This thesis presents a new technique for the reconstruction of a smooth surface from a set of 3D data points. The reconstructed surface is represented by an everywhere -continuous subdivision surface which interpolates all the given data points. And the topological structure of the reconstructed surface is exactly the same as that of the data points. The new technique consists of two major steps. First, use an efficient surface reconstruction method to produce a polyhedral approximation to the given data points. Second, construct a Doo-Sabin subdivision surface that smoothly passes through all the data points in the given data set. A new technique is presented for the second step in this thesis. The new technique iteratively modifies the vertices of the polyhedral approximation 1CM until a new control meshM, whose Doo-Sabin subdivision surface interpolatesM, is reached. It is proved that, for any mesh M with any size and any topology, the iterative process is always convergent with Doo-Sabin subdivision scheme. The new technique has the advantages of both a local method and a global method, and the surface reconstruction process can reproduce special features such as edges and corners faithfully.

Concentration of microorganisms from a sample volume would increase the limits of detection of samples used for rapid-detection methods. Rapid detection methods are is advantageous for the food industry to rapidly test for bacteria in order release products on a timely basis. Ultrasonic concentration was considered a promising method for manipulation of microorganisms. An ultrasonic chamber consisting of parallel piezoceramic discs with a reticulated polyurethane foam mesh was used to concentrate Saccharomyces cerevisiae yeast and Escherichia coli bacteria. The concentration of yeast was seen to increase by 200% (from 8.0 x 104 cells mL-1 to 2.4 x 105 cells mL-1) while almost zero concentration of bacteria was observed. The poor concentration effect seen with the smaller microorganisms was explained by the volume dependent acoustic radiation force exerted on the particles; the concentration forces are 1,000 times smaller for a 1 μm bacteria cell versus a 10 μm yeast cell.

This thesis presents a new system that reconstructs the 3D representation of dental casts. To maintain the integrity of the 3D representation, a standard model is built to cover the blind spots that the camera cannot reach. The standard model is obtained by scanning a real human mouth model with a laser scanner. Then the model is simplified by an algorithm which is based on iterative contraction of vertex pairs. The simplified standard model uses a local parametrization method to obtain the curvature information. The system uses a digital camera and a square tube mirror in front of the camera to capture multi-view images. The mirror is made of stainless steel in order to avoid double reflections. The reflected areas of the image are considered as images taken by the virtual cameras. Only one camera calibration is needed since the virtual cameras have the same intrinsic parameters as the real camera. Depth is computed by a simple and accurate geometry based method once the corresponding points are identified. Correspondences are selected using a feature point based stereo matching process, including fast normalized cross-correlation and simulated annealing.

Many manual biomedical annotation tasks can be categorized as instances of the typical multi-label classification problem where several categories or labels from a fixed set need to assigned to an input instance. MeSH term assignment to biomedical articles and diagnosis code extraction from medical records are two such tasks. To address this problem automatically, in this thesis, we present a way to utilize latent associations between labels based on output label sets. We used random indexing as a method to determine latent associations and use the associations as a novel feature in a learning-to-rank algorithm that reranks candidate labels selected based on either k-NN or binary relevance approach. Using this new feature as part of other features, for MeSH term assignment, we train our ranking model on a set of 200 documents, test it on two public datasets, and obtain new state-of-the-art results in precision, recall, and mean average precision. In diagnosis code extraction, we reach an average micro F-score of 0.478 based on a large EMR dataset from the University of Kentucky Medical Center, the first study of its kind to our knowledge. Our study shows the advantages and potential of random indexing method in determining and utilizing implicit relationships between labels in multi-label classification problems.

This thesis of 15 hp has been implemented at Halmstad University, in collaboration with Saab Dynamics in Linköping. Saab Dynamics is a company operating in the defence industry where competition is tough. This necessitates new ways to increase efficiency in the company, which is the basis for this thesis. Saab Dynamics wants to introduce simulation driven design. Since Saab Dynamics engineers have little experience of simulation, required a user methodology with clear guidelines. Due to lack of time, they chose to assign the task to students, which resulted in this thesis. The aim of the thesis is to develop a methodology in mechanical design, where the designer uses the FE analysis early in the design process to develop the structures' mechanical properties. The methodology should be seen as a guide and a source of information to enable an iterative approach with FE-analysis, which is the basis of simulation-driven design. The iterative process of simulation driven design, which can lead to reduced lead times and cost savings in the design process. The work was carried out by three students from the mechanical engineering program between December 2014 and May 2015. Because of the scale of the project, it has been carried out by a total of three students with individual focus areas. The work has followed a self-developed method and the project began with theoretical studies of the topic to get an understanding of what has been done and what research in simulation driven design. Then conducted an empirical study on the Saab Dynamics in Linköping, in order to increase understanding of how the design process looks like. Meanwhile, sustainable development and ethical aspects has been taken into account. Much time has been devoted to investigate the possibilities and limitations of 3D Experience, which is Dassault Systèmes latest platform for 3D modelling- and simulation software. 3D Experience is the software, the methodology is based on. This thesis has resulted in a methodology for simulating at the designer level that the project team in consultation with the supervisor at Saab Dynamics managed to adapt to the company's requirements.

This work developed a stylized three dimensional benchmark problem based on Argonne National Laboratory's conceptual Advanced Burner Test Reactor design. This reactor is a sodium cooled fast reactor designed to burn recycled fuel to generate power while transmuting long term waste. The specification includes heterogeneity at both the assembly and core levels while the geometry and material compositions are both fully described. After developing the benchmark, 15 group cross sections were developed so that it could be used for transport code method verification. Using the aforementioned benchmark and 15 group cross sections, the Coarse-Mesh Transport Method (COMET) code was compared to Monte Carlo code MCNP5 (MCNP). Results were generated for three separate core cases: control rods out, near critical, and control rods in. The cross section groups developed do not compare favorably to the continuous energy model; however, the primary goal of these cross sections is to provide a common set of approachable cross sections that are widely usable for numerical methods development benchmarking. Eigenvalue comparison results for MCNP vs. COMET are strong, with two of the models within one standard deviation and the third model within one and a third standard deviation. The fission density results are highly accurate with a pin fission density average of less than 0.5% for each model.

Gas lift is a means of enhancing oil recovery from hydrocarbon reservoirs. Gas injected at the production riser base reduces the gravity component of the pressure drop and thereby, increases the supply of oil from the reservoir. Also, gas injection at the base of a riser helps to mitigate slugging and thus, improving the performance of the topside facility. In order to improve the efficiency of the gas lifting technique, a good understanding of the characteristics of gas-liquid multiphase flow in vertical pipes is very important. In this study, experiments of gas/liquid (air/water) two-phase flows, liquid/liquid of oil/water two-phase flows and gas/liquid/liquid (air/oil/water) three-phase flows were conducted in a 10.5 m high 52 mm ID vertical riser. These experiments were performed at liquid and gas superficial velocities ranging from 0.25 to 2 m/s and ~0.1 to ~6.30 m/s, respectively. Dielectric oil and tap water were used as test fluids. Instruments such as Coriolis mass flow meter, single beam gamma densitometer and wire-mesh sensor (WMS) were employed for investigating the flow characteristics. For the experiments of gas/liquid (air/water) two-phase flow, flow patterns of Bubbly, slug, churn flow regimes and transition regions were identified under the experimental conditions. Also, for flow pattern identification and void fraction measurements, the capacitance WMS results are consistent with those obtained simultaneously by the gamma densitometer. Generally, the total pressure gradient along the vertical riser has shown a significant decrease as the injected gas superficial velocity increased. In addition, the rate of decrease in total pressure gradient at the lower injected gas superficial velocities was found to be higher than that for higher gas superficial velocities. The frictional pressure gradient was also found to increase as the injected gas superficial velocity increased. For oil-water experiments, mixture density and total pressure gradient across the riser were found to increase with increasing water cut (ranging between 0 - 100%) and/or mixture superficial velocity. Phase slip between the oil and water was calculated and found to be significant at lower throughputs of 0.25 and 0.5 m/s. The phase inversion point always takes place at a point of input water cut of 42% when the experiments started from pure oil to water, and at an input water cut of 45% when the experiment’s route started from water to pure oil. The phase inversion point was accompanied by a peak increase of pressure gradient, particularly at higher oil-water mixture superficial velocities of 1, 1.5 and 2 m/s. The effects of air injection rates on the fluid flow characteristics were studied by emphasizing the total pressure gradient behaviour and identifying the flow pattern by analysing the output signals from gamma and WMS in air/oil/water experiments. Generally, riser base gas injection does not affect the water cut at the phase inversion point. However, a slight shift forward for the identified phase inversion point was found at highest flow rates of injected gas where the flow patterns were indicated as churn to annular flow. In terms of pressure gradient, the gas lifting efficiency (lowering pressure gradient) shows greater improvement after the phase inversion point (higher water cuts) than before and also at the inversion point. Also, it was found that the measured mean void fraction reaches its lowest value at the phase inversion point. These void fraction results were found to be consistent with previously published results.

Previous work on progressive mesh compression focused on triangle meshes but meshes containing other types of faces are commonly used. Therefore, we propose a new progressive mesh compression method that can efficiently compress meshes with arbitrary face degrees. Its compression performance is competitive with approaches dedicated to progressive triangle mesh compression. Progressive mesh compression is linked to mesh decimation because both applications generate levels of detail. Consequently, we propose a new simple volume metric to drive the polygon mesh decimation. We apply this metric to the progressive compression and the simplification of polygon meshes. We then show that the features offered by progressive mesh compression algorithms can be exploited for 3D adaptation by the proposition of a new framework for remote scientific visualization. Progressive random accessible mesh compression schemes can better adapt 3D mesh data to the various constraints by taking into account regions of interest. So, we propose two new progressive random-accessible algorithms. The first one is based on the initial segmentation of the input model. Each generated cluster is compressed independently with a progressive algorithm. The second one is based on the hierarchical grouping of vertices obtained by the decimation. The advantage of this second method is that it offers a high random accessibility granularity and generates one-piece decompressed meshes with smooth transitions between parts decompressed at low and high levels of detail. Experimental results demonstrate the compression and adaptation efficiency of both approaches.

Three-dimensional (3-D) medical imaging creates notable opportunities as input toward engineering analyses, whether for basic understanding of the normal function or patho-physiology of an organ, or for the simulation of virtual surgical procedures. These analyses most often require finite element (FE) models to be constructed from patient-specific 3-D medical images. However, creation of such models can be extremely labor-intensive; in addition, image processing and mesh generation are often operator-dependent, lack robustness and may be of suboptimal quality. Focusing on the human aorta, the goal of the present work is to create a fast and robust methodology for quadrilateral surface and hexahedral volume meshing from 3-D medical images with minimal user input. By making use of the segmentation capabilities of the 3-D gradient vector flow field combined with original ray-tracing and orientation control algorithms, we will demonstrate that it is possible to incrementally grow a structured quadrilateral surface mesh of the inner wall of the aorta. The process does not only require minimal input from the user, it is also robust and very fast compared to existing methods; it effectively combines segmentation and meshing into one single effort. After successfully testing the methodology and measuring the quality of the meshes produced by it from synthetic as well as real medical image datasets, we will make use of the surface mesh of the inner aortic wall to derive hexahedral meshes of the aortic wall thickness and of the fluid domain inside the aorta. We will finally outline a tentative approach to merge several structured meshes to process the main branches of the aorta.

Transient multi-phase flow problems in porous media are ubiquitous in engineering and environmental systems and processes; examples include heat exchangers, reservoir simulation, environmental remediation, magma flow in the earth crust and water management in porous electrodes of PEM fuel cells. This thesis focuses on the development of accurate and computationally efficient numerical models to simulate such flows. The research challenges addressed in this work fall in two areas. For a numerical standpoint, conventional numerical methods including Newton-Raphson linearization and a simple upwind scheme do not always provide the required computational efficiency or sufficiently accurate resolution of the flow field. From a modelling perspective, closure schemes required in volume-averaged formulations, such as the generalized Leverett J function for capillary pressure, are specific to certain media (e.g. lithologic media) and are not valid for fibrous porous media, which are of central interest in fuel cells. This thesis presents a set of algorithms that are integrated efficiently to achieve computations that are more than two orders of magnitude faster compared to traditional techniques. The method uses an adaptive operator splitting method based on an a posteriori criterion to separate the flow from the transport equations which eliminates unnecessary and costly solution of the implicit pressure-velocity term at every time step; adaptive meshing to reduce the size of the discretized problem; efficient block preconditioned solver techniques for fast solution of the discrete equations; and a recently developed artificial diffusion strategy to stabilize the numerical solution of the transport equation. The significant improvements in accuracy and efficiency of the approach is demosntrated using numerical experiments in 2D and 3D. The method is also extended to advection-dominated problems to specifically investigate two-phase flow in heterogeneous porous media involving capillary transport. Both hydrophilic and hydrophobic media are considered, and insights relevant to fuel cell electrodes are discussed.