to spread differently according to the initial core position and a complete 3-part dissociation is not found, which may mean that such a dissociation is not easily obtainable from an initially perfect dislocation core. As segregation to SF means a decrease of the SF energy, the presence of O may make the SF formation energetically more difficult, contrary to H case. H strongly segregates to the a screw dislocation core region with segregation energies varing from 0.06 to 0.3 eV while O hardly segregates to it. Both H and O in core sites change the meta-stable gliding prismatic dissociation to π1 plane or a prism-π1 plane mixed configuration. According to our measurements of Peierls energy barriers with H or O in different sites and concentrations, H makes the gliding more difficult, thus increasing the CRSS in prismatic plane, in agreement with experimental measurements. The effect of H is not big enough to induce a cross-slip of the gliding a-screw dislocation to the π1 plane and that screw will prefer to keep on gliding in its same prismatic plane. The Peierls energy barrier is extremely increased when an O is present in the core position, much higher than the barrier for π1 plane glide or a glide in the nearest prismatic plane. A cross-slip could happen in this case. In the last part, three different deformations are applied to TBs. Their structural stabilities depend not only on their intrinsic characters at the atomistic level but also on the deformation mode applied. {10-12}, {11-22} TB structures fail for deformations as low as 1% or 2% along the c-axis. The {11-21} and the {10-11} TBs are much more resistant. The presence of segregated H and O enhances the {10-12} and {11-22} TB limited stability. A twinning disconnection dipole model is proposed which allows the simulation of a TD in a size limited supercell. Segregation energy calculations with the {10-12} TB and its TD validate the model at the TB level and show that H and O should distribute more or less homogeneously to the TD core and the TB, with only a slight preference to the TD core although not at the interstitial sites of the atomic layer related to the disconnection step itself.

京都大学 / 0048 / 新制・論文博士 / 博士(農学) / 乙第13021号 / 論農博第2831号 / 新制||農||1042(附属図書館) / 学位論文||H28||N4967(農学部図書室) / 32949 / 京都大学大学院農学研究科地域環境科学専攻 / (主査)教授 藤原 正幸, 教授 村上 章, 准教授 宇波 耕一 / 学位規則第4条第2項該当 / Doctor of Agricultural Science / Kyoto University / DFAM