Doctor of Philosophy (PhD) / The glass-transition traverses continuously from liquid to solid behaviour, yet the role of structure in this large and gradual dynamic transition is poorly understood. This thesis presents a theoretical study of the relationship between structure and dynamics in two-dimensional glass-forming alloys, and provides new tools and real-space insight into the relationship at a microscopic level. The work is divided into two parts. Part I is concerned with the role of structure in the appearance of spatially heterogeneous dynamics in a supercooled glass-forming liquid. The isoconfigurational ensemble method is introduced as a general tool for analysing the effect that a configuration has on the subsequent particle motion, and the dynamic propensity is presented as the aspect of structural relaxation that can be directly related to microscopic variations in the structure. As the temperature is reduced, the spatial distribution of dynamic propensity becomes increasingly heterogeneous. This provides the first direct evidence that the development of spatially heterogeneous dynamics in a fragile glass-former is related to spatial variations in the structure. The individual particle motion also changes from Gaussian to non- Gaussian as the temperature is reduced, i.e. the configuration expresses its character more and more intermittently. The ability of several common measures of structure and a measure of structural ‘looseness’ to predict the spatial distribution of dynamic propensity are then tested. While the local coordination environment, local potential energy, and local free volume show some correlation with propensity, they are unable to predict its spatial variation. Simple coarse-graining does not help either. These results cast doubt on the microscopic basis of theories of the glass transition that are based purely on concepts of free volume or local potential energy. In sharp contrast, a dynamic measure of structural ‘looseness’ - an isoconfigurational single-particle Debye-Waller (DW) factor - is able to predict the spatial distribution of propensity in the supercooled liquid. This provides the first microscopic evidence for previous correlations found between short- and long-time dynamics in supercooled liquids. The spatial distribution of the DW factor changes rapidly in the supercooled liquid and suggests a picture of structural relaxation that is inconsistent with simple defect diffusion. Overall, the work presented in Part I provides a real-space description of the transition from structure-independent to structure-dependent dynamics, that is complementary to the configuration-space description provided by the energy landscape picture of the glass transition. In Part II, an investigation is presented into the effect of varying the interparticle potential on the phase behaviour of the binary soft-disc model. This represents a different approach to studying the role of structure in glass-formation, and suggests many interesting directions for future work. The structural and dynamic properties of six different systems are characterised, and some comparisons are made between them. A wide range of alloy-like structures are formed, including substitutionally ordered crystals, amorphous solids, and multiphase materials. Approximate phase diagrams show that glass-formation generally occurs between competing higher symmetry structures. This work identifies two new glass-forming systems with effective chemical ordering and substantially different short- and medium-range structure compared to the glassformer studied in Part I. These represent ideal candidates for extending the study presented in Part I. There also appears to be a close connection between quasicrystal and glass-formation in 2D via random-tiling like structures. This may help explain the experimental observation that quasicrystals sometimes vitrify on heating. The alignment of asymmetric unit cells is found to be the rate-limiting step in the crystal nucleation and growth of a substitutionally ordered crystal, and another system shows amorphous-crystal coexistence and appears highly stable to complete phase separation. The generality of these results and their implications for theoretical descriptions of the glass transition are also discussed.

<p>This dissertation presents the first experiments on radio frequency (rf) spectroscopy of a quasi-two dimensional strongly interacting ultracold atomic Fermi gas. A 50-50 mixture of spin-up and spin-down atoms is confined in a series of pancake-shaped traps produced using an optical standing-wave. To make the system quasi-two dimensional, I adjust the Fermi energy in the weakly confined direction to be comparable to the harmonic oscillator energy level spacing in the tightly confined direction.</p><p>For a perfectly two dimensional system, at low enough temperature, spin-up and spin-down atoms should form dimers in the ground state of the tightly confined direction. However, in our quasi-two dimensional system I find that the simple dimer theory does not agree with the measured radio-frequency spectra. Instead, the data can be explained by polaron to polaron transitions, which is a many-body effect. Here, a polaron is a spin-down impurity surrounded by a cloud of particle-hole pairs in a spin-up Fermi sea. With this unique strongly interacting quasi-two dimensional system, I am able to study the interplay between confinement induced two-body pairing and many-body physics in confined mesoscopic systems of several hundred atoms, which has not been previously explored and offers new challenges for predictions.</p> / Dissertation

Salmonella species continue to be commonly associated with cases of food-borne disease in developed countries. In the United States in 2001, the incidence per 100,000 people was highest for salmonellosis (15.1), followed by campylobacteriosis (13.8) and shigellosis (6.4). Enteric pathogens usually contaminate the surface of raw animal products during slaughter and primary processing (scalding, defeathering or dehiding, rinsing, cutting, mixing, and grinding, etc.) and can attach and/or reside in the regular and irregular surfaces of the skin, multiply and, thereafter, contaminate food preparation surfaces, hands and utensils. Trisodium phosphate (TSP) has been approved by the USDA as a sanitizer to reduce surface loads of Salmonella on chicken carcasses. A number of studies had demonstrated that TSP effectively removes surface contamination of carcasses by food-borne pathogens. However, very little scientific evidence is available which identifies the actual mechanisms of TSP antimicrobial activity and the response of food-borne pathogens exposed to TSP. This study examined both the physiological and molecular response of Salmonella enterica serovar Enteritidis to TSP treatment. The role of high pH during TSP treatment on its antimicrobial activity was examined. Adaptation of S. enterica serovar Enteritidis to TSP treatment was also examined by analyzing the proteome of serovar Enteritidis cells using two-dimensional gel electrophoresis and mass spectrometry. The role of high pH on the antimicrobial activity of TSP was examined using comparative studies involving treatment solutions containing different concentrations of TSP, treatment solutions adjusted to the equivalent pH as in each of the TSP treatments and TSP solutions pH adjusted to 7.0. Direct and indirect indices of cell survival, membrane damage, and cellular leakage were also employed to examine specific antimicrobial effects. Cell viability, loss of membrane integrity, cellular leakage, release of lipopolysaccharides and cell morphology were accordingly examined and quantified under the above treatment conditions. Exposure of serovar Enteritidis cells to TSP or equivalent alkaline pH made with NaOH resulted in the loss of cell viability and membrane integrity in a TSP concentration- or NaOH-alkaline pH-dependent manner. In contrast, cells treated with different concentrations of TSP whose pH was adjusted to 7.0 did not show any loss of cell viability or membrane integrity. These results indicate that TSP is a potent membrane-acting agent, and provide compelling evidence that high pH during TSP treatment was responsible for its antimicrobial activity. Adaptation of S. enterica serovar Enteritidis with a sublethal concentration of TSP resulted in the induction of the alkaline stress response. Alkaline stress response involves induced thermotolerance, resistance to higher concentrations of TSP, high pH and sensitivity to acid. Examination of the proteome of TSP-adapted cells revealed differential expression of a number of proteins but did not include the common heat shock proteins involved in thermotolerance. However, TSP adaptation caused a shift in the membrane fatty acid composition from unsaturated to a higher saturated and cyclic fatty acid. This shift in fatty acid composition increases the melting point of the cytoplasmic membrane so that it remains functional at high temperatures. Biofilm bacteria are more resistant to sanitizers, heat and antimicrobial agents than their planktonic counterparts. Examination of the proteome of TSP-adapted biofilm cell of S. enterica serovar Enteritidis revealed little overlap in the protein profile compared to TSP-adapted planktonic cells. Proteomic examination of planktonic and biofilm cells of S. enterica serovar Enteritidis revealed differential expression of a number of proteins involved in DNA replication, stress survival and transport of newly synthesized proteins. These results clearly indicate that changes in the expression of specific genes are involved in the biofilm mode of growth, which could play a significant role in resistance to antimicrobial agents. The results of the current study provide a better understanding of the mechanisms of antimicrobial action of TSP and also elucidate the response of S. enterica serovar Enteritidis to TSP and high pH adaptation. The study also raises new questions regarding stress tolerance of S. Enteritidis following TSP or alkaline pH adaptation with relevance to food safety.

Salmonella species continue to be commonly associated with cases of food-borne disease in developed countries. In the United States in 2001, the incidence per 100,000 people was highest for salmonellosis (15.1), followed by campylobacteriosis (13.8) and shigellosis (6.4). Enteric pathogens usually contaminate the surface of raw animal products during slaughter and primary processing (scalding, defeathering or dehiding, rinsing, cutting, mixing, and grinding, etc.) and can attach and/or reside in the regular and irregular surfaces of the skin, multiply and, thereafter, contaminate food preparation surfaces, hands and utensils. Trisodium phosphate (TSP) has been approved by the USDA as a sanitizer to reduce surface loads of Salmonella on chicken carcasses. A number of studies had demonstrated that TSP effectively removes surface contamination of carcasses by food-borne pathogens. However, very little scientific evidence is available which identifies the actual mechanisms of TSP antimicrobial activity and the response of food-borne pathogens exposed to TSP. This study examined both the physiological and molecular response of Salmonella enterica serovar Enteritidis to TSP treatment. The role of high pH during TSP treatment on its antimicrobial activity was examined. Adaptation of S. enterica serovar Enteritidis to TSP treatment was also examined by analyzing the proteome of serovar Enteritidis cells using two-dimensional gel electrophoresis and mass spectrometry. The role of high pH on the antimicrobial activity of TSP was examined using comparative studies involving treatment solutions containing different concentrations of TSP, treatment solutions adjusted to the equivalent pH as in each of the TSP treatments and TSP solutions pH adjusted to 7.0. Direct and indirect indices of cell survival, membrane damage, and cellular leakage were also employed to examine specific antimicrobial effects. Cell viability, loss of membrane integrity, cellular leakage, release of lipopolysaccharides and cell morphology were accordingly examined and quantified under the above treatment conditions. Exposure of serovar Enteritidis cells to TSP or equivalent alkaline pH made with NaOH resulted in the loss of cell viability and membrane integrity in a TSP concentration- or NaOH-alkaline pH-dependent manner. In contrast, cells treated with different concentrations of TSP whose pH was adjusted to 7.0 did not show any loss of cell viability or membrane integrity. These results indicate that TSP is a potent membrane-acting agent, and provide compelling evidence that high pH during TSP treatment was responsible for its antimicrobial activity. Adaptation of S. enterica serovar Enteritidis with a sublethal concentration of TSP resulted in the induction of the alkaline stress response. Alkaline stress response involves induced thermotolerance, resistance to higher concentrations of TSP, high pH and sensitivity to acid. Examination of the proteome of TSP-adapted cells revealed differential expression of a number of proteins but did not include the common heat shock proteins involved in thermotolerance. However, TSP adaptation caused a shift in the membrane fatty acid composition from unsaturated to a higher saturated and cyclic fatty acid. This shift in fatty acid composition increases the melting point of the cytoplasmic membrane so that it remains functional at high temperatures. Biofilm bacteria are more resistant to sanitizers, heat and antimicrobial agents than their planktonic counterparts. Examination of the proteome of TSP-adapted biofilm cell of S. enterica serovar Enteritidis revealed little overlap in the protein profile compared to TSP-adapted planktonic cells. Proteomic examination of planktonic and biofilm cells of S. enterica serovar Enteritidis revealed differential expression of a number of proteins involved in DNA replication, stress survival and transport of newly synthesized proteins. These results clearly indicate that changes in the expression of specific genes are involved in the biofilm mode of growth, which could play a significant role in resistance to antimicrobial agents. The results of the current study provide a better understanding of the mechanisms of antimicrobial action of TSP and also elucidate the response of S. enterica serovar Enteritidis to TSP and high pH adaptation. The study also raises new questions regarding stress tolerance of S. Enteritidis following TSP or alkaline pH adaptation with relevance to food safety.

The biggest limitation to conventional gas chromatography (GC) is limited peak capacity, making the analysis of complex mixtures a difficult or even impossible task. Comprehensive two-dimensional gas chromatography (GC×GC) significantly increases peak capacity and resolution, improves sensitivity and generates structured 3D chromatograms. This is achieved by connecting two columns coated with different stationary phases through a special interface (modulator). The interface samples the first column effluent and periodically injects fractions of this material, as narrow injection pulses, onto the second column for further separation. Commercial instruments achieve this with cryogenic agents. Since this expensive approach permits only in-laboratory analysis, the development of simple, economical and field-capable GC×GC systems is in demand. This report summarizes the fundamentals governing GC×GC separations and a brief history of technological advances in the field. It also documents the construction of a simple interface, devoid of moving parts and cryogenic consumables, and hence highly suitable for field analysis and monitoring applications. Evaluation of the interface suggests on-par performance with more complicated cryogenic modulators. GC×GC separations of technical mixtures of fatty acid methyl esters (FAMEs), common environmental pollutants (EPA 8270), polychlorinated biphenyls (PCBs), pesticides (toxaphene), as well as selected essential oils and major distillation fractions of crude oil indicate very good performance. Most notably, the interface prototype was applied for the first ever time-resolved on-site analysis of the semivolatile organic fraction of urban air particulate matter (PM2.5).

The biggest limitation to conventional gas chromatography (GC) is limited peak capacity, making the analysis of complex mixtures a difficult or even impossible task. Comprehensive two-dimensional gas chromatography (GC×GC) significantly increases peak capacity and resolution, improves sensitivity and generates structured 3D chromatograms. This is achieved by connecting two columns coated with different stationary phases through a special interface (modulator). The interface samples the first column effluent and periodically injects fractions of this material, as narrow injection pulses, onto the second column for further separation. Commercial instruments achieve this with cryogenic agents. Since this expensive approach permits only in-laboratory analysis, the development of simple, economical and field-capable GC×GC systems is in demand. This report summarizes the fundamentals governing GC×GC separations and a brief history of technological advances in the field. It also documents the construction of a simple interface, devoid of moving parts and cryogenic consumables, and hence highly suitable for field analysis and monitoring applications. Evaluation of the interface suggests on-par performance with more complicated cryogenic modulators. GC×GC separations of technical mixtures of fatty acid methyl esters (FAMEs), common environmental pollutants (EPA 8270), polychlorinated biphenyls (PCBs), pesticides (toxaphene), as well as selected essential oils and major distillation fractions of crude oil indicate very good performance. Most notably, the interface prototype was applied for the first ever time-resolved on-site analysis of the semivolatile organic fraction of urban air particulate matter (PM2.5).

The increasing demand for high density storage devices has led to innovative data recording paradigms like optical holographic memories that record and read data in a two-dimensional page-oriented manner. In order to overcome the effects of inter-symbol-interference and noise in holographic channels, sophisticated constrained modulation codes and error correction codes are needed in these systems. This dissertation deals with the information-theoretic and signal processing aspects of holographic storage. On the information-theoretic front, the capacity of two-dimensional runlength-limited channels is analyzed. The construction of two-dimensional runlength-limited codes achieving the capacity lower bounds is discussed. This is a theoretical study on one of the open problems in symbolic dynamics and mathematical physics. The analysis of achievable storage density in holographic channels is useful for building practical systems. In this work, fundamental limits for the achievable volumetric storage density in holographic channels dominated by optical scattering are analyzed for two different recording mechanisms, namely angle multiplexed holography and localized recording. Pixel misregistration is an important signal processing problem in holographic systems. In this dissertation, algorithms for compensating two-dimensional translation and rotational misalignments are discussed and analyzed for Nyquist size apertures with low fill factors. These techniques are applicable for general optical imaging systems

Elastic cylinder vibration due to different shear parameter in the water flow is investigated experimentally in this research. The water flow ranges from 0.4 m/s to 1.06 m/s. It is found from the experiment that shear parameter has a significant influence on the amplitude of the cylinder vibration. The greater the shear parameter becomes, the later the delaying phenomenon also becomes. The delaying phenomenon will bring about resonant procrastination. Additionally, the greater shear parameter lessens the cylinder¡¦s drag force, but the lift force will be augmented, and the vibration orbit will be asymmetric. At lower flow velocity, cylinder¡¦s displacement is greater. With the enhancement of the shear parameter or the reduced velocity, the flow type and the vortex street behind the cylinder will turn more and more impalpable, and eventually become chaotic.

In this thesis, we propose a new way to generate orthogonal code distinct from complete complementary (CC) code and Super CC code but it still have ideal auto-correlation and cross-correlation property. We also introduce the concept of correlation and propose six rules to determine if the code generated by different ways are the same.After that we use the rules on orthogonal matrix and find a new way to generate orthogonal matrix different from Hadamard marix. Then we will use this marix in 2-D orthogonal variable spreading factor (OVSF) code and generate similar codes.

The cyanide-degradation bacteria Klebsiella oxytoca SYSU-110 was isolated from the waste water of a metal-plating plant in southern Taiwan. K. oxytoca can utilize many nitrile compounds [including acetonitrile (100 mM), benzonitrile (1 mM), butyronitrile (100 mM), glutaronitrile (50 mM), methacrylnitrile (100 mM), phenylacetonitrile (1 mM), propionitrile (25 mM), succinonitrile (25 mM) and valeronitrile (50 mM)] as its sole nitrogen source. In this study, we found out that K. oxytoca was capable of degrading acetonitrile and propionitrile. Frome GC analysis, we recognized amide was an intermediate compound, while the carboxylic acid and ammonia were the final end-products. Therefore, we presume that K. oxytoca biodegraded nitrile compounds by two enzymes, the nitrile hydratase and amidase. We also analyzed the total cell proteins by 2-D polyacrylamide gel electrophoresis after the cells were cultured in medium containing 25mM succinonitrile. There were 23 proteins could be induced or overexpressed by nitrile and we had identified 11 by Mascot Peptide mass Fingerprint and Blast. Six proteins that can protect the cells from oxidative damage are: superoxide dismutase, glutathione s-transferase, dyp-type peroxidase, metal binding protein PsaA (that can transport metal ions into the cells), LraI, and FepA (used to transport inorganic ions into the cells). Three enzymes glutamine synthetase, methylenetetrahydrofolate reductase,¡@and dihydroxyacid dehydratase were used to synthesize amino acids. One protein was identified as ribosomal protein L9. The last identified protein is nucleoside triphosphates kinase which can convert nucleoside diphosphates to nucleoside triphosphates non-specifically. From the activity analysis, superoxide dismutase and glutathione S-transferase activities were escalated when the cells were cultured in 25mM succinonitrile, and the concentration of ROS has rise. These results suggested that succinonitrile could cause oxidative damage to the cells and induce some anti-oxidative damage proteins to protect them.