Knowledge of the detailed flow dynamics at the interior of branching corals is critical for a full understanding of nutrient uptake, mass transport, wave dissipation, and other essential processes. These physiological processes depend on the local velocity field, local concentration gradients of nutrients and waste, and the turbulent stresses developed on and above the coral surface. Though the large-scale hydrodynamics over coral reefs are well studied, the interior hydrodynamics, between the branches, remains uncharacterized due to limited optical and acoustic access to the interior. In the current thesis, a three-dimensional immersed boundary method in the large eddy simulation framework was used to compute the flow inside several branching coral colony geometries in order to study the effects of branch density and surface structure on the flow fields in the coral interiors. Two different Pocillopora colony species were studied at different Reynolds numbers. A ray-tracing algorithm was used for capturing the arbitrary branches of these complex geometries to obtain the three-dimensional flow fields within these colonies for the first time. The analysis showed the formation of vortices at the colony interior that stir the water column and thus passively enhance mass transport, compensating for the reduced mean velocity magnitude compared to the free stream value, within the densely branched Pocillopora meandrina colony. Further analysis showed that the mean streamwise velocity profile changes shape along the streamwise direction inside P. meandrina, whereas the mean velocity profile did not change shape from the front to the back for the loosely branched Pocillopora colony, Pocillopora eydouxi. Moreover, turbulent flow field quantities were computed for both these structures, and for two almost identical Montipora capitata colony geometries, one with, and one without roughness elements called verrucae. The analyses demonstrated significant differences in the mean velocity profiles, Reynolds stress, and other flow quantities with changes in colony branch density and surface structure. / Doctor of Philosophy / Coral reefs are the largest marine ecosystem, and play a critical role in protecting coastal areas against flooding and erosion. The majority of the world's corals are currently under threat from rising ocean temperatures, which disrupt the symbiotic relationship between the coral polyp and its symbiont algae causing coral bleaching. Bleaching involves processes mediated by the flow at the coral surface, but relatively little is known regarding the local flow dynamics between the branches of coral reefs. The current research seeks to characterize internal coral hydrodynamics, leading to insights about many critical physiological and other processes in corals, like drag formation, mixing, and mass or nutrient transport to and from the coral. In the current study, the influence of the coral branch density and surface structure on the resulting interbranch flow field were investigated by simulating the flow resulting from uniform oncoming ocean flow conditions using three-dimensional immersed boundary large eddy simulations. The detailed velocity and pressure fields were found throughout the interior of the colonies studied. A distinct mass transport mechanism was found inside one densely branched colony studied. For this coral, Pocillopora meandrina, the flow speed reduces substantially inside the coral because of the high branch density. But corals depend on the ocean flow to bring nutrients to the polyps on their surface. We found that P. meandrina sheds hundreds of small vortices from its branches, which stir the overlying water column, increasing the mass transport rate, and compensating almost exactly for the reduced flow in the interior. The study also included computing the flow through three other coral colony geometries, and comparisons of their mean velocity profiles and turbulent flow statistics in order to examine the impact of the colony branch density and surface structures on the resulting hydrodynamic flow field. The current investigation of coral hydrodynamics may lead to an increased understanding of coral health and physiological activity, and may help in designing effective interventions for the challenges facing corals, which could have impacts in the fields of coral restoration, coastal protection, and public policy in the United States and abroad.

No description available.

京都大学 / 0048 / 新制・課程博士 / 博士(工学) / 甲第21753号 / 工博第4570号 / 新制||工||1712(附属図書館) / 京都大学大学院工学研究科機械理工学専攻 / (主査)教授 西脇 眞二, 教授 松原 厚, 教授 黒瀬 良一 / 学位規則第4条第1項該当 / Doctor of Philosophy (Engineering) / Kyoto University / DFAM

The present thesis focuses on evaluating a conjugate heat transfer (CHT) simulation in a ribbed cooling passage with a fully developed flow assumption using LES with the immersed boundary method (IBM-LES-CHT). The IBM with the LES model (IBM-LES) and the IBM with CHT boundary condition (IBM-CHT) frameworks are validated prior to the main simulations by simulating purely convective heat transfer (iso-flux) in the ribbed duct, and a developing laminar boundary layer flow over a two-dimensional flat plate with heat conduction, respectively. For the main conjugate simulations, a ribbed duct geometry with a blockage ratio of 0.3 is simulated at a bulk Reynolds number of 10,000 with a conjugate boundary condition applied to the rib surface. The nominal Biot number is kept at 1, which is similar to the comparative experiment. As a means to overcome a large time scale disparity between the fluid and the solid regions, the use of a high artificial solid thermal diffusivity is compared to the physical diffusivity. It is shown that while the diffusivity impacts the instantaneous fluctuations in temperature, heat transfer and Nusselt numbers, it has an insignificantly small effect on the mean Nusselt number. The comparison between the IBM-LES-CHT and iso-flux simulations shows that the iso-flux case predicts higher local Nusselt numbers at the back face of the rib. Furthermore, the local Nusselt number augmentation ratio (EF) predicted by IBM-LES-CHT is compared to the body fitted grid (BFG) simulation, experiment and another LES conjugate simulation. Even though there is a mismatch between IBM-LES-CHT prediction and other studies at the front face of the rib, the area-averaged EF compares reasonably well in other regions between IBM-LES-CHT prediction and the comparative studies. / Master of Science / The present thesis focuses on the computational study of the conjugate heat transfer (CHT) investigation on the turbine internal ribbed cooling channel. Plenty of prior research on turbine internal cooling channel have been conducted by considering only the convective heat transfer at the wall, which assumes an iso-flux (constant heat flux) boundary condition at the surface. However, applying an iso-flux condition on the surface is far from the realistic heat transfer mechanism occurring in internal cooling systems. In this work, a conjugate heat transfer analysis of the cooling channel, which considers both the conduction within the solid wall and the convection at the ribbed inner wall surface, is conducted for more realistic heat transfer coefficient prediction at the inner ribbed wall. For the simulation, the computational mesh is generated by the immersed boundary method (IBM), which can ease the mesh generation by simply immersing the CAD geometry into the background volume grid. The IBM is combined with the conjugate boundary condition to simulate the internal ribbed cooling channel. The conjugate simulation is compared with the experimental data and another computational study for the validation. Even though there are some discrepancy between the IBM simulation and other comparative studies, overall results are in good agreement. From the thermal prediction comparison between the iso-flux case and the conjugate case v using the IBM, it is found that the heat transfer predicted by the conjugate case is different from the iso-flux case by more than 40 percent at the rib back face. The present study shows the potential of the IBM framework with the conjugate boundary condition for more complicated geometry, such as full turbine blade model with external and internal cooling system.

The delivery of drugs into solid tumors is not trivial due to obstructions in the tumor microenvironment. Innovative drug delivery vehicles are currently being designed to overcome this challenge. In this research, computational fluid dynamics (CFD) simulations were used to evaluate the behavior of several drug delivery vectors in tumor capillaries—specifically motile bacteria, non-motile bacteria, and nanoparticles. Red blood cells, bacteria, and nanoparticles were imposed in the flow using the immersed boundary method. A human capillary model was developed using a novel method of handling deformable red blood cells (RBC). The capillary model was validated with experimental data from the literature. A stochastic model of bacteria motility was defined based on experimentally observed run and tumble behavior. The capillary and bacteria models were combined to simulate the intracapillary transport of bacteria. Non-motile bacteria and nanoparticles of 200 nm, 300 nm, and 405 nm were also simulated in capillary flow for comparison to motile bacteria. Motile bacteria tended to swim into the plasma layer near the capillary wall, while non-motile bacteria tended to get caught in the bolus flow between the RBCs. The nanoparticles were more impacted by Brownian motion and small scale fluid fluctuations, so they did not trend toward a single region of the flow. Motile bacteria were found to have the longest residence time in a 1 mm long capillary as well as the highest average radial velocity. This suggests motile bacteria may enter the interstitium at a higher rate than non-motile bacteria or nanoparticles of diameters between 200–405 nm. / Master of Science

This thesis presents a numerical method for the phase-resolving simulation of rigid particles and deformable bubbles in viscous, magnetohydrodynamic flows. The presented approach features solid robustness and high numerical efficiency. The implementation is three-dimensional and fully parallel suiting the needs of modern high-performance computing. In addition to the steps towards magnetohydrodynamics, the thesis covers method development with respect to the immersed boundary method which can be summarized in simple words by From rigid spherical particles to deformable bubbles. The development comprises the extension of an existing immersed boundary method to non-spherical particles and very low particle-to-fluid density ratios. A detailed study is dedicated to the complex interaction of particle shape, wake and particle dynamics. Furthermore, the representation of deformable bubble shapes, i.e. the coupling of the bubble shape to the fluid loads, is accounted for. The topic of bubble interaction is surveyed including bubble collision and coalescence and a new coalescence model is introduced. The thesis contains applications of the method to simulations of the rise of a single bubble and a bubble chain in liquid metal with and without magnetic field highlighting the major effects of the field on the bubble dynamics and the flow field. The effect of bubble coalescence is quantified for two closely adjacent bubble chains. A framework for large-scale simulations with many bubbles is provided to study complex multiphase phenomena like bubble-turbulence interaction in an efficient manner.

This thesis presents a numerical method for the simulation of fluid-structure interaction (FSI) problems on high-performance computers. The proposed method is specifically tailored to interactions between Newtonian fluids and a large number of slender viscoelastic structures, the latter being modeled as Cosserat rods. From a numerical point of view, such kind of FSI requires special techniques to reach numerical stability. When using a partitioned fluid-structure coupling approach this is usually achieved by an iterative procedure, which drastically increases the computational effort. In the present work, an alternative coupling approach is developed based on an immersed boundary method (IBM). It is unconditionally stable and exempt from any global iteration between the fluid part and the structure part. The proposed FSI solver is employed to simulate the flow over a dense layer of vegetation elements, usually designated as canopy flow. The abstracted canopy model used in the simulation consists of 800 strip-shaped blades, which is the largest canopy-resolving simulation of this type done so far. To gain a deeper understanding of the physics of aquatic canopy flows the simulation data obtained are analyzed, e.g., concerning the existence and shape of coherent structures.

This thesis presents a numerical method for the phase-resolving simulation of rigid particles and deformable bubbles in viscous, magnetohydrodynamic flows. The presented approach features solid robustness and high numerical efficiency. The implementation is three-dimensional and fully parallel suiting the needs of modern high-performance computing. In addition to the steps towards magnetohydrodynamics, the thesis covers method development with respect to the immersed boundary method which can be summarized in simple words by From rigid spherical particles to deformable bubbles. The development comprises the extension of an existing immersed boundary method to non-spherical particles and very low particle-to-fluid density ratios. A detailed study is dedicated to the complex interaction of particle shape, wake and particle dynamics. Furthermore, the representation of deformable bubble shapes, i.e. the coupling of the bubble shape to the fluid loads, is accounted for. The topic of bubble interaction is surveyed including bubble collision and coalescence and a new coalescence model is introduced. The thesis contains applications of the method to simulations of the rise of a single bubble and a bubble chain in liquid metal with and without magnetic field highlighting the major effects of the field on the bubble dynamics and the flow field. The effect of bubble coalescence is quantified for two closely adjacent bubble chains. A framework for large-scale simulations with many bubbles is provided to study complex multiphase phenomena like bubble-turbulence interaction in an efficient manner.

The article describes direct numerical simulations using an Euler–Lagrange approach with an immersed-boundary method to resolve the geometry and trajectory of particles moving in a flow. The presentation focuses on own work of the authors and discusses elements of physical and numerical modeling in some detail, together with three areas of application: microfluidic transport of spherical and nonspherical particles in curved ducts, flows with bubbles at different void fraction ranging from single bubbles to dense particle clusters, some also subjected to electro-magnetic forces, and bedload sediment transport with spherical and nonspherical particles. These applications with their specific requirements for numerical modeling illustrate the versatility of the approach and provide condensed information about main findings.

In meshfree methods, partial differential equations are solved on an unstructured cloud of points distributed throughout the computational domain. In collocated meshfree methods, the differential operators are directly approximated at each grid point based on a local cloud of neighboring points. The set of neighboring nodes used to construct the local approximation is determined using a variable search radius. The variable search radius establishes an implicit nodal connectivity and hence a mesh is not required. As a result, meshfree methods have the potential flexibility to handle problem sets where the computational grid may undergo large deformations as well as where the grid may need to undergo adaptive refinement. In this work we develop the sharp interface formulation of the immersed boundary method for collocated meshfree approximations. We use the framework to implement three meshfree methods: General Finite Differences (GFD), Smoothed Particle Hydrodynamics (SPH), and Moving Least Squares (MLS). We evaluate the numerical accuracy and convergence rate of these methods by solving the 2D Poisson equation. We demonstrate that GFD is computationally more efficient than MLS and show that its accuracy is superior to a popular corrected form of SPH and comparable to MLS. We then use GFD to solve several canonic steady state fluid flow problems on meshfree grids generated using uniform and variable radii Poisson disk algorithm.