Apoptosis, or programmed cell death, is an essential process in all multi-cellular organisms. It is indispensable to an organism's survival, preventing the malicious propagation of DNA damage and pathogenic alterations, through the clean disposal of afflicted cells. The BAD/tBID/BAK pathway is a portion of the apoptosis molecular pathway, albeit an important pathway since it is known to be deregulated and lead to pathological ailments such as cancer. Using chemical kinetics the BAD/tBID/BAK signaling pathway is modeled as a set of (nonlinear) ordinary differential equations. A first-cut numerical analysis reveals a mechanism where BAD sensitizes a switch from tBID activation to BAK activation. The phosphorylation of BAD is shown to inhibit this sensitizing effect. All behaviors are supported by experimental data, thereby validating the model of the BAD/tBID/BAK pathway. Moreover, modeling the phosphorylation of BAD as one of two modes, some conflicting experimental data about BAD's phosphorylation can be disentangled. Parameter values (in this case the kinetic rate constants) are prone to error or missing altogether. Chemical reaction network theory, however, provides a theoretical approach to complement the initial numerical analysis without having to specify rate constant values. We extend the global asymptotic stability and robustness results in [92] to include any complex-balanced mass-action network. This enables us to study the BAD/tBID/BAK signaling network by breaking it into two sub-networks: one with BAD and tBID, and the other with tBID and BAK. The complex-balanced BAD/tBID sub-network is shown to possess a unique steady state which is globally asymptotically stable. This verifies the simple and dynamically well-behaved exchange of BAD for Bcl-2 proteins which guard against tBID activation. The second sub-network, tBID/BAK, is formulated as a complex-balanced network with a perturbation representing the reaction of tBID catalyzing the activation of BAK. Our theoretical results produce a non-conservative, though state-dependent, condition which can be used to prove global convergence to a neighborhood of the unperturbed steady state. We then illustrate the biological importance of the result for tBID/BAK sub-network with an example design for a drug delivery system. / Ph. D.

This thesis is concerned with the numerical simulation of mixtures of chemically reacting fluids at high pressures. Mixture rules are established, accommodating components that do not follow the thermally perfect Equation of State (EoS), and including formulas for the fugacities. Particular attention has been given to the species EoS originally developed by Hirschfelder, Buehler, McGee and Sutton. The Law of Mass Action that governs chemical equilibrium of mixtures of fluids is presented. The common assumption of neglecting fugacities contributions when calculating the equilibrium composition is assessed by comparing complete thermochemical predictions with those obtained by reduced models. For air mixtures at high pressures and moderate temperatures, species thermally imperfect EoS effects are significant. However, the contribution of fugacities to the Law of Mass Action is found to be small, at least for mixtures of super-critical dissociating gases. Similar conclusions apply to combustion mixtures (involving hydrogen and oxygen).

Submitted by Marilene Donadel (marilene.donadel@unioeste.br) on 2017-08-23T20:19:47Z No. of bitstreams: 1 Pietro E Franco 2011.pdf: 990760 bytes, checksum: fee1787afa670f26170e23dc070a0075 (MD5) / Made available in DSpace on 2017-08-23T20:19:47Z (GMT). No. of bitstreams: 1 Pietro E Franco 2011.pdf: 990760 bytes, checksum: fee1787afa670f26170e23dc070a0075 (MD5) Previous issue date: 2011-02-07 / This study evaluated the removal of heavy metal íons Zn+2 and Ni+2 through the íon exchange process using a cationic resin Amberlite IR-120/Na+. The characterization of wastewater from an industry of electroplating was performed and the results were the basis for obtaining the aqueous solution used at work. Experiments were performed in batch system for the valuation of ion exchange kinetics of the binary systems Ni+2–Na+, Zn+2–Na+ and the ternary system Ni+2–Zn+2–Na+ in the initial concentrations of 20ppm and 200ppm, in the conditions of pH 4.5, agitation speed of 150rpm and 25ºC. Two models were tested to obtain kinetic parameters of ion exchange. In the simulation of kinetic model in which the ion exchange reaction was considered the limiting step during the model does not fit the experimental data. A second simulation, where the diffusion in the resin (linear driving force model) was assumed to be limiting step had better fit and evidence for the hypothesis that the experimental conditions the ion exchange process presents diffusional limitations. The value of mass transfer coefficients in the resin (ks) varied from 0.0032 to 0.043min-1. Kinetic studies showed that equilibrium is reached around 400 minutes for the systems with initial concentration of 20ppm and 60 minutes for systems with initial concentration of 200ppm. Experiments to obtain data of ion exchange equilibrium were performed for the binary systems Ni+2–Na+, Zn+2–Na+ and for the ternary system Ni+2–Zn+2–Na+ at concentrations of 160ppm and 300ppm (pH 4.5, agitation speed of 150rpm and 25ºC). The isotherms were modeled using the law of mass action ideal and not ideal. The Bromley and Wilson models were used to calculate the activity coefficient in solution and resin. Simulations were conducted for determining the value of the constant and equilibrium thermodynamics of the interaction parameters of Wilson. The results showed that the law of mass action is not ideal fits well the experimental data of binary systems. The simulation of the ternary equilibrium system was accomplished using a predictive, based on the interaction parameters of Wilson and equilibrium constants provided by the modeling of binary systems. The data predicted by the model were compared with experimental data and the results showed that the model was able to predict the behavior of the ternary system. The affinity of the studied ions with Amberlite IR-120 showed the following order: Zn+2 Ni+2 > Na+. For all experiments conducted in this study, the variation of pH and stoichiometry during the experiments were evaluated. For the parameter pH, speciation graphics were done using the HYDRA software and the results show that ions of interest in the solutions (Zn+2 and Ni+2) were above 95%. The average deviation from stoichiometry was less than 8%. / O presente trabalho avaliou a remoção dos íons de metais pesados Zn+2 e Ni+2 através do processo de troca iônica utilizando a resina catiônica Amberlite IR-120/Na+. A caracterização do efluente de uma indústria do ramo de galvanoplastia foi realizada e os resultados obtidos serviram de base para a obtenção da solução aquosa utilizada no trabalho. Experimentos foram realizados em sistema batelada para a avaliação da cinética de troca iônica dos sistemas binários Ni+2–Na+, Zn+2–Na+ e para o sistema ternário Ni+2–Zn+2–Na+ nas concentrações iniciais de 20ppm e 200ppm, nas condições de pH de 4.5, velocidade de agitação de 150rpm e temperatura de 25ºC. Dois modelos foram testados para obtenção de parâmetros de cinética de troca iônica. Na simulação do modelo cinético em que a reação de troca iônica foi considerada a etapa limitante o modelo não se ajustou aos dados experimentais. Uma segunda simulação, em que a difusão na resina (modelo da força motriz linear) foi assumida como etapa limitante apresentou melhor ajuste e evidencia a hipótese de que para as condições experimentais adotadas o processo de troca iônica apresenta limitações difusionais. O valor dos coeficientes de transferência de massa na resina (ks) apresentaram valores entre 0,0032-0,043min-1. Estudos cinéticos mostraram que o equilíbrio é atingido em torno de 400 minutos para os sistemas com concentração inicial de 20ppm e de 60 minutos para os sistemas com concentração inicial de 200ppm. Experimentos para obtenção de dados de equilíbrio de troca iônica foram realizados para os sistemas binários Ni+2–Na+, Zn+2–Na+ e para o sistema ternário Ni+2–Zn+2–Na+ nas concentrações de 160ppm e 300ppm (pH de 4.5, velocidade de agitação de 150rpm e temperatura de 25ºC). As isotermas foram modeladas com uso da lei da ação das massas ideal e não ideal. Os modelos de Bromley e Wilson foram utilizados para o cálculo do coeficiente de atividade na solução e na resina. Realizou-se simulação para a determinação do valor da constante termodinâmica de equilíbrio e dos parâmetros de interação de Wilson. Os resultados mostraram que a lei da ação das massas não ideal se ajustou bem aos dados experimentais dos sistemas binários. A simulação do sistema de equilíbrio ternário foi realizada de forma preditiva, baseada nos parâmetros de interação de Wilson e constantes de equilíbrio fornecidas pelas modelagens dos sistemas binários. Os dados preditos pelo modelo foram comparados com os dados experimentais e os resultados mostraram que o modelo foi capaz de prever o comportamento do sistema ternário. A afinidade dos íons estudados com a resina Amberlite IR-120 mostrou a seguinte ordem: Zn+2 Ni+2 > Na+. Para todos os experimentos realizados neste trabalho, a variação de pH e de estequiometria ao longo dos experimentos foram avaliados. Para o parâmetro pH, gráficos de especiação foram realizados com o uso do software HYDRA e os resultados mostram que os íons de interesse nas soluções (Zn+2 e Ni+2) estavam acima de 95%. O desvio médio da estequiometria não foi superior a 8%.

<p>Proteins are among the most complex molecules in the cell and they play a major role in life itself. The complexity is not restricted to just structure and function, but also embraces the protein folding reaction. Within the field of protein folding, the focus of this thesis is on the features of the folding transition state in terms of growing contacts, common nucleation motifs and the contribution of charged residues to stability and folding kinetics. </p><p>During the resent decade, the importance of a certain residue in structure formation has been deduced from Φ-value analysis. As a complement to Φ-value analysis, I present how scatter in a Hammond plot is related to site-specific information of contact formation, Φ´(β^TS), and this new formalism was experimentally tested on the protein L23. The results show that the contacts with highest Φ growth at the barrier top were distributed like a second layer outside the folding nucleus. This contact layer is the critical interactions needed to be formed to overcome the entropic barrier. </p><p>Furthermore, the nature of the folding nucleus has been shown to be very similar among proteins with homologous structures and, in the split β-α-β family the proteins favour a two-strand-helix motif. Here I show that the two-strand-helix motif is also present in the ribosomal protein S6 from<i> A. aeolicus</i> even though the nucleation and core composition of this protein differ from other related structure-homologues. </p><p>In contrast to nucleation and contact growth, which are events driven by the hydrophobic effect, my most recent work is focused on electrostatic effects. By pH titration and protein engineering the charge content of S6 from <i>T. thermophilus</i> was altered and the results show that the charged groups at the protein surface might not be crucial for protein stability but, indeed, have impact on folding kinetics. Furthermore, by site-specific removal of all acidic groups the entire pH dependence of protein stability was depleted.</p>

Proteins are among the most complex molecules in the cell and they play a major role in life itself. The complexity is not restricted to just structure and function, but also embraces the protein folding reaction. Within the field of protein folding, the focus of this thesis is on the features of the folding transition state in terms of growing contacts, common nucleation motifs and the contribution of charged residues to stability and folding kinetics. During the resent decade, the importance of a certain residue in structure formation has been deduced from Φ-value analysis. As a complement to Φ-value analysis, I present how scatter in a Hammond plot is related to site-specific information of contact formation, Φ´(βTS), and this new formalism was experimentally tested on the protein L23. The results show that the contacts with highest Φ growth at the barrier top were distributed like a second layer outside the folding nucleus. This contact layer is the critical interactions needed to be formed to overcome the entropic barrier. Furthermore, the nature of the folding nucleus has been shown to be very similar among proteins with homologous structures and, in the split β-α-β family the proteins favour a two-strand-helix motif. Here I show that the two-strand-helix motif is also present in the ribosomal protein S6 from A. aeolicus even though the nucleation and core composition of this protein differ from other related structure-homologues. In contrast to nucleation and contact growth, which are events driven by the hydrophobic effect, my most recent work is focused on electrostatic effects. By pH titration and protein engineering the charge content of S6 from T. thermophilus was altered and the results show that the charged groups at the protein surface might not be crucial for protein stability but, indeed, have impact on folding kinetics. Furthermore, by site-specific removal of all acidic groups the entire pH dependence of protein stability was depleted.

This dissertation addresses the development of integrative modeling strategies capable of combining deterministic and stochastic, discrete and continuous, as well as multi-scale features. The first set of studies combines the purely deterministic modeling methodology of Biochemical Systems Theory (BST) with a hybrid approach, using Functional Petri Nets, which permits the account of discrete features or events, stochasticity, and different types of delays. The efficiency and significance of this combination is demonstrated with several examples, including generic biochemical networks with feedback controls, gene regulatory modules, and dopamine based neuronal signal transduction. A study expanding the use of stochasticity toward systems with small numbers of molecules proposes a rather general strategy for converting a deterministic process model into a corresponding stochastic model. The strategy characterizes the mathematical connection between a stochastic framework and the deterministic analog. The deterministic framework is assumed to be a generalized mass action system and the stochastic analogue is in the format of the chemical master equation. The analysis identifies situations where internal noise affecting the system needs to be taken into account for a valid conversion from a deterministic to a stochastic model. The conversion procedure is illustrated with several representative examples, including elemental reactions, Michaelis-Menten enzyme kinetics, a genetic regulatory motif, and stochastic focusing. The last study establishes two novel, particle-based methods to simulate biochemical diffusion-reaction systems within crowded environments. These simulation methods effectively simulate and quantify crowding effects, including reduced reaction volumes, reduced diffusion rates, and reduced accessibility between potentially reacting particles. The proposed methods account for fractal-like kinetics, where the reaction rate depends on the local concentrations of the molecules undergoing the reaction. Rooted in an agent based modeling framework, this aspect of the methods offers the capacity to address sophisticated intracellular spatial effects, such as macromolecular crowding, active transport along cytoskeleton structures, and reactions on heterogeneous surfaces, as well as in porous media. Taken together, the work in this dissertation successfully developed theories and simulation methods which extend the deterministic, continuous framework of Biochemical Systems Theory to allow the account of delays, stochasticity, discrete features or events, and spatial effects for the modeling of biological systems, which are hybrid and multiscale by nature.

Made available in DSpace on 2017-07-10T18:08:16Z (GMT). No. of bitstreams: 1 Thiago DArisbo.pdf: 2108504 bytes, checksum: 7b8aad29ec7d75a6fd370e54a95cd849 (MD5) Previous issue date: 2011-02-24 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Ion exchange is a process that is used in the treatment of aqueous industrial effluents containing organic compounds and heavy metals. The fixed bed columns are longer applied by allowing the process to occur continuously (cycles of regeneration). The design and process optimization of the ion exchange column requires the use of mathematical models. Phenomenological models of these systems involve the solution of partial differential and algebraic equations. The equilibrium data for ion exchange processes are usually described by the Mass Action Law (MAL), which can be considered non-ideality of aqueous and solid phases. Artificial Neural Networks (ANN) are being used successfully for the study of equilibrium data because they are empirical models and don t demand a mathematical rigor. This work aimed to evaluate the applicability of the hybrid model to describe the dynamics of ion exchange in fixed beds of binary systems. This system consists of partial differential equations obtained from mass balance in fluid phases in the ion exchanger and ANN to describe the balance. LAM was adjusted to experimental data of ion exchange equilibrium and then were generated 4200 data sets for each binary pair studied, which served as training for RNA. We tested networks with different structures, with one and two input layers. The 3-3-2 structure was used in the simulations of the hybrid model because it was the best represented the systems during the training phase. The differential equations were solved by the lines method. A computer program in FORTRAN language was developed for solving the model equations. DASSL subroutine was used to solve the equations. The performance of the hybrid model was evaluated from the results obtained with the phenomenological model, in which case the equilibrium description was made with the use of MAL. It also was the analysis of results from the comparison of experimental data. To evaluate the model we used data from the literature of ion exchange in Amberlite IR 120 resin on the systems Cu-Na and Zn-Na and in NaY zeolite on Fe-Na and Zn-Na. Both models were efficient to describe the dynamics of ion-exchange fixed bed columns, and the hybrid model had the advantage of the reduced computational time (82% reduction on average) as a result of not needing to solve a nonlinear equation. / A troca iônica é um processo muito utilizado no tratamento de efluentes industriais aquosos contendo compostos orgânicos e metais pesados. As colunas de leito fixo são mais aplicadas por permitir que o processo ocorra de maneira contínua (ciclos de regeneração). O projeto e a otimização de processos de troca iônica em coluna requer o uso de modelos matemáticos. Os modelos fenomenológicos destes sistemas envolvem a resolução de equações diferenciais parciais e algébricas. Os dados de equilíbrio de processos de troca iônica geralmente são descritos pela Lei da Ação das Massas (LAM), na qual podem ser consideradas as não idealidades das fases aquosa e sólida. As Redes Neurais Artificiais (RNA) estão sendo utilizadas com sucesso para o estudo destes dados de equilíbrio por serem modelos empíricos e não demandarem tal rigor matemático. Esta dissertação teve por objetivo avaliar a aplicabilidade do modelo híbrido para descrever a dinâmica do processo de troca iônica em leito fixo de sistemas binários. Este sistema é constituído de equações diferenciais parciais obtidas por meio de balanço de massa nas fases fluida e no trocador iônico e de RNA para descrever o equilíbrio. A LAM foi ajustada a dados experimentais de equilíbrio de troca iônica e, então, foram gerados conjuntos de 4200 dados para cada par binário estudado, os quais serviram como treinamento para a RNA. Foram testadas redes com diferentes estruturas, com uma e com duas camadas de entrada. A estrutura 3-3-2 foi utilizada nas simulações do modelo híbrido, pois foi a que melhor representou os sistemas na etapa de treinamento. As equações diferenciais foram resolvidas pelo método das linhas. Um programa computacional em linguagem FORTRAN foi desenvolvido para a resolução das equações do modelo. Foi utilizada a sub-rotina DASSL para resolver as equações. O desempenho do modelo híbrido foi avaliada a partir dos resultados obtidos com o modelo fenomenológico, sendo que neste caso a descrição do equilíbrio foi feita pelo uso da LAM. Também foi feita a análise dos resultados a partir da comparação dos dados experimentais. Para avaliar o modelo foram utilizados dados da literatura de troca iônica em resina Amberlite IR 120 dos sistemas Cu-Na e Zn-Na e na zeólita NaY dos sistemas Fe-Na e Zn-Na. Ambos os modelos foram eficientes para descrever a dinâmica de troca iônica de colunas de leito fixo, sendo que o modelo híbrido apresentou como vantagem o menor tempo computacional (82% de redução em média) em decorrência de não necessitar resolver a equação não-linear.