A three-dimensional, parallel, anisotropic, block-based, adaptive mesh refinement (AMR) algorithm is proposed and described for the solution of fluid flows on body-fitted, multi-block, hexahedral meshes. Refinement and de-refinement in any grid block computational direction, or combination of directions, allows the mesh to rapidly adapt to anisotropic flow features such as shocks, boundary layers, or flame fronts, common to complex flow physics. Anisotropic refinements and an efficient and highly scalable parallel implementation lead to a potential for significant reduction in computational cost as compared to a more typical isotropic approach. Unstructured root-block topology allows for greater flexibility in the treatment of complex geometries. The AMR algorithm is coupled with an upwind finite-volume scheme for the solution of the Euler equations governing inviscid, compressible, gaseous flow. Steady-state and time varying, three-dimensional, flow problems are investigated for various geometries, including the cubed-sphere mesh.

<p>In recent years, there has been a great interest towards the higher order numerical methods for singularly perturbed problems. As compared to their lower order counterparts, they provide better accuracy with fewer mesh points. Construction and/or implementation of direct higher order methods is usually very complicated. Thus a natural choice is to use some convergence acceleration techniques, e.g., Richardson extrapolation, defect correction, etc. In this thesis, we will consider various classes of problems described by singularly perturbed ordinary and partial differential equations. For these problems, we design some novel numerical methods and attempt to increase their accuracy as well as the order of convergence. We also do the same for existing numerical methods in some instances. We &macr / nd that, even though the Richardson extrapolation technique always improves the accuracy, it does not perform equally well when applied to different methods for certain classes of problems. Moreover, while in some cases it improves the order of convergence, in other cases it does not. These issues are discussed in this thesis for linear and nonlinear singularly perturbed ODEs as well as PDEs. Extrapolation techniques are analyzed thoroughly in all the cases, whereas the limitations of the defect correction approach for certain problems is indicated at the end of the thesis</p>

A three-dimensional, parallel, anisotropic, block-based, adaptive mesh refinement (AMR) algorithm is proposed and described for the solution of fluid flows on body-fitted, multi-block, hexahedral meshes. Refinement and de-refinement in any grid block computational direction, or combination of directions, allows the mesh to rapidly adapt to anisotropic flow features such as shocks, boundary layers, or flame fronts, common to complex flow physics. Anisotropic refinements and an efficient and highly scalable parallel implementation lead to a potential for significant reduction in computational cost as compared to a more typical isotropic approach. Unstructured root-block topology allows for greater flexibility in the treatment of complex geometries. The AMR algorithm is coupled with an upwind finite-volume scheme for the solution of the Euler equations governing inviscid, compressible, gaseous flow. Steady-state and time varying, three-dimensional, flow problems are investigated for various geometries, including the cubed-sphere mesh.

L’avancée des infrastructures informatiques a permis l’émergence de la modélisation moléculaire. À cet effet, une multitude de modèles mathématiques sont aujourd’hui disponibles pour simuler différents systèmes chimiques. À l’aide de la modélisation moléculaire, différents types d’interactions chimiques ont été observés. À partir des systèmes les plus simples permettant l’utilisation de modèles quantiques rigoureux, une série d’approximations a été considérée pour rendre envisageable la simulation de systèmes moléculaires de plus en plus complexes. En premier lieu, la théorie de la fonctionnelle de densité dépendante du temps a été utilisée pour simuler les énergies d’excitation de molécules photoactives. De manière similaire, la DFT indépendante du temps a permis la simulation du pont hydrogène intramoléculaire de structures analogues au 1,3,5-triazapentadiène et la rationalisation de la stabilité des états de transition. Par la suite, la dynamique moléculaire et la mécanique moléculaire ont permis de simuler les interactions d’un trimère d’acide cholique et d’un pyrène dans différents solvants. Cette même méthodologie a été utilisée pour simuler les interactions d’un rotaxane-parapluie à l’interface d’un système biphasique. Finalement, l’arrimage moléculaire et les fonctions de score ont été utilisés pour simuler les interactions intermoléculaires entre une protéine et des milliers de candidats moléculaires. Les résultats ont permis de mettre en place une stratégie de développement d’un nouvel inhibiteur enzymatique. / The evolution of computer systems has led to the emergence of molecular modeling. To this end, a variety of mathematical models are now available to simulate various chemical systems. Using molecular modeling, different types of chemical interactions were observed. From the simplest systems allowing the use of rigorous quantum models, a series of approximations were considered in order to make possible the simulation of increasingly complex molecular systems. First, time-dependent density fonctional theory has been used to simulate the excitation energies of photoactive molecules. Similarly, time-independent DFT has enabled the simulation of intramolecular hydrogen bonding in the 1,3,5-triazapentadiene system and the rationalization of the stability of the transition states. Subsequently, molecular dynamics and molecular mechanics were used to simulate the interactions of a trimer of cholic acid with a pyrene in different solvents. This methodology was then used to simulate the interactions of an umbrella-rotaxane at the interface of a biphasic system. Finally, molecular docking and the concept of scoring functions were used to simulate the intermolecular interactions between a protein molecule and thousands of potential ligands. The results were then used to create a strategy for the development of a new enzyme inhibitor.

Philosophiae Doctor - PhD / In recent years, there has been a great interest towards the higher order numerical methods for singularly perturbed problems. As compared to their lower order counterparts, they provide better accuracy with fewer mesh points. Construction and/or implementation of direct higher order methods is usually very complicated. Thus a natural choice is to use some convergence acceleration techniques, e.g., Richardson extrapolation, defect correction, etc. In this thesis, we will consider various classes of problems described by singularly perturbed ordinary and partial differential equations. For these problems, we design some novel numerical methods and attempt to increase their accuracy as well as the order of convergence. We also do the same for existing numerical methods in some instances. We find that, even though the Richardson extrapolation technique always improves the accuracy, it does not perform equally well when applied to different methods for certain classes of problems. Moreover, while in some cases it improves the order of convergence, in other cases it does not. These issues are discussed in this thesis for linear and nonlinear singularly perturbed ODEs as well as PDEs. Extrapolation techniques are analyzed thoroughly in all the cases, whereas the limitations of the defect correction approach for certain problems is indicated at the end of the thesis. / South Africa

The Aw-Rascle-Zhang (ARZ) model has become a favorable ``second order" macroscopic traffic model, which corrects several shortcomings of the Payne-Whitham (PW) model. The ARZ model possesses a family of flow rate versus density (FD) curves, rather than a single one as in the ``first order" Lighthill-Whitham-Richards (LWR) model. This is more realistic especially during congested traffic state, where the historic fundamental diagram data points are observed to be set-valued. However, the ARZ model also possesses some obvious shortcomings, e.g., it assumes multiple maximum traffic densities which should be a ``property" of road. Instead, we propose a Generalized ARZ (GARZ) model under the generic framework of ``second order" macroscopic models to overcome the drawbacks of the ARZ model. A systematic approach is presented to design generic ``second order" models from historic data, e.g., we construct a family of flow rate curves by fitting with data. Based on the GARZ model, we then propose a phase-transition-like model that allows the flow rate curves to coincide in the free flow regime. The resulting model is called Collapsed GARZ (CGARZ) model. The CGARZ model keeps the flavor of phase transition models in the sense that it assume a single FD function in the free-flow phase. However, one should note that there is no real phase transition in the CGARZ model. To investigate to which extent the new generic ``second order" models (GARZ, CGARZ) improve the prediction accuracy of macroscopic models, we perform a comparison of the proposed models with two types of LWR models and their ``second order" generalizations, given by the ARZ model, via a three-detector problem test. In this test framework, the initial and boundary conditions are derived from real traffic data. In terms of using historic traffic data, a statistical technique, the so-called kernel density estimation, is applied to obtain density and velocity distributions from trajectory data, and a cubic interpolation is employed to formulate boundary condition from single-loop sensor data. Moreover, a relaxation term is added to the momentum equation of selected ``second order" models to address further unrealistic aspects of homogeneous models. Using these inhomogeneous ``second order" models, we study which choices of the relaxation term &tau are realistic. / Mathematics

The unsteady aerodynamic and aeroelastic analysis of flapping flight under various kinematics and flow parameters is presented in this dissertation. The main motivation for this study arises from the challenges facing the development of micro air vehicles. Micro air vehicles by requirement are compact with dimensions less than 15-20 cm and flight speeds of around 10-15 m/s. These vehicles operate in low Reynolds number range of 10,000 to 100,000. At these low Reynolds numbers, the aerodynamic efficiency of conventional fixed airfoils significantly deteriorates. On the other hand, flapping flight employed by birds and insects whose flight regime coincides with that of micro air vehicles offers a viable alternate solution. For the analysis of flapping flight, a boundary fitted moving grid algorithm is implemented in a flow solver, GenIDLEST. The dynamic movement of the grid is achieved using a combination of spring analogy and trans-finite interpolation on displacements. The additional conservation equation of space required for moving grid is satisfied. The solver is validated with well known flow problems such as forced oscillation of a cylinder, a heaving airfoil, a moving indentation channel, and a hovering fruitfly. The performance of flapping flight is analyzed using Large Eddy Simulation (LES) for a wide range of Reynolds numbers and under various kinematic parameters. A spiral Leading Edge Vortex (LEV) forms during the downstroke due to the high angle of attack, which results in high force production. A strong spanwise flow of the order of the flapping velocity is observed along the core of the LEV. In addition, the formation of a negative spanwise flow is observed due to the tip vortex, which slows down the removal of vorticity from the LEV. This leads to the instability of the LEV at around mid-downstroke. Analysis with different rotation kinematics shows that a continuous rotation results in better propulsive efficiency as it generates thrust during the entire flapping cycle. Analysis with different angles of attack shows that a moderate angle of attack which results in complete shedding of the LEV offers high propulsive efficiency. The analysis of flapping flight at Reynolds numbers ranging from 100 to 100,000 shows that higher lift and thrust values are obtained for Re?100. The critical reasons are that at higher Reynolds numbers, the LEV is closer to the surface and as it sheds and convects it covers most of the upper surface. However, the Reynolds number has no or little effect on the lift and thrust as identical values are obtained for Re=10,000 and 100,000. The analysis with different tip shapes shows that tip shapes do not have a significant effect on the performance. Introduction of stroke deviation to kinematics leads to drop in average lift as wing interacts with the LEV shed during the downstroke. A linear elastic membrane model with applied aerodynamic load is developed for aeroelastic analysis. Analysis with different wing stiffnesses shows that the membrane wing outperforms the rigid wing in terms of lift, thrust and propulsive efficiency. The main reason for the increase in force production is attributed to the gliding of the LEV along the camber, which results in a high pressure difference across the surface. In addition, a high stiffness along the spanwise direction and low stiffness along the chordwise direction results in a uniform camber and high lift and thrust production. / Ph. D.

La tesis tracta diferents aspectes relacionats amb el càlcul de la semblança quàntica, així com la seva aplicació en la racionalització i predicció de l'activitat de fàrmacs. Es poden destacar dos progressos importants en el desenvolupament de noves metodologies que faciliten el càlcul de les mesures de semblança quàntica. En primer lloc, la descripció de les molècules mitjançant les funciones densitat aproximades PASA (Promolecular Atomic Shell Approximation) ha permès descriure amb suficient precisió la densitat electrònica dels sistemes moleculars analitzats, reduint substancialment el temps de càlcul de les mesures de semblança. En segon lloc, el desenvolupament de tècniques de superposició molecular específiques de les mesures de semblança quàntica ha permès resoldre el problema de l'alineament en l'espai dels compostos comparats. El perfeccionament d'aquests nous procediments i algoritmes matemàtics associats a les mesures de semblança molecular quàntica, ha estat essencial per poder progressar en diferents disciplines de la química computacional, sobretot les relacionades amb les anàlisis quantitatives entre les estructures moleculars i les seves activitats biològiques, conegudes amb les sigles angleses QSAR (Quantitative Structure-Activity Relationships). Precisament en l'àrea de les relacions estructura-activitat s'han presentat dues aproximacions fonamentades en la semblança molecular quàntica que s'originen a partir de dues representacions diferents de les molècules. La primera descripció considera la densitat electrònica global de les molècules i és important, entre altres, la disposició dels objectes comparats en l'espai i la seva conformació tridimensional. El resultat és una matriu de semblança amb les mesures de semblança de tots els parells de compostos que formen el conjunt estudiat. La segona descripció es fonamenta en la partició de la densitat global de les molècules en fragments. S'utilitzen mesures d'autosemblança per analitzar els requeriments bàsics d'una determinada activitat des del punt de vista de la semblança quàntica. El procés permet la detecció de les regions moleculars que són responsables d'una alta resposta biològica. Això permet obtenir un patró amb les regions actives que és d'evident interès per als propòsits del disseny de fàrmacs. En definitiva, s'ha comprovat que mitjançant la simulació i manipulació informàtica de les molècules en tres dimensions es pot obtenir una informació essencial en l'estudi de la interacció entre els fàrmacs i els seus receptors macromoleculars. / There is probably no other concept that contributed to the development of chemistry so remarkably as the ill-defined, qualitative concept of similarity. From the intuitively understood meaning of similarity arises also one of the most powerful chemical principles - the principle of analogy - which in early days of chemistry served as the basis for the classification and systematization of molecules and reactions. The same principle underlies also the widely used idea that similar structures have similar properties which, in turn, is the basis for the existence of various empirical relations between the structure and activity known as QSAR relationships. Because of the fundamental role which similarity plays in so many different situations it is not surprising that its systematic investigation has become the focus of intense scientific interest. Main attention in this respect was devoted to the design of new quantitative measures of molecular similarity. The philosophy underlying the development of quantitative, similarity measures based on quantum theory, arises from the idea that properties of molecules, whether chemical, physical or biological are predetermined by the molecular structure. The rationalization of empirical structure-activity relationships is to considerable extent connected with the recent efforts in the design of new molecular descriptors based on quantum theory. The simplest of such quantities is the electron density function and most of the theoretical molecular descriptors are derived just from this quantity. Among them, a privileged place belongs to the so-called Molecular Quantum Similarity Measures (MQSM). These measures are generally based on the pairwise comparison of electron density functions of the corresponding molecules.This contribution pretends to present an up-to-date revision of Quantum Similarity concepts and their application to QSAR. The general form of MQSM is introduced, and the concrete definitions for practical implementations are specified. Two important topics related to the application of MQSM are discussed: first the Promolecular Atomic Shell Approximation (PASA), a method for fitting first-order molecular density functions for a fast and efficient calculation of the MQSM. Afterwards, a possible solution to the problem of molecular alignment, a determinant procedure in all 3D QSAR methodologies. Finally, the application of Quantum Similarity to QSAR is discussed in detail. Two kind of descriptors derived from molecular quantum similarity theory were used to construct QSAR models: molecular quantum similarity matrices and fragment quantum self-similarity measures. The practical implementation of those ideas has led to the publication of several papers, and finally, to the present work.

A number of recent research studies have investigated the performance of panel zones in seismic-resistant steel Special Moment Resisting Frames (SMF). These recent studies investigated various options for attaching doubler plates to the column at beam-column joints in SMF for purpose of increasing the shear strength of the panel zone. This previous work was primarily focused on doubler plates that extend beyond the top and bottom of the attached beams, and considered cases both with and without continuity plates. As an extension to this previous research, this thesis explores the situation when a doubler plate is fitted between the continuity plates. The objective of this research was to evaluate various options for welding fitted doubler plates to the column and continuity plates through the use of finite element analysis, and to provide recommendations for design. The development and validation of the finite element model are described, along with the results of an extensive series of parametric studies on various panel zone configurations and attachment details for fitted doubler plates. Based on the results of these analyses, recommendations are provided for design of welds used for attaching fitted doubler plates in the panel zone of SMF systems. / text

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