For elucidating catalytic processes and enhancing process efficiency, the characterisation of porous catalysts is crucial. While the chemical characterisation of the catalyst surface, e.g. by infrared and X-ray photoelectron spectroscopy, is standard practice, the energetic characterisation of surface sites is often neglected, although all heterogeneously catalyzed reactions take place at the surface. Inverse gas chromatography is a gas phase method to investigate a large number of physico-chemical, morphological and energetical surface properties of particles, granulates or fibers. In this dissertation, silica materials with well-defined surface properties and a large specific surface area (porous glass beads, pyrogenic silica) were investigated. For potential catalytic and sensoric applications, the silica material was additionally grafted with organofunctional silanes. The overall aim of this Thesis was to apply IGC-theories to different silicas before and after surface modification, to examine the potential of this characterisation method. The validity of the results was set against its limitations, to verify the IGC as sensitive method even for small changes of physico-chemical surface properties. It was observed that the physicochemical properties of the surface are predominatly determined by silanol and siloxane groups. In particular the LEWIS-acid silanol groups strongly interact with LEWIS-basic polar probe molecules. This results in high values for free surface energy with a dominant polar component and an overall LEWIS-acidity of the silica. Measurements indicated specific surface areas respectively to the applied probe molecule. In particular 2-propanol showed strong interactions, a very high surface area, but also a heterogenous adsorption behaviour. According to PAPIRERs Patchwork model of condensation approximation, two different states of adsorption were found. With DFT-simulation these were identified as low energetic hydrogen bonds between 2-propanol and siloxan and as high energetic hydrogen bonds between 2-propanol and silanol groups. Nevertheless, all of the IGC findings point to a reduction of the acidity of silica and an increase in hydrophobicity by surface modification due to the loss of silanol groups with the silane grafting. Finally, the IGC can be presented as a many-faceted useful tool for surface characterisation. Its variability and sensitivity expands most other classical methods. Complex surface properties like free surface energies, acid-base functionality, kinetic parameters, specific surface area and surface heterogenity can be determined from single chromatographic peaks with the respective theories. Throughout the investigation, a new non-linear parameter estimation approach was introduced in contrast to the common linear computation models. Therefore, an increasing number of involved probe molecules and also the use of bipolar probes yields in statistical more reliable results.

Synthetic biology is a rapidly growing discipline that aims to rationally design the behavior of living organisms for an array of applications, ranging from environmental monitoring to one of particular interest –medicine. For instance, given bacteria’s inherent ability to passively localize to tumor sites and previous work of engineering bacteria to sense compounds of interest utilizing genetic circuits, synthetic biologists can engineer bacteria to proactively sense the tumor for various applications. In this dissertation, we will discuss two such critical applications; one is ensuring safety of living therapeutics by having bacteria limit their growth to disease sites in order to prevent off-target toxicity. The other is a novel method of diagnostic readout, using bacterial production of a volatile compound. The aim of this thesis is to develop safe and robust bacteria-based technologies as living therapies. To confine bacterial growth within defined regions of interest, we engineer enhanced bacterial tropism with genetic circuits that couple bacterial sensing and growth in response to physiological signatures in vivo. Specifically, we construct oxygen, pH, and lactate biosensors with tunable features for activation at distinct physiological concentrations. We use these biosensors to control the expression of essential genes, which results in significant bacterial growth differences in permissive vs non-permissive conditions. Using pH and oxygen sensors, we demonstrate preferential growth in physiologically-relevant acidic and oxygen conditions. Upon oral delivery in mice, these engineered strains lowered bacteria numbers outside of the host. Multiplexing hypoxia and lactate biosensors with an AND logic-gate architecture resulted in improved performance, reducing bacterial off-target colonization in a syngeneic mouse tumor model. Taken together, these results demonstrate a synthetic biology approach to enhance precision localization of bacteria to specified organ niches. In additional to engineering bacteria localization, we also want to take advantage of E. coli’s programmable nature to produce diagnostic molecules. The engineering of microbial metabolic pathways over the last two decades has led to numerous examples of cell factories used for the production of small molecules. These molecules have an array of utility in commercial industries and as in-situ expressed biomarkers or therapeutics in microbial applications. While most efforts have focused on the production of molecules in the liquid phase, there has been increasing interest in harnessing microbes’ inherent ability to generate volatile compounds. Here, we optimized and characterized the production of methyl salicylate, an aromatic compound found mainly in plants, using a common lab strain of E. coli. We utilized genetic components from both microbes and plants to construct the volatile metabolite circuit cassette. In order to maximize production, we explored expressing methyl salicylate precursors, upregulating expression by increasing ribosomal binding strength and codon optimizing methyl transferase gene obtain from plant Petunia x hybrida. Lastly, we validated and quantified the production of methyl salicylate with liquid chromatography and gas chromatography mass spectrometry (LC-MS or GC-MS) and found that the codon optimized strain with precursor supplementation yield the highest production compared to the other strains. This work characterizes an optimized metabolite producing-genetic circuit and sets the stage for creation of an engineered bacteria diagnostic to be used in volatile assays.Finally we conclude by discussing the current efforts to adapt technology described in this thesis dissertation for clinical research and applying them in genetic mouse models for further validation. This underlying work contributes to rapidly growing field in synthetic biology to engineer microbial based living therapy.

Following an unexpected event in an underground mine, it is important to know the state of the mine immediately to manage the situation effectively. Particularly when part or the whole mine is inaccessible, remotely and quickly ascertaining the ventilation status is one of the pieces of essential information that can help mine personnel and rescue teams make decisions. This study developed a methodology that uses tracer gas techniques and CFD modeling to analyze underground mine ventilation system status remotely. After an unanticipated event that has damaged ventilation controls, the first step of the methodology is to assess and estimate the level of the damage and the possible ventilation changes based on the available information. Then CFD models will be built to model the normal ventilation status before the event, as well as possible ventilation damage scenarios. At the same time, tracer gas tests will be designed and performed on-site. Tracer gas will be released at a designated location with constant or transient release techniques. Gas samples will be collected at other locations and analyzed using Gas Chromatography (GC). Finally, through comparing the CFD simulated results and the tracer on-site test results, the general characterization of the ventilation system can be determined. A review of CFD applications in mining engineering is provided in the beginning of this dissertation. The basic principles of CFD are reviewed and six turbulence models commonly used are discussed with some examples of their application and guidelines on choosing an appropriate turbulence model. General modeling procedures are also provided with particular emphasis on conducting a mesh independence study and different validation methods, further improving the accuracy of a model. CFD applications in mining engineering research and design areas are reviewed, which illustrate the success of CFD and highlight challenging issues. Experiments were conducted both in the laboratory and on-site. These experiments showed that the developed methodology is feasible for characterizing underground ventilation systems remotely. Limitations of the study are also addressed. For example, the CFD model requires detailed ventilation survey data for an accurate CFD modeling and takes much longer time compared to network modeling. Some common problems encountered when using tracer gases in underground mines are discussed based on previously completed laboratory and field experiments, which include tracer release methods, sampling and analysis techniques. Additionally, the use of CFD to optimize the design of tracer gas experiments is also presented. Finally, guidelines and recommendations are provided on the use of tracer gases in the characterization of underground mine ventilation networks. / Ph. D.

For the first time, germania-based hybrid organic-inorganic sol-gel materials were developed for analytical sample preparation and chromatographic separation. Being an isostructural analog of silica (SiO2), germania (GeO2) is compatible with silica network. This structural similarity, which is reflected by the relative positions of germanium and silicon in the periodic table, stimulated our investigation on the development of germania-based sol-gel hybrid organic-inorganic coatings for analytical applications. Sol-gel sorbents and stationary phases reported to date are predominantly silica-based. Poor pH stability of silica-based materials is a major drawback. In this work, this problem was addressed through development of germania-based organic-inorganic hybrid sol-gel materials. For this, tetramethoxygermane (TMOG) and tetraethyoxygermane (TEOG) were used as precursors to create a sol-gel network via hydrolytic polycondensation reactions to provide the inorganic component (germania) of the organic-inorganic hybrid coating. The growing sol-gel germania network was simultaneously reacted with an organic ligand that contained sol-gel-active sites in its chemical structure. Hydroxy-terminated polydimethylsiloxane (PDMS) and 3-cyanopropyltriethoxysilane (CPTES) served as sources of nonpolar and polar organic components, respectively. The sol-gel reactions were performed within fused silica capillaries. The prepared sol-gel germania coatings were found to provide excellent pH and thermal stability. Their extraction characteristics remained practically unchanged after continuous rinsing of the sol-gel germania-PDMS capillary for 24 hours with highly basic (pH=13) and/or acidic (pH = 1.3) solution. They were very efficient in extracting non-polar and moderately polar analytes such as polycyclic aromatic hydrocarbons, aldehydes, ketones. Possessing the polar cyanopropyl moiety, sol-gel germania cyanopropyl-PDMS capillaries were found to effectively extract polar analytes such as alcohols, fatty acids, and phenols. Besides, they also showed superior thermal stability compared with commercial cyano-PDMS coatings thanks to the covalent attachment of the coating to capillary surface achieved through sol-gel technology. Their extraction characteristics remained unchanged up to 330°C which is significantly higher than the maximum operation temperature ( < 280 ºC) for commercial cyano-PDMS coatings. Low ng/L detection limits were achieved for both non-polar and polar test solutes. Our preliminary results also indicated that sol-gel hybrid germania coatings have the potential to offer great analytical performance as GC stationary phases.

The methyl ester of an unsaturated fatty acid, methyllinoleate was reacted with oxygen in a pressurized system at a controlled temperature. A natural autoxidation of methyl linoleate was observed without the addition of an initiating reagent. This autoxidation process could be used to mimic the course of lipid peroxidation, which is the major cause ofradical damage to living cells. The technology of GC-MS was employed to monitor the autoxidation of methyllinoleate. Eight of the autoxidation products separated by GC column were identified by interpreting the corresponding EI ion mass spectra. The products from 9-alkoxy methyl linoleate radical were methyl octanate, 2,4-decadienal, nonanoic acid, 9-oxo-methyl ester, and its further oxidation product, nonanedioic acid, monomethyl ester. All of them formed through a pathway of beta-cleavage. The products from 13-alkoxy methyl linoleate radical were tridecanoic acid, 9, 11-diene-13-oxo-methyl ester, hex anal, and its further oxidation product, hexanoic acid. They were also formed through a mechanism of beta-cleavage. The fourth product from 13-alkoxy methyllinoleate radical was 13-keto-9, 11-octadecadienoic acid, methyl ester, which was obtained through a pathway of keto formation. Observation of their concentrations in the samples at different autoxidation periods revealed the time-course of formation of these products.

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Eastern Cistern B on the Ad-Deir Plateau is unusual in its breadth and variety of ceramic vessels represented by thousands of sherds. These sherds raised significant questions about the purpose and use of the vessels that they originally came from. This thesis argues that the ceramic vessels that were deposited in Eastern Cistern B represent the deposited remains of an ancient Nabataean ritual feast. Furthermore, this thesis also helps to answer the questions surrounding what the ceramic containers once held and their relationship to that ritual meal. This thesis identified residues absorbed within the ceramic fragments through the use of a gas chromatographer-mass spectrometer analysis. The data demonstrated that the vessels once contained remains of medicinal plants, such as crocus, oleander, and others as well as post deposition contaminants throughout the majority of the samples. Those contaminations and other limitations mentioned in this thesis may provide a basis for future investigations for absorbed residue analysis in Petra, Jordan. In turn, the relationship between the medicinal plants and the feast at Eastern Cistern B suggests that a healing ritual possibly accompanied a meal suggesting archaeologists begin examining this and other associated events that accompanied ritual feasts in and among the Nabataeans and in the ancient Near East more broadly.

An analytical method was developed for detection and quantitation of diazinon and chlorpyrifos, two widely used pesticides in local water pathway. Solid phase extraction combined with GC/MS detection with selected ion monitoring was employed. In establishing calibration curves for GC/MS analysis, it may be impractical to use isotope-labeled analogs as internal standards for all analytes in a complicated matrix. Compounds may have to be used as internal standards which could cause non-linear effects because of different response of analytes and internal standards. A novel sample introduction method, which could eliminate this negative effect of non-linearity, was proposed. Calibration data were acquired using the traditional constant volume injection method, and a new method: constant mass injection of analytes. Calibration curves by the constant mass injection method show a better linearity and y-intercept. The nonlinear effect observed with data obtained in low concentration ranges using the constant volume injection method was eliminated. The effectiveness of these curves by two methods was also tested. Better accuracy was obtained with the constant mass injection method. This constant mass injection of analytes method could be very useful in quantitative studies of a complicated sample matrix, such as those encountered in the environmental analysis of pesticides, or in the quality control analysis of medical and industrial product. In solid phase extraction, Varian Bondelute SPE C8 cartridge was selected for extraction. With the standard water sample spiked at 500 ng/L for the two analytes, the recovery for diazinon was about 50% and for chlorpyrifos about 60%. With the standard water sample at 1000 ng/L, the recovery for diazinon was about 60% and for chlorpyrifos about 70%. Among three samples from three different sampling sites, diazinon was detected and confirmed. The quantitation of diazinon was done to water sample from the Calaveras River near the Sanguetti Street crossing Stockton, California, with observed concentration 143.2 ng/L.