Browsing by Subject "SEM"
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Item An Experimental Study of Mn12-Family Molecular Magnets in Isolation with High Spatial Resolution(2014-12-17) Reaves, Kelley ThomasI report my studies of Mn12O12(C6H5COO)16(H2O)4, which will be referred to as Mn12-Ph, a single molecule magnet, on Cu(111) and HOPG (highly oriented pyrolytic graphite) surfaces by scanning tunneling microscopy (STM). A technique of vacuum spray injection for room temperature deposition of films of a tunable density, between very diffuse isolated molecules and complete surface coverage, onto sample substrates was developed and used to create sub-monolayer films of Mn12-Ph on Cu(111) for low temperature observation. Scanning tunneling spectroscopy (STS) of samples at low temperatures produced insights into the local density of states (LDOS) with a high degree of precision with spatial location (X,Y,Z) and energy (eV).These spectroscopic data were analyzed and compared to results in the literature from competing groups. A theoretical model of spinstability in an interacting graph of spins was developed and simulations were carried out to find a weak topological invariant to perturbation of a given spinstate for a class of ferromagnetically interacting spingraphs. A phenomenological (post hoc) model built upon poor coupling between the molecule's wave function and the Cu surface wave function is proposed to explain the spectroscopic data. Normalized (to the Cu background) junction impedance is calculated and compared in different regions of the molecular interior to form a better view of the evolution of the tunnel junction current with respect to applied bias voltage.Item Application of enzymatic catalysis and galvanic processes for biosensor development(2011-08) Zaccheo, Brian Andrew; Crooks, Richard M. (Richard McConnell); Browning, Karen; Hoffman, David; Johnston, Keith P.; Stevenson, KeithMethods for integrating enzyme systems with electrochemical reactions having applications to diagnostic sensing are described. Diagnostic tests that include biological molecules can be classified as biosensors. Existing testing methods often require trained technicians to perform, and laboratory settings with complex infrastructure. The theme of this dissertation is the development of methods that are faster, easier to use, and more applicable for non-laboratory environments. These goals are accomplished in systems using enzymatic catalysis and galvanic processes. Two biosensors with specific model pathologies have been designed and demonstrated in this study. The first assay senses a DNA fragment representing the Epstein Barr virus and uses enzyme-mediated Ag deposition over a v microfabricated chip. The chip contains a specially designed pair of electrodes in an interdigitated array (IDA). Detection is signaled by a change in the resistance between the two electrodes. The second biosensor discussed in this study is targeted towards the digestive enzyme trypsin. It is selfpowered due to its construction within an open-circuit galvanic cell. In this system, a small volume of blood serum is introduced onto the device over barriers made of protein and Al that block the anode from solution. In the presence of trypsin, the protein gel is rendered more permeable to sodium hydroxide. Adding hydroxide initiates the dissolution of the Al layer, closing the cell circuit and illuminating a light-emitting diode (LED). A relationship was observed between LED illumination time and trypsin concentration. Biosensors that utilize enzymes to generate or amplify a detectable signal are widely used, and the final project of this study uses a nanoparticle based approach to protect the catalytic activity of alkaline phosphatase (AlkP) from hostile chemicals. By incubating Au colloid with AlkP overnight and adding Ag+, core@shell nanoparticles of Au@Ag2O can be isolated that show AlkP activity. The resulting enzyme-metal composite material was analytically characterized and demonstrated greater activity in the presence of organic inhibitors relative to either wild type vi or Au colloid-associated AlkP without the Ag2O shell. The stabilization procedure is complete in one day using a onepot synthesis. This method may provide opportunities to carry out biosensing chemistry in previously incompatible chemical environments.Item Associations between health behaviors and adolescents life satisfaction using structural equation modeling (SEM)(2016-08) Wang, Wanyi; Lin, Lizhen, Ph. D.; Whittaker, Tiffany ALife satisfaction is an important indicator in suicidal behavior. The purpose of this study was to investigate the influences of health-related behaviors on adolescent life satisfaction using structural equation modeling (SEM). Data were obtained from the Health Behavior in School-Age Children (HBSC), 2001-2002. Because of the complex nature, SEM was preferred to be used over regression models in the present study. The results indicated that good eating habits and high scores of self-reported health played the greatest roles in promoting life satisfaction. The effects of both factors on life satisfaction were also mediated by academic achievement. Physical activity was a positive predictor of life satisfaction, but its effect appears to be mediated by health and academic achievement, rather than affecting life satisfaction directly. Moreover, physical activity was positively associated with good eating habits. These results generated from SEM were also compared with that from multiple linear regressions. Slight differences in the standardized coefficients for the total effects between SEM and regression models were detected due to the existing latent variable in SEM, but the general proportion variance accounted for in each outcome variable were similar across the two analyses. In summary, although there were some limitations for the study design and the building of the model, this study suggested that good habits with respect to diets may be beneficial for improvements in health and academic achievement, which in turn lead to positive scores of adolescent life satisfaction. High frequent physical activity and low BMI were poor but acceptable predictors of life satisfaction.Item Characterizing the petrophysical properties of shallow marine environments and their potential as methane hydrate reservoirs(2015-05) Nole, Michael Anthony; Daigle, Hugh; Mohanty, KishoreIn shallow marine sedimentary environments, characterization of sediment petrophysical and thermodynamic properties is imperative for understanding the subsurface transport of fluids and their chemical constituents. This work first presents an objective method of scanning electron microscope image analysis that directly quantifies microporosity in clay-rich, fine-grained sediments typical of the shallow marine subsurface. The method is powerful because it is fast, easy, and provides a direct microporosity estimation technique to augment or replace experimental data. When used appropriately, the method can be implemented on microporous sediments and sedimentary rock in general. With an understanding of how microporosity manifests in shallow marine sediments, the impact of small pore sizes on methane hydrate solubility is then examined for core samples taken from 3 sites in the Nankai Trough offshore Japan, an area that has been heavily surveyed in recent years for its potential to host economically recoverable deposits of methane hydrate for use as a natural gas resource. Small pores in fine-grained shaley intervals are shown to significantly increase the aqueous solubility of methane in pore water relative to surrounding coarser-grained sediment strata, which can have broad implications for methane hydrate formation, including lack of formation in the clayey intervals and strong diffusive fluxes of methane into coarser sediment layers. Finally, an existing methane hydrate reservoir simulator is modified to model methane hydrate accumulations in marine environments with heterogeneous layered sediments. The impact of pore size on solubility is included in the model along with steady state microbial methanogenesis and diffusion of salt in the pore water. The simulator is then used to successfully model methane hydrate accumulations in 1D and 2D at Walker Ridge Site 313 in the Gulf of Mexico, where well logs and seismic surveys throughout the region abound. This work is an important step in building a general 3D methane hydrate reservoir simulator for shallow marine environments around the globe.Item Evolutionary ecology of Malpighiaceae pollination at the species and community levels(2011-08) Cappellari, Simone Caroline; Simpson, Beryl Brintnall; Neff, John L.Plant-pollinator interactions figure as key elements promoting the natural regeneration of terrestrial vegetation, as most plants depend on animals to transfer their gametes between flowers and produce seeds. Bees are the most common pollinators of plants and their interactions with flowers have served as model systems for the study of specialized mutualisms since Darwin's time. While most plants offer nectar as a reward and attract a variety of floral visitors, others produce distinctive types of resources which are sought by particular groups of pollinators. Such associations may involve specialization at the morphological, behavioral, or physiological levels and are especially common in tropical habitats. The interactions between oil-producing flowers of Neotropical Malpighiaceae and oil-collecting bees are an example of a specialized mutualism in which plants offer lipids to attract pollinators that use the resource to build nest cells and feed their offspring. Although several studies have focused on specialized pollination at the species level, their effects on the organization of tropical communities remain largely unexplored. This dissertation aims to help fill this gap through an analysis of the mechanisms of pollinator partitioning in multi-species assemblages of specialists as well as a study of the organization of communities in which they occur. The motivation for pursuing the study of specialized interactions using Neotropical species of Malpighiaceae as a model system is outlined in the first chapter. In Chapter 2, I present an evaluation of the structural properties of a plant-pollinator community from the Cerrado, a seasonal ecosystem that hosts a large diversity of oil flowers. The third chapter analyzes pollinator partitioning and reproductive strategies promoting the coexistence of closely related Malpighiaceae. A possible outcome for the selective pressures imposed by the coexistence of specialists is presented in Chapter 4 by a case study providing evidence for a shift from specialized to generalized pollination in a Neotropical Malpighiaceae species. The last chapter includes reports of active floral oil foraging by males of Tetrapedia and a description of an oil storage structure without precedence among bees and unique to males of this genus suggesting that floral oils may also play a role in bees mating systems.Item The implementation of phylogenetic structural equation modeling for biological data from variance-covariance matrices, phylogenies, and comparative analyses(2009-12) Santos, Juan Carlos; Wilke, Claus O.; Bryant, JamesOne statistical approach with a long history in the social sciences is a multivariate method called Structural Equation Modeling (SEM). The development of SEM followed the evolution of factor and path analyses, multiple regression analysis and MACOVA. One of the key innovations of factor analysis and SEM is that they group a set of multivariate statistical approaches that condense variability among a set of variables in fewer latent (unobserved) factors. Most biological systems are multivariate, which are not easily dissected into their component parts. However, most biologists use only univariate statistical methods, which have definitive limitations in accounting for more than a few variables simultaneously. Therefore, the implementation of methodologies like SEM into biological research is necessary. However, SEM cannot be applied directly to most biological datasets or generalized across species because of the hierarchical pattern of evolutionary history (i.e., phylogenetic non-independence or signal). This report includes the theoretical grounds for the development of Phylogenetic SEM in preparation of the development of utilitarian algorithms. I have divided this report in six parts: (1) a brief introduction to factor analysis and SEM from historical perspective and a brief description of its utility; (2) a summary of the implications of using biological data and the underlying hierarchical structure due to shared common ancestry or phylogeny; (3) a summary of the two most common comparative methods to incorporate the phylogeny in univariate analyses (i.e., phylogenetic independent contrasts and phylogenetic generalized least squares); (4) I describe how some intermediate output from both comparative methods can be used to estimate the variance–covariance matrix that has been corrected for phylogenetic signal; (5) I describe how to perform a exploratory factor analysis, specifically principal component analysis, with the corrected variance–covariance matrix; and (6) I describe the development of the phylogenetic confirmatory factor analysis and phylogenetic SEM. I hope that this report encourages other researchers to develop adequate multivariate analysis that incorporate the evolutionary principles in its analyses.Item Investigating the Use of Biosorbents to Remove Arsenic from Water(2011-02-22) Erapalli, ShreyasEvaluating the ability of biosorbents to remove arsenic from water has global significance due to the widespread availability and low cost of biosorbent materials. In this study, the ability of coffee grounds and coconut substrate (two previously unreported biosorbents) to remove arsenic from water was compared against the performance of arsenic removal on rice husk (a recognized and widely tested biosorbent). The three biosorbents were individually screened for their ability to remove arsenite, As (III), and arsenate, As (V), from water. Batch reactors were employed to assess the percent removal, reaction kinetics, adsorption capacity, and desorption of each arsenic species onto/from biosorbents under pH buffered and non?buffered conditions. The resulting experimental data was statistically interpreted using analysis of variance and ttesting of the means. The experimental results were also fit to existing kinetic and isotherm models to provide kinetic rate constants, the maximum adsorption capacity, and to help interpret the nature of the reactions on the biosorbent surface. While all three biosorbents removed arsenic with similar initial reaction kinetics (pseudo 1st order reaction rate constant for As (III) was 0.13 hr^?1 for all three biosorbents and for As (V) was 0.17 hr^?1 for coffee grounds and rice husk and 0.15 hr^?1 for coconut substrate), the amount of arsenite and arsenate removed was highest for coffee grounds (84 and 91 percent, respectively), followed by rice husk (68 and 72 percent, respectively), and then coconut substrate (26 and 24 percent, respectively). The maximum adsorption capacity of arsenite and arsenate was determined for coffee grounds (0.66 and 0.70 mg/g, respectively) and rice husk (0.55 and 0.66 mg/g, respectively). While desorption was observed for both coffee grounds and rice husk, the total amount of desorption accounted for less than 15 percent of the total retained mass. The results of this thesis work reveal that coffee can be used as an effective biosorbent when compared to rice husk; however, coconut substrate is less effective than rice husk at removing As (III) and As (V).Item Nonconforming formulations with spectral element methods(Texas A&M University, 2004-11-15) Sert, CuneytA 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.Item Self-control, social integration, and bullying behavior : an application of structural equation modeling (SEM)(2016-12) Hooper, Sophia Man Yang; Daniels, Michael JosephThe current study examined the longitudinal relations among self-control problems, social integration in school, bullying behavior, and later aggression. Latent growth models showed that self-control problems decreased while bullying behavior increased from 3rd grade to 6th grade. A parallel growth model demonstrated the longitudinal relationship between self-control problems and bullying behavior over time. Furthermore, the initial status and the decrease in self-control problems were associated with social integration, which in turn influenced students’ proximal (i.e., 6th bullying behavior) and distal outcomes (i.e., aggression at age 15). Moreover, the initial status and the decrease in self-control problems influenced proximal and distal outcomes indirectly through their influence on social integration. The findings suggested that intervening to promote students’ feelings of social integration in the school context could have important and lasting effects on bullying and aggressive behaviors.Item Spelling English Words: Contributions of Phonological, Morphological and Orthographic Knowledge in Speakers of English and Chinese(2011-08-08) Zhao, JingA growing body of literature has provided evidence of the contribution of various metalinguistic skills to children's English literacy development; however, most of the studies focused on reading outcomes while spelling outcomes have been under-researched. Further, very few studies have been conducted to investigate if the results based on native English speakers can be generalized to speakers of other languages who are learning to read and spell in English. In this study, the simultaneous influence of phonological, morphological and orthographic knowledge that may impact English spelling acquisition, among Chinese students learning English as a foreign language in Grade 8 (n = 339) in mainland China and native English-speaking students in Grade 3 (n = 166) in the United States, was investigated. Measures in English tapping into the three aspects of metalinguistic skills?phonological awareness (PA), morphological awareness (MA) and orthographic awareness (OA)?were administered to both groups. Multi-group structural equation models were used to compare models between the Chinese and the American group. Results showed that 1) the overall model of metalinguistic skills predicting spelling outcome was highly similar between the American and the Chinese groups; 2) metalinguistic skills were correlated and worked in concert to compose the linguistic repertoire construct which concurrently predicted the spelling outcome; 3) MA was the major component, compared to PA and OA, of Linguistic Repertoire (LING) across the two groups. Linguistic repertoire explained 64.1 percent and 40.2 percent of the total variance in the spelling outcome for the American and the Chinese groups, respectively; and 4) the contribution of OA was greater in the Chinese group than it was in the American group, whereas the contribution of PA was greater in the American group than it was in the Chinese group. This study highlights the important contribution of MA to literacy development among both the American students and the Chinese students. It also sheds light on the influence of first language (L1) orthography on English literacy acquisition. That OA contributed more than PA to the LING construct may reflect that the English learners with L1-Chinese background have enhanced visual-orthographic processing skills. This study challenges phase models of literacy development that claim MA only contributes to literacy acquisition late in the process and offers some empirical evidence to support the emerging "linguistic repertoire" theory of literacy development.Item Surface enhanced Raman spectroscopy of olivine type battery cathode LiFePO4(2010-08) Delone, Nicholas Ryan; Stevenson, Keith J.; Vanden Bout, David A.This thesis explores the use of Raman Spectroscopy to study the battery cathode material LiFePO4. Surface Enhanced Raman Spectroscopy (SERS) was incorporated into the study due to fluorescence that traditionally plagues Raman. By imaging LiFePO4 nanoparticles, an understanding can be gained of the complex chemistry taking place when the material is lithiated and delithiated at the nanoscale level and the phase changes of the material that occur during this process. The use of bimetallic (Au/Ag) SERS substrates allowed for more stable substrates with longer shelf life compared single metal Ag substrates. Further tuning of these substrates can be applied to the ever evolving science of energy storage material technology as a way to track phase changes in the material.Item The Determination and Comparison of the in vitro Lectin, Antimicrobial and Anti-HIV Reverse Transcriptase Activities of Three South Texas Fabaceae Leaf ExtractsPalacios, Patrick James; Ynalvez, Ruby APlant extracts have proteins that possess significant biological properties. Studies on plant lectins reported that a number of lectins possess antibacterial, antifungal and antiviral properties. Lectins are carbohydrate-binding proteins that are of non-immunological origin and possess agglutination capabilities. The objective of this study was to determine lectin activity and biological activities of therapeutic potential of three South Texas Fabaceae leaf extracts. These were Senegalia berlandieri (Bentham), S. greggii (Gray) and Vachelia rigidula (Bentham). There was no significant difference in lectin activity among the three leaf extracts. Scanning electron microscopy images showed S. berlandieri extracts caused extracellular damage to Aspergillus niger. All three leaf extracts exhibited high anti-HIV1 RT activity when tested using an enzyme linked immunoadsorbent assay (ELISA). In order to determine any correlation between lectin activity and anti-HIV activity, ammonium sulfate precipitation was done. Correlational analyses suggest that another molecule other than the lectin may be responsible for the high anti-HIV1 RT activity exhibited by the leaf extracts. Further analyses and biomolecule isolation would prove beneficial in concluding the results of this study.