All living creatures, despite their profound diversity, share a common architectural building block: the cell. Cells are the basic functional units of life, yet are themselves comprised of numerous components with distinct mechanical characteristics. It is well established that cells have the ability to sense and respond to externally applied forces. However, the detailed mechanism of mechanosensation is still not clearly understood, and is an active area of research involving experimental and theoretical works. Mathematical modeling of the mechanical stimulus correlating to different experimental stimulation procedures forms the first step to understanding the mechanosensation in cellular system. In this thesis, a continuum -based computational model of living cells that explicitly incorporate the material properties of various cellular components are developed. In the constitutive modeling of cell, the continuum standard linear solid viscoelastic model (SLS), its natural extension for large scale deformation standard Neo-Hookean solid viscoelastic model (SnHS) as well as polymer mechanics- based dynamic shear modulus model was introduced. Finite element simulations of three widely used experiments- atomic force microscopy (AFM), magnetic twisting cytometry (MTC) and micropipette aspiration in the quantification of cell properties were carried out to verify the developed constitutive model. From the results of AFM finite element simulation, it was observed that the force-deformation and strain-relaxation curves obtained fit the experimental results very well. The influences of cytoplasm shear modulus which varies due to the formation of stress fiber, and cortex shear modulus which alters with the actin filament concentration factors and load frequency were systematically studied. Similarly, in magnetic twisting cytometry (MTC) simulation, the role of cytoplasm material properties, constant/sinusoidal forcing rates and various frequencies on the overall mechanical response of a cell was obtained. Numerical results are validated against experiments results. Micropipette aspiration simulation was also carried out in which the typical creep deformation test was carried out to study the viscoelastic behavior of the cell. Based on the results from finite element simulation, the effect of pipette radius, effect of cortex shear modulus and effect of pressure rate have been derived for the interpretation of the mechanical parameters from the micropipette aspiration.

All living creatures, despite their profound diversity, share a common architectural building block: the cell. Cells are the basic functional units of life, yet are themselves comprised of numerous components with distinct mechanical characteristics. It is well established that cells have the ability to sense and respond to externally applied forces. However, the detailed mechanism of mechanosensation is still not clearly understood, and is an active area of research involving experimental and theoretical works. Mathematical modeling of the mechanical stimulus correlating to different experimental stimulation procedures forms the first step to understanding the mechanosensation in cellular system. In this thesis, a continuum -based computational model of living cells that explicitly incorporate the material properties of various cellular components are developed. In the constitutive modeling of cell, the continuum standard linear solid viscoelastic model (SLS), its natural extension for large scale deformation standard Neo-Hookean solid viscoelastic model (SnHS) as well as polymer mechanics- based dynamic shear modulus model was introduced. Finite element simulations of three widely used experiments- atomic force microscopy (AFM), magnetic twisting cytometry (MTC) and micropipette aspiration in the quantification of cell properties were carried out to verify the developed constitutive model. From the results of AFM finite element simulation, it was observed that the force-deformation and strain-relaxation curves obtained fit the experimental results very well. The influences of cytoplasm shear modulus which varies due to the formation of stress fiber, and cortex shear modulus which alters with the actin filament concentration factors and load frequency were systematically studied. Similarly, in magnetic twisting cytometry (MTC) simulation, the role of cytoplasm material properties, constant/sinusoidal forcing rates and various frequencies on the overall mechanical response of a cell was obtained. Numerical results are validated against experiments results. Micropipette aspiration simulation was also carried out in which the typical creep deformation test was carried out to study the viscoelastic behavior of the cell. Based on the results from finite element simulation, the effect of pipette radius, effect of cortex shear modulus and effect of pressure rate have been derived for the interpretation of the mechanical parameters from the micropipette aspiration.

This thesis documents the development of a computational method for wave induced longitudinal bending in ships. First, there will be a discussion about the importance of longitudinal bending in ship design. The paper will then outline the basic physics at work in the system. It will review the wave forcing computation as well as the response of the vessel. It will then document the progression of the program, which was constructed in Fortran 90, as it solves the linear differential equation for the vessel bending caused by an incoming wave. The entire program then appears at the end of the paper. While the current program is not complete the theory behind it is valid and the code can be augmented to include non-linear components in the future.

Ce travail de thèse concerne la modélisation numérique fine des processus locaux dans le transport sédimentaire, à l'échelle d'un à plusieurs centaines de grains. Une méthode aux éléments discrets (DEM) basée sur la méthode dite des sphères molles et prenant en compte les contacts entre les grains a été développée et couplée à une méthode de frontière immergée (IBM) qui calcule l'écoulement autour d'objets solides mobiles dans un fluide Newtonien incompressible. Dans ce couplage, une force de lubrification est incluse pour représenter les interactions entre le fluide et les particules proches d'un contact. Il est montré que la méthode numérique reproduit de manière satisfaisante le coefficient de restitution effective mesuré dans des expériences de rebonds normal et oblique d'un grain sur un plan, ainsi que de rebond entre deux grains dans un fluide visqueux. Deux modèles analytiques associés au phénomène de rebond sont proposés et montrent l'importance de la rugosité de surface du grain et du nombre de Stokes sur le phénomène. La méthode numérique est ensuite utilisée pour simuler deux configurations tridimensionnelles d'écoulements granulaires pilotés par la gravité en milieu fluide : l'avalanche de grains sur un plan incliné rugueux et l'effondrement d'une colonne de grains. Dans le premier cas, les résultats permettent de caractériser les différents régimes d'écoulement granulaires (visqueux, inertiel et sec) observés dans les expériences en fonction du rapport de masse volumique grain-fluide et du nombre de Stokes. En particulier, les simulations apportent des informations originales quant aux profils de vitesse de grains et du fluide ainsi qu'aux forces prédominantes dans chacun des régimes. Dans le second cas, les résultats sont en bon accord avec les expériences et le mécanisme dit de « pore pressure feedback », qui dépend de la compacité initiale de la colonne, est pour la première fois observé dans des simulations numériques directes. / This work deals with direct numerical simulations of sediment transport at the scale of O(103) grains. A soft-sphere discrete element method (DEM) taking into account grain contacts is developed and coupled to an immersed boundary method (IBM) which computes the flow around moving solid objects in an incompressible Newtonian fluid. A lubrication force is added for representing fluid-particles interaction near contact. The numerical method is shown to adequately reproduce the effective coefficient of restitution measured in experiments of the normal and oblique rebound of a grain on a plane and the rebound between two grains in a viscous fluid. Two analytical models are proposed and highlight the importance of the grain roughness and Stokes number on the rebound phenomenon. This numerical method is then used for simulating two three-dimensional configurations of gravity-driven dense granular flow in a fluid, namely the granular avalanche on a rough inclined plane and the collapse of a granular column. In the first case, results allow to characterize the granular flow regimes (viscous, inertial and dry) observed in experiments as a function of the grain-to-fluid density ratio and the Stokes number. In particular, the simulations provide insight on the grain and fluid velocity profiles and force balance in each regime. In the second case, results agree well with experiments and in particular the pore pressure feedback, which depends on the initial volume fraction of the column, is observed for the first time in direct numerical simulations.

<p> This thesis details the application of computational methods to the problem of determining custom data representations when building hardware accelerators for numerical computations. A majority of scientific applications which require hardware acceleration are implemented in IEEE-754 double precision. However, in many cases the error tolerance requirements of the application are much less than the accuracy which IEEE-754 double precision provides. By leveraging custom data representations, a more resource efficient hardware implementation arises thereby enabling greater parallelism and thus higher performance of the accelerator. </p> <p> The existing custom representation methods are unable to guarantee robust representations while at the same time adequately supporting ill-conditioned operators. Support for both of these scenarios is necessary for accelerating scientific calculations. To address this, we propose the use of a computational method based on Satisfiability-Modulo Theory (SMT). By capturing a calculation as a set of constraints, an SMT instance can be formulated which provides meaningful bounds even in the presence of ill-conditioned operators. At the same time, the analytical nature of SMT satisfies the need for robustness. Utilizing block vector arithmetic, our SMT approach is extended to provide scalability to large instances involving vector calculus which arise in scientific calculations. Atop this foundation, a unified error model is proposed which deals simultaneously with absolute and relative error, thereby providing the means of supporting both fixed-point and custom floating-point data types. Iterative algorithm analysis is leveraged to derive constraints for the SMT method. The application of the method to several scientific algorithms is discussed by way of case studies. </p> / Thesis / Doctor of Philosophy (PhD)

A Large Eddy-Simulation code, based on a mesh transparent algorithm, for hybrid unstructured meshes is presented to deal with complex geometries that are often found in engineering flow problems. While tetrahedral elements are very effective in dealing with complex geometry, excessive numerical diffusion often affects results. Thus, prismatic or hexahedral elements are preferable in regions where turbulence structures are important. A second order reconstruction methodology is used since an investigation of a higher order method based upon Lele's compact scheme has shown this to be impractical on general unstructured meshes. The convective fluxes are treated with the Roe scheme that has been modified by introducing a variable scaling to the dissipation matrix to obtain a nearly second order accurate centred scheme in statistically smooth flow, whilst retaining the high resolution TVD behaviour across a shock discontinuity. The code has been parallelised using MPI to ensure portability. The base numerical scheme has been validated for steady flow computations over complex geometries using inviscid and RANS forms of the governing equations. The extension of the numerical scheme to unsteady turbulent flows and the complete LES code have been validated for the interaction of a shock with a laminar mixing layer, a Mach 0.9 turbulent round jet and a fully developed turbulent pipe flow. The mixing layer and round jet computations indicate that, for similar mesh resolution of the shear layer, the present code exhibits results comparable to previously published work using a higher order scheme on a structured mesh. The unstructured meshes have a significantly smaller total number of nodes since tetrahedral elements are used to fill to the far field region. The pipe flow results show that the present code is capable of producing the correct flow features. Finally, the code has been applied to the LES computation of the impingement of a highly under-expanded jet that produces plate shock oscillation. Comparison with other workers' experiments indicates good qualitative agreement for the major features of the flow. However, in this preliminary computation the computed frequency is somewhat lower than that of experimental measurements.

Orientador: Jorge Isaias Llagostera Beltran / Dissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Engenharia Mecanica / Made available in DSpace on 2018-08-08T17:53:07Z (GMT). No. of bitstreams: 1 Lopes_FernandodeOliveira_M.pdf: 4254683 bytes, checksum: 3714a253c99b8967319409a00b69058a (MD5) Previous issue date: 2007 / Resumo: Este trabalho apresenta o desenvolvimento de um programa computacional para modelagem inicial de compressores axiais de vários estágios pertencentes ao conjunto de turbinas a gás. O desenvolvimento do programa se baseia na metodologia adotada por Saravanamutto et al. (2001), faz uso da Primeira Lei da Termodinâmica para cálculo de potência consumida pelo compressor e da Segunda Lei da Termodinâmica para determinar o grau de irreversibilidade do sistema. O programa calcula a quantidade de estágios necessária para uma dada relação de pressão, a quantidade de palhetas por estágio e outros dados construtivos do compressor. O trabalho analisa a eficiência global de uma turbina a gás, avalia rendimento utilizando diferentes tipos combustíveis, estuda a influência da temperatura de entrada do ar no compressor, temperatura de entrada dos gases na turbina, e eficiência isentrópica do compressor e da turbina. Fatores que geram instabilidade no compressor são discutidos e algumas sugestões são apresentadas para evitar que compressores operem fora das condições iniciais. O trabalho apresenta procedimentos claros e detalhados para o préprojeto de um compressor de fluxo axial. Finalmente, o trabalho apresenta uma breve discussão sobre eficiência exergética de máquinas térmicas / Abstract: This work presents the developing of a computational program for designing axial compressors that hold multistage belonged gas turbine. The developing of the program is based on methodology adopted by Saravanamutto et al.(2001), it makes use of the First Law of Thermodynamic to calculate the power required by the axial compressor e the Second Law to calculate the level of irreversibilities. Beside of this the program presents the numbers of stages required for a given pressure ratio, the amount of blades per stage and other building parameters has been included to make a better analyze about the equipment. The work contains thermal efficiency analyzes of a gas turbines, where parameters such as fuels, temperature intlet turbine, environmental conditions, efficiency of the compressor and turbine are included. Other factors such as unstable conditions are discussed and solutions to avoid that axial compressors running in off design conditions. In summary the work provides a global view about thermal machines and how their parameters can influence both in the thermal and exergetic efficiency / Mestrado / Termica e Fluidos / Mestre em Engenharia Mecânica

Les neurosciences computationnelles sont une grande source d'inspiration pour le traitement de données. De nos jours, aussi bon que soit l'état de l'art de la vision par ordinateur, il reste moins performant que les possibilités offertes par nos cerveaux ou ceux d'autres animaux ou insectes. Cette thèse se base sur cette observation afin de développer de nouvelles méthodes de calcul pour la vision par ordinateur ainsi que pour le calcul de manière générale reposant sur les données issues de capteurs événementiels tels que les "rétines artificielles". Ces capteurs copient la biologie et sont utilisés dans ces travaux pour le caractère épars de leurs données ainsi que pour leur précision temporelle : l'information est codée dans des événements qui sont générés avec une précision de l'ordre de la microseconde. Ce concept ouvre les portes d'un paradigme complètement nouveau pour la vision par ordinateur, reposant sur le temps plutôt que sur des images. Ces capteurs ont été utilisés pour développer des applications comme le suivi ou la reconnaissance d'objets ou encore de l'extraction de motifs élémentaires. Des plate-formes de calcul neuromorphiques ont aussi été utilisées pour implémenter plus efficacement ces algorithmes, nous conduisant à repenser l'idée même du calcul. Les travaux présentés dans cette thèse proposent une nouvelle façon de penser la vision par ordinateur via des capteurs événementiels ainsi qu'un nouveau paradigme pour le calcul. Le temps remplace la mémoire permettant ainsi des opérations complètement locales, ce qui permet de réaliser des machines hautement parallèles avec une architecture non-Von Neumann. / Computational Neurosciences are a great source of inspiration for data processing and computation. Nowadays, how great the state of the art of computer vision might be, it is still way less performant that what our brains or the ones from other animals or insects are capable of. This thesis takes on this observation to develop new computational methods for computer vision and generic computation relying on data produced by event-based sensors such as the so called “silicon retinas”. These sensors mimic biology and are used in this work because of the sparseness of their data and their precise timing: information is coded into events which are generated with a microsecond precision. This opens doors to a whole new paradigm for machine vision, relying on time instead of using images. We use these sensors to develop applications such as object tracking or recognition and feature extraction. We also used computational neuromorphic platforms to better implement these algorithms which led us to rethink the idea of computation itself. This work proposes new ways of thinking computer vision via event-based sensors and a new paradigm for computation. Time is replacing memory to allow for completely local operations, enabling highly parallel machines in a non-Von Neumann architecture.

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No / The use of the hybrid method of moments/finite difference time domain technique can be effective for solution of electromagnetic problems which are intractable for a single numerical method. Using this method, a study of the effects of human proximity on the polarisation purity of different types of circularly-polarised handset antennas for personal satellite communications was undertaken. Associated with this, assessments of the specific absorption rate in the head were made. The method gave stable results, in accordance with physical expectations; good agreement with the pure method of moments was shown in simplified cases omitting the head