Immersed boundary methods are a class of techniques in computational fluid dynamics where the Navier-Stokes equations are simulated on a computational grid that does not conform to the interfaces in the domain of interest. This facilitates the simulation of flows with complex moving and deforming geometries without considerable effort wasted in generating the mesh. The first part of this dissertation is concerned with the aerodynamics of the cross-section of a species of flying snake, Chrysopelea paradisi (paradise tree snake). Past experiments have shown that the unique cross-section of this snake, which can be described as a lifting bluff body, produces an unusual lift curve--with a pronounced peak in lift coefficient at an angle of attack of 35 degrees for Reynolds numbers 9000 and beyond. We studied the aerodynamics of the cross-section using a 2-D immersed boundary method code. We were able to qualitatively reproduce the spike in the lift coefficient at the same angle of attack for flows beyond a Reynolds number of 2000. This phenomenon was associated with flow separation at the leading edge of the body that did not result in a stall. This produced a stronger vortex and an associated reduction in pressure on the dorsal surface of the snake cross-section, which resulted in higher lift. The second part of this work deals with the analysis of the direct forcing method, which is a popular immersed boundary method for flows with rigid boundaries. We begin with the fully discretized Navier-Stokes equations along with the appropriate boundary conditions applied at the solid boundary, and derive the fractional step method as an approximate block LU decomposition of this system. This results in an alternate formulation of the direct forcing method that takes into consideration mass conservation at the immersed boundaries and also handles the pressure boundary conditions more consistently. We demonstrate that this method is between first and second-order accurate in space when linear interpolation is used to enforce the boundary conditions on velocity. We then develop a theory for the order of accuracy of the direct forcing method with linear interpolation. For a simple 1-D case, we show that the method can converge at a range of rates for different locations of the solid body with respect to the mesh. But this effect averages out in higher dimensions and results in a scheme that has the same order of accuracy as the expected order of accuracy of the interpolation at the boundary. The discrete direct forcing method for the Navier-Stokes equations exhibits an order of accuracy between 1 and 2 because the velocities at the boundary are linearly interpolated, but the resulting boundary conditions on the pressure gradient turn out to be only first-order accurate. We recommend linearly interpolating the pressure gradient as well to make the method fully second-order accurate. We have also developed two open source codes in the course of these studies. The first, cuIBM, is a two-dimensional immersed boundary method code that runs on a single GPU. It can simulate incompressible flow around rigid bodies with prescribed motion. It is based on the general idea of a fractional step method as an approximate block LU decomposition, and can incorporate any type of immersed boundary method that can be made to fit within this framework. The second code, PetIBM, can simulate both two and three-dimensional incompressible flow and runs in parallel on multiple CPUs. Both codes have been validated using well-known test cases.

Simulação de fluidos tem sido um dos focos principais de pesquisa em computação gráfica nos últimos anos. O interesse por tal assunto é motivado pelas aplicações na indústria cinematográfica, jogos e sistemas voltados para simulação de fenômenos físicos realísticos em tempo real. Neste trabalho atacamos um problema ainda pouco explorado pela comunidade de computação gráfica, a simulação de fluidos em imagens digitais. Adotamos uma abordagem relacionando fluidos multifásicos, onde propriedades da imagem são incorporadas às equações de Navier-Stokes a fim de permitir que objetos contidos nas imagens \"escoem\" interagindo a forças que agem no sistema / In the last years, fluid simulation has been one of the main focus in Computer Graphics. Such a reason is related to applications to film industry, games and frameworks for realtime physical problem simulations. In this work we aim at accessing a problem which is not so much explored in Computer Graphics: fluid simulation in digital images. We adopt a approach related to multiphase fluids, where properties of the image are set to the Navier-Stokes equations in order to allow that objects into the images \"flow\"in accordance to the forces in the system

The aim of this work is to find a stable scheme which would solve the Stokes problem of the fluid flow, in which an elastic structure is immersed. Unlike most of the schemes solving fluid-structure interaction problems, in our scheme meshes of fluid and structure do not have to coincide. We have restricted ourselves to two-dimensional domain occupied by fluid with one-dimensional im- mersed structure. To describe a fluid-structure interaction, we have used an Immersed boundary method. At first we consider the strucure to be massless. We have modified an existing scheme and made it unconditionally stable, which was mathematically proven and numerically tested. Then we have proposed a modification where the structure is not massless and also proved the uncondi- tional stability in this case. The proposed schemes were implemented using the Freefem++ software and tested on aneurysm-like geometry. We have tested the behavior of our scheme in case when the qrowing aneurysm touches an obstacle, for example a bone (with no-slip condition on the bone boundary). Powered by TCPDF (www.tcpdf.org)

<p>Mathematical and computational modeling allow for the rationalization of complex phenomenon observed in our reality. Through the careful selection of assumptions, the intractable task of simulating reality can be reduced to the simulation of a practical system whose behavior can be replicated. The development of computational models allow for the full comprehension of the defined system, and the model itself can be used to evaluate the results of thousands of simulate experiments to aid in the rational design process.</p> <p>Biomedical engineering is the application of engineering principles to the field of medicine and biology. This discipline is composed of numerous diverse subdisciplines that span from genetic engineering to biomechanics. Each of these subdisciplines is concerned with its own complex and seemingly chaotic systems, whose behavior is difficult to characterize. The development and application of computational modeling to rationalize these systems is often necessary in this field and will be the focus of this thesis.</p> <p>This thesis is centered on the development and application of mathematical and computational modeling in three diverse systems in biomedical engineering. First, computational modeling is employed to investigate the behavior of key proteins in the post-synapse centered around learning and memory. Second, computational modeling is utilized to characterize the drug release rate from implantable drug delivery depots, and produce a tool to aid in the tailoring of the release rate. Finally, computational modeling is utilized to understand the motion of particles through an inertial focusing microfluidics chip and optimize the size selective capture efficiency.</p> <p> </p>

This dissertation develops a computational method for simulating laser-induced cavitation and investigates the mechanism behind the formation of non-spherical bubbles induced by long-pulsed lasers. The proposed computational method accounts for the laser emission and absorption, phase transition, and the dynamics and thermodynamics of a two-phase fluid flow. In this new method, the model combines the Navier-Stokes (NS) equations for a compressible inviscid two-phase fluid flow, a new laser radiation equation, and a novel local thermodynamic model of phase transition. The Navier-Stokes equations are solved using the FInite Volume method with Exact two-phase Riemann solvers (FIVER). Following this method, numerical fluxes across phase boundaries are computed by constructing and solving one-dimensional bi-material Riemann problems. The new laser radiation equation is derived by customizing the radiative transfer equation (RTE) using the special properties of laser, including monochromaticity, directionality, high intensity, and a measurable focusing or diverging angle. An embedded boundary finite volume method is developed to solve the laser radiation equation on the same mesh created for the NS equations. The fluid mesh usually does not resolve the boundary and propagation directions of the laser beam, leading to the challenges of imposing the boundary conditions on the laser domain. To overcome this challenge, ghost nodes outside the laser domain are populated by mirroring and interpolation techniques. The existence and uniqueness of the solution are proved for the two-dimensional case, leveraging the special geometry of the laser domain. The method is up to second-order accuracy, which is also proved, and verified using numerical tests. A method of latent heat reservoir is developed to predict the onset of vaporization, which accounts for the accumulation and release of latent heat. In this work, the localized level set method is employed to track the bubble surface. Furthermore, the continuation of phase transition is possible in laser-induced cavitation problems, especially for long-pulsed lasers. A method of local correction and reinitialization is developed to account for continuous phase transitions. Several numerical tests are presented to verify the convergence of these methods. This multiphase laser-fluid coupled computational model is employed to simulate the formation and expansion of bubbles with different shapes induced by different long-pulsed lasers. The simulation results show that the computational method can capture the key phenomena in the laser-induced cavitation problems, including non-spherical bubble expansion, shock waves, and the ``Moses effect''. Additionally, the observed complex non-spherical shapes of vapor bubbles generated by long-pulsed laser reflect some characteristics (e.g., direction, width) of the laser beam. The dissertation also investigates the relation between bubble shapes and laser parameters and explores the transition between two commonly observed shapes -- namely, a rounded pear-like shape and an elongated conical shape -- using the proposed computational model. Two laboratory experiments are simulated, in which Holmium:YAG and Thulium fiber lasers are used respectively to generate bubbles of different shapes. In both cases, the predicted bubble nucleation and morphology agree reasonably well with the experimental observation. The full-field results of laser radiance, temperature, velocity, and pressure are analyzed to explain bubble dynamics and energy transmission. It is found that due to the lasting energy input, the vapor bubble's dynamics is driven not only by advection, but also by the continued vaporization at its surface. Vaporization lasts less than 1 microsecond in the case of the pear-shaped bubble, compared to over 50 microseconds for the elongated bubble. It is thus hypothesized that the bubble's morphology is determined by a competition between the speed of bubble growth due to advection and continuous vaporization. When the speed of advection is higher than that of vaporization, the bubble tends to grow spherically. Otherwise, it elongates along the laser beam direction. To test this hypothesis, the two speeds are defined analytically using a model problem and then estimated for the experiments using simulation results. The results support the hypothesis and also suggest that when the laser's power is fixed, a higher laser absorption coefficient and a narrower beam facilitate bubble elongation. / Doctor of Philosophy / Laser-induced cavitation is a process where laser beams create bubbles in a liquid. This phenomenon is widely applied in research and microfluidic applications for precise control of bubble dynamics. It also naturally occurs in various laser-based processes involving liquid environments. Understanding laser-induced cavitation is important for enhancing the effectiveness and safety of related technologies. However, experimental studies encounter limitations, highlighting the development of numerical methods to advance the understanding of laser-induced cavitation. The laser-induced cavitation can be roughly described as localized boiling through thermal radiation. The detailed physics involves the absorption of laser light by a liquid, the formation of vapor bubbles due to localized heating, and the dynamics of both the bubbles and the surrounding liquid. The first part of the dissertation introduces a new computational method for modeling these phenomena. The dynamics of the two-phase flow are modeled by the Navier-Stokes equations, which are solved using the FInite Volume method with Exact two-phase Riemann solvers (FIVER). The absorption of the laser light is modeled by a new laser radiation equation, which is derived from laser energy conservation and special properties of the laser. An embedded boundary finite volume method is developed to solve this equation on the same mesh created for the NS equations. Additionally, a method of latent heat reservoir is developed to predict the onset of vaporization. In this work, the level set method is employed to track the bubble surface, and a method of local correction and reinitialization is developed to account for possible continuous phase transitions. After developing this new method, several test cases are simulated. The simulation results show that the method can capture the key phenomena in the laser-induced cavitation problems, including the absorption of laser light, non-spherical bubble expansion, and shock waves. When the laser pulse is comparable to or longer than the acoustic time scale (long-pulsed laser), vapor bubbles generated often have complex non-spherical shapes. The bubble shapes reflect some characteristics (e.g., direction, width) of the laser beam. The second part of the dissertation investigates the relation between bubble shapes and laser parameters. Two laboratory experiments are simulated, in which two different lasers are used to generate bubbles of different shapes, namely, a rounded pear-like shape and an elongated conical shape. In both cases, the simulated bubbles exhibit shapes and sizes that reasonably match the experimental results. The simulation results of temperature, pressure, and velocity fields are analyzed to explain bubble dynamics and energy transmission. The analysis shows that the expansion of bubbles induced by long-pulsed lasers is determined not only by advection but also by the continued vaporization at its surface. Vaporization lasts less than $1$ microsecond in the case of the pear-shaped bubble, compared to over $50$ microseconds for the elongated bubble. It is thus hypothesized that the bubble expansion is determined by a competition between the speed of bubble growth due to advection and continuous vaporization. When the speed of advection is higher than that of vaporization, the bubble tends to grow spherically. Otherwise, it elongates along the laser beam direction. To test this hypothesis, the two speeds are defined analytically using a model problem and then estimated for the experiments using simulation results. The results support the hypothesis and also suggest that when the laser's power is fixed, a higher laser absorption coefficient and a narrower beam facilitate bubble elongation.

Flush-mounted cavity hot-wire probes have been around since two decades, but have typically not been applied as often compared to the traditional wall hot-wires mounted several wire diameters above the surface. While the latter suffer from heat conduction from the hot wire to the substrate in particular when used in air flows, the former is belived to significantly enhance the frequency response of the sensor. The recent work using a cavity hotwire by Gubian et al. (2019) came to the surprising conclusion that the magnitute of the fluctuating wall-shear stress τ+w,rms reaches an asymptotic value of 0.44 beyond the friction Reynolds number Re τ ∼ 600. In an effort to explain this result, which is at odds with the majority of the literature, the present work combines direct numerical simulations (DNS) of a turbulent channel flow with a cavity modelled using the immersed boundary method, as well as an experimental replication of the study of Gubian et al. in a turbulent boundary layer to explain how the contradicting results could have been obtained. It is shown that the measurements of the mentioned study can be replicated qualitatively as a result of measurement problems. We will present why cavity hot-wire probes should neither be used for quantitative nor qualitative measurements of wall-bounded flows, and that several experimental short-comings can interact to sometimes falsely yield seemingly correct results.

This dissertation presents a detailed account of the study undertaken on the subject of heat and mass transfer phenomena in porous media. The current work specifically targets the general reaction-diffusion systems arising in separation processes using porous sorbent particles. These particles are comprised of pore channels spanning length scales over almost three orders of magnitude while involving a variety of physical processes such as mass diffusion, heat transfer and surface adsorption-desorption. A novel methodology is proposed in this work that combines models that account for the multi-scale and multi-physics phenomena involved. Pore-resolving DNS calculations using an immersed boundary method (IBM) framework are used to simulate the macro-scale physics while the phenomena at smaller scales are modeled using a sub-pore modeling technique. The IBM scheme developed as part of this work is applicable to complex geometries on curvilinear grids, while also being very efficient, consuming less than 1% of the total simulation time per time-step. A new method of implementing the conjugate heat transfer (CHT) boundary condition is proposed which is a direct extension of the method used for other boundary conditions and does not involve any complex interpolations like previous CHT implementations using IBM. Detailed code verification and validation studies are carried out to demonstrate the accuracy of the developed method. The developed IBM scheme is used in conjunction with a stochastic reconstruction procedure based on simulated annealing. The developed framework is tested in a two-dimensional channel with two types of porous sections - one created using a random assembly of square blocks and another using the stochastic reconstruction procedure. Numerous simulations are performed to demonstrate the capability of the developed framework. The computed pressure drops across the porous section are compared with predictions from the Darcy-Forchheimer equation for media composed of different structure sizes. The developed methodology is also applied to CO2 diffusion studies in porous spherical particles of varying porosities. For the pore channels that are unresolved by the IBM framework, a sub-pore modeling methodology developed as part of this work which solves a one-dimensional unsteady diffusion equation in a hierarchy of scales represented by a fractal-type geometry. The model includes surface adsorption-desorption, and heat generation and absorption. It is established that the current framework is useful and necessary for reaction-diffusion problems in which the adsorption time scales are very small (diffusion-limited) or comparable to the diffusion time scales. Lastly, parametric studies are conducted for a set of diffusion-limited problems to showcase the powerful capability of the developed methodology. / Ph. D.

La méthode de projection et l'approche variationnelle de Sasaki sont deux techniques permettant d'obtenir un champ vectoriel à divergence nulle à partir d'un champ initial quelconque. Pour une vitesse d'un vent en haute altitude, un champ de vitesse sur une grille décalée est généré au-dessus d'une topographie donnée par une fonction analytique. L'approche cartésienne nommée Embedded Boundary Method est utilisée pour résoudre une équation de Poisson découlant de la projection sur un domaine irrégulier avec des conditions aux limites mixtes. La solution obtenue permet de corriger le champ initial afin d'obtenir un champ respectant la loi de conservation de la masse et prenant également en compte les effets dûs à la géométrie du terrain. Le champ de vitesse ainsi généré permettra de propager un feu de forêt sur la topographie à l'aide de la méthode iso-niveaux. L'algorithme est décrit pour le cas en deux et trois dimensions et des tests de convergence sont effectués. / The Projection method and Sasaki's variational technique are two methods allowing one to extract a divergence-free vector field from any vector field. From a high altitude wind speed, a velocity field is generated on a staggered grid over a topography given by an analytical function. The Cartesian grid Embedded Boundary method is used for solving a Poisson equation, obtained from the projection, on an irregular domain with mixed boundary conditions. The solution of this equation gives the correction for the initial velocity field to make it such that it satisfies the conservation of mass and takes into account the effects of the terrain. The incompressible velocity field will be used to spread a wildfire over the topography with the Level Set Method. The algorithm is described for the two and three dimensional cases and convergence tests are done.

O estudo do comportamento de um perfil de uma seção aerolástica típica, com Reynolds na faixa de microaeronaves, constitui o principal foco deste trabalho, tomando como objetivo a estimativa de parâmetros do fenômeno de flutter. A pesquisa analisa o escoamento de um fluido sobre um corpo (cilindro e perfil de aerofólio) em estado estacionário e oscilante, em escoamento de velocidade constante, e, especificamente, o fenômeno de flutter. As equações de Navier-Stokes, com termo de força, são resolvidas pelo método da fronteira virtual para modelagem da interface escoamento/estrutura, representada pela geometria de um corpo de geometria complexa. Na discretização das equações governantes foi utilizado o método de diferenças finitas, sobre malhas deslocadas, com avanço temporal das velocidades do escoamento por meio de um esquema de Runge-Kutta de ordem 4. Os códigos computacionais, para as simulações das diretrizes e a lógica de cálculo, foram criados no contexto deste trabalho. A verificação foi feita através do método da solução manufaturada por meio de um problema fictício, que tem uma solução analítica conhecida, e que preenche as condições de contorno implementadas no código. O modelo da fronteira virtual é testado para os casos de escoamento sobre cilindro de base quadrada, cilindro de base circular e perfil de aerofólio tipo NACA0012, com malhas regular e não regular, e para condições estacionária e sob oscilação forçada. Foi estudado o comportamento de formação de vórtices, provocados por escoamento uniforme sobre o perfil de aerofólio, através dos coeficientes de arrasto, sustentação e pressão com visualização por meio da vorticidade e linhas de corrente, para vários ângulos de ataque e oscilação forçada com elevação e rotação em torno de um pivô posicionado no centro geométrico do perfil (50% da corda). Finalmente, é apresentada uma determinação numérica das características aeroelásticas para o perfil de aerofólio NACA0012, em escoamento de número de Reynolds ultra baixo (Re = 1.000), e parâmetros de flutter para um caso de baixa frequência de oscilação. / The behavior study of a profile of a typical aerolastic section, with Reynolds in range of micro aerial vehicle, is the main focus of this work, taking as objective the estimation of parameters of flutter phenomenon. The research analyzes of the flow of a incompressible fluid on a body (cylinder and airfoil profile) at steady state and oscillating with constant speed and, specifically, the flutter phenomenon. The Navier-Stokes equations, with force term, are solved by virtual boundary method for modeling interface flow/structure, represented by the geometry of a body of complex geometry. In discretization of the governing equations, the method of finite differences on staggered grid, with temporal advancement of discharge velocity through a Runge-Kutta of order 4. The computer codes, for simulations guidelines and logic calculation, were created in the context of this work. The verification was done by method ofmanufactured solution through a fictional problem, which has a known analytical solution, and satisfies the boundary conditions implemented in code. The model of the virtual boundary is tested for cases of flow over a square cylinder, circular cylinder and profile of a NACA0012 airfoil type, with regular and non-regular meshes, over stationary and forced oscillation conditions. We studied the behavior of vortex formation, caused by uniform flow over the airfoil profile, by the drag, lift and pressure coefficients with view through the vorticity and streamlines for various attack angles and forced oscillation with plunge and pich around a pivot witch was positioned at the geometric airfoil profile (half chord). Finally, it is presented a numerical determination of aeroelastic characteristics for the NACA0012 airfoil profile, flow under ultra low Reynolds number, and flutter parameters for a case of low oscillation frequency.

O escoamento em torno de corpos tem sido objeto de estudo de muitos pesquisadores e é muito explorado experimental e computacionalmente, devido a sua grande aplicabilidade na engenharia. No entanto, simular computacionalmente este tipo de escoamento requer uma atenção especial ao escolher o tipo malha a ser utilizado. Em muitos casos faz-se necessário o uso de uma malha que se adapte ao contorno do obstáculo, o que pode ocasionar um aumento no esforço computacional. Um maneira de contornar este problema é a utilização do Método das Fronteiras Imersas, que possibilita o uso de malha cartesiana na simulação computacional do escoamento em torno de obstáculos. Isso é possível através da adição de um termo forçante nas equações que modelam o escoamento, e assim as forças que agem sobre o contorno do corpo são transferidas diretamente para a malha. O objetivo deste trabalho de mestrado foi implementar o método das Fronteiras Imersas e simular o escoamento em torno de um cilindro circular em repouso, movimentando-se na mesma direção do escoamento, na direção perpendicular ao escoamento, ou rotacionando em torno do próprio eixo. As simulações computacionais possibilitaram a captura do fenômeno de Atrelagem Síncrona, caracterizado pela sincronia entre a frequência de desprendimento natural de vórtices e a frequência de oscilação do mesmo. O Método das Fronteiras Imersas mostrou um ótimo desempenho quando comparado a resultados experimentais e numéricos encontrados na literatura / The flow around bodies have been studied by many researchers. Both experimental and computational approaches have been extensively explored in researches on flow around bodies and have been applied in many engeneering problems. However, to choose an appropriate type of mesh to perform computational simulations of this type of problem requires special attention. In many cases, it is necessary to use a mesh that is able to conform to the boundary if a given obstacle. The need to perform this adaptation may increase the computational effort. The Immersed Boundary Method enables the use of cartesian meshes to perform computational simulations of flows around obstacles. The idea of this method is to add a forcing term in the equations that model the flow. Thus, the forces applied on the body boundaries are directly transfered to the mesh. The aim of this work was to perform a computational implementation of the Immersed Boundary Method to simulate the flow over a oscilating circular cylinder. This oscilation may be inline with the flow, cross-flow, or rotating. The computational simulations enabled the capture of the lock-in phenomena, which consists of the syncronization between the vortex shedding frequency and the cylinder oscilation frequency. The results obtained from the computational simulations using the Immersed Boundary Method were in good agreement with the numerical and experimental results found in the literature