The Sutton Chen and quantum Sutton Chen potentials are used in molecular dynamics simulations to describe the structural, thermodynamical, and transport properties of Pd, Ni and their binary alloys in solid, liquid, and glass phases. Static properties including elastic constants, pair distribution function, static structure factor, and dynamical properties consisting of phonon dispersion relation, diffusion coefficient, and viscosity are computed at various temperatures. The melting temperatures for Pd-Ni system are obtained. The transferability of the potentials is tested by simulating the solid and liquid states. The eutectic concentration Pd0.45Ni0.55 is quenched at four different cooling rates. The system goes into glass formation at fast cooling rates, while it evolves to crystal at slow cooling rate. Comparison of calculated structural and dynamical properties with the available experiments and other calculations shows satisfactory consistency.

Single-particle tracking (SPT) is a method used to study the diffusion of various molecules within the cell. SPT involves tagging proteins with optical labels and observing their individual two-dimensional trajectories with a microscope. The analysis of this data provides important information about protein movement and mechanism, and is used to create multistate biological models. One of the challenges in SPT analysis is the variety of complex environments that contribute to heterogeneity within movement paths. In this thesis, we explore the limitations of current methods used to analyze molecular movement, and adapt analytical methods used in animal movement analysis, such as correlated random walks and first-passage time variance, to SPT data of leukocyte function-associated antigen-1 (LFA-1) integral membrane proteins. We discuss the consequences of these methods in understanding different types of heterogeneity in protein movement behaviour, and provide support to results from current experimental work. / Applied Mathematics

Fundação Carlos Chagas Filho de Amparo a Pesquisa do Estado do Rio de Janeiro / Neste trabalho é apresentado a aplicação de um método de otimização a fim de estimar parâmetros que normalmente estão presentes na modelagem matemática da dinâmica de espécies químicas na interface água-sedimento. O Problema Direto aqui consistiu na simulação das concentrações das espécies orgânicas e inorgânicas (amônia e nitrato) de nitrogênio, num ambiente idealizado, o qual foi fracionado em quatro camadas: uma camada de água (1 metro) e três camadas de sedimento (0-1 cm, 1-2 cm e 2-10 cm). O Problema Direto foi resolvido pelo Método de Runge Kutta, tendo sido gerada uma simulação de 50 dias. Na estimativa dos coeficientes de difusão e porosidade foi aplicado o Método Simulated Annealing (SA). A eficiência da estratégia aqui adotada foi avaliada através do confronto entre dados experimentais sintéticos e as concentrações calçadas pela solução do Problema Direto, adotando-se os parâmetros estimados pela SA. O melhor ajuste entre dados experimentais e valores calculados se deu quando o parâmetro estimado foi a porosidade. Com relação à minimização da função objetivo, a estimativa desse parâmetro também foi a que exigiu menor esforço computacional. Após a introdução de um ruído randômico às concentrações das espécies nitrogenadas, a técnica SA não foi capaz de obter uma estimativa satisfatória para o coeficiente de difusão, com exceção da camada 0-1 cm sedimentar. Para outras camadas, erros da ordem de 10 % foram encontrados (para amônia na coluna dágua, pro exemplo). Os resultados mostraram que a metodologia aqui adotada pode ser bastante promissora enquanto ferramenta de gestão de corpos dágua, especialmente daqueles submetidos a um regime de baixa energia, como lagos e lagoas costeiras. / This work presents the application of an optimization method to estimate parameters that are usually present in the mathematical modeling of chemical species dynamics in the water-sediment interface . Here, the Direct Problem was the simulation of organic and inorganic (ammonium and nitrate) nitrogen species concentrations in an idealized environment, which was fractionated into four layers: a layer of water (1 meter depth) and three layers of sediment (0-1 cm 1-2 cm and 2-10 cm). The Direct Problem was solved by the Runge Kutta method, yielding a 50 days simulation. Thus, the Simulated Annealing (SA) Method was applied to estimate diffusion coefficients and porosity. The strategy efficiency was evaluated by comparing synthetic experimental data with those yielded by the direct problem solution, adopting the parameters estimated by SA Method. The best fitting between experimental and calculated concentrations was achieved when the porosity was the estimated parameter. Regarding the Objective Function minimization, the estimative of this parameter also required lower computational effort. After introducing a random noise to the concentrations of nitrogenous species, SA technique was unable to obtain a satisfactory estimate for the diffusion coefficient, with the exception of sediment layer 0-1 cm. For the other layers, concentrations errors as high as 10% were found (for the ammonia concentration in the water layer, for example). The results showed that the methodology adopted here can be a quite promising tool in the water bodies management, especially in those submitted to low energy, as lakes and coastal lagoons.

L’opération de transfert de matière gaz/liquide est une étape essentielle en génie desprocédés. Elle conditionne directement les performances des contacteurs gaz/liquide en représentantbien souvent l’étape limitant l’efficacité du procédé. L'objectif de cette étude est de proposer denouvelles investigations afin d'étudier l'effet de la présence dans l'eau pure, de certains composésgénéralement rencontrés dans les procédés biologiques, sur les coefficients de diffusion de l'oxygèneet de quantifier leurs conséquences sur les coefficients de transfert de matière côté liquide. Lescoefficients de diffusion de l'oxygène DO2 ont été mesurés dans diverses phases liquides contenant dusel (NaCl), du sucre (glucose) ou des tensio-actifs (laurylsulfate de sodium). Comparé à l'eau pure,des réductions de coefficient de diffusion DO2 ont été observées, la variation de DO2 avec laconcentration C de composé a été modélisée, elle dépend de la nature du composé ajouté. Ensuite,des expériences réalisées sur un train de bulles et sur les mêmes phases liquides ont permis ladétermination des coefficients de transfert de matière côté liquide kL. Quelle que soit la solutionaqueuse étudiée, une diminution des valeurs de kL est observée avec l'augmentation de C. Cesrésultats mettent en évidence que, même si les propriétés de l'eau pure (densité, viscosité, tensionsuperficielle) ne sont pas significativement modifiées par l'ajout de sels (NaCl), les coefficients detransfert de matière côté liquide kL peuvent être modifiés. Pour les solutions aqueuses de glucose, laréduction de kL avec DO2 est bien corrélée, et principalement due à la variation de viscosité avec laconcentration. Pour les solutions de tensio-actif, les nombres de Reynolds restent presque constantspour toutes les concentrations. Le seul responsable de la réduction du coefficient de transfert dematière côté liquide kL est donc le coefficient de diffusion de l’oxygène qui diminue avec laconcentration. La présente étude a clairement confirmé la nécessité de compléter et/ou rendre comptedes données liées aux coefficients de diffusion de l’oxygène DO2 et aux coefficients de transfert dematière côté liquide kL dans des milieux complexes (solution électrolytique, solution organique ettensioactif). Ces informations sont nécessaires pour décrire et modéliser correctement lesphénomènes de transfert de matière gaz/liquide / The gas/liquid mass transfer is an essential step in process engineering. It directly affects theperformance of gas/liquid reactor in being often limiting process efficiency. The objective of this studyis to propose new investigations in order to study (i) the effect on oxygen diffusion coefficients underthe presence in clean water of some compounds usually found in biological process and (ii) quantifytheir consequences on liquid-side mass transfer coefficients. The oxygen diffusioncoefficients DO2 were measured in various synthetic liquid phases containing either salt (NaCl), sugar(glucose) or surfactant (sodium laurylsulphate). When compared to clean water, reductionsof DO2 were observed; the variation of DO2 with the compound concentration C was modeled andfound dependent on the nature of the compound added. Then, to determine the liquid side masstransfer coefficient kL, experiments on a train of bubbles rising in a quiescent liquid phase were carriedout by the same synthetic liquid phases. For all cases, whatever the aqueous solutions, a decreaseof kL with increasing C was clearly observed. These results firstly showed that, even if the properties ofclean water (density, viscosity, surface tension) were not significantly changed by the addition of salts(NaCl), the liquid-side mass transfer coefficients could be modified. For the aqueous solutions ofglucose, the reduction of kL with DO2 was well correlated, and mainly due to the change in viscositywith concentration. For surfactants, the hydrodynamic conditions (i.e. bubble Reynolds number) beingalmost kept constant for all concentrations, only the change in DO2 was thus responsible for thedecrease of kL. The present study clearly confirmed the need to complete and/or account for thedatabase related to oxygen diffusion coefficients and liquid side mass transfer coefficient in complexmedia (electrolytic solution, organic solution and surfactant). This condition is imperatively required todescribe and to model appropriately the gas-liquid mass transfer phenomena

Fundação Carlos Chagas Filho de Amparo a Pesquisa do Estado do Rio de Janeiro / Neste trabalho é apresentado a aplicação de um método de otimização a fim de estimar parâmetros que normalmente estão presentes na modelagem matemática da dinâmica de espécies químicas na interface água-sedimento. O Problema Direto aqui consistiu na simulação das concentrações das espécies orgânicas e inorgânicas (amônia e nitrato) de nitrogênio, num ambiente idealizado, o qual foi fracionado em quatro camadas: uma camada de água (1 metro) e três camadas de sedimento (0-1 cm, 1-2 cm e 2-10 cm). O Problema Direto foi resolvido pelo Método de Runge Kutta, tendo sido gerada uma simulação de 50 dias. Na estimativa dos coeficientes de difusão e porosidade foi aplicado o Método Simulated Annealing (SA). A eficiência da estratégia aqui adotada foi avaliada através do confronto entre dados experimentais sintéticos e as concentrações calçadas pela solução do Problema Direto, adotando-se os parâmetros estimados pela SA. O melhor ajuste entre dados experimentais e valores calculados se deu quando o parâmetro estimado foi a porosidade. Com relação à minimização da função objetivo, a estimativa desse parâmetro também foi a que exigiu menor esforço computacional. Após a introdução de um ruído randômico às concentrações das espécies nitrogenadas, a técnica SA não foi capaz de obter uma estimativa satisfatória para o coeficiente de difusão, com exceção da camada 0-1 cm sedimentar. Para outras camadas, erros da ordem de 10 % foram encontrados (para amônia na coluna dágua, pro exemplo). Os resultados mostraram que a metodologia aqui adotada pode ser bastante promissora enquanto ferramenta de gestão de corpos dágua, especialmente daqueles submetidos a um regime de baixa energia, como lagos e lagoas costeiras. / This work presents the application of an optimization method to estimate parameters that are usually present in the mathematical modeling of chemical species dynamics in the water-sediment interface . Here, the Direct Problem was the simulation of organic and inorganic (ammonium and nitrate) nitrogen species concentrations in an idealized environment, which was fractionated into four layers: a layer of water (1 meter depth) and three layers of sediment (0-1 cm 1-2 cm and 2-10 cm). The Direct Problem was solved by the Runge Kutta method, yielding a 50 days simulation. Thus, the Simulated Annealing (SA) Method was applied to estimate diffusion coefficients and porosity. The strategy efficiency was evaluated by comparing synthetic experimental data with those yielded by the direct problem solution, adopting the parameters estimated by SA Method. The best fitting between experimental and calculated concentrations was achieved when the porosity was the estimated parameter. Regarding the Objective Function minimization, the estimative of this parameter also required lower computational effort. After introducing a random noise to the concentrations of nitrogenous species, SA technique was unable to obtain a satisfactory estimate for the diffusion coefficient, with the exception of sediment layer 0-1 cm. For the other layers, concentrations errors as high as 10% were found (for the ammonia concentration in the water layer, for example). The results showed that the methodology adopted here can be a quite promising tool in the water bodies management, especially in those submitted to low energy, as lakes and coastal lagoons.

Orientador: Sergio Persio Ravagnani / Tese (doutorado) - Universidade Estadual de Campinas, Faculdade de Engenharia Quimica / Made available in DSpace on 2018-08-07T03:49:14Z (GMT). No. of bitstreams: 1 Trochmann_JoseLuizLino_D.pdf: 1070584 bytes, checksum: 3407aee7ad6d88d9de0a1326aaf3d29d (MD5) Previous issue date: 2006 / Resumo: Neste trabalho de tese foi realizado um estudo do potencial de predição de propriedades de transporte em matrizes poliméricas de poli - imidas, utilizando a simulação dinâmica molecular de gases simples como Oxigênio, Nitrogênio e Dióxido de Carbono. A propriedade de transporte de interesse prático, a permeabilidade de uma membrana polimérica a um dado penetrante, envolve a determinação de propriedades de ordem cinética e termodinâmica, respectivamente a determinação do coeficiente de difusão e da solubilidade deste penetrante na matriz polimérica. Atenção especial foi conferida à propriedade cinética, pela predição do coeficiente de autodifusão dos penetrantes. Num procedimento experimental clássico é de vital importância para significância das conclusões derivadas dos experimentos, o uso de amostras de membranas poliméricas adequadamente preparadas quanto à composição química, estrutura física e morfologia. Analogamente, quando se utiliza a simulação molecular para a predição de propriedades, tais como o coeficiente de autodifusão, também é de fundamental relevância para os resultados obtidos, a qualidade dos modelos moleculares das matrizes poliméricas, que serão usados como base. Assim para a preparação de modelos moleculares com o adequado empacotamento, um procedimento para a obtenção de modelos bem equilibrados foi desenvolvido neste trabalho. Os modelos moleculares desenvolvidos foram usados para a obtenção dos valores de massa específica em função da temperatura, e comparados aos valores experimentais disponíveis e quando necessário a, valores preditos por meio da expressão de massa específica em função da temperatura, acima e abaixo da temperatura de transição. A capacidade do modelo molecular desenvolvido em predizer a massa especifica e temperatura de transição vítrea foi usada como critério para a validação da adequação do empacotamento proposto para o referido modelo molecular da matriz polimérica. Os modelos validados de empacotamento, células amorfas, foram utilizados para o cálculo do coeficiente de autodifusão dos gases acima mencionados, através do da simulação dinâmica molecular. A comparação dos coeficientes de autodifusão obtidos das poli-imidas aromáticas e éster imidas, BAAF, 6FDA-ODA, PMDA-ODA e BA-20DA, para os gases O2, N2 e CO2, com os dados experimentais, permitiu concluir a adequação das células amorfas e do esquema de simulação dinâmica molecular para a predição do coeficiente de autodifusão.. A versão preditiva de Vrentas e Duda, baseada na teoria do volume livre, foi utilizada para a predição dos coeficientes de autodifusão da água e do etanol para as poli-imidas acima. , Estes valores, quando comparados com os valores obtidos através da simulação dinâmica molecular mostram a validade de ambas as teorias para a predição da cinética de difusão de penetrantes em matrizes poliméricas complexas / Abstract: In this thesis a study of the predictive potential of the molecular dynamic simulation was performed for transport properties of light gases in polyimide matrix. From de practical point of view permeability is the property of most interest, and involves kinetics as well as thermodynamics properties, diffusion coefficient and solubility of the penetrants molecule in the bulk polymeric matrix, this work will be focus in the former. As important as is in as experimental work, a well prepared polymeric membrane is essential for the significance of the draw conclusions. Therefore a special attention was take in the preparation of the bulk molecular polymeric model, the so called amorphous cell, in order to obtain well-equilibrated molecular packing models for the polyimide matrixes. The amorphous cells were prepared throughout thermodynamic transforms, using one or more of the statistical ensembles and cell specific volume obtained as a function of temperature, this data was compared against the experimental data available, and when necessary to data obtained via predictive methods. The molecular packing model ability to predict the glass transition temperature was used as criteria to validate de amorphous cell, to be used in the molecular dynamic' simulations allow the matrix to be locally flexible and coupled to the classic molecular dynamics simulation. The resulting self diffusion coefficients for the polyimide, BAAF, 6FDA-ODA, PMDA­ODA and BA-20DA for the gases O2, N2 e CO2 were compared to the experimental data. The lack of quality experimental diffusion data available for polyimide membranes for larger penetrants as water and ethanol, showed up as a good opportunity to assess the predictive capability of the molecular dynamic simulation for self diffusion coefficients, considering the relevant technological relevance of polyimide membranes for pervaporation process. The data of self diffusion coefficient produced by the predictive version of free-volume theory after Vrentas and Duda, was compared with the data produced via coupled molecular dynamic simulation for the water and ethanol penetrants, showing the relevance of both theories for the prediction of penetrants kinetic in complex polymeric matrixes / Doutorado / Ciencia e Tecnologia de Materiais / Doutor em Engenharia Química

Made available in DSpace on 2017-07-10T19:23:38Z (GMT). No. of bitstreams: 1 Rafaela.pdf: 1254631 bytes, checksum: 3d834f48484b52c9ceff46d1a42fb49a (MD5) Previous issue date: 2013-03-12 / The cowpea bean, a culture traditionally planted in the Brazilian Northeast, has been expanding to other regions of Brazil, mostly to the Midwest, in the states of Mato Grosso and Mato Grosso do Sul, on account of its wide adaptability to tropical conditions and low production cost. Most of the seeds after harvest do not have appropriate characteristics for the storage, mainly due to high water content at harvest time. Drying is the most widely used process to preserve the quality of the product. The operation consists in removing some water contained in the fresh beans. In this context, the aim of this study was to determine and model the drying curves of cowpea beans at temperatures of 30, 40 and 50 °C, adjusting different mathematical models to experimental data, to select the one that best represents the phenomenon, determine the effective diffusion coefficient, and evaluate the physiological quality of seeds. They were seeds of cowpea bean cultivars BRS Guariba and BRS Novaera, harvested by hand, with water content of 0.21 (bs) and 0.16 (bs) respectively, dried to the level 0.11 (bs). The drying process was carried out in an experimental dryer under controlled temperatures of 30, 40 and 50 ° C and relative humidity of the drying air between 14% and 59%. The drying time for the cowpea bean seeds (BRS Guariba cultivar) was 10.4, 5.6 and 2.1 hours at temperatures of 30, 40 and 50 ° C respectively. For BRS Novaera, the drying lasted 8.7, 4.7 and 2.0 hours at temperatures of 30, 40 and 50 °C respectively. The mathematical model of Midilli was the one that best adapted to the experimental data for both cultivars. The diffusion coefficient increases with the temperature, with values from 5.047 to 12.011 x 10-11 x 10-11 m² s-1, for BRS Guariba, and from 2.482 x 10-11 to 5.187 x 10-11 m² s-1 for BRS Novaera in the temperature range from 30 to 50 °C. The relation between the effective diffusion coefficient and the drying temperature can be described by the Arrhenius equation, which has activation energy of 35.04 kJ.mol-1 and 29.76 kJ.mol-1 for liquid diffusion in the drying process of cowpea bean seeds. After the drying process, the seeds percentage of normal seedlings were more than 87%, and under the different conditions of study they presented low force, since the drying under a temperature of 40 °C was the one which produced the most satisfactory results. / O feijão-caupi, cultura tradicionalmente cultivada no Nordeste brasileiro, vem se expandindo para diversas regiões do Brasil, principalmente para o Centro-Oeste, nos estados do Mato Grosso e Mato Grosso do Sul, em razão da sua ampla adaptabilidade às condições tropicais e ao baixo custo de produção. Após a colheita, a maior parte das sementes possui características inadequadas para o armazenamento, devido principalmente ao alto conteúdo de água na época da colheita. A secagem é o processo mais utilizado para a preservação da qualidade desse produto. A operação consiste na remoção de parte da água contida no feijão recém colhido. Neste contexto, o objetivo deste trabalho foi determinar e modelar as curvas de secagem do feijão-caupi, nas temperaturas de 30, 40 e 50 °C, ajustando-se diferentes modelos matemáticos aos dados experimentais e selecionar aquele que melhor representa o fenômeno, bem como determinar o coeficiente de difusão efetivo e avaliar a qualidade fisiológica das sementes. Foram utilizadas sementes de feijão-caupi das cultivares BRS Guariba e BRS Novaera, colhidas manualmente, com teor de água de 0,21 (b.s) e 0,16 (b.s), respectivamente, secas até o teor 0,11 (b.s.). O processo de secagem foi realizado em secador experimental sob as temperaturas controladas de 30, 40 e 50 °C, e umidade relativa do ar de secagem entre 14 e 59%. O tempo de secagem para as sementes de feijão-caupi (cultivar BRS guariba) foi de 10,4, 5,6 e 2,1 horas para as temperaturas de 30, 40 e 50 °C, respectivamente; para a cultivar BRS Novaera a secagem foi de 8,7, 4,7 e 2,0 horas para as temperaturas de 30, 40 e 50 °C, respectivamente. O modelo matemático de Midilli foi o que melhor se ajustou aos dados experimentais de ambas as cultivares, apontando que o coeficiente de difusão aumenta com a elevação da temperatura, apresentando valores entre 5,047 x 10-11 a 12,011 x 10-11 m² s-1, para a cultivar BRS Guariba e 2,482 x 10-11 a 5,187 x 10-11 m² s-1, na cultivar BRS Novaera, para a faixa de temperatura de 30 a 50 °C. A relação entre o coeficiente de difusão efetivo e a temperatura de secagem pode ser descrita pela equação de Arrhenius, que apresenta uma energia de ativação de 35,04 kJ.mol-1 e de 29,76 kJ.mol-1 para a difusão líquida no processo de secagem das sementes de feijão-caupi. Após o processo de secagem, as sementes apresentaram percentuais de plântulas normais superiores a 87%; nas diferentes condições de estudo apresentaram baixo vigor, sendo a secagem sob a temperatura de 40 °C a que produziu os resultados mais satisfatórios.

The diploma thesis deals with the issue of electrochemical cells and deals in detail with lithium-ion batteries. The thesis describes the history of development of lithium-ion batteries, basic information about lithium and basic types of electrochemical cells. The work is devoted in detail to the description of characteristics and operating principle of lithium-ion batteries with emphasis on the negative electrode and negative electrode materials. Of the negative electrode materials, both the most widely used material graphite and modern materials with a great potential for the future are described. In the measurement methods the work describes methods CV, GCPL and EIS. Great emphasis is placed on the explanation of the principle of the function of electrochemical impedance spectroscopy and its application in measurement of electrochemical properties of materials used in lithium-ion batteries. There is also described the procedure of calculation of diffusion coefficients using the results of electrochemical impedance spectroscopy. In the practical part, two methods are used to calculate the diffusion coefficients of lithium ions into the negative electrode made of expanded flake graphite using the results of a series of electrochemical measurements.

This diploma thesis deals with the issue of lithium-ion accumulators. The thesis focuses on the negative electrode of lithium-ion accumulators made of natural graphite. The first part of this thesis points to the issue of electrochemical cells. In the theoretical part the thesis deals with the SEI layer, advantages, disadvantages, characteristics, operating principle and the use of lithium-ion accumulators. The practical part focuses on the electrochemical properties of negative electrode, especially the determination of the diffusion coefficient. Thesis also deals with electrochemical impedance spectroscopy (EIS) and its use in determining the equivalent replacement circuit and calculating the diffusion coefficient.

This thesis is focused on diffusion of dyes in biopolymer-based hydrogels. These hydrogels are based on interaction between biopolymer-like electrolytes with oppositely charged surfactants. When polyelectrolytes interact with oppositely charged surfactants, micelle-like nano-containers can be formed. These nano-containers are able of binding hydrophobic compounds. In this study, combination of modified dextran (diethylaminoethyl dextran) with positive charge and oppositely charged sodium dodecylsulphate as surfactant was used for preparation of hydrogels. Next type of hydrogel was based on hyaluronan and positive charged surfactant Septonex (carbethoxypendecinium bromide). As a diffusion probes in hydrogels dyes Nile red and ATTO 488 were used. The diffusion of these dyes from aqeous solutions of NaCl or surfactants into hydrogels was monitored in time. Transport of dyes into structure of hydrogels was characterized by diffusion coefficients and structural parameters of hydrogels.