In this thesis, we would like to present a new way to enhance the “depth map” image which is called as the fusion of depth images. The goal of our thesis is to try to enhance the “depth images” through a fusion of different classification methods. For that, we will use three similar but different methodologies, the Graph-Cut, Super-Pixel and Principal Component Analysis algorithms to solve the enhancement and output of our result. After that, we will compare the effect of the enhancement of our result with the original depth images. This result indicates the effectiveness of our methodology. / Room 401, No.56, Lane 21, Yin Gao Road, Shanghai, China

CO₂ injection in oil reservoirs provides the dual benefit of increasing oil recovery as well as sequestration. Compositional simulations using phase behavior calculations are used to model miscibility and estimate oil recovery. The injected CO₂, however, is known to react with brine. The precipitation and dissolution reactions, especially with carbonate rocks, can have undesirable consequences. The geochemical reactions can also change the mole numbers of components and impact the phase behavior of hydrocarbons. A Gibbs free energy framework that integrates phase equilibrium computations and geochemical reactions is presented in this dissertation. This framework uses the Gibbs free energy function to unify different phase descriptions - Equation of State (EOS) for hydrocarbon components and activity coefficient model for aqueous phase components. A Gibbs free energy minimization model was developed to obtain the equilibrium composition for a system with not just phase equilibrium (no reactions) but also phase and chemical equilibrium (with reactions). This model is adaptable to different reservoirs and can be incorporated in compositional simulators. The Gibbs free energy model is used for two batch calculation applications. In the first application, solubility models are developed for acid gases (CO₂ /H2 S) in water as well as brine at high pressures (0.1 - 80 MPa) and high temperatures (298-393 K). The solubility models are useful for formulating acid gas injection schemes to ensure continuous production from contaminated gas fields as well as for CO₂ sequestration. In the second application, the Gibbs free energy approach is used to predict the phase behavior of hydrocarbon mixtures - CO₂ -nC₁₄ H₃₀ and CH₄ -CO₂. The Gibbs free energy model is also used to predict the impact of geochemical reactions on the phase behavior of these two hydrocarbon mixtures. The Gibbs free energy model is integrated with flow using operator splitting to model an application of cation exchange reactions between aqueous phase and the solid surface. A 1-D numerical model to predict effluent concentration for a system with three cations using the Gibbs free energy minimization approach was observed to be faster than an equivalent stoichiometric approach. Analytical solutions were also developed for this system using the hyperbolic theory of conservation laws and are compared with experimental results available at laboratory and field scales. / text

The peridynamic theory is a generalization of classical continuum mechanics and takes into account the interaction between material points separated by a finite distance within a peridynamic horizon δ. The parameter δ corresponds to a length scale and is treated as a material property related to the microstructure of the body. Since the balance of linear momentum is written in terms of an integral equation that remains valid in the presence of discontinuities, the peridynamic theory is suitable for studying the material behavior in regions with singularities. The first part of this work concerns the evaluation of the properties of a linear elastic peridynamic material in the context of a three-dimensional state-based peridynamic theory, which uses the difference displacement quotient field in the neighborhood of a material point and considers both length and relative angle changes. This material model is based upon a free energy function that contains four material constants, being, therefore, different from other peridynamic models found in the literature, which contain only two material constants. Using convergence results of the peridynamic theory to the classical linear elasticity theory in the limit of small horizons and a correspondence argument between the free energy function and the strain energy density function from the classical theory, expressions were obtained previously relating three peridynamic constants to the classical elastic constants of an isotropic linear elastic material. To calculate the fourth peridynamic material constant, which couples both bond length and relative angle changes, the correspondence argument is used once again together with the strain field of a linearly elastic beam subjected to pure bending. The expression for the fourth constant is obtained in terms of the Poisson\'s ratio and the shear elastic modulus of the classical theory. The validity of this expression is confirmed through the consideration of other experiments in mechanics, such as bending of a beam by terminal loads and anti-plane shear of a circular cylinder. In particular, numerical results indicate that the expressions for the constants are independent of the experiment chosen. The second part of this work concerns an investigation of the behavior of a one-dimensional linearly elastic bar of length L in the context of the peridynamic theory; especially, near the ends of the bar, where it is expected that the behavior of the peridynamic bar may be very different from the behavior of a classical linear elastic bar. The bar is in equilibrium without body force, is fixed at one end, and is subjected to an imposed displacement at the other end. The bar has micromodulus C, which is related to the Young\'s modulus E in the classical theory through different expressions found in the literature. Depending on the expression for C, the displacement field may be singular near the ends, which is in contrast to the linear behavior of the displacement field observed in classical linear elasticity. In spite of the above, it is also shown that the peridynamic displacement field converges to its classical counterpart as the peridynamic horizon tends to zero. / A teoria peridinâmica é uma generalização da teoria clássica da mecânica do contínuo e considera a interação de pontos materiais devido a forças que agem a uma distância finita entre si, além da qual considera-se nula a força de interação. Por ter o balanço de momento linear formulado como uma equação integral que permanece válida na presença de descontinuidades, a teoria peridinâmica é adequada para o estudo do comportamento de materiais em regiões com singularidades. A primeira parte deste trabalho consiste no cálculo das propriedades de um material peridinâmico elástico linear no contexto de uma teoria peridinâmica de estado, linearmente elástica e tridimensional, que utiliza o campo quociente de deslocamento relativo na vizinhança de um ponto material e leva em conta mudanças relativas angulares e de comprimento. Esse modelo utiliza uma função energia livre que apresenta quatro constantes materiais, sendo, portanto, diferente de outros modelos peridinâmicos investigados na literatura, os quais contêm somente duas constantes materiais. Utilizando resultados de convergência da teoria peridinâmica para a teoria de elasticidade linear clássica no limite de pequenos horizontes e um argumento de correspondência entre as funções energia livre proposta e densidade de energia de deformação da teoria clássica, expressões para três constantes peridinâmicas foram obtidas em função das constantes de um material elástico e isotrópico da teoria clássica. O argumento de correspondêmcia, em conjunto com o campo de deformações de uma viga submetida à flexão pura, é utilizado para calcular a quarta constante peridinâmica do material, que relaciona mudanças angulares relativas e de comprimentos das ligações entre as partículas. Obtem-se uma expressão para a quarta constante em termos do coeficiente de Poisson e do módulo de elasticidade ao cisalhamento da teoria clássica. A validade dessa expressão é confirmada por meio da consideração de outros experimentos da mecânica, tais como flexão de um viga por cargas terminais e cisalhamento anti-plano de um eixo cilíndrico. Em particular, os resultados numéricos indicam que as expressões para as constantes são independentes do experimento escolhido. A segunda parte deste trabalho consiste em uma investigação do comportamento de uma barra unidimensional linearmente elástica de comprimento L no contexto da teoria peridinâmica; especialmente, próximo às extremidades da barra, onde espera-se que o comportamento da barra peridinâmica possa ser muito diferente do comportamento de uma barra elástica linear clássica. A barra está em equilíbrio e sem força de corpo, fixa em uma extremidade, e sujeita a deslocamento imposto na outra extremidade. A barra possui micromódulo C, o qual está relacionado ao módulo de Young E da teoria clássica por meio de diferentes expressões encontradas na literatura. Dependendo da expressão para C, o campo de deslocamento pode ser singular próximo às extremidades, o que contrasta com o comportamento linear do campo de deslocamento observado na elasticidade linear clássica. Apesar disso, é mostrado também que o campo de deslocamento peridinâmico converge para o campo de deslocamento da teoria clássica quando o horizonte peridinâmico tende a zero.

Este trabalho está dividido em duas partes distintas que constituem contribuições inéditas ao estudo da estabilidade em sistemas elétricos de potência. A primeira parte do trabalho é a mais importante e trata do problema da identificação das soluções de baixa tensão críticas do fluxo de carga. Esta parte do trabalho se presta a análise de estabilidade de tensão a pequenas perturbações. Os últimos capítulos deste trabalho apresentam também uma proposta de função energia estendida que modela as cargas dependentes da tensão segundo o modelo ZIP de carga, considerando a estrutura da rede preservada. Assim, a função energia proposta pode ser utilizada para analisar tanto a estabilidade de tensão como a estabilidade de ângulo em sistemas de potência. Esta proposta também é inédita na literatura. Embora a função energia proposta tenha sido aplicada apenas a sistemas de dimensão reduzidas, os resultados apresentados neste trabalho nos levam a acreditar que essa mesma função energia pode ser utilizada na análise de estabilidade de sistemas de potência de grandes dimensões. Já o método proposto para identificação das soluções de baixa tensão das equações de fluxo de carga se utiliza de um sistema dinâmico auxiliar das equações de fluxo de carga. O sistema dinâmico auxiliar utilizado não tem significado físico, mas pode ser escolhido de tal forma que a solução usual das equações de fluxo de carga seja um ponto de equilíbrio estável do sistema dinâmico auxiliar, eque as soluções de baixa tensão do fluxo de carga sejam pontos de equilíbrio instáveis do sistema dinâmico auxiliar. Dessa forma, é possível calcular as soluções de baixa tensão do fluxo de carga, calculando-se os pontos de equilíbrio instáveis do sistema dinâmico auxiliar. Assim, é possível utilizar partes da teoria de sistemas dinâmicos para estudar as soluções das equações de fluxo de carga. Baseado nestes princípios, foi desenvolvido um programa para calcular trajetórias do sistema dinâmico auxiliar, que se iniciam e se mantêm nas vizinhanças da fronteira da área de atração do ponto de equilíbrio estável do SEP. Dessa forma é possível afirmar que a trajetória calculada tende a convergir para a solução crítica das equações de fluxo de carga. O programa foi inicialmente concebido para calcular as soluções de baixa tensão de sistemas elétricos sem perdas. Em seguida o programa desenvolvido foi adaptado para calcular as soluções de baixa tensão de sistemas de potência completos, incluindo também as resistências das linhas de transmissão. Esta última versão do programa foi testada para os sistemas IEEE 39 e IEEE 118 barras, e os resultados obtidos se mostraram bastante satisfatórios. Assim, o método proposto é uma ferramenta original e eficaz para a solução do problema de calcular a solução crítica das equações de fluxo de carga de sistemas elétricos de potência. / This work may be divided into two distinct parts. Both of them are new contributions to stability analysis of power systems. In the first part it is proposed a new method to calculate the critical load flow low voltage solutions, and it is the main part of this work. Meanwhile, the last two chapters of this work presents a proposed extended energy function that consider the common load ZIP models. It allows the analysis of angle and voltage stability for power systems subjected to large disturbances. This work proposes a method to calculate the low voltage solutions (LVS) of the load flow equations of an electrical power system. The proposed method identifies the LVS involved in the saddle-node bifurcation leading the power system to a voltage collapse. This solution is known as the critical low voltage solution. In order to perform the proposed calculation, an auxiliary dynamical gradient system is used. It is shown that the equilibrium points of that associated auxiliary dynamical gradient system are the solutions of the load flow equations. In such manner, the paper proposes identifying the critical LVS calculating the equilibrium points of an auxiliary dynamical gradient system. The proposed method was tested on the Stagg 5-bus, on the IEEE 39-bus and on IEEE 118-bus test systems, and the results are presented at the end of the text.

Proteins are an important component of living organisms, composed of one or more polypeptide chains, each containing hundreds or even thousands of amino acids of 20 standard types. The structure of a protein from the sequence determines crucial functions of proteins such as initiating metabolic reactions, DNA replication, cell signaling, and transporting molecules. In the past, proteins were considered to always have a well-defined stable shape (structured proteins), however, it has recently been shown that there exist intrinsically disordered proteins (IDPs), which lack a fixed or ordered 3D structure, have dynamic characteristics and therefore, exist in multiple states. Based on this, we extend the mapping of protein sequence not only to a fixed stable structure but also to an ensemble of protein conformations, which help us explain the complex interaction within a cell that was otherwise obscured. The objective of this dissertation is to develop effective ab initio methods and tools for protein un/structure prediction by developing effective statistical energy function, conformational search method, and disulfide connectivity patterns predictor. The key outcomes of this dissertation research are: i) a sequence and structure-based energy function for structured proteins that includes energetic terms extracted from hydrophobic-hydrophilic properties, accessible surface area, torsion angles, and ubiquitously computed dihedral angles uPhi and uPsi, ii) an ab initio protein structure predictor that combines optimal energy function derived from sequence and structure-based properties of proteins and an effective conformational search method which includes angular rotation and segment translation strategies, iii) an SVM with RBF kernel-based framework to predict disulfide connectivity pattern, iv) a hydrophobic-hydrophilic property based energy function for unstructured proteins, and v) an ab initio conformational ensemble generator that combines energy function and conformational search method for unstructured proteins which can help understand the biological systems involving IDPs and assist in rational drugs design to cure critical diseases such as cancer or cardiovascular diseases caused by challenging states of IDPs.

The Support Vector Machine (SVM) classifier seeks to find the separating hyperplane wx=r that maximizes the margin distance 1/||w||2^2. It can be formalized as an optimization problem that minimizes the hinge loss Ʃ[subscript i](1-y[subscript i] f(x[subscript i]))₊ plus the L₂-norm of the weight vector. SVM is now a mainstay method of machine learning. The goal of this dissertation work is to solve different biomedical data analysis problems efficiently using extensions of SVM, in which we augment the standard SVM formulation based on the application requirements. The biomedical applications we explore in this thesis include: cancer diagnosis, biomarker discovery, and energy function learning for protein structure prediction. Ovarian cancer diagnosis is problematic because the disease is typically asymptomatic especially at early stages of progression and/or recurrence. We investigate a sample set consisting of 44 women diagnosed with serous papillary ovarian cancer and 50 healthy women or women with benign conditions. We profile the relative metabolite levels in the patient sera using a high throughput ambient ionization mass spectrometry technique, Direct Analysis in Real Time (DART). We then reduce the diagnostic classification on these metabolic profiles into a functional classification problem and solve it with functional Support Vector Machine (fSVM) method. The assay distinguished between the cancer and control groups with an unprecedented 99\% accuracy (100\% sensitivity, 98\% specificity) under leave-one-out-cross-validation. This approach has significant clinical potential as a cancer diagnostic tool. High throughput technologies provide simultaneous evaluation of thousands of potential biomarkers to distinguish different patient groups. In order to assist biomarker discovery from these low sample size high dimensional cancer data, we first explore a convex relaxation of the L₀-SVM problem and solve it using mixed-integer programming techniques. We further propose a more efficient L₀-SVM approximation, fractional norm SVM, by replacing the L₂-penalty with L[subscript q]-penalty (q in (0,1)) in the optimization formulation. We solve it through Difference of Convex functions (DC) programming technique. Empirical studies on the synthetic data sets as well as the real-world biomedical data sets support the effectiveness of our proposed L₀-SVM approximation methods over other commonly-used sparse SVM methods such as the L₁-SVM method. A critical open problem in emph{ab initio} protein folding is protein energy function design. We reduce the problem of learning energy function for extit{ab initio} folding to a standard machine learning problem, learning-to-rank. Based on the application requirements, we constrain the reduced ranking problem with non-negative weights and develop two efficient algorithms for non-negativity constrained SVM optimization. We conduct the empirical study on an energy data set for random conformations of 171 proteins that falls into the {it ab initio} folding class. We compare our approach with the optimization approach used in protein structure prediction tool, TASSER. Numerical results indicate that our approach was able to learn energy functions with improved rank statistics (evaluated by pairwise agreement) as well as improved correlation between the total energy and structural dissimilarity.

Indiana University-Purdue University Indianapolis (IUPUI) / Computational protein design aims at designing amino acid sequences that can fold into a target structure and perform a desired function. Many computational design methods have been developed and their applications have been successful during past two decades. However, the success rate of protein design remains too low to be of a useful tool by biochemists whom are not an expert of computational biology. In this dissertation, we first developed novel computational assessment techniques to assess several state-of-the-art computational techniques. We found that significant progresses were made in several important measures by two new scoring functions from RosettaDesign and from OSCAR-design, respectively. We also developed the first machine-learning technique called SPIN that predicts a sequence profile compatible to a given structure with a novel nonlocal energy-based feature. The accuracy of predicted sequences is comparable to RosettaDesign in term of sequence identity to wild type sequences. In the last two application chapters, we have designed self-inhibitory peptides of Escherichia coli methionine aminopeptidase (EcMetAP) and de novo designed barstar. Several peptides were confirmed inhibition of EcMetAP at the micromole-range 50% inhibitory concentration. Meanwhile, the assessment of designed barstar sequences indicates the improvement of OSCAR-design over RosettaDesign.

Calcific aortic valve disease (CAVD) is one of the most common causes of cardiovascular disease in North America. Mechanical factors have been closely linked to the pathogenesis of CAVD and may contribute to the disease by actively regulating the mechanobiology of valve interstitial cells (VICs). Mechanical forces affect VIC function through interactions between the VIC and the extracellular matrix (ECM). Studies have shown that the transfer of mechanical stimulus during cell-ECM interaction depends on the local material properties at hierarchical length scales encompassing tissue, cell and cytoskeleton. In this thesis, biomechanical tools were developed and applied to investigate hierarchical cell-ECM interactions, using VICs and valve tissue as a model system. Four topics of critical importance to understanding VIC-ECM interactions were studied: focal biomechanical material properties of aortic valve tissue; viscoelastic properties of VICs; transduction of mechanical deformation from the ECM to the cytoskeletal network; and the impact of altered cell-ECM interactions on VIC survival. To measure focal valve tissue properties, a micropipette aspiration (MA) method was implemented and validated. It was found that nonlinear elastic properties of the top layer of a multilayered biomaterial can be estimated by MA by using a pipette with a diameter smaller than the top layer thickness. Using this approach, it was shown that the effective stiffness of the fibrosa layer is greater than that of the ventricularis layer in intact aortic valve leaflets (p<0.01). To characterize the viscoelastic properties of VICs, an inverse FE method of single cell MA was developed and compared with the analytical half-space model. It was found that inherent differences in the half-space and FE models of single cell MA yield different cell viscoelastic material parameters. However, under particular experimental conditions, the parameters estimated by the half-space model are statistically indistinguishable from those predicted by the FE model. To study strain transduction from the ECM to cytoskeleton, an improved texture correlation algorithm and a uniaxial tension release device were developed. It was found that substrate strain fully transfers to the cytoskeletal network via focal adhesions in live VICs under large strain tension release. To study the effects of cell-ECM interactions on VIC survival, two mechanical stimulus systems that can simulate the separate effects of cell contraction and cell monolayer detachment were developed. It was found that cell sheet detachment and disrupted cell-ECM signaling is likely responsible for the apoptosis of VICs grown in culture on thin collagen matrices, leading to calcification. The studies presented in this thesis refine existing biomechanical tools and provide new experimental and analytical tools with which to study cell-ECM interactions. Their application resulted in an improved understanding of hierarchical valve biomechanics, mechanotransduction, and mechanobiology.

Calcific aortic valve disease (CAVD) is one of the most common causes of cardiovascular disease in North America. Mechanical factors have been closely linked to the pathogenesis of CAVD and may contribute to the disease by actively regulating the mechanobiology of valve interstitial cells (VICs). Mechanical forces affect VIC function through interactions between the VIC and the extracellular matrix (ECM). Studies have shown that the transfer of mechanical stimulus during cell-ECM interaction depends on the local material properties at hierarchical length scales encompassing tissue, cell and cytoskeleton. In this thesis, biomechanical tools were developed and applied to investigate hierarchical cell-ECM interactions, using VICs and valve tissue as a model system. Four topics of critical importance to understanding VIC-ECM interactions were studied: focal biomechanical material properties of aortic valve tissue; viscoelastic properties of VICs; transduction of mechanical deformation from the ECM to the cytoskeletal network; and the impact of altered cell-ECM interactions on VIC survival. To measure focal valve tissue properties, a micropipette aspiration (MA) method was implemented and validated. It was found that nonlinear elastic properties of the top layer of a multilayered biomaterial can be estimated by MA by using a pipette with a diameter smaller than the top layer thickness. Using this approach, it was shown that the effective stiffness of the fibrosa layer is greater than that of the ventricularis layer in intact aortic valve leaflets (p<0.01). To characterize the viscoelastic properties of VICs, an inverse FE method of single cell MA was developed and compared with the analytical half-space model. It was found that inherent differences in the half-space and FE models of single cell MA yield different cell viscoelastic material parameters. However, under particular experimental conditions, the parameters estimated by the half-space model are statistically indistinguishable from those predicted by the FE model. To study strain transduction from the ECM to cytoskeleton, an improved texture correlation algorithm and a uniaxial tension release device were developed. It was found that substrate strain fully transfers to the cytoskeletal network via focal adhesions in live VICs under large strain tension release. To study the effects of cell-ECM interactions on VIC survival, two mechanical stimulus systems that can simulate the separate effects of cell contraction and cell monolayer detachment were developed. It was found that cell sheet detachment and disrupted cell-ECM signaling is likely responsible for the apoptosis of VICs grown in culture on thin collagen matrices, leading to calcification. The studies presented in this thesis refine existing biomechanical tools and provide new experimental and analytical tools with which to study cell-ECM interactions. Their application resulted in an improved understanding of hierarchical valve biomechanics, mechanotransduction, and mechanobiology.

The issue of angle instability has been widely discussed in the power engineering literature. Many control techniques have been proposed to provide the complementary synchronizing and damping torques through generators and/or network connected power apparatus such as FACTs, braking resistors and DC links. The synchronizing torque component keeps all generators in synchronism while damping torque reduces oscillations and returns the power system to its pre-fault operating condition. One of the main factors limiting the transfer capacity of the electrical transmission network is the separation of the power system at weak links which can be understood by analogy with a large spring-mass system. However, this weak-links related problem is not dealt with in existing control designs because it is non-trivial during transient period to determine credible weak links in a large power system which may consist of hundreds of strong and weak links. The difficulty of identifying weak links has limited the performance of existing controls when it comes to the synchronization of generators and damping of oscillations. Such circumstances also restrict the operation of power systems close to its transient stability limits. These considerations have led to the primary research question in this thesis, "To what extent can the synchronization of generators and damping of oscillations be maximized to fully extend the transient stability limits of power systems and to improve the transfer capacity of the network?" With the recent advances in power electronics technology, the extension of transfer capacity is becoming more readily achievable. Complementary to the use of power electronics technology to improve transfer capacity, this research develops an improved control strategy by examining the dynamics of the modes of separation associated with the strong and weak links of the reduced transmission network. The theoretical framework of the control strategy is based on Energy Decomposition and Unstable Equilibrium Points. This thesis recognizes that under extreme loadings of the transmission network containing strong and weak links, weak-links are most likely to dictate the transient stability limits of the power system. We conclude that in order to fully extend the transient stability limits of power system while maximizing the value of control resources, it is crucial for the control strategy to aim its control effort at the energy component that is most likely to cause a separation. The improvement in the synchronization amongst generators remains the most important step in the improvement of the transfer capacity of the power system network.