This dissertation is a combination of both research and teaching experience. Part I will cover research done in the area of organocatalyzed synthesis of optically active 4-substituted 2-cyclohexenones, while Part II will cover teaching experience at University of West Florida. 4-substituted 2-cyclohexenones are important building blocks for natural products. Both racemic and enantioselective syntheses of these small molecules have been reported, however, most methodologies are limited to very few substrates and necessitate four to more number of steps. A two step syntheses of 4-substituted 2-cyclohexenones were recently provided independently by Baran and Nicolaou groups en route to dihydrojunenol and ent-7-epizingiberene respectively. Both groups used base-mediated intramolecular aldol condensation of optically pure monosubstituted acyclic ketoladehydes. Applying Baran's LiOH-mediated aldol condensation to both the benzyl and ethyl substituted ketoaldehydes afforded cyclization products with significant erosion of optical purity. A mechanistic study of the reaction and a reasonable justification of such erosion in optical purity are provided. Inspired by the base-catalyzed aldol condensation, we sought synthesizing optically active 4-substituted 2-cyclohexenones via organocatalyzed Robinson annulation approach (Michael addition-Aldol condensation). Finding a set of organocatalyzed conditions to promote the enolendo intramolecular aldol condensation of acyclic ketoaldehydes with low erosion of optical purity is discussed. Finally a neutral set of organocatalyzed conditions is offered and expanding the methodology to synthesize a library of ten optically active 4-susbtituted 3-cyclohexenones is reported. Part II of this dissertation covers the experience in applying the Seven Principles for Good Practice in teaching organic chemistry II course at University of West Florida. It is generally accepted that organic chemistry is one of the fields where the Seven Principles are least applied. Working as teaching assistant for different organic chemistry professors at FSU was extremely helpful in (1) observing the different teaching strategies applied in classroom and (2) examining the response of students to certain activities done in class, laboratory or recitation. In fall 2010, a chance of applying personal teaching strategies was offered, efforts to apply the seven principles is described, finishing with conclusions. / A Dissertation submitted to the Department of Chemistry and Biochemistry in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Fall Semester, 2012. / November 5, 2012. / 4-substituted 2-Cyclohexenones, Aldol condensation, Michael addition, Organocatalyzed, Proline derivative, Seven Principle for Good Practice / Includes bibliographical references. / D. Tyler McQuade, Professor Directing Dissertation; Sherry A. Southerland, University Representative; Qing-Xiang (Amy) Sang, Committee Member; Gregory B. Dudley, Committee Member; Igor V. Alabugin, Committee Member.

One of the mechanisms of cardiac arrhythmias is the self-organization of electrical waves in the heart. These waves can anchor to scar tissue, collagen fibers, and coronary vessels. The anchoring generates stationary electrical signals that compete with the heart's natural pacemakers. When anchored, the electrical wave acquires a geometry of a spiral in a two-dimensional system and of a scroll in three-dimensions. These patterns are also observed in the chemical medium provided by the Belousov-Zhabotinsky reaction. These two systems share the property of excitability. Reason for which, the chemical system is used as a model medium to determine the effects and mechanisms during the anchoring of scroll waves. This dissertation describes experimental and numerical results of the dynamics of three-dimensional waves in heterogeneous Belousov-Zhabotinsky reaction media. Here, the focus is on scroll rings which are scroll waves with circular geometry. These waves are characterized by their rotation around a closed filament loop. In a homogeneous medium with positive filament tension, these free filament rings contract and collapse at a rate that is a function of their curvature. In non-homogeneous media, scroll rings can anchor to hetero- geneities (i.e. unexcitable regions within the reaction medium); depending on the obstacle's size, the pinning can be a success or a failure. In this research cylindrical, spherical and toroidal-shaped heterogeneities are used to pin scroll rings. The pinning process affects the stability and the collapsing time of the filament loops. This stability means that the contraction and collapse of the filament are prevented; consequently the filament loop becomes stationary. The stabilization may be induced by filament-filament interaction in the proximity of the pinning sites. This interaction seems to induce the self-wrapping of the filament along the heterogeneity. In general, this dissertation reports the characterization of these stationary filaments and the discussion of the possible mechanism that allows the vortex stabilization. The dynamics of pinned scroll rings is also analyzed in terms of the curvature-flow model, the Burgers' equation and the Barkley model. The unpinning of filament loops anchored to spherical heterogeneities is also investigated. For this purpose electric fields of different strength are applied to the BZ-medium. In general, the electric field forces the pinned scroll ring to change its initial shape, unpin, rotate, and drift. Strong fields induces the scroll wave to expand instead of collapse and also the formation of new filaments by a wavebreak mechanism. More experimental and computational research is needed to a) explain in detail the mechanism behind the stabilization of vortices by pinning, b) understand the role of the excitability of the heterogeneity in the pinning process, and c) elucidate the robustness of the pinned structure and its dependence on the heterogeneity's characteristics. / A Dissertation submitted to the Department of Chemistry and Biochemistry in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Fall Semester, 2012. / November 6, 2012. / Belousov-Zhabotinsky, Excitabile media, Filament dynamics, Scroll waves, Spiral waves, Ventricular Arrhythmias / Includes bibliographical references. / Oliver Steinbock, Professor Directing Thesis; Richard Bertram, University Representative; Naresh Dalal, Committee Member; Lei Zhu, Committee Member.

Controlling cell fate via mechanical properties of the culture substrates provides an important tool for biomedical applications. Thin films of polyelectrolyte multilayers (PEMUs) have been used as substrates for cell culture due to their biocompatibility. Photocrosslinkable polyelectrolyte multilayers were prepared from poly(acrylic acid) grafted with photosensitive benzophenone (PAABp) as the polyanion and poly(allylamine hydrochloride) (PAH) as the polycation. Young's modulus measured by force spectroscopy using nano-indentation showed smooth controlled increase after irradiation with UV light. The permeability of PEMUs for iodide ions, measured with a rotating disc electrode, decreased significantly. The surface wettability and charge density were not affected by irradiation, suggesting that surface chemistry and charge remained essentially unaltered. This provides substrate material for cell culture applications where the only variable is the mechanical stiffness. Since photocrosslinking provided control over the region of crosslinking, photomasks were used to prepare substrates with gradient elasticity. The behavior of rat aortic smooth muscle cells (A7r5) and osteosarcoma (U2OS) was followed on uniform substrates of increasing stiffness and on substrates with gradient elasticity. A7r5 cells detected the elasticity gradient and those that were on the soft side could polarize and orient towards the stiff side, where they showed better adhesion. U2OS cells also showed preference to the stiff side; however U2OS cells that were on the soft side did not adhere and underwent apoptosis. Nano-indentation was used to study some important fundamental properties of polyelectrolyte multilayer from poly(diallyldimethylammounium chloride) PDADMAC as the polycation and sodium poly(styrene sulfonate) (NaPSS) as the polyanion, which allowed proposing mechanism for PEMU build-up. The degree of swelling varied depending on the type of polyelectrolyte on the surface, with PDADMA-ending films more swollen than PSS ending films. This observation correlated well with the change in modulus. This suggested that PDADMA-ending films are extrinsically compensated while PSS-ending films are more intrinsically compensated. Also using nano-indentation, we demonstrated that the surface features and roughness of polyelectrolyte multilayers were not due to phase separation. Using nano-indentation, we demonstrated the role of water in controlling the mechanical properties of PEMUs. Previously, it was shown that salt plasticizes PEMUs and they were termed "saloplastics". A complimentary study was done to investigate the plasticizing effect of water. We used osmotic stress to control the amount of water in the films without affecting the degree of ionic crosslinks. Poly(ethylene glycol) (PEG) was used as the osmotic stressor. We showed that water increases free volume between the polyelectrolyte chains and acted as lubricant and the elastic modulus increases with decreasing water content. Water was also found to contribute to the viscoelastic properties of the polyelectrolyte multilayer, suggesting that water acts in plasticizing polyelectrolyte multilayers. / A Dissertation submitted to the Department of Chemistry and Biochemistry in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Fall Semester, 2012. / October 31, 2012. / cell adhesion, modulus, multilayer, nanoindentations, plasticizer, polyelecrolytes / Includes bibliographical references. / Joseph B. Schlenoff, Professor Directing Dissertation; Teng Ma, University Representative; Igor Alabugin, Committee Member; Mike Roper, Committee Member; Alan Marshall, Committee Member.

Carbon nanotubes (CNTs) possess extraordinary electrical properties including conductivity that is comparable to metals and breakdown current density that is orders of magnitude higher than copper. In order to take advantage of the electrical performance of CNTs in engineering applications, macroscopic carbon nanotube networks (NTN) are fabricated by entangling large amounts of CNTs into thin sheets. However, the electrical properties of these networks are much lower than those of individual nanotubes. Stretch-induced alignment of CNTs is an effective approach to enhance the electrical conductivity of the NTNs. However, the alignment mechanism of NTNs during the stretching process has not been fully investigated. This study employed in-situ X-ray and Raman scattering techniques to characterize the NTN structural evolution during stretch-induced alignment. The observed inhomogeneous alignment of NTNs prompts the need for a method that accurately determines the degree of nanotube alignment in bulk materials. A method that combines X-ray scattering and electrical anisotropy measurement was explored and proposed to determine the aligned fractions of nanotubes. Based on the characterization results, the structure-property relationship of NTNs and their electrical conductivity was studied through a 3D physics-based electrical model. The model was built in two stages. First, the structural model of NTNs was built using coarse-grained molecular dynamics, which provides high fidelity representation of the waviness, contacts and self-assembly of constituent nanotubes and ropes that originated from the van der Waals interactions. By applying tensile strains, the dynamics model also enabled the direct simulation of the dynamics of networks aligned through stretching. After the network structure was established, the simulated NTNs were translated into equivalent electrical circuits. The electrical model was developed based on the Simulation Program with Integrated Circuit Emphasis, which allows us to directly conduct device design and analysis using NTNs. This model is able to capture the effects of alignment and contact changes on the electrical properties of NTNs. Based on the understanding of the unique contact resistance dominated transport mechanism of NTNs, sensor applications of the novel materials were explored. By manipulating the tunneling barrier through either polymer molecule insertion or increasing the tunneling distances, NTNs were studied for potential applications in detecting organic solvent leakage and sensing tensile strains. Scaling-up of sensor fabrication using aligned NTNs and advanced printing technology was also explored and demonstrated. / A Dissertation submitted to the Department of Industrial and Manufacturing Engineering in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Fall Semester, 2012. / November 2, 2012. / Includes bibliographical references. / Richard Liang, Professor Directing Thesis; Petru Andrei, University Representative; Arda Vanli, Committee Member; Chuck Zhang, Committee Member.

In the present work, we investigate the internal fields generated by the dislocation structures that form during the deformation of copper single crystals. In particular, we perform computational modeling of the statistical and morphological characteristics of the dislocation structures obtained by dislocation dynamics simulation method and compare the results with X-ray microscopy measurements of the same data. This comparison is performed for both the dislocation structure and their internal elastic fields for the cases of homogeneous deformation and indentation of copper single crystals. A direct comparison between dislocation dynamics predictions and X-ray measurements plays a key role in demonstrating the fidelity of discrete dislocation dynamics as a predictive computational mechanics tool and in understanding the X-ray data. For the homogeneous deformation case, dislocation dynamics simulations were performed under periodic boundary conditions and the internal fields of dislocations were computed by solving an elastic boundary value problem of many-dislocation system using the finite element method. The distribution and pair correlation functions of all internal elastic fields and the dislocation density were computed. For the internal stress field, the availability of such statistical information paves the way to the development of a density-based mobility law of dislocations in continuum dislocation dynamics models, by correlating the internal-stress statistics with dislocation velocity statistics. The statistical analysis of the lattice rotation and the dislocation density fields in the deformed crystal made possible the direct comparison with X-ray measurements of the same data. Indeed, a comparison between the simulation and experimental measurements has been possible, which revealed important aspects of similarity and differences between the simulation results and the experimental data. In the case of indentation, which represents a highly inhomogeneous deformation, a contact boundary value problem was solved in conjunction with a discrete-dislocation dynamics simulation model; the discrete dislocation dynamics simulation was thus enabled to handle finite domains under mixed traction/displacement boundary conditions. The load-displacement curves for indentation experiments were analyzed with regard to cross slip, indentation speed and indenter shape. The lattice distortion fields obtained by indentation simulations were directly compared with their experimental counterparts. Other indentation simulations were also carried out, giving insight into different aspects of micro-scale indentation deformation. / A Dissertation submitted to the Department of Scientific Computing in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Fall Semester, 2012. / November 2, 2012. / Copper, Dislocation Dynamics, Indentation, Plasticity, Size effects / Includes bibliographical references. / Anter El-Azab, Professor Directing Thesis; Leon van Dommelen, University Representative; Gordon Erlebacher, Committee Member; Ming Ye, Committee Member; Xiaoqiang Wang, Committee Member.

Metallic nodules are common in metamorphosed ordinary chondrites. The origin of metal nodules has been debated because the mechanism of the formation of metal nodules is not known. Several proposed scenarios, e.g., the metal nodules and veins could be shock melted products of chondritic metal grains (Widom et al., 1986, Rubin 1999), and/or could be formed by shock-induced vaporization of bulk chondrite material consisting of small metal grains, silicates, and troilite (Widom et al., 1986), or formed by sub-solidus growth (Kong et al., 1998). Nebular origins proposed for nodules were not very compelling because such nodules are not found in unequilibrated ordinary chondrites. In this study, we tested these hypotheses of origin and formation of metal nodules and veins in L chondrites by collection of a comprehensive set of siderophile element analyses, which include many refractory (e.g., W, Re, Os, Ir, Pt, Ru, Rh, Mo) and volatile (Au, As, Sb, Cu, Ga, Ge, Sn) elements by laser ablation ICP-MS. The siderophile element patterns of metal grains measured as spots and tracks show large enrichments and depletions in the more compatible siderophile elements (Re, Os, Ir); a limited range of W and Mo abundances; Pd abundances that plot both above and below bulk L chondrite metal; high Au-As abundances; and systematic depletions of Cu, Sb and Sn. Therefore, the results of this study indicate that the origin of observed compositional variations of siderophile elements from metallic nodules in samples is partial melts of L chondritic composition that have undergone some fractional crystallization. Models involving sub-solidus growth or troilite volatilization/recondensation fail to meet the constraints imposed by the siderophile element patterns of the nodule metal. Sub-solidus cooling resulted in kamacite-taenite fractionation which disturbed magmatic relationships between Co and Ni and Au and As, but retained those of Re and Ir with Os. A grain retaining a diffusive profile provided constraints on temperature (T=1573±100 K) and timescale ~1 year, for the melting processes that implies a well-insulated post-shock environment for cooling of the nodules. A comparison of the bulk nodule composition with calculated bulk metallic fractions of H, L and LL chondrites indicates that the nodules are more reduced than the composition of L chondrite metallic fractions and are similar to the metallic fractions of H chondrites. / A Thesis submitted to the Department of Earth, Ocean, and Atmospheric Science in partial fulfillment of the requirements for the degree of Master of Science. / Summer Semester, 2012. / July 2, 2012. / Compositions and origin, L-Chondrites, Metal nodules, Ordinary chondrites / Includes bibliographical references. / Munir Humayun, Professor Directing Thesis; Vincent Salters, Committee Member; Leroy Odom, Committee Member.

RNA-RNA interactions involved in recognition associated with ribozyme catalysis are essential for ribozyme function. Research described in this dissertation focuses on RNA-RNA interactions at, and in the vicinity of two splice sites of two splicing systems: the U2-dependent spliceosome and a yeast mitochondrial group II intron ai5gamma;. In the U2-dependent spliceosomes, an RNA complex is formed by the U2 and U6 snRNAs, creating a network of indispensable helices, which are believed to be the active components of the spliceosome. Helix III has been shown to be essential in mammals. The goal of our study was to analyze structural evidence for formation of U2-U6 Helix III in an in vitro protein-free system, including the possibility of interaction with the intron strand. The questions addressed were: a) which pairing of the three available strands dominates; b) alternatively, if the three strands form a complex, is there an RNA triple helix in solution? NMR studies of the three strand complex representing the U2-intron-U6 pairing showed formation of the U2-intron duplex and the U2-U6 duplex, but no interaction of the U6 snRNA with the U2-intron duplex in the region of the putative Helix III. NMR studies of the extended Helix III samples corroborate this finding and confirm that the U6 snRNA immediately upstream of the ACAGAGA sequence does not interact with the U2-intron duplex in the region of the proposed Helix III. Group II introns, large ribozymes and mobile genetic elements found in prokaryotes and eukaryotic organelles, share common structural and catalytic features with the spliceosome in eukaryotes. At the functional core of group II introns is the pairing of the EBS1-IBS1 sequences (exon binding sequence one and intron binding sequence one, respectively), which is essential for preserving fidelity of the splice site. The EBS1 guide sequence is a part of an 11-nucleotide loop at the terminus of the ID3 stem loop, which is a subdomain of Domain one (D1), the largest of the group II intron domains. The goal of the latter part of this dissertation was to investigate the structural features of the ID3 stem loop and the ID3-IBS1 complex. We investigated the effects of the ID3 stem loop structure on the EBS1-IBS1 pairing. A question addressed was whether the large 11-nucleotide loop forms a stable structure. We tested whether the EBS1-IBS1 pairing forms in solution and what structural changes the ID3 loop undergoes upon formation of the EBS1-IBS1 pairing. We wanted to determine the effects of ID3 structure on the availability of bases of EBS1 for base pairing and thus for the 5' splice site selection. Solution NMR structure of the ID3 stem loop shows a structured stem and a fairly structured base of the loop, as well as an unstructured or dynamic loop, involving residues of the EBS1 sequence. NMR spectroscopic study of the ID3-IBS1 complex in solution indicates that the unstructured region of the ID3 loop becomes structured upon interaction with the IBS1 sequence, in an apparent induced-fit mechanism, by which both the guide sequence and the target become structured upon interaction. An important observation here is that the double stranded EBS1-IBS1 region ends at the 5' splice site, placing it at the single/double stranded junction, which may play an important role in recognition and/or accessibility of the 5' splice site. The placement of the EBS1 sequence in the specific structural context of the ID3 loop may be an important feature, which aids the recognition of the 5' splice site. We show here that by virtue of being placed within the loop of a certain size, the two potential base pairs downstream of the 5' splice site, which could form in a free duplex, do not form in the context of the loop. These findings are important because we show that positioning of a guide sequence within a loop determines the availability of bases for pairing and controls the extent of base pairing and thus the position of the 5' splice site. / A Dissertation submitted to the Department of Chemistry and Biochemistry in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Spring Semester, 2012. / March 29, 2012. / EBS1-IBS1, group II intron, ID3, spliceosome / Includes bibliographical references. / Nancy L. Greenbaum, Professor Co-Directing Dissertation; Timothy M. Logan, Professor Co-Directing Dissertation; Jack R. Quine, University Representative; Hong Li, Committee Member; Rafael P. Brüschweiler, Committee Member.

Given the important role of contact in improving attitudes toward outgroup members, it is necessary to examine factors that reduce majority group members' likelihood of having contact with minority group members. Recent research illustrates the role of social contagion concerns (i.e., heterosexuals' concerns that contact with lesbians and gay men will result in being misidentified as homosexual) in heterosexuals' desire to avoid lesbians and gay men. One potential consequence for heterosexuals who are misidentified as homosexual is the potential loss of mating opportunities. The current work examined the role that mating motives play in social contagion concerns and heterosexuals' desires to avoid lesbians and gay men. Consistent with predictions, heterosexual participants whose mating goals were not being met reported greater contagion concerns than participants whose mating goals were being met (Study 1). Further, when mating motives were manipulated, heterosexual participants whose mating motives were activated reported a greater desire to avoid contact with a hypothetical gay/lesbian roommate than control participants (Study 2). This desire to avoid was especially pronounced in heterosexuals with high levels of general contagion concerns. The implications of these findings for inter-orientation contact are discussed. / A Thesis submitted to the Department of Psychology in partial fulfillment of the requirements for the degree of Master of Science. / Fall Semester, 2011. / August 31, 2011. / Includes bibliographical references. / E. Ashby Plant, Professor Directing Thesis; Jon Maner, Committee Member; Colleen Kelley, Committee Member.

Between 1933-1945, Rabbi Stephen Samuel Wise did more than any other American Jewish leader to fight against Hitlerism. Wise was one of the earliest outspoken critics of Adolf Hitler, speaking out against him and the National Socialist German Workers Party even before they assumed power in Germany. Yet, in recent years, he has come under constant scrutiny for his perceived inactions during the Holocaust. This dissertation seeks to investigate these criticisms, and explore their validity, by examining the actions of Stephen Wise during this era. This includes analyzing his relationship with President Franklin D. Roosevelt, his role in the American and World Jewish Congresses, his fight against American apathy and anti-Semitism, as well as his multitudinous plans for the rescue and relief of European Jews. / A Dissertation submitted to the Department of History in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Spring Semester, 2012. / March 2, 2012. / America, American Jewish Congress, Franklin D. Roosevelt, Holocaust, Stephen S. Wise, World War II / Includes bibliographical references. / James P. Jones, Professor Directing Dissertation; John Fenstermaker, University Representative; Jonathan Grant, Committee Member; Maxine D. Jones, Committee Member; Edward Wynot, Committee Member.

These nine stories are a reflection of the shifting culture and rapid economic growth of Northwest Arkansas, the birthplace of Walmart and Tyson Foods. While the stories may have a distinctly Southern flavor in their setting, they are essentially global in their perspective of the homogenization of culture. / A Dissertation submitted to the Department of English in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Fall Semester, 2011. / September 14, 2011. / Creative Writing, English, Fiction, Short Story Collection / Includes bibliographical references. / Mark Winegardner, Professor Directing Dissertation; Neil Jumonville, University Representative; Diane Roberts, Committee Member; Elizabeth Stuckey-French, Committee Member.