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ItemNon-equilibrium current fluctuations in graphene(Georgia Institute of Technology, 2012-12-20) Wiener, Alexander DavidWe analyze experimental evidence of transport through evanescent waves in graphene, reconciling existing experimental data with theory. We propose novel experimental geometries that provide even more compelling evidence of evanescent waves. We investigate the shot noise generated by evanescent modes in graphene for several experimental setups. For two impurity-free graphene strips kept at the Dirac point by gate potentials, separated by a long highly doped region, we find that the Fano factor takes the universal value F=1/4. For a large superlattice consisting of many strips gated to the Dirac point, interspersed among doped regions, we find F=1/(8ln2). These results differ from the value F=1/3 predicted for a disordered metal, providing an unambiguous experimental signature of evanescent mode transport in graphene. For a graphene nano-ribbon transistor geometry, we explain that the experimentally observed anomalous voltage scale of the shot noise can arise from doping by the contacts to the electrical circuit. These observations provide strong evidence of evanescent mode transport in graphene.
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ItemDevelopment of algorithms for metagenomics and applications to the study of evolutionary processes that maintain microbial biodiversity(Georgia Institute of Technology, 2012-12-20) Luo, ChengweiUnderstanding microbial evolution lies at the heart of microbiology and environmental sciences. Numerous studies have been dedicated to elucidating the underlying mechanisms that create microbial genetic diversity and adaptation. However, due to technical limitations such as the high level of uncultured cells in almost every natural habitat, most of current knowledge is primarily based on axenic cultures grown under laboratory conditions, which typically do not simulate well the natural environment. How well the knowledge from isolates translates to in-situ processes and natural microbial communities remains essentially speculative. The recent development of culture-independent genomic techniques (aka metagenomics) provides possibilities to bypass some of these limitations and provide new insights into microbial evolution in-situ. To date, most of metagenomic studies have been focused on a few reduced-diversity model communities, e.g., acid mine drainage. Highly complex communities such as those of soil and sediment habitats remain comparatively less understood. Furthermore, a great power of metagenomics, which has not been fully capitalized yet, is the ability to follow the evolution of natural microbial communities over time and environmental perturbations, i.e., times-series metagenomics. Although the recent developments in DNA sequencing technologies have enabled (inexpensive) time-series studies, the bioinformatics approaches to analyze the resulting data have clearly fallen behind. Taken together, to scale up metagenomics for complex community studies, three major challenges remain: 1) the difficulty to process and analyze massive short read sequencing data, often at the terabyte level; 2) the difficulty to effectively assemble genomes from complex metagenomes; and 3) the lack of methods for tracking genotypes and mutational events such as horizontal gene transfer (HGT) through time. Therefore, developing efficient bioinformatics approaches to address these challenges represents an important and timely issue. This thesis aimed to develop novel bioinformatics pipelines and algorithms for high performance computing, and, subsequently, apply these tools to natural microbial communities to generate quantitative insights into the relative importance of the molecular mechanisms creating or maintaining microbial diversity. The tools are not specific to a particular habitat or group of organisms and thus, can be broadly used to advance our understanding of microbial evolution in different settings. In particular, the comparative whole-genome analysis of 24 Escherichia isolates form various habitats, including human and non-human associated habitats such as freshwater ecosystems and beaches, showed that organisms with more similar ecologies tend to exchange more genes, which has important implications for the prokaryotic species concept. To more directly test these findings from isolates and quantify the patterns of genetic exchange among co-occurring populations, three years of time-series metagenomics data from planktonic samples from Lake Lanier (Atlanta, GA) were analyzed. For this, it was first important to develop bioinformatics algorithms to robustly assemble population genomes from complex community metagenomes, identify the phylogenetic affiliation of assembled genome and contig sequences, and detect horizontal gene transfer among these sequences. Using these novel algorithms, in situ bacterial lineage evolution was quantitatively assessed, especially with respect to whether or not ecologically distinct lineages evolve according to the recently proposed fragmented speciation model (Retchless and Lawrence, Science 2008). Evidence in support of this model was rarely observed. Instead, it appeared that rampant HGT disseminated ecologically important genes within the population, maintaining intra-population diversity. By expanding the previous approaches to include methods to assess differential gene abundance and selection pressure between samples, it was possible to quantify how soil microbial communities respond to a decade of warming by 2 0C, which simulated the predicted effects of climate change. It was found that the heated communities showed significant shifts in composition and predicted metabolism, reflecting the release of additional soil carbon compared to the unheated (control) communities, and these shifts were community-wide as opposed to being attributable to a few taxa. These findings indicated that the microbial communities of temperate grassland soils play important roles in mediating the feedback responses to climate change. Collectively, the findings presented here advance our understanding of the modes and tempo of microbial community adaptation to environmental perturbations and have important implications for better modeling the microbial diversity on the planet. The bioinformatics algorithms and approaches developed as part of this thesis are expected to facilitate future genomic and metagenomic studies across the fields of microbiology, ecology, evolution and engineering.
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ItemAn FPGA-based microarchitecture for the implementation of quantum gates with trapped ions(Georgia Institute of Technology, 2012-12-18) Nichols, Charles SpencerQuantum computing promises to revolutionize computing by providing exponential speed improvements to classically difficult problems. Over the past 30 years, experimental research has progressed from manipulating quantum systems to creating elementary gates in many quantum mechanical systems. One of the most successful media for implementing quantum gates is trapped ions. Current trapped-ion quantum computing architectures have very high gate fidelities and long coherence times, but creating quantum gates with low error rates with trapped ions is challenging since it requires precise trap and laser control. In order to implement quantum gates with trapped ions, I have created a field-programmable-gate-array- (FPGA) based microarchitecture for constructing laser-pulse sequences and controlling ancillary equipment. The microarchitecture is centralized to minimize experimental timing errors and is programmable to provide the generality necessary for implementing a vast range of experiments.
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ItemSynthesis of a triple-decker π-conjugated system to explore charge migration in organic semiconductors(Georgia Institute of Technology, 2012-12-18) Castaneda, Alma DeliaClosely stacked π-systems exhibit physical properties that are a consequence of π- π interactions. The primary focus of this study is the production of a triple-decker π-conjugated system. Although many studies have investigated the use of para and meta-cyclophanes, research on ortho-cyclophanes in which arene rings are held in a stacked arrangement has been limited. This thesis describes a synthesis of the scaffold to hold conjugated units together. Ultimately, the stacked analog will be obtained by ketalization of a bicyclic ketone with ethylene glycol to lock the bicyclic core into a chair-chair conformation in which oligo(phenylene ethynylene)s are stacked atop one another. The optical properties of the stacked compound will be studied using UV-Vis and fluorescence spectroscopy. The electrochemical properties of the stacked compounds will be characterized using cyclic voltametry (CV) and differential pulse voltammetry (DPV).
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ItemThe effect of host food quality on host and parasite fitness in an invertebrate-parasite system(Georgia Institute of Technology, 2012-12-18) Snell, Sara JeanneParasites achieve their fitness by reducing the fitness of the hosts they infect. The relationship between host and parasite fitness is often mediated by environmental conditions, such as the quality of food consumed by the host. We used the crustacean Daphnia dentifera and its virulent yeast parasite Metschnikowia bicuspidata to examine how the quality of the food consumed by the Daphnia affected the probability of the host being infected by the parasite and the fitness consequences of infection for the host (measured as offspring production and survival) and for the parasite (measured as the production of transmission spores within the host following infection). We fed Daphnia either high quality food (Ankistrodesmus falcatus) or low quality food (Oocystis sp.) before exposure to Metschnikowia spores, and then either high quality or low quality food after parasite exposure (according to a fully factorial design). We found that when hosts were fed high quality food as juveniles and adults, they were able to invest more energy in preventing loss of fitness due to parasites without limiting parasite growth; high quality food therefore benefits both parasite and host. High food quality benefited both host and parasite when hosts are infected. We saw that infected hosts that produced more offspring also contained more parasite spores. One possible explanation for this is the individuals that produced more offspring and spores were larger, allowing them to take in more resources.
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ItemHigh-contrast metal-responsive fluorescent probes based on synergistic electronic and conformational switching(Georgia Institute of Technology, 2012-12-18) Sarwar, MyshaWe have prepared and characterized a Mg(II)-responsive fluorescent probe, constructed using a large tetradentate, 15-membered crown ether ligand and a 1,3,5-triaryl-substituted pyrazoline fluorophore. The photoinduced electron transfer (PET) driving force between the ligand and fluorophore controls the fluorescence contrast ratio when an analyte is bound to the probe. Previous studies have shown that the maximum obtainable fluorescence probes based on macrocyclic ligands was impaired due to ternary complex formation of the metal-ligand complex with the solvent molecules. We redesigned the metal ion receptor by incorporating the aniline ring into the ligand. We selected four fluoro substituents to increase the electron withdrawing ability of the 1-aryl-ring, yielding a very high fluorescence enhancement upon saturation with Mg(II) in acetonitrile. The quantum yield of this pyrazoline probe was found to be 79%.We expect that the described approach should be applicable for rationally designing high-contrast pyrazoline-based PET probes selective towards other metal cations as well.
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ItemExpression and purification of internalin a ligand for internalization studies on non-professional phagocytic epithelial cells(Georgia Institute of Technology, 2012-12-18) Haddad, NatalieInfection by intracellular pathogens is a growing concern as these microorganisms can cross their host s cellular barrier and use the host s own cellular proteins for replication, making treatment very difficult (Kenneth et al., 2008). A further restriction for treatment is that a proposed drug must be able to cross the same barriers in order to reach these pathogens. Our study investigates the same protein used by a particular intracellular pathogen, Listeria monocytogenes, as a possible internalization method for intracellular delivery of materials or drugs. A pGEX-6p plasmid vector containing a gene for the bacterial surface protein Internalin A (InlA) and a glutathione S-transferase (GST) tag, was restored and transformed into Escherichia coli MAX Efficiency DH5αF`IQ competent cells in order to increase insert stability and DNA quality. The plasmid was then purified and subsequently transformed into One Shot BL21(DE3)pLysS expression competent E. coli cells. Thereafter, the InlA-GST fusion protein was expressed in the BL21 cells using Isopropyl β-D-1-thiogalactopyranoside (IPTG). It has been shown, through selective plating and gel electrophoresis, that the plasmid was successfully transformed and purified. Our next steps will be to purify the InlA-GST fusion protein using glutathione affinity based chromatography, cleave and remove the GST tag from the InlA protein of interest, fluorescently label InlA using Alexa Flour, and bind InlA to microbeads of various sizes in a range of densities. We will then carry out internalization assays of the InlA-coated beads in different epithelial cell lines to demonstrate the versatility of this method as a possible material or drug delivery option.
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ItemAmazon River influence on nitrogen fixation and export production in the western tropical north Atlantic(Georgia Institute of Technology, 2012-12-17) Weber, Sarah CatherineAs part of the multidisciplinary ANACONDAS program, we characterized the distributions of nutrients, particulate organic matter, phytoplankton, and stable carbon and nitrogen isotopes in the Amazon plume region during the spring high-flow period of May-June 2010. We encountered the lowest salinities (16.6 psu) near the southern end of our study region where the plume showed the greatest spatial coherence, and the highest salinities (36.0 psu) to the east of the plume. The major nutrients showed distinct patterns of variation with salinity, with NO₃- largely absent from the surface plume and SiO₂ and PO₄³⁻ showing different degrees of conservative behavior. SiO₂ distributions were more strongly conservative, but with clear negative deviations that reflected biological consumption. In contrast, PO₄³⁻ concentrations showed clear positive deviations as large as 0.7 µM across a broad range of salinities as particle- and organically-bound P was released. These nutrient distributions resulted in strong nitrogen limitation and delivery of substantial amounts of SiO₂ and PO₄³⁻ to offshore waters, creating conditions that favored diazotrophy rather than simple eutrophication. We found a variety of diazotrophs in our study area, with interesting regional variation in their distributions. Mesohaline waters to the northwest of the plume axis were strongly dominated by Diatom-Diazotroph Associations (DDAs), particularly the Hemiaulus hauckii Richelia intracellularis association. In contrast, Trichodesmium spp. were most abundant to the southeast of the plume. These two diazotrophs appeared to contribute to the nitrogen and carbon budgets of the upper water column in fundamentally different ways, with H. hauckii making a much greater contribution to the particulate nitrogen pool than Trichodesmium spp. (100% versus 50%, respectively), while contributing to a greater reduction in pCO₂ in the upper water column. These contrasts have important implications for the fate of new production, with DDAs supporting higher export flux than Trichodesmium spp. Our findings provide an important constraint on the role of the Amazon plume in creating distinct niches for diazotrophic phytoplankton, and for their role in the nutrient and carbon budgets of the Western Tropical North Atlantic
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ItemGoodness-of-fit test and bilinear model(Georgia Institute of Technology, 2012-12-12) Feng, HuijunThe Empirical Likelihood method (ELM) was introduced by A. B. Owen to test hypotheses in the early 1990s. It's a nonparametric method and uses the data directly to do statistical tests and to compute confidence intervals/regions. Because of its distribution free property and generality, it has been studied extensively and employed widely in statistical topics. There are many classical test statistics such as the Cramer-von Mises (CM) test statistic, the Anderson-Darling test statistic, and the Watson test statistic, to name a few. However, none is universally most powerful. This thesis is dedicated to extending the ELM to several interesting statistical topics in hypothesis tests. First of all, we focus on testing the fit of distributions. Based on the CM test, we propose a novel Jackknife Empirical Likelihood test via estimating equations in testing the goodness-of-fit. The proposed new test allows one to add more relevant constraints so as to improve the power. Also, this idea can be generalized to other classical test statistics. Second, when aiming at testing the error distributions generated from a statistical model (e.g., the regression model), we introduce the Jackknife Empirical Likelihood idea to the regression model, and further compute the confidence regions with the merits of distribution free limiting chi-square property. Third, the ELM based on some weighted score equations are proposed for constructing confidence intervals for the coefficient in the simple bilinear model. The effectiveness of all presented methods are demonstrated by some extensive simulation studies.
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ItemUltra-high Energy Cosmic Rays from Blazars(Georgia Institute of Technology, 2012-12-10) Dermer, CharlesBlazar astronomy is rapidly progressing thanks in large part to the successes of the Fermi Gamma-ray Space Telescope and the ground-based gamma-ray telescopes. More than 1000 active galaxies have been detected at GeV energies, and nearly 50 at Very-High Energies (VHE, > 100 GeV). We can now explore multiwavelength and multi-messenger connections in unprecedented detail, and derive the astroparticle implications of those results. In this presentation, leptonic and hadronic spectral modeling of blazars is reviewed with the intent of identifying ultra-high energy cosmic rays (UHECRs) in the spectral energy distributions of these objects. We consider a number of unusual results that could be explained by UHECRs in blazars: (1) distinct spectral components revealed by deabsorption of blazar VHE spectra; (2) flattening at moderate redshift in the Stecker-Scully relation showing the GeV - TeV spectral index difference versus redshift; (3) conflicting results for the location of the gamma-ray emission site in blazars; (4) the unusually short variability times of luminous blazars. The arguments for and against radio galaxies and blazars being the sources of the UHECRs are reviewed, and predictions for UHECR composition is made if BL Lac objects accelerate most of the UHECRs. Unusual effects of UHECR acceleration in blazars is illustrated by the strange case of 4C +21.35. We also discuss effects of hypothetical axions, a dark matter candidate, in the interpretation of unusual blazar behavior, and a recent Fermi-LAT search for axions in occultations of bright AGNs by the Sun.