Doctor of Philosophy

dissertationOne of the fundamental building blocks of many computational sciences is the construction and use of a discretized, geometric representation of a problem domain, often referred to as a mesh. Such a discretization enables an otherwise complex domain to be represented simply, and computation to be performed over that domain with a finite number of basis elements. As mesh generation techniques have become more sophisticated over the years, focus has largely shifted to quality mesh generation techniques that guarantee or empirically generate numerically well-behaved elements. In this dissertation, the two complementary meshing subproblems of vertex placement and element creation are analyzed, both separately and together. First, a dynamic particle system achieves adaptivity over domains by inferring feature size through a new information passing algorithm. Second, a new tetrahedral algorithm is constructed that carefully combines lattice-based stenciling and mesh warping to produce guaranteed quality meshes on multimaterial volumetric domains. Finally, the ideas of lattice cleaving and dynamic particle systems are merged into a unified framework for producing guaranteed quality, unstructured and adaptive meshing of multimaterial volumetric domains

Meshing for Multimaterial Biological Volumes

poste

Dietary Analysis of Batfishes (Lophiiformes: Ogcocephalidae) in the Gulf of Mexico

Stomach content analyses, performed on three species of batfishes, Halieutichthys aculeatus, Ogcocephalus declivirostris, and Ogcocephalus pantosticus collected in the Gulf of Mexico in summer (June-July) and fall (Oct.-Nov.) 2002 and 2003, revealed a variety of benthic invertebrates, particularly gastropods, polychaete worms, and xanthid crabs. Schoener\u27s dietary overlap indices (Sl) were calculated between the three species within the same seasons, and within each species between seasons. SI values indicated that each species consumed a different assemblage of prey and that two of the species exhibited temporal variation in diet

Lattice cleaving: a multimaterial tetrahedral meshing algorithm with guarantees

pre-printWe introduce a new algorithm for generating tetrahedral meshes that conform to physical boundaries in volumetric domains consisting of multiple materials. The proposed method allows for an arbitrary number of materials, produces high-quality tetrahedral meshes with upper and lower bounds on dihedral angles, and guarantees geometric fidelity. Moreover, the method is combinatoric so its implementation enables rapid mesh construction. These meshes are structured in a way that also allows grading, to reduce element counts in regions of homogeneity. Additionally, we provide proofs showing that both element quality and geometric fidelity are bounded using this approach

Effects of Aqueous Solutions on the Slow Crack Growth of Soda-Lime-Silicate Glass

The slow crack growth (SCG) parameters of soda-lime-silicate were measured in distilled and saltwater of various concentrations in order to determine if the presence of salt and the contaminate formation of a weak sodium film affects stress corrosion susceptibility. Past research indicates that solvents affect the rate of crack growth; however, the effects of salt have not been studied. The results indicate a small but statistically significant effect on the SCG parameters A and n at high concentrations; however, for typical engineering purposes, the effect can be ignored

Effect of Control Mode and Test Rate on the Measured Fracture Toughness of Advanced Ceramics

The effects of control mode and test rate on the measured fracture toughness of ceramics were evaluated by using chevron-notched flexure specimens in accordance with ASTM C1421. The use of stroke control gave consistent results with about 2% (statistically insignificant) variation in measured fracture toughness for a very wide range of rates (0.005 to 0.5 mm/min). Use of strain or crack mouth opening displacement (CMOD) control gave approx. 5% (statistically significant) variation over a very wide range of rates (1 to 80 m/m/s), with the measurements being a function of rate. However, the rate effect was eliminated by use of dry nitrogen, implying a stress corrosion effect rather than a stability effect. With the use of a nitrogen environment during strain controlled tests, fracture toughness values were within about 1% over a wide range of rates (1 to 80 micons/m/s). CMOD or strain control did allow stable crack extension well past maximum force, and thus is preferred for energy calculations. The effort is being used to confirm recommendations in ASTM Test Method C1421 on fracture toughness measurement

Effect of Control Mode and Test Rate on Fracture Toughness of Advanced Ceramics

The effects of control mode and rate on the fracture toughness of ceramics were measured by using chevron-notched flexure specimen in accordance with ASTM C1421. The use of stroke control gave consistent results with about 2% variation in measured fracture toughness for a very wide range of rates (0.005 to 0.5 mm/min). Use of strain or CMOD control gave ~5% variation over a very wide range of rates, with the measurements being a function of rate. However, the effect was eliminated by use of dry nitrogen, implying a stress corrosion effect rather than a stability effect. With the use of nitrogen for strain control, fracture toughness values were within about 1% over a wide range of rates (1 to 80 /s). CMOD or strain control did allow stable crack extension well past maximum load, and thus is preferred for energy calculations. The effort is being used to confirm recommendations in ASTM International standard C1421 on fracture toughness measurement

Navigating exponentially large spaces in biology : methods for directed evolution and smFRET time series analysis

The recent explosion of high throughput technologies in many fields of biology has necessitated the use of sophisticated algorithms to guide experimental design and analyze results. This thesis explores two such fields: directed protein evolution and single molecule fluorescence resonance energy transfer analysis. Although the methodologies and applications of the fields differ greatly, they are both limited by a process which scales exponentially with problem size. In the former case, the problem is determining which combination of amino acids should be mutated to enhance or create protein function. In the latter case, the problem is inferring the number of conformations a molecule explores during an experiment and the probability of being in each state at each time point in the experiment. Methods to address both problems will be presented in this thesis

Hierarchically-coupled hidden Markov models for learning kinetic rates from single-molecule data

We address the problem of analyzing sets of noisy time-varying signals that all report on the same process but confound straightforward analyses due to complex inter-signal heterogeneities and measurement artifacts. In particular we consider single-molecule experiments which indirectly measure the distinct steps in a biomolecular process via observations of noisy time-dependent signals such as a fluorescence intensity or bead position. Straightforward hidden Markov model (HMM) analyses attempt to characterize such processes in terms of a set of conformational states, the transitions that can occur between these states, and the associated rates at which those transitions occur; but require ad-hoc post-processing steps to combine multiple signals. Here we develop a hierarchically coupled HMM that allows experimentalists to deal with inter-signal variability in a principled and automatic way. Our approach is a generalized expectation maximization hyperparameter point estimation procedure with variational Bayes at the level of individual time series that learns an single interpretable representation of the overall data generating process.Comment: 9 pages, 5 figure

Allosteric collaboration between elongation factor G and the ribosomal L1 stalk directs tRNA movements during translation

Determining the mechanism by which transfer RNAs (tRNAs) rapidly and precisely transit through the ribosomal A, P and E sites during translation remains a major goal in the study of protein synthesis. Here, we report the real-time dynamics of the L1 stalk, a structural element of the large ribosomal subunit that is implicated in directing tRNA movements during translation. Within pre-translocation ribosomal complexes, the L1 stalk exists in a dynamic equilibrium between open and closed conformations. Binding of elongation factor G (EF-G) shifts this equilibrium towards the closed conformation through one of at least two distinct kinetic mechanisms, where the identity of the P-site tRNA dictates the kinetic route that is taken. Within post-translocation complexes, L1 stalk dynamics are dependent on the presence and identity of the E-site tRNA. Collectively, our data demonstrate that EF-G and the L1 stalk allosterically collaborate to direct tRNA translocation from the P to the E sites, and suggest a model for the release of E-site tRNA