This thesis has two major goals; first to develop scalable scripts for steady-state analysis, then to perform a case study on the dynamic properties of a vertical pile. The scripts are based on the numerical library PETSc for parallel linear algebra. This opens up the opportunity to use the scripts to solve large-scale models on supercomputers. The performance of the scripts are verified against problems with analytical solutions and the commercial software ABAQUS. The case study compares the numerical results with those obtained from an approximate solution.   The results from this thesis are verified scripts that can find a steady-state solution for linear-elastic isotropic solids on supercomputers. The case study has shown differences between numerical and semi-analytical solutions for a vertical pile. The dynamic stiffness show differences within reasonable limits but the equivalent viscous damping show larger differences. This is believed to come from the material damping in the soil that has been excluded from the approximate solution.   These two results make it possible for further case studies on typical three-dimensional problems, that result in large-scale models, such as the dynamic properties of a slanted pile or pile-groups. The scripts can easily be expanded and used for other interesting research projects and this is the major outcome of from this thesis.

The natural variation of strength properties within brittle materials leads to size effect, a well-known phenomenon whereby the mean strength of a material is observed to decrease as the stressed volume increases. An important implication of size effect is that size adjustment parameters must be incorporated into multi-axial constitutive and failure models used in numerical simulations to predict material response to loading. This experimental study seeks to verify and quantify the presence of depth effect under shear failure in the orthotropic principal material directions of parallel strand lumber (PSL) and laminated veneer lumber (LVL). Torsion tests have been performed on specimens of fixed length and differing cross section to get a pure shear failure, by using a Universal Test Machine. The experimental results indicate that there is no depth effect for LVL from torsional shear stresses. PSL testing was limited to one size, and depth effect was not evaluated. A finite element model was built to simulate the torsional test for the 44x140mm LVL specimen. Comparing the experimental test results and the simulation results, the model provided an accurate prediction of the torsional test for Structural Composite Lumber.

A substantial amount of research has been done in the field of engineering knowledge management, where countless ontologies have been developed for various applications within the engineering community. However, despite the success shown in these research efforts, the techniques have not been adopted by industry. This research aims to uncover the reasons for the slow adoption of engineering knowledge frameworks, namely ontologies, in industry. There are two projects covered in this thesis. The first project is the development of a cross-domain ontology for the Biomesh Project, which spans the fields of mechanical engineering, biology, and anthropology. The biology community is known for its embrace of ontologies and has made their use quite popular with the creation of the Gene Ontology. This ontology spawned the establishment of the Open Biological and Biomedical Ontologies (OBO) Foundry, a consortium which approves and curates ontologies in the biology field. No such consortium exists in the field of engineering. This project demonstrates the usefulness of curated reference ontologies. Ontological knowledge bases in four different domains were imported and integrated together to connect previously disparate information. A case study with data from the Biomesh Project demonstrates cross-domain queries and inferences that were not possible before the creation of this ontology. In the second part of this thesis we investigate the usability of current ontology tools. Protégé, the most popular ontology editing tool, is compared to OntoWiki, a semantic wiki. This comparison is done using proven techniques from the field of Human-computer interaction to uncover usability problems and point out areas where each system excels. A field of 16 subjects completed a set of tasks in each system and gave feedback based on their experience. It is shown that while OntoWiki offers users a satisfying interface, it lacks in some areas that can be easily improved. Protégé provides users with adequate functionality, but it is not intended for a novice user.

In order to understand the relationship between feeding behavior and the evolution of mammalian skull form, it is essential to evaluate the impact of bite force over large regions of skull. There are about 1,100 bat species worldwide, which represent about 20% of all classified mammal species. Hence, a study in the evolution of bat skull form may provide general understanding of the overall evolution of skull form in mammals. These biomechanical studies are generally performed by first building solid Finite Element (FE) models of skull from micro CT scans. This process of building FE models from micro CT scans is both tedious and time consuming. Therefore a new approach is developed in this research project to build these FE models quickly and efficiently. I have used SolidWorks to build a parameterized, three dimensional surface CAD model of a skull of the short-tailed fruit bat, Carollia perspicillata, by using coordinate data from an STL model of the species. The overall shape of this model closely resembled that of solid model of C. perspiciallata constructed from micro CT scans. Finite element analyses of the solid and surface models yielded comparable results in terms of magnitude and distribution of von Mises stress and mechanical advantage. Using this parametric surface model, the FE plate or shell element models of different bat species were generated by varying two parameters, palate length and palate width. Parametric analyses were performed on these FE plate models of skulls and response surfaces of performance criteria: von Mises stress, strain energy and mechanical advantage were generated by varying the input parameters. After generating response surfaces, species of bats from the morphologically diverse family of New World leaf-nosed bats (Family Phyllostomidae) were overlain on these response surfaces to determine which portions of the performance design space (palate length X width) are and are not occupied. These plots serve as a foundation for understanding the affect of different performance criteria on the evolution of bat skull form.

This study proposed a finite element procedure for protein normal mode analysis (NMA). The finite element model adopted the protein solvent-excluded surface to generate a homogeneous and isotropic volume. A simplified triangular approximation of coarse molecular surface was generated from the original surface model by using the Gaussian-based blurring technique. Similar to the widely adopted elastic network model, the finite element model holds a major advantage over standard all-atom normal mode analysis: the computationally expensive process of energy minimization that may distort the initial protein structure has been eliminated. This modification significantly increases the efficiency of normal mode analysis. In addition, the finite element model successfully brings out the capability of normal mode analysis in low-frequency/high collectivity molecular motion by capturing protein shape properties. Fair results from six protein models in this study have fortified the capability of the finite element model in protein normal mode analysis.

Artificial Neural Network (ANN) ensemble and Response Surface Method (RSM) surrogate models were generated from Finite Element (FE) simulations to predict the overpressure load and vehicle impact response of a novel rapidly deployable protective structure. A Non-dominated Sorting Genetic Algorithm-II (NSGA-II) was used in conjunction with the surrogate models to determine structure topology input variable configurations which were suited to produce the optimal balance of minimum mass, minimum rotation angle, minimum displacement, and maximum total length of the deployable structure. The structure was designed to retract into a container, be lightweight to facilitate transportation, and be able to adapt to varying terrain slopes. This research demonstrates that, in comparison to the RSM, ANN ensembles can more accurately and efficiently be used for identifying optimal design solutions for multi-objective design problems when two surrogate models from the same method corresponding to separate FE models are used simultaneously in a NSGA-II.

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A new spline space, the hierarchical structure-preserving B-spline space, is introduced and implemented in the analysis of Stokes flow. The space, when properly constrained, is shown to be stable and to have at least optimal convergence rates in the velocity field and suboptimal convergence rates in the pressure field. However, results show that superoptimal convergence can often be expected in the pressure field, likely due to error reduction in the velocity field. Like other hierarchical spline spaces, these splines are shown to greatly increase accuracy and to drastically lower computation times for analyses on domains whose solution fields have singularities or could otherwise benefit from local refinement. With the advent of this adaptive, locally-refineable, high-fidelity technology, isogeometric methods can become more feasible for use in fluid analyses.

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