Numerical modeling of fluid flow and dissolved species transport in the subsurface is a challenging task, given variability and measurement uncertainty in the physical properties of the rock, the complexities of multi-fluid interaction, and limited computational resources. Nonetheless, this thesis seeks to expand our modeling capabilities in the context of contaminant hydrogeology. We describe the numerical simulator CompFlow Bio and use it to model invasion of a nonaqueous phase liquid (NAPL) contaminant through the vadose zone and below the water table in a fractured porous rock. CompFlow Bio is a three-phase, multicomponent, deterministic numerical model for fluid flow and dissolved species transport; it includes capillary pressure and equilibrium partitioning relationships. We have augmented the model to include randomly generated, axis-aligned, discrete fracture networks (DFNs). The DFN is coupled with the porous medium (PM) to form a single continuum. The domain is discretized using a finite-volume scheme in an unstructured mesh of rectilinear control volumes (CVs). Herein we present the governing equations, unstructured mesh creation scheme, algebraic development of fracture intersection CV elimination, and coupling of PM CVs over a fracture plane to permit asperity contact bridged flow. We include: small scale two-phase water-air and NAPL-water simulations to validate the practice of intersection CV elimination; small scale simulations with water-air, NAPL-water, and NAPL-water-air systems in a grid refinement exercise and to demonstrate the effect of asperity contact bridged flow; intermediate scale 3D simulations of NAPL invading the saturated zone, based on the Smithville, Ontario, site; intermediate scale 2D and 3D simulations of NAPL invading the vadose zone and saturated zone with transient recharge, based on the Santa Susana Field Laboratory site, California. Our findings indicate that: the formulation provides a practical and satisfactory way of modeling three-phase flow in discretely fractured porous rock; numerical error caused by spatial discretization manifests itself as several biases in physical flow processes; that asperity contact is important in establishing target water saturation conditions in the vadose zone; and simulation results are sensitive to relative permeability-saturation-capillary pressure relationships. We suggest a number of enhancements to CompFlow Bio to overcome certain computational limitations.

The development of high-order solution methods remain a very active field of research in Computational Fluid Dynamics (CFD). These types of schemes have the potential to reduce the computational cost necessary to compute solutions to a desired level of accuracy. The goal of this thesis has been to develop a high-order Central Essentially Non Oscillatory (CENO) finite volume scheme for multi-block unstructured meshes. In particular, solutions to the compressible, inviscid Euler equations are considered. The CENO method achieves a high-order spatial reconstruction based on the k-exact method, combined with hybrid switching to limited piecewise linear reconstruction in non-smooth regions to maintain monotonicity. Additionally, fourth-order Runge-Kutta time marching is applied. The solver described has been validated through a combination of high-order function reconstructions, and solutions to the Euler equations. Cases have been selected to demonstrate high-orders of convergence, the application of the hybrid switching method, and the multi-block techniques which has been implemented.

The development of high-order solution methods remain a very active field of research in Computational Fluid Dynamics (CFD). These types of schemes have the potential to reduce the computational cost necessary to compute solutions to a desired level of accuracy. The goal of this thesis has been to develop a high-order Central Essentially Non Oscillatory (CENO) finite volume scheme for multi-block unstructured meshes. In particular, solutions to the compressible, inviscid Euler equations are considered. The CENO method achieves a high-order spatial reconstruction based on the k-exact method, combined with hybrid switching to limited piecewise linear reconstruction in non-smooth regions to maintain monotonicity. Additionally, fourth-order Runge-Kutta time marching is applied. The solver described has been validated through a combination of high-order function reconstructions, and solutions to the Euler equations. Cases have been selected to demonstrate high-orders of convergence, the application of the hybrid switching method, and the multi-block techniques which has been implemented.

Most chloroplast proteins are encoded in the nucleus and translated in the cytosol with an N-terminal transit peptide, which facilitates recognition by the receptors of the translocon at the outer membrane of chloroplasts (Toc). The Toc159 family of receptors in Arabidopsis thaliana are the primary chloroplast preprotein receptors. Members of this family differentially associate with either atToc33 or atToc34 (“at” designates the species of origin, Arabidopsis thaliana) to form structurally and functionally distinct Toc complexes; atToc159/33-containing complexes import photosynthetic preproteins, and atToc132(120)/34-containing complexes import non-photosynthetic, plastid house-keeping proteins. The Toc159 receptors are most variable in their N-terminal A-domain, suggesting that this domain may contribute to their functional specificity. The A-domain has structural properties characteristic of intrinsically unstructured protein (IUP) domains, including an abundance of acidic amino acid residues, aberrant mobility during SDS-PAGE and sensitivity to proteolysis. The overall objective of this study was to gain insight into the function of the A-domain. First, to investigate the role of the A-domain in the assembly of structurally distinct Toc complexes, full-length, truncated and domain-swapped variants of atToc159 and atToc132 were targeted in vitro to chloroplasts isolated from wild type (WT) Arabidopsis, and atToc33 and atToc34 null mutants (ppi1 and ppi3, respectively). Insertion of atToc132 was less efficient than atToc159, and was not affected by the removal or swapping of the A-domain. In contrast, removal of the A-domain of atToc159 resulted in decreased insertion, most notably into ppi1 chloroplasts, suggesting that the A-domain is important for insertion, especially into atToc34-containing complexes. These results indicate that the A-domain does play a role in targeting, and may also suggest different roles for the A-domain in targeting of atToc159 and atToc132. Second, a structural analysis of the A-domain of atToc132 and atToc159 was performed using CD and fluorescence spectroscopy to gain insight into their potential function(s). The A-domains were found to be unstructured at physiological pH, and their secondary structure increased with increasing temperature and decreasing pH, which are characteristics of IUPs. IUPs are commonly involved in protein-protein interactions, and their unstructured nature may suggest a role for the A-domains in binding transit peptides, accounting for the ability of the Toc159 receptors to differentially distinguish between a large number of diverse transit peptides that possess low sequence conservation.

The plant leaf is one of the most challenging natural objects to be realistically depicted by computer graphics due to its complex morphological and optical characteristics. Although many studies have been done on plant modeling, previous research on leaf modeling required for close-up realistic plant images is very rare. In this thesis, a novel method for modeling of the leaf shape based on the leaf venation is presented. As the first step of the method, the leaf domain is defined by the enclosure of the leaf boundary. Second, the leaf venation is interactively modeled as a hierarchical skeleton based on the actual leaf image. Third, the leaf domain is triangulated with the skeleton as constraints. The skeleton is articulated with nodes on the skeleton. Fourth, the skeleton is interactively transformed to a specific shape. A user can manipulate the skeleton using two methods which are complementary to each other: one controls individual joints on the skeleton while the other controls the skeleton through an intermediate spline curve. Finally, the leaf blade shape is deformed to conform to the skeleton by interpolation. An interactive modeler was developed to help a user to model a leaf shape interactively and several leaves were modeled by the interactive modeler. The ray-traced rendering images demonstrate that the proposed method is effective in the leaf shape modeling.

Most chloroplast proteins are encoded in the nucleus and translated in the cytosol with an N-terminal transit peptide, which facilitates recognition by the receptors of the translocon at the outer membrane of chloroplasts (Toc). The Toc159 family of receptors in Arabidopsis thaliana are the primary chloroplast preprotein receptors. Members of this family differentially associate with either atToc33 or atToc34 (“at” designates the species of origin, Arabidopsis thaliana) to form structurally and functionally distinct Toc complexes; atToc159/33-containing complexes import photosynthetic preproteins, and atToc132(120)/34-containing complexes import non-photosynthetic, plastid house-keeping proteins. The Toc159 receptors are most variable in their N-terminal A-domain, suggesting that this domain may contribute to their functional specificity. The A-domain has structural properties characteristic of intrinsically unstructured protein (IUP) domains, including an abundance of acidic amino acid residues, aberrant mobility during SDS-PAGE and sensitivity to proteolysis. The overall objective of this study was to gain insight into the function of the A-domain. First, to investigate the role of the A-domain in the assembly of structurally distinct Toc complexes, full-length, truncated and domain-swapped variants of atToc159 and atToc132 were targeted in vitro to chloroplasts isolated from wild type (WT) Arabidopsis, and atToc33 and atToc34 null mutants (ppi1 and ppi3, respectively). Insertion of atToc132 was less efficient than atToc159, and was not affected by the removal or swapping of the A-domain. In contrast, removal of the A-domain of atToc159 resulted in decreased insertion, most notably into ppi1 chloroplasts, suggesting that the A-domain is important for insertion, especially into atToc34-containing complexes. These results indicate that the A-domain does play a role in targeting, and may also suggest different roles for the A-domain in targeting of atToc159 and atToc132. Second, a structural analysis of the A-domain of atToc132 and atToc159 was performed using CD and fluorescence spectroscopy to gain insight into their potential function(s). The A-domains were found to be unstructured at physiological pH, and their secondary structure increased with increasing temperature and decreasing pH, which are characteristics of IUPs. IUPs are commonly involved in protein-protein interactions, and their unstructured nature may suggest a role for the A-domains in binding transit peptides, accounting for the ability of the Toc159 receptors to differentially distinguish between a large number of diverse transit peptides that possess low sequence conservation.

Borders of flow field around immersed bodies can be extended to long distances since there are no physical boundaries. In computational practice however, the flow domain must be restricted to a reasonable size by imposing appropriate boundary conditions at the edges of the computational space. In this thesis work, streamlines obtained from potential flow solution in a relatively large spatial domain are utilized to specify the boundaries and boundary conditions for a more restricted computational domain to be used for detailed viscous flow computations. A grid generation code is adopted for generation of unstructured triangular grid systems for domains involving multiple immersed bodies of any shape at arbitrary orientations such as a group of tall buildings in horizontal plane. Finite volume method is used in the solution of Laplace equation for the stream function. A deformation modulus is introduced as a probe parameter to aid locating the viscous flow boundaries. The computer code acts as a preprocessor for viscous flow computations, specifying the computational boundaries, the boundary conditions and generating the computational grid.

The multigrid technique is one of the most effective techniques to achieve the reduction of the CPU cost for flow solvers. The multigrid strategy uses the multilevel grids which are the coarsening subsets of fine grid. An explicit solver rapidly reduces the high frequency errors on the computational grids. Since high frequency errors on coarse grids correspond to low frequency errors on fine grids, cycling through the coarse grid levels rapidly reduces the errors ranging from high-to-low frequency. The aim of this study is, therefore, to accelerate SENSE3D solver developed by TUBITAK-SAGE by implementating multigrid concept. In this work, a novel grid coarsening method suitable for cell-centered hybrid/unstructured grids is developed to provide the cells with high aspect ratio. This new grid coarsening technique relies on the agglomeration of cells based on their distribution on octree data structure. Then, the multigrid strategy is implemented to the baseline flow solver. During this implementation, the flux calculation along the face loops is modified without changing cell-centered scheme. The performance of the coarsening algorithm is investigated for all grid types in two and three dimension. The grid coarsening algorithm produces well defined, nested, body fitted coarser grids with aspect ratios of one and the coarse grids have similar characteristics of Cartesian grids. Then, the multigrid flow solutions are obtained at inviscid, laminar and turbulent flows. It is shown that, the convergence accelerations are up to 14 times for inviscid flows and in a range of 4 to 110 fold for turbulent flow solutions.

In the past, information was stored more or less well-structured in database. Nowadays, a lot of information is presented in unstructured format. The management of and retrieval from such large vast of textual information has been a challenging issue for organizations or individuals. Information extraction is the process of extracting relevant data from semi-structured or unstructured documents and transforming them into structured representations. Many information extraction learning techniques have been proposed. However, they are ineffectiveness on unstructured documents. Thus, in the research, we proposed a new information extraction learning algorithm, called LIEF, that enhancing existing information extraction learning techniques. According to the empirical evaluations on news documents that are unstructured format, the LIEF algorithm proposed showed its capabilities in accuracy rate.

A spectral element algorithm for solution of the incompressible Navier-Stokes and heat transfer equations is developed, with an emphasis on extending the classical conforming Galerkin formulations to nonconforming spectral elements. The new algorithm employs both the Constrained Approximation Method (CAM), and the Mortar Element Method (MEM) for p-and h-type nonconforming elements. Detailed descriptions, and formulation steps for both methods, as well as the performance comparisons between CAM and MEM, are presented. This study fills an important gap in the literature by providing a detailed explanation for treatment of p-and h-type nonconforming interfaces. A comparative eigenvalue spectrum analysis of diffusion and convection operators is provided for CAM and MEM. Effects of consistency errors due to the nonconforming formulations on the convergence of steady and time dependent problems are studied in detail. Incompressible flow solvers that can utilize these nonconforming formulations on both p- and h-type nonconforming grids are developed and validated. Engineering use of the developed solvers are demonstrated by detailed parametric analyses of oscillatory flow forced convection heat transfer in two-dimensional channels.