A general framework is described for the solution of two-phase fluid-object interaction problems on the basis of coupling a distributed-Lagrange-multiplier fictitious domain method and a level-set method, intended for application to the problem of seabed scour by ice ridges. The resulting equations are discretized in space using stabilized finite-element methods and integrated in time using the generalized-α method. This approach is simple to implement and applicable to both structured and unstructured meshes in two and three dimensions. By means of examples, it is shown that despite the simplicity of the approach, good results are obtained in comparison with other more computationally demanding methods. A robust approach is utilized for constructing signed-distance functions on arbitrary meshes by introducing artificial numerical diffusivity to improve the robustness of classical signed-distance construction approaches without resorting to common pseudo-time relaxation. Under this approach, signed-distance functions can be rapidly constructed while preserving the numerical convergence properties and, generally, having minimal interfacial perturbation. The method is then applied with a modified deformation procedure for fast and efficient mesh adaptivity, including a discussion how it may be used in computational fluid dynamics. The two-phase fluid-object interaction approach is then customized for modeling of the seabed scour and soil-pipe interaction. In this approach, complex history-dependent soil constitutive models are replaced with a simple strain-rate dependent model. Utilization of this constitutive model along with the framework developed earlier leads to the treatment of seabed scour as a two-phase fluid-object interaction, and the soil-pipe interaction as a fluid-structure interaction problem without the need for remeshing. Good agreement with past experimental and numerical studies are obtained using our approach. The dissertation is concluded by conducting a parametric study of seabed scour in two- and three-dimensions. / text

The purpose of this thesis is to further develop numerical methods for solving surface problems by utilizing tangential calculus and the trace finite element method. Direct computation on the surface is possible by the use of tangential calculus, in contrast to the classical approach of mapping 2D parametric surfaces to 3D surfaces by means of differential geometry operators. Using tangential calculus, the problem formulation is only dependent on the position and normal vectors of the 3D surface. Tangential calculus thus enables a clean, simple and inexpensive formulation and implementation of finite element methods for surface problems. Meshing techniques are greatly simplified from the end-user perspective by utilizing an unfitted finite element method called the Trace Finite Element Method, in which the basic idea is to embed the surface in a higher dimensional mesh and use the shape functions of this background mesh for the discretization of the partial differential equation. This method makes it possible to model surfaces implicitly and solve surface problems without the need for expensive meshing/re-meshing techniques especially for moving surfaces or surfaces embedded in 3D solids, so called embedded interface problems. Using these two approaches, numerical methods for solving three surface problems are proposed: 1) minimal surface problems, in which the form that minimizes the mean curvature was computed by iterative update of a level-set function discretized using TraceFEM and driven by advection, for which the velocity field was given by the mean curvature flow, 2) elastic membrane problems discretized using linear and higher order TraceFEM, which makes it straightforward to embed complex geometries of membrane models into an elastic bulk for reinforcement and 3) stabilized, accurate vertex normal and mean curvature estimation with local refinement on triangulated surfaces. In this thesis the basics of the two main approaches are presented, some aspects such as stabilization and surface reconstruction are further developed, evaluated and numerically analyzed, details on implementations are provided and the current state of work is presented.

Level set method is a boundary tracking method that uses an implicit function to define the boundary location. By using the implicit function to define the structural boundary the level set method can be used for topology optimisation. The level set method has previously been used to solve a range of structural optimisation problems. The aim of this thesis is to extend the application of the level set method to additional applications of structural optimisation. A robust method of 3D level set topology optimisation is developed and tested. The use of a hole insertion method was found to be advantageous, but not vital, for 3D level set topology optimisation. The level set method is used to optimise the internal structure of a proximal femur. Similarities between the optimal structure and real internal trabecular bone architecture suggest that the internal bone structure may be mechanically optimal. Stress constrained level set topology optimisation is performed in 2D. Stress shape sensitivities are derived and interpolated to obtain smooth boundary sensitivity, resulting in feasible stress constrained solution in numerical examples. A new generic objective hole insertion method is used to reduce dependence on the initial solution. A level set method for optimising the design of fibre angles in composite structures is also introduced. Fibre paths are implicitly defined using the level set function. Sensitivity analysis is used to update the level set function values and optimise the fibre path. The method implicitly ensures continuous fibre paths in the optimum solution, that could be manufactured using advanced fibre placement.

Research in the biomedical sciences is incredibly diverse and often involves the interaction of specialists in a variety of fields. In particular, quantitative, mathematical, and computational methods are increasingly playing significant roles in studying problems arising in biomedical science. This is particularly exciting for mathematical modeling as the complexity of biological systems poses new challenges to modelers and leads to interesting mathematical problems. On the other hand mathematical modeling can provide considerable insight to laboratory and clinical researchers. In this thesis we develop mathematical representations for three biological processes that are of current interest in biomedical science. A deeper understanding of these processes is desirable not only from the standpoint of basic science, but also because of the connections these processes have with certain diseases. The processes we consider are collective cell motility, bone remodeling, and injury response in articular cartilage. Our goals are to develop mathematical representations of these processes that can provide a conceptual framework for understanding the processes at a fundamental level, that make rigorous the intuition biological researchers have developed about these processes, and that help to translate theoretical and experimental work into information that can be used in clinical settings where the primary concern is in treating diseases associated with the process.

Cardiovascular modeling has the capability to provide valuable information allowing clinicians to better classify patients and aid in surgical planning. Modeling is advantageous for being non-invasive, and also allows for quantification of values not easily obtained from physical measurements. Hemodynamics are heavily dependent on vessel geometry, which varies greatly from patient to patient. For this reason, clinically relevant approaches must perform these simulations on patient-specific geometry. Geometry is acquired from various imaging modalities, including magnetic resonance imaging, computed tomography, and ultrasound. The typical approach for generating a computational model requires construction of a triangulated surface mesh for use with finite volume or finite element solvers. Surface mesh construction can result in a loss of anatomical features and often requires a skilled user to execute manual steps in 3rd party software. An alternative to this method is to use a Cartesian grid solver to conduct the fluid simulation. Cartesian grid solvers do not require a surface mesh. They can use the implicit geometry representation created during the image segmentation process, but they are constrained to a cuboidal domain. Since patient-specific geometry usually deviate from the orthogonal directions of a cuboidal domain, flow extensions are often implemented. Flow extensions are created via a skilled user and 3rd party software, rendering the Cartesian grid solver approach no more clinically useful than the triangulated surface mesh approach. This work presents an alternative to flow extensions by developing a method of applying vessel inlet and outlet boundary conditions to regions inside the Cartesian domain.

This dissertation presents a study on the development of a numerical model aimed at simulating free surface flow, which still remains an active research area. Modeling these processes is very challenging since the interface between air and water is characterized by sharp discontinuities in fluid properties and flow characteristics due to different densities, viscosities, surface tension and consequent discontinuities in spatial gradients of velocity and pressure. The constraint of incompressibility poses another difficulty on the efficient design of algorithms. Recently, the level set method has emerged as a powerful tool for evolving interfaces in computational science and engineering for a wide range of applications while the finite element method has been long known for its geometrical flexibility. An effort to combine these two methods is made in this study. Several benchmark problems are used for the test of the developed code in view of temporal and spatial accuracy. Then, the capability and efficiency of the model are extended with advanced turbulence models and parallel algorithm. The model is applied to problems of practical importance in hydraulics, including hydraulic jump under a sluice gate and the design of spillways for fish migration. The main focus is on the capturing of free surface and identifying and understanding of the vortical structures and nonhydrostatic pressure distribution. The model has proved to be very effective for these purpose. The new technique dealing with air-water interface in a more physically accurate way is introduced for future development and the new method is applied to the problems of static equilibrium for validation.

<p>Image segmentation is the problem of partitioning an image into meaningful parts, often consisting of an object and background. As an important part of many imaging applications, e.g. face recognition, tracking of moving cars and people etc, it is of general interest to design robust and fast segmentation algorithms. However, it is well accepted that there is no general method for solving all segmentation problems. Instead, the algorithms have to be highly adapted to the application in order to achieve good performance. In this thesis, we will study segmentation methods for blood vessels in medical images. The need for accurate segmentation tools in medical applications is driven by the increased capacity of the imaging devices. Common modalities such as CT and MRI generate images which simply cannot be examined manually, due to high resolutions and a large number of image slices. Furthermore, it is very difficult to visualize complex structures in three-dimensional image volumes without cutting away large portions of, perhaps important, data. Tools, such as segmentation, can aid the medical staff in browsing through such large images by highlighting objects of particular importance. In addition, segmentation in particular can output models of organs, tumors, and other structures for further analysis, quantification or simulation.</p><p>We have divided the segmentation of blood vessels into two parts. First, we model the vessels as a collection of lines and edges (linear structures) and use filtering techniques to detect such structures in an image. Second, the output from this filtering is used as input for segmentation tools. Our contributions mainly lie in the design of a multi-scale filtering and integration scheme for de- tecting vessels of varying widths and the modification of optimization schemes for finding better segmentations than traditional methods do. We validate our ideas on synthetical images mimicking typical blood vessel structures, and show proof-of-concept results on real medical images.</p>

In the present study, a fifth-order weighted essentially non-oscillatory (WENO) scheme was built for solving the surface-capturing level-set equation. Combined with the level-set equation, the three-dimensional Reynolds averaged Navier-Stokes (RANS) equations were employed for the prediction of nonlinear wave-interaction and wave-breaking phenomena over sloping beaches. In the level-set finite-analytic Navier-Stokes (FANS) method, the free surface is represented by the zero level-set function, and the flows are modeled as immiscible air-water two phase flows. The Navier-Stokes equations for air-water two phase flows are formulated in a moving curvilinear coordinate system and discretized by a 12-point finite-analytical scheme using the finite-analytic method on a multi-block over-set grid system. The Pressure Implicit with Splitting of Operators / Semi-Implicit Method for Pressure-Linked Equation Revised (PISO/SIMPLER) algorithm was used to determine the coupled velocity and pressure fields. The evolution of the level-set method was solved using the third-order total variation diminishing (TVD) Runge-Kutta method and fifth-order WENO scheme. The accuracy was confirmed by solving the Zalesak's problem. Two major subjects are discussed in the present study. First, to identify the WENO scheme as a more accurate scheme than the essentially non-oscillatory scheme (ENO), the characteristics of a nonlinear monochromatic wave were studied systematically and comparisons of wave profiles using the two schemes were conducted. To eliminate other factors that might produce wave profile fluctuation, different damping functions and grid densities were studied. To damp the reflection waves efficiently, we compared five damping functions. The free-surface elevation data collected from gauges distributed evenly in a numerical wave tank are analyzed to demonstrate the damping effect of the beach. Second, as a surface-tracking numerical method built on curvilinear coordinates, the level-set RANS model was tested for nonlinear bichromatic wave trains and breaking waves on a sloping beach with a complex free surface. As the wave breaks, the velocity of the fluid flow surface became more complex. Numerical modeling was performed to simulate the two-phase flow velocity and its corresponding surface and evolution when the wave passed over different sloping beaches. The breaking wave test showed that it is an efficient technique for accurately capturing the breaking wave free surface. To predict the breaking points, different wave heights and beach slopes are simulated. The results show that the dependency of wave shape and breaking characteristics to wave height and beach slope match the results provided by experiments.

Vibration control is inevitable in many fields, including mechanical and civil engineering. This matter becomes more crucial for lightweight systems, like those made of magnesium. One of the most commonly practiced methods in vibration control is to apply constrained layer damping (CLD) patches to the surface of a structure. In order to consider the weight efficiency of the structure, the best shape and locations of the patches should be determined to achieve the optimum vibration suppression with the lowest amount of damping patch. In most research work done so far, the shape of patches are assumed to be known and only their optimum locations are found. However, the shape of the patches plays an important role in vibration suppression that should be included in the overall optimization procedure. In this research, a novel topology optimization approach is proposed. This approach is capable of finding the optimum shape and locations of the patches simultaneously for a given surface area. In other words, the damping optimization will be formulated in the context of the level set technique, which is a numerical method used to track shapes and locations concurrently. Although level set technique offers several key benefits, its application especially in time-varying problems is somewhat cumbersome. To overcome this issue, a unique programming technique is suggested that utilizes MATLAB© and COMSOL© simultaneously. Different 2D structures will be considered and CLD patches will be optimally located on them to achieve the highest modal loss factor. Optimization will be performed while having different amount of damping patches to check the effectiveness of the technique. In all cases, certain constraints are imposed in order to make sure that the amount of damping material remains constant and equal to the starting value. Furthermore, different natural frequencies will be targeted in the damping optimization, and their effects will also be explained. The level set optimization technique will then be expanded to 3D structures, and a novel approach will be presented for defining an efficient 4D level set function to initialize the optimization process. Vibrations of a satellite dish will be optimally suppressed using CLD patches. Dependency of the optimum shape and location of patches to different parameters of the models such as natural frequencies and initial starting point will be examined. In another practical example, excessive vibrations of an automotive dash panel will be minimized by adding damping materials and their optimal distribution will be found. Finally, the accuracy of the proposed method will be experimentally confirmed through lab tests on a rectangular plate with nonsymmetrical boundary conditions. Different damping configurations, including the optimum one, will be tested. It will be shown that the optimum damping configuration found via level set technique possesses the highest loss factor and reveals the best vibration attenuation. The proposed level set topology optimization method shows high capability of determining the optimum damping set in structures. The effective coding method presented in this research will make it possible to easily extend this method to other physical problems such as image processing, heat transfer, magnetic fields, etc. Being interconnected, the physical part will be modeled in a finite element package like COMSOL and the optimization advances by means of Hamilton-Jacobi partial differential equation. Thus, the application of the proposed method is not confined to damping optimization and can be expanded to many engineering problems. In summary, this research: - offers general solution to 2D and 3D CLD applications and simultaneously finds the best shape and location of the patches for a given surface area (damping material); - extends the level set technique to concurrent shape and location optimization; - proposes a new numerical implementation to handle level set optimization problems in any complicated structure; - makes it possible to perform level set optimization in time dependent problems; - extends level set approach to higher order problems.

The level set method is a powerful way of tracking surfaces by defining the surface as a zero level set of a continuous function that is usually a signed distance function. The level set method is one of the best methods for simulating multi-phase flow because it can easily handle fast topological changes, as well as splitting and merging of fluids. In this thesis, a standard level set method was implemented in C++, using the finite element method library deal.II, to simulate incompressible two-phase flow on some benchmark problems. The results show a significant change of mass in the simulations, something that should not be allowed to happen when simulating incompressible fluids. The mass changes mainly occur in the reinitialization phase, where the level set function is rebuilt to look more like a signed distance function.