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ItemNanojets – Formation, characterization and applications(Georgia Institute of Technology, 2008-12-21) Landman, Uzi ; Glezer, Ari ; Allen, Mark G. ; King, William ; Brand, Oliver ; Luedtke, William ; Gao, Jianping
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ItemElectronic and mechanical properties of chemically functionalized nanowires(Georgia Institute of Technology, 2008-12-16) Bidasaria, Sanjay K.Organic and inorganic nanostructured materials, nano- and mesoscale objects and devices, and their integration into existing microelectronic technologies have been at the center of recent fundamental and applied research in nanotechnology. One of the critical needs is to develop an enhanced predictive capability of structure-property correlations and enable robust high performance systems by design. My thesis work was concerned with the theoretical and experimental studies of electronic and mechanical properties of chemically functionalized nanowires. I will describe a theoretical approach for investigating structure-property correlations in atomic-sized metallic wires based on the Density Functional Theory (DFT) for structure calculations and the Non-equilibrium Green's Function (NEGF) technique for electronic transport properties simulations. This synergistic approach is shown to yield the atomic structure of the smallest niobium nanowires. Furthermore, the method was applied to simulate electronic properties of chemically functionalized graphene nanoribbons. Further, I will demonstrate an experimental technique for simultaneous measurements of force and conductance in atomic-size objects based on quartz tuning fork piezoelectric sensors. A peculiar scaling effect, relevant for a broad range of test and measurement applications, namely the squeeze film effect, was observed during the development of the sensors. Using theoretical analysis based on finite element simulations of the hydrodynamic behavior of the sensors in a broad range of ambient conditions, I explain the observed phenomenon.
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ItemStudies in the mass 160 decay chain. gamma-ray and conversion electron spectroscopy for the 160lu-160yb, 160yb-160tm, 160tm-160er decay schemes.(Georgia Institute of Technology, 2008-12-16) Brown, Nathaniel J.Excited states in the transitional nucleus 160Yb have been studied using gamma-ray and conversion electron spectroscopy following the beta+/EC decay of 160Lu. Excited states in the nuclei 160Tm and 160Er have been studied following the beta+/EC decay of 160Yb and 160Tm, respectively. The data for the present study were obtained at TRIUMF in Vancouver, Canada at the ISAC-1 facility through radioactive sources moved into the combination of the 8pi gamma-ray spectrometer array and the Pentagonal Array for Conversion Electron Spectroscopy (PACES). Analysis of gamma-ray gated gamma-ray, gamma-ray gated conversion electron and conversion electron gated gamma-ray spectra resulted in the discovery of a new first excited state and the establishment of a level scheme for 160Tm which differs from the one adopted; as well as a test of the rotational characteristics of 160Er with intensity comparisons to both the spin-5 beta-decaying isomer study of by Singh et al. and the spin-parity 1- beta decay study of by Strusny et al. and Bykov et al.
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ItemMatter-light entanglement with cold atomic ensembles(Georgia Institute of Technology, 2008-12-16) Lan, Shau-YuIn this thesis I present the investigations of matter-light entanglement in cold atomic samples. Particularly, entanglement of mixed species ensembles and bichromatic light fields is proposed and demonstrated experimentally. This approach avoids the use of two interferometrically separate paths for qubits entanglement distribution. I also present the first implementation of multiplexed quantum memory, and experimentally demonstrate entanglement involving arbitrary pairs of elements within this memory array. Finally, quantum interference of electromagnetic fields emitted by remote quantum memory elements separated by 5.5 m is realized.
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ItemLateral gene transfer of pandemic Vibrio parahaemolyticus genomic island genes(Georgia Institute of Technology, 2008-12-15) Silberger, Daniel JamesVibrio parahaemolyticus is an emerging enteric pathogen. The O3:K6 serotype has become pandemic, and the genome has been sequenced for the RIMD2210633 strain of this serotype (20). The thermostabile direct hemolysin (tdh), thermostabile related hemolysin (trh), and two distinct Type III Secretion Systems (T3SS) have been implicated in virulence. Deletion studies have determined that the T3SS alone are sufficient to induce eukaryotic cell apoptosis. The T3SS loci are found within two separate genomic islands. Because genomic islands are known to be disseminated by Lateral Gene Transfer (LGT), we examined the distribution of the pandemic genomic island genes among clinical and environmental V. parahaemolyticus isolates and also among closely-related environmental Vibrio spp. using primers designed to amplify hemolysins and T3SS effectors previously characterized for V. parahaemolyticus strain RIMD2210633 (23). We also examined the distribution of a hypothetical bacteriocin, encoded by vpa1263, within another genomic island that is similar to the bacteriocins produced by Escherichia coli. Preliminary screens for the bacteriocin gene suggest that many clinical strains and some environmental strains contain vpa1263. PCR screens for the T3SS effector genes have shown that 22% of closely-related environmental Vibrio spp. contain at least one T3SS1 or one T3SS2 effector gene. Sequencing of housekeeping genes is ongoing to confirm these findings.
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ItemFr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score(Georgia Institute of Technology, 2008-12-12) Pandit, Shashi Bhushan ; Skolnick, JeffreyBackground: Protein tertiary structure comparisons are employed in various fields of contemporary structural biology. Most structure comparison methods involve generation of an initial seed alignment, which is extended and/or refined to provide the best structural superposition between a pair of protein structures as assessed by a structure comparison metric. One such metric, the TM-score, was recently introduced to provide a combined structure quality measure of the coordinate root mean square deviation between a pair of structures and coverage. Using the TM-score, the TM-align structure alignment algorithm was developed that was often found to have better accuracy and coverage than the most commonly used structural alignment programs; however, there were a number of situations when this was not true. Results: To further improve structure alignment quality, the Fr-TM-align algorithm has been developed where aligned fragment pairs are used to generate the initial seed alignments that are then refined using dynamic programming to maximize the TM-score. For the assessment of the structural alignment quality from Fr-TM-align in comparison to other programs such as CE and TMalign, we examined various alignment quality assessment scores such as PSI and TM-score. The assessment showed that the structural alignment quality from Fr-TM-align is better in comparison to both CE and TM-align. On average, the structural alignments generated using Fr-TM-align have a higher TM-score (~9%) and coverage (~7%) in comparison to those generated by TM-align. Fr- TM-align uses an exhaustive procedure to generate initial seed alignments. Hence, the algorithm is computationally more expensive than TM-align. Conclusion: Fr-TM-align, a new algorithm that employs fragment alignment and assembly provides better structural alignments in comparison to TM-align. The source code and executables of Fr- TM-align are freely downloadable at: http://cssb.biology.gatech.edu/skolnick/files/FrTMalign/.
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ItemAurora kinase inhibitors synergize with paclitaxel to induce apoptosis in ovarian cancer cells(Georgia Institute of Technology, 2008-12-11) Scharer, Christopher D. ; Laycock, Noelani ; Osunkoya, Adeboye O. ; Logani, Sanjay ; McDonald, John F. ; Benigno, Benedict B. ; Moreno, Carlos S.Background: A large percentage of patients with recurrent ovarian cancer develop resistance to the taxane class of chemotherapeutics. While mechanisms of resistance are being discovered, novel treatment options and a better understanding of disease resistance are sorely needed. The mitotic kinase Aurora-A directly regulates cellular processes targeted by the taxanes and is overexpressed in several malignancies, including ovarian cancer. Recent data has shown that overexpression of Aurora-A can confer resistance to the taxane paclitaxel. Methods: We used expression profiling of ovarian tumor samples to determine the most significantly overexpressed genes. In this study we sought to determine if chemical inhibition of the Aurora kinase family using VE-465 could synergize with paclitaxel to induce apoptosis in paclitaxel-resistant and sensitive ovarian cancer cells. Results: Aurora-A kinase and TPX2, an activator of Aurora-A, are two of the most significantly overexpressed genes in ovarian carcinomas. We show that inhibition of the Aurora kinases prevents phosphorylation of a mitotic marker and demonstrate a dose-dependent increase of apoptosis in treated ovarian cancer cells. We demonstrate at low doses that are specific to Aurora-A, VE-465 synergizes with paclitaxel to induce 4.5-fold greater apoptosis than paclitaxel alone in 1A9 cells. Higher doses are needed to induce apoptosis in paclitaxel-resistant PTX10 cells. Conclusion: Our results show that VE-465 is a potent killer of taxane resistant ovarian cancer cells and can synergize with paclitaxel at low doses. These data suggest patients whose tumors exhibit high Aurora-A expression may benefit from a combination therapy of taxanes and Aurora-A inhibition.
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ItemRandom sampling of lattice configurations using local Markov chains(Georgia Institute of Technology, 2008-12-01) Greenberg, SamAlgorithms based on Markov chains are ubiquitous across scientific disciplines, as they provide a method for extracting statistical information about large, complicated systems. Although these algorithms may be applied to arbitrary graphs, many physical applications are more naturally studied under the restriction to regular lattices. We study several local Markov chains on lattices, exploring how small changes to some parameters can greatly influence efficiency of the algorithms. We begin by examining a natural Markov Chain that arises in the context of "monotonic surfaces", where some point on a surface is sightly raised or lowered each step, but with a greater rate of raising than lowering. We show that this chain is rapidly mixing (converges quickly to the equilibrium) using a coupling argument; the novelty of our proof is that it requires defining an exponentially increasing distance function on pairs of surfaces, allowing us to derive near optimal results in many settings. Next, we present new methods for lower bounding the time local chains may take to converge to equilibrium. For many models that we study, there seems to be a phase transition as a parameter is changed, so that the chain is rapidly mixing above a critical point and slow mixing below it. Unfortunately, it is not always possible to make this intuition rigorous. We present the first proofs of slow mixing for three sampling problems motivated by statistical physics and nanotechnology: independent sets on the triangular lattice (the hard-core lattice gas model), weighted even orientations of the two-dimensional Cartesian lattice (the 8-vertex model), and non-saturated Ising (tile-based self-assembly). Previous proofs of slow mixing for other models have been based on contour arguments that allow us prove that a bottleneck in the state space constricts the mixing. The standard contour arguments do not seem to apply to these problems, so we modify this approach by introducing the notion of "fat contours" that can have nontrivial area. We use these to prove that the local chains defined for these models are slow mixing. Finally, we study another important issue that arises in the context of phase transitions in physical systems, namely how the boundary of a lattice can affect the efficiency of the Markov chain. We examine a local chain on the perfect and near-perfect matchings of the square-octagon lattice, and show for one boundary condition the chain will mix in polynomial time, while for another it will mix exponentially slowly. Strikingly, the two boundary conditions only differ at four vertices. These are the first rigorous proofs of such a phenomenon on lattice graphs.
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ItemGene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training(Georgia Institute of Technology, 2008-12) Ter-Hovhannisyan,Vardges ; Lomsadze, Alexandre ; Chernoff, Yury O. ; Borodovsky, MarkWe describe a new ab initio algorithm, GeneMark-ES version 2, that identifies protein-coding genes in fungal genomes. The algorithm does not require a predetermined training set to estimate parameters of the underlying hidden Markov model (HMM). Instead, the anonymous genomic sequence in question is used as an input for iterative unsupervised training. The algorithm extends our previously developed method tested on genomes of Arabidopsis thaliana, Caenorhabditis elegans, and Drosophila melanogaster. To better reflect features of fungal gene organization, we enhanced the intron submodel to accommodate sequences with and without branch point sites. This design enables the algorithm to work equally well for species with the kinds of variations in splicing mechanisms seen in the fungal phyla Ascomycota, Basidiomycota, and Zygomycota. Upon self-training, the intron submodel switches on in several steps to reach its full complexity. We demonstrate that the algorithm accuracy, both at the exon and the whole gene level, is favorably compared to the accuracy of gene finders that employ supervised training. Application of the new method to known fungal genomes indicates substantial improvement over existing annotations. By eliminating the effort necessary to build comprehensive training sets, the new algorithm can streamline and accelerate the process of annotation in a large number of fungal genome sequencing projects
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ItemCollaborative research: particulate organic carbon in the air and snow at Summit, Greenland(Georgia Institute of Technology, 2008-11-30) Bergin, Michael H.