# Browsing by Subject "computational fluid dynamics"

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Item Open Access A New Method for Modeling Free Surface Flows and Fluid-structure Interaction with Ocean Applications(2016) Lee, CurtisThe computational modeling of ocean waves and ocean-faring devices poses numerous challenges. Among these are the need to stably and accurately represent both the fluid-fluid interface between water and air as well as the fluid-structure interfaces arising between solid devices and one or more fluids. As techniques are developed to stably and accurately balance the interactions between fluid and structural solvers at these boundaries, a similarly pressing challenge is the development of algorithms that are massively scalable and capable of performing large-scale three-dimensional simulations on reasonable time scales. This dissertation introduces two separate methods for approaching this problem, with the first focusing on the development of sophisticated fluid-fluid interface representations and the second focusing primarily on scalability and extensibility to higher-order methods.

We begin by introducing the narrow-band gradient-augmented level set method (GALSM) for incompressible multiphase Navier-Stokes flow. This is the first use of the high-order GALSM for a fluid flow application, and its reliability and accuracy in modeling ocean environments is tested extensively. The method demonstrates numerous advantages over the traditional level set method, among these a heightened conservation of fluid volume and the representation of subgrid structures.

Next, we present a finite-volume algorithm for solving the incompressible Euler equations in two and three dimensions in the presence of a flow-driven free surface and a dynamic rigid body. In this development, the chief concerns are efficiency, scalability, and extensibility (to higher-order and truly conservative methods). These priorities informed a number of important choices: The air phase is substituted by a pressure boundary condition in order to greatly reduce the size of the computational domain, a cut-cell finite-volume approach is chosen in order to minimize fluid volume loss and open the door to higher-order methods, and adaptive mesh refinement (AMR) is employed to focus computational effort and make large-scale 3D simulations possible. This algorithm is shown to produce robust and accurate results that are well-suited for the study of ocean waves and the development of wave energy conversion (WEC) devices.

Item Open Access Analyzing Hydrodynamic Properties of the North Atlantic Right Whales with Computer Solutions(2020) Wu, Chen-YiAnimals experience hydrodynamic forces (lift, drag, and side) and moments (pitching, yawing, and rolling) as a result of motion in an aqueous medium. Under selective pressure, most cetaceans, including porpoises, dolphins, and whales, developed a streamlined body shape and modified limbs, which delay the separation of flow, create lower drag when they swim, and therefore decrease their locomotor cost. In order to calculate the locomotor cost and propulsive efficiency of cetaceans, accurate estimates of drag on marine animals are required. However, extra momentum imparted into the fluid from lift and side forces as well as pitching, rolling, and yawing moments (here, the parasitic loads) results in extra drag force on the animal. Therefore, in addition to streaming and delaying flow separation, animals must also minimize excess fluid momentum resulting from parasitic loads. Given the endangered status of the North Atlantic right whale (Eubalaena glacialis; hereafter NARW), analyzing the hydrodynamic characteristics of the NARWs was the focus of this work. Additionally, previous studies showed that body shape of NARWs changes with life stages, reproduction status, nutritive conditions or prey abundance, and the effects of entanglement in fishing gear. Therefore, in this study, computational fluid dynamics (CFD) analysis was performed on multiple 10 m three-dimensional NARW models with different body shapes (e.g., normal condition, emaciated, and pregnant) to measure baseline measurements of flow regimes and hydrodynamic loads on the animal. Swimming speeds covering known right whale speed range (0.125 m/s to 8 m/s) were simulated in most scenarios. In addition to the hydrodynamic effects of different body shapes, drag was also considered a function of parasitic loads. The NARW models were embedded with bone segments that allowed one to manipulate the body pose of the model via adjusting the flippers or the spine of the animal before measuring hydrodynamic drag. By doing so, momentum from parasitic loads was expected to be eliminated. CFD simulations revealed that drag on NARWs is dictated by its irregular outline and that the drag coefficient (0.0071-0.0059; or dimensionless drag) of on NARWs is approximately twice that of many previous estimates for large cetaceans. It was also found that pregnant NARW model encounters the lowest drag coefficient due to delayed flow separation resulting from enlarged abdomen, whereas the emaciated NARW model experiences the highest drag coefficient possibly due to the concavity at the post-nuchal region. These results suggested that drag on NARWs and their thrust power requirements were indeed affected by its body shape but the differences between the three NARW models tested were small. Lastly, minimum drag, which corresponds to the elimination of the parasitic loads, can be obtained by adjusting the pose of the animal. Thus, minimum drag occurs at the neutral trim pose. For the static, normo-nourished NARW model, simulations revealed that by changing the angle of attack of the flippers by 4.03° (relative to the free-stream flow) and pitching the spine downward by 5° while maintaining fluke angle, the drag was lowered by approximately 11% across the flow speeds tested. This drag reduction was relative to the drag study conducted on the same animal model but without body pose adjustments. Together the studies included in the present work explored and highlighted the capability of numerical methods in investigating the hydrodynamics and energetics of cetaceans. Future studies should address how computer solutions can be used to solve problems from a wider aspect. For instance, extra parasitic loads caused by attached gear as well as possible injuries due to the encounter with fishing gear should also be considered while evaluating the energy budget of the North Atlantic right whales.

Item Open Access Investigating the Influence of Red Blood Cell Interactions on Large-Scale Cancer Cell Transport: Bridging the Gap through Advances in Computational Techniques(2023) Roychowdhury, SayanMetastatic cancer, the leading cause of cancer mortality, involves the complex process of circulating tumor cells (CTCs) spreading through the bloodstream and forming secondary tumors far away from the primary mass, which often travel a distance many thousand times its size. The interactions between CTCs and their neighboring red blood cells (RBCs), as well as the local hemodynamics in vessels, play a crucial role in determining these cells' fate; however, the mechanisms guiding their transit are still unclear. Predicting secondary tumor sites remains challenging due to the intricate dynamics of CTC migration. Thus, there remains a need to understand the interplay between the fluid dynamics, intercellular interactions, and vessel topology which can determine the fate of the CTC and subsequent likelihood of cancer progression.

Investigating CTC transport has involved a range of \textit{in vivo} and \textit{in vitro} studies to unravel the intricate mechanisms that dictate cellular outcomes. However, the process of tracking an individual CTC's trajectory through the massive vascular system is still not possible today \textit{in vivo}. The integration of \textit{in silico} models has proven instrumental, complementing traditional experimental approaches. In this work, we utilize our advanced fluid dynamics solver HARVEY to perform high-fidelity hemodynamic simulations to capture CTC dissemination. We outline several key contributions, including the addition of new physics interactions models and software optimizations, to enable these simulations to better capture biological phenomena and run to completion within a reasonable timeframe.

Numerical optimizations for \textit{in silico} models are still necessary: the drastic difference in length scales of CTC size versus distance traveled hinders current simulation models. To accurately capture intercellular dynamics, interactions must be modeled with sub-micrometer precision; meanwhile, the characteristic length scale of CTC traversal through the blood stream can be on the order of hundreds of millimeters, over 5 orders of magnitude larger. Numerically modeling hundreds of millions of individual cells at a sub-micron resolution over this timescale would require the entirety of multiple leadership-class supercomputers over the course of several weeks, if not months. Therefore, there still exists a disparity between these two ranges that needs to be addressed to make simulations of CTC transport with the presence of neighboring RBCs tractable.

We also address one of the pillars of the inherent variability in cell transport: the fate of a single CTC can exhibit significant variations due to its interactions with neighboring RBCs in the context of an \textit{in vivo} experiment,. A single simulation of a CTC may not encompass the range of outcomes, necessitating the consideration of many simulations with different RBC distributions. Multiplying the number of simulations required to capture this variability by the computational workload of a single simulation results in a computationally intractable workload, making it essential to optimize the number of simulations required for proper results. The number of potential cell configurations is vast, which makes it essential to identify representative configurations that encompass the full range of possible outcomes while optimizing computational feasibility.

This dissertation explores the influence of several hemodynamic and geometric parameters, microvasculature interactions, and the impact of RBCs on CTC movement, including the presence of RBC aggregation, RBC volume fraction, microvessel size, and shear rate. Furthermore, it discusses the enhancement of adaptive physics refinement methods to model cellular transport phenomena and highlights the capabilities of fluid-structure interaction models in capturing the dynamics of CTCs and RBCs across the system-scale. The dissertation concludes by discussing the development of a novel framework to account for the range of outcomes in CTC transport due to the variability in neighboring RBCs; it addresses the importance of generating representative configurations using quantitative metrics such as the Jaccard index applied to sets of sphere and RBC data sets. By integrating these advances, we further reduce the gap towards biologically accurate computational models of cancer cell transport, which holds promise for improving our understanding of cancer metastasis and developing effective strategies for cancer treatment.

Item Open Access Probabilistic Modeling of Decompression Sickness, Comparative Hydrodynamics of Cetacean Flippers, Optimization of CT/MRI Protocols and Evaluation of Modified Angiocatheters: Engineering Methods Applied to a Diverse Assemblage of Projects(2010) Weber, Paul WilliamThe intent of the work discussed in this dissertation is to apply the engineering methods of theory/modeling, numerics/computation, and experimentation to a diverse assemblage of projects. Several projects are discussed: probabilistic modeling of decompression sickness, comparative hydrodynamics of cetacean flippers, optimization of CT/MRI protocols, evaluation of modified catheters, rudder cavitation, and modeling of mass transfer in amphibian cone outer segments.

The first project discussed is the probabilistic modeling of decompression sickness (DCS). This project involved developing a system for evaluating the success of decompression models in predicting DCS probability from empirical data. Model parameters were estimated using maximum likelihood techniques, and exact integrals of risk functions and tissue kinetics transition times were derived. Agreement with previously published results was excellent including maximum likelihood values within one log-likelihood unit of previous results and improvements by re-optimization, mean predicted DCS incidents within 1.4% of observed DCS, and time of DCS occurrence prediction. Alternative optimization and homogeneous parallel processing techniques yielded faster model optimization times. The next portion of this project involved investigating the nature and utility of marginal decompression sickness (DCS) events in fitting probabilistic decompression models to experimental dive trial data. Three null models were developed and compared to a known decompression model that was optimized on dive trial data containing only marginal DCS and no-DCS events. It was found that although marginal DCS events are related to exposure to decompression, empirical dive data containing marginal and full DCS outcomes are not combinable under a single DCS model; therefore, marginal DCS should be counted as no-DCS events when optimizing probabilistic DCS models with binomial likelihood functions. The final portion of this project involved the exploration of a multinomial DCS model. Two separate models based on the exponential-exponential/linear-exponential framework were developed: a trinomial model, which is able to predict the probabilities of mild, serious and no-DCS simultaneously, and a tetranomial model, which is able to predict the probabilities of mild, serious, marginal and no-DCS simultaneously. The trinomial DCS model was found to be qualitatively better than the tetranomial model, for reasons found earlier concerning the utility of marginal DCS events in DCS modeling.

The next project discussed is comparative hydrodynamics of cetacean flippers. Cetacean flippers may be viewed as being analogous to modern engineered hydrofoils, which have hydrodynamic properties such as lift coefficient, drag coefficient and associated efficiency. The hydrodynamics of cetacean flippers have not previously been rigorously examined and thus their performance properties are unknown. By conducting water tunnel testing using scale models of cetacean flippers derived via computed tomography (CT) scans, as well as computational fluid dynamic (CFD) simulations, a baseline work is presented to describe the hydrodynamic properties of several cetacean flippers. It was found that flippers of similar planform shape had similar hydrodynamic performance properties. Furthermore, one group of flippers of planform shape similar to modern swept wings was found to have lift coefficients that increased with angle of attack nonlinearly, which was caused by the onset of vortex-dominated lift. Drag coefficient versus angle of attack curves were found to be less dependent on planform shape. Larger cetacean flippers were found to have degraded performance at a Re of 250,000 compared to flippers of smaller odontocetes, while performance of larger and smaller cetacean flippers was similar at a swim speed of 2 m/s. Idealization of the planforms of cetacean flippers was found to capture the relevant hydrodynamic effects of the real flippers, although unintended consequences such as the lift curve slope changing from linear to nonlinear were sometimes observed. A numerical study of an idealized model of the humpback whale flipper showed that the leading-edge tubercles delay stall compared to a baseline (no tubercle) flipper because larger portions of the flow remaining attached at higher angles of attack.

The third project discussed is optimization of CT/MRI protocols. In order to optimize contrast material administration protocols for Computed Tomography (CT) and Magnetic Resonance Imaging (MRI), a custom-built physiologic flow phantom was constructed to model flow in the human body. This flow phantom was used to evaluate the effect of varying volumes, rates, and types of contrast material, use of a saline chase, and cardiac output on aortic enhancement characteristics. For CT, reducing the volume of contrast material decreased duration peak enhancement and reduced the maximum value of peak enhancement. Increasing the rate of contrast media administration increased peak enhancement and decreased duration of peak enhancement. Use of a saline chase resulted in an increase in peak enhancement. Peak aortic enhancement increased when reduced cardiac output was simulated. For MRI, when the same volume of contrast material was injected at the same rate, the type of contrast material used has a significant effect on the greatest peak signal intensity and duration peak signal intensity. A higher injection rate of saline chaser is more advantageous than a larger volume of saline chaser to increase the peak aortic signal intensity using low contrast material doses. Furthermore, for higher volumes of contrast material, the effect of increasing the volume of saline chaser makes almost no difference while increasing the rate of injection makes a significant difference. When a saline chaser with a high injection rate is used, the dose of the contrast material may be reduced by 25-50% and more than 86% of the non-reduced dose peak aortic enhancement will be attained.

The next project discussed is evaluation of modified angiocatheters. In this study, a standard peripheral end hole angiocatheter was compared to those modified with side holes or side slits by using experimental techniques to qualitatively compare the contrast material exit jets, and by using numeric techniques to provide flow visualization and quantitative comparisons. A Schlieren imaging system was used to visualize the angiocatheter exit jet fluid dynamics at two different flow rates, and a commercial computational fluid dynamics (CFD) package was used to calculate numeric results for various catheter orientations and vessel diameters. Experimental images showed that modifying standard peripheral intravenous angiocatheters with side holes or side slits qualitatively changed the overall flow field and caused the exiting jet to become less well-defined. Numeric calculations showed that the addition of side holes or slits resulted in a 9-30% reduction of the velocity of contrast material exiting the end hole of the angiocatheter. With the catheter tip directed obliquely to the wall, the maximum wall shear stress was always highest for the unmodified catheter and always lowest for the 4 side slit catheter. Modified angiocatheters may have the potential to reduce extravasation events in patients by reducing vessel wall shear stress.

The next project discussed involves studying the effect of leading-edge tubercles on cavitation characteristics for marine rudders. Three different rudders were constructed and tested in a water tunnel: baseline, 3-tubercle leading edge, and 5-tubercle leading edge. In the linear (non-stall) regime, tubercled rudders performed equally to the smooth rudder. Hydrodynamic stall occurred at smaller angles of attack for the tubercled rudders than for the smooth rudder. When stall did occur, it was more gradual for the tubercled rudders, whereas the smooth rudder demonstrated a more dramatic loss of lift. At lower Re, the tubercled rudders also maintained a higher value of lift post-stall than the smooth rudder. Cavitation onset for the tubercled rudders occurred at lower angles of attack and higher values of cavitation number than for the smooth rudder, but cavities on the tubercled rudders were localized in the slots as opposed to the smooth rudder where the cavity spread across the entire leading edge.

In the final project discussed, modeling of mass transfer in amphibian cone outer segments, a detailed derivation of a simplified (continuum, one-dimensional) mathematical model for the radio-labeled opsin density profile in the amphibian cone outer segment is presented. This model relies on only one free parameter, which was the mass transfer coefficient between the plasmalemma and disc region. The descriptive equations were nondimensionalized, and scale analysis showed that advective effects could be neglected as a first approximation for early times so that a simplified system could be obtained. Through numeric computation the solution behavior was found to have three distinct stages. The first stage was marked by diffusion in the plasmalemma and no mass transfer in the disc region. The second stage first involved the plasmalemma reaching a metastable state whereas the disc region density increased, then involved both the plasmalemma and disc regions increasing in density with their distributions being qualitatively the same. The final stage involved a slow relaxation to the steady-state solution.