The ultimate goal of this research is to develop the capability of direct numerical simulation of a flow containing numerous rigid finite size particles. In order to reach this goal, we have implemented the smoothed profile method (SPM) in the University of Iowa in-house solver, pELAFINT3D and overcame several challenges related to the method. This includes a proposed formulation for the interface thickness and many validations and comparisons with experimental data as well as with a second-order accurate sharp interface method. As one of the issues related to low-density particles is the instability, SPM has been improved by developing to a fully implicit scheme. Moreover, use of higher order integration formulation and implementation of Euler parameters have been shown to be helpful in stabilization of the calculations. To preserve the efficiency when the number of the particles increases, local mesh refinement is shown to be a very effective tool. A revised version of SPM that has only one projection step is proposed to improve the efficiency of the method. A comprehensive efficiency study is performed and it has been shown that the new method is less expensive in problems with high added mass effect when strongly coupled fluid-structure interaction schemes are used. Moreover, the code is massively parallelized using MPI and PETSc libraries. The parallelization includes I/O, operations leading to construction of the linear solver as well as the solver itself. Simulation of a particle laden flow involves particles collisions. Two novel collision models are suggested which are able to avoid particle overlapping for arbitrary shape particles. The methods are efficient as they are not involved with extra grid refinement related to implementing lubrication forces. The issue of handling continuously changing number of particles in a particle laden flow is solved by implementation of a linked list data structure for the particles. By studying a flow over a constricted region we showed that the platelets’ activation is more likely to happen for the particles that pass from the middle of the upper bump region because those particles will have longer exposure time to the high shear flow behind the bump. PDF contour of particles’ presence show the more concentrated presence of the particles near the bump. Moreover, the interaction of RBCs and platelets pushes the platelets toward the wall after the bottom wall.

This thesis presents an automatic animation system for jellyfish that is based on a physical simulation of the organism and its surrounding fluid. Our goal is to explore the unusual style of locomotion, namely jet propulsion, which is utilized by jellyfish. The organism achieves this propulsion by contracting its body, expelling water, and propelling itself forward. The organism then expands again to refill itself with water for a subsequent stroke. We endeavor to model the thrust achieved by the jellyfish, and also the evolution of the organism's geometric configuration. <p> We restrict our discussion of locomotion to fully grown adult jellyfish, and we restrict our study of locomotion to the resonant gait, which is the organism's most active mode of locomotion, and is characterized by a regular contraction rate that is near one of the creature's resonant frequencies. We also consider only species that are axially symmetric, and thus are able to reduce the dimensionality of our model. We can approximate the full 3D geometry of a jellyfish by simulating a 2D slice of the organism. This model reduction yields plausible results at a lower computational cost. From the 2D simulation, we extrapolate to a full 3D model. To prevent our extrapolated model from being artificially smooth, we give the final shape more variation by adding noise to the 3D geometry. This noise is inspired by empirical data of real jellyfish, and also by work with continuous noise functions from the graphics community. <p> Our 2D simulations are done numerically with ideas from the field of computational fluid dynamics. Specifically, we simulate the elastic volume of the jellyfish with a spring-mass system, and we simulate the surrounding fluid using the semi-Lagrangian method. To couple the particle-based elastic representation with the grid-based fluid representation, we use the immersed boundary method. We find this combination of methods to be a very efficient means of simulating the 2D slice with a minimal compromise in physical accuracy.

This thesis presents an automatic animation system for jellyfish that is based on a physical simulation of the organism and its surrounding fluid. Our goal is to explore the unusual style of locomotion, namely jet propulsion, which is utilized by jellyfish. The organism achieves this propulsion by contracting its body, expelling water, and propelling itself forward. The organism then expands again to refill itself with water for a subsequent stroke. We endeavor to model the thrust achieved by the jellyfish, and also the evolution of the organism's geometric configuration. <p> We restrict our discussion of locomotion to fully grown adult jellyfish, and we restrict our study of locomotion to the resonant gait, which is the organism's most active mode of locomotion, and is characterized by a regular contraction rate that is near one of the creature's resonant frequencies. We also consider only species that are axially symmetric, and thus are able to reduce the dimensionality of our model. We can approximate the full 3D geometry of a jellyfish by simulating a 2D slice of the organism. This model reduction yields plausible results at a lower computational cost. From the 2D simulation, we extrapolate to a full 3D model. To prevent our extrapolated model from being artificially smooth, we give the final shape more variation by adding noise to the 3D geometry. This noise is inspired by empirical data of real jellyfish, and also by work with continuous noise functions from the graphics community. <p> Our 2D simulations are done numerically with ideas from the field of computational fluid dynamics. Specifically, we simulate the elastic volume of the jellyfish with a spring-mass system, and we simulate the surrounding fluid using the semi-Lagrangian method. To couple the particle-based elastic representation with the grid-based fluid representation, we use the immersed boundary method. We find this combination of methods to be a very efficient means of simulating the 2D slice with a minimal compromise in physical accuracy.

Fluid-structure interaction (FSI) is an important physical phenomenon in many applications and across various disciplines including aerospace, civil and bio-engineering. In civil engineering, applications include the design of wind turbines, pipelines, suspension bridges and offshore platforms. Ocean structures such as drilling risers, mooring lines, cables, undersea piping and tension-leg platforms can be subject to strong ocean currents, and such structures may suffer from Vortex-Induced Vibrations (VIV's), where vortex shedding of the flow interacts with the structural properties, leading to large amplitude vibrations in both in-line and cross-flow directions. Over the past years, many experimental and numerical studies have been conducted to comprehend the underlying physical mechanisms. However, to date there is still limited understanding of the effect of oscillatory interactions between fluid flow and structural behavior though such interactions can cause large deformations. This research proposes a mathematical framework to accurately predict FSI for elastically supported rigid structures. The numerical method developed solves the Navier-Stokes (NS) equations for the fluid and the Equation of Motion (EOM) for the structure. The proposed method employs Finite Differences (FD) on Cartesian grids together with an improved, efficient and oscillation-free Immersed Boundary Method (IBM), the accuracy of which is verified for several test cases of increasing complexity. A variety of two and three dimensional FSI simulations are performed to demonstrate the accuracy and applicability of the method. In particular, forced and a free vibration of a rigid cylinder including Vortex-Induced Vibration (VIV) of an elastically supported cylinder are presented and compared with reference simulations and experiments. Then, the interference between two cylinders in tandem arrangement at two different spacing is investigated. In terms of VIV, three different scenarios were studied for each cylinder arrangement to compare resonance regime to a single cylinder. Finally, the IBM is implemented into a three-dimensional Large-Eddy Simulation (LES) method and two high Reynolds number (Re) flows are studied for a stationary and transversely oscillating cylinder. The robustness, accuracy and applicability of the method for high Re number flow is demonstrated by comparing the turbulence statistics of the two cases and discussing differences in the mean and instantaneous flows.

Resumo: A compreensão do escoamento em válvulas de compressores herméticos alternativos é de fundamental importância para introduzir modificações no projeto delas de maneira a aumentar a performance dos compressores, e por fim, dos ciclos de refrigeração. A válvula do compressor é um dispositivo ímpar, umas vez que seu funcionamento se dá pela ação da pressão exercida pelo escoamento, caracterizando um problema de forte interação fluido- estrutura. O uso da modelagem numérica através das ferramentas da mecânica dos fluidos computacional (CFD) tem se destacado como a alternativa mais dinâmica para o estudo do fenômeno. O trabalho desenvolvido foi voltado para o estudo numérico do escoamento através do difusor radial, o qual é um modelo simplificado da válvula, com o emprego do Método da Fronteira Imersa com Modelo Físico Virtual para a modelagem do disco superior do difusor (palheta). O ponto forte desta metodologia é que a representação de regiões sólidas é feita pelo cálculo de um campo de força, o qual é introduzido nas equações das células na vizinhança do sólido. Este procedimento dispensa o uso de malhas que se adaptam ao corpo, possibilitando o uso de malhas cartesianas convencionas para modelar geometrias complexas e móveis. A metodologia foi acoplada com a solução das equações governantes do escoamento em coordenadas cilíndricas através do Método dos Volumes Finitos. Inicialmente, a metodologia foi validada, utilizando como dados de referência resultados provenientes de estudos numéricos e experimentais, e foi avaliada a influência dos parâmetros do procedimento na qualidade final dos resultados. Na segunda etapa foram desenvolvidos estudos preliminares referentes ao movimento do disco superior, com a imposição artificial dos processos de abertura e fechamento da válvula. Os resultados obtidos mostraram que a metodologia adotada ... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: The fully understanding of the flow through automatic valves of alternative hermetic compressors is essentiall to introduce modifications in its project aiming the improvement of the compressor performance and, also, the refrigeration cycle. The compressor valve is a singular device, once its operation is ruled by the flow pressure, characterizing a case with a strong fluid-structure interaction. The using of numerical tools trough the methods of computational fluid dynamics (CFD) has gained especial attention due to its flexibility to study the phenomenon. The present work was developed to study numerically the flow through the radial diffuser, which is a simplified model of the valve, with the employment of the Immersed Boundary Method with Virtual Physical Model to modeling the superior disk (valve reed). The main advantage of this methodology is that the modeling of solid boundaries is performed with the calculus of a force field, which is introduced in the cells equations nearby the solid. This procedure dispenses the using of body-fitted meshes, enabling the adoption of conventional Cartesian meshes to model complex and moving geometries. The methodology was coupled with the solution of the governing equations in cylindrical coordinates though the Finite Volume Method. Firstly, the methodology was validated, confronting the results obtained with data from numerical and experimental studies, where the influence of the main parameters in the quality of the final results was evaluated. In the second step were developed preliminary studies concerning the movement of the superior disk, whose opening and closing movements were artificially imposed. The results obtained showed that the adopted methodology is quit promising and flexible, and can be employed in more refined studies to the comprehension of the flow through the valve regarding the fluid-structure interaction that rules the problem / Orientador: José Luiz Gasche / Coorientador: Júlio Militzer / Banca: Cassio Roberto Macedo Maia / Banca: Elie Luis Martinez Padilla / Mestre

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>

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.