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“Matrix effects” in Near Edge X-ray Absorption Fine Structure (NEXAFS) spectroscopy are the spectroscopic changes induced by intermolecular interactions, providing sensitivity to local structure and order in solids and liquids. This project aims to identify the effect of intermolecular interactions caused by different n-alkane solid state structures on their NEXAFS spectra. Changes to the carbon 1s NEXAFS spectra are studied as a function of their solid state structure and organization. Two experimental approaches were proposed in this project. In the first approach, different n-alkane crystal structures (orthorhombic, monoclinic, etc.) are examined which arise as a function of n-alkane chain length. In the second approach, changes observed through the pre-melting point order-disorder phase transition found in n-alkanes are examined. This work will explore the characteristic spectroscopic differences observed between n-alkanes in different crystalline forms as well as in the disordered phase below the melting points. In this project, well-ordered diamond shape n-alkane single crystals were obtained by solution casting, using experimental conditions optimized for each n-alkane. As circularly polarized radiation will average the effect of molecular orientation, circularly polarized radiation was used to obtain the NEXAFS spectra of n-alkanes. However, in the analysis of the NEXAFS spectra of n-alkanes recorded with the left circularly polarized X-rays, a significant linear polarization contamination was found. Therefore, linearly polarized X-rays were used to acquire angle dependent NEXAFS spectra, where the X-ray polarization was deliberately aligned along the principal axes (X, Y) of the n-alkane crystal. It was observed that the room temperature carbon 1s NEXAFS spectrum of n-octacosane (C28H58) was different from that of the other n-alkanes, n-tetracosane (C24H50), n-tricosane (C23H48) and n-tetracontane (C40H82). This difference can be attributed due to the different crystal packing of n-octacosane (C28H58 - monoclinic) relative to the other n-alkanes (triclinic and orthorhombic), suggesting different intermolecular interactions (matrix effects) in n-octacosane (C28H58). The analysis of the temperature dependent NEXAFS spectra of n-alkanes reveals that samples of the short chain n-alkane crystals, specially n-tricosane (C23H48), n-tetracosane (C24H50) and n-octacosane (C28H58), sublimed in the STXM microscope. Changes observed in the carbon 1s NEXAFS spectra of n-tetracontane (C40H82) with temperature were attributed to the order-disorder transition. This further illustrates the existence of matrix effects in the NEXAFS spectra of n-alkanes.

Inductively coupled plasma-mass spectrometers (ICP-MS) have become the workhorses of many analytical labs over the past few decades. Despite the instruments' high sensitivities and low detection limits there is still a demand for improvements in several aspects of their performance. One area of improvement is in the understanding of "space charge effects" Space charge effects are classified as problems associated with the ion beam. Problems are created when the mutual repulsions of the ions make consistent focusing of the ion beam difficult. This is particularly problematic with samples containing a low concentration analyte contained within a high salt solution matrix, resulting in lower instrument sensitivity and inaccurate results. The research presented here used laser-induced fluorescence (LIF) imaging to characterize the ion beam as it enters the mass analyzer of a commercial ICP-MS. To perform the LIF imaging a laser system with two ring cavities was constructed to frequency double a CW titanium-sapphire laser to the calcium ion transition at 393.4 nm or to the barium ion transition at 455.4 nm. Ion beam images for both elements were taken under different instrument modes and matrix compositions. The same trends in shift and distortion of the barium ion beam with the addition of a lead matrix was observed as in previous experiments with calcium. A shift in the focal point of the ion beams of both elements was also observed in normal sensitivity mode and with the instrument's collisional reaction interface (CRI). This work indicates that a shift in beam focusing is responsible for the change in ion transmission due to changes in matrix composition and instrument modes.

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The Life Marker Chip instrument, which has been selected to fly as part of the 2018 ExoMars rover mission payload, aims to detect up to 25 organic molecules in martian rocks and regolith, as markers of extant life, extinct life, meteoritic in-fall and spacecraft contamination. Martian samples will be extracted with a solvent and the resulting liquid extracts will be analysed using multiplexed microarray-format immunoassays. The LMC is under development by an international consortium led by the University of Leicester and the work described within this thesis was carried out at Cranfield University as part of the consortium’s broader program of work preparing the LMC instrument for flight in 2018. Within this thesis four specific areas of LMC instrument development are addressed: the investigation of immunoassay compatible liquid extraction solvents, the study of likely interactions of martian sample matrix with immunoassays, the development of antibodies for the detection of markers of extinct life and demonstration of solvent extraction and immunoassay detection in a flight representative format. Cont/d.

A novel method for determination of tetrabromobisphenol-A (TBBPA), was developed using gas chromatography-negative ion chemical ionization-mass spectrom- etry (GC-NCI-MS). Samples of municipal wastewater treatment plant (WWTP) influent were analyzed for TBBPA. Levels ranged from 1 to 41 ng/L, with an average of 20 ± 14 ng/L. Matrix effects were shown to be 30 ± 17 % in the influent and -30 ± 11 % in membrane permeate. The method limit of quantitation was 0.1 ng/L TBBPA. Sorption of TBBPA to fresh mixed-liquor suspended solids (MLSS) from a membrane bioreactor (MBR) were studied. In a kinetic study, sorption was found to be essentially complete after 12 hours of exposure to MLSS. Log Koc and log Kd were measured at 4.7 ± 0.8 and 1.9 ± 0.8 respectively (n = 22). These values were much higher than modelled estimates based on Kow (p ≥ 0.05), and higher than modelled estimates based on Kow and pKa (p ≥ 0.05). Data was successfully modelled using the Freundlich isotherm, having a Kf value of 8.5 and an n value of 1.7. TBBPA adsorbed to borosilicate glassware, with a wall-loss coefficient (Kw) of 0.15 ± 0.1 (n ≥ 3). TBBPA levels in WWTP influent varied from 13 to 29 ng/L while effluent concentrations varied from 0 to 2.2 ng/L over the same period. Three pilot-scale membrane bioreactors (MBRs) removed less TBBPA during the same time period, though MBR removal was also significant (p ≥ 0.05). Increasing MBR sludge residence time (SRT) increased removal at the 86 % confidence interval (p = 0.14). A nitrifying MABR was shown to remove TBBPA significantly when spiked with ammonia and TBBPA (p ≥ 0.05), showing that nitrifying bacteria can degrade TBBPA. An MABR hollow fibre was found to adsorb TBBPA. Various soluble microbial products (SMP) were studied from MBRs fed munici- pal influent. Using current measurement practices, SMP were shown to be sensitive to matrix effects. Use of the standard addition technique (SA) can compensate for this. Measurements using SA showed SMP degrades rapidly during storage in the fridge and due to freezing. SA was also used to compare commonly used SMP extraction techniques, and showed that extraction method influences recovery.

Master of Science / Department of Biology / Alice Boyle / Species extinctions over the past two centuries have mainly been caused by habitat destruction. Landscape change typically reduces habitat area, and can fragment contiguous habitat into remnant patches that are more subject to anthropogenic disturbance. Furthermore, changes in the landscape matrix and land-use intensification within remaining natural areas can reduce habitat quality and exacerbate the consequences of habitat loss and fragmentation. Accordingly, wildlife conservation requires an understanding of how landscape structure influences habitat selection. However, most studies of habitat selection are conducted at fine spatial scales and fail to account for landscape context. Temperate grasslands are a critically endangered biome, and remaining prairies are threatened by woody encroachment and disruptions to historic fire-grazing regimes. Here, I investigated the effects of habitat area, fragmentation, woody cover, and rangeland management on habitat selection by two species of declining grassland-obligate sparrows: Henslow’s Sparrows (Ammodramus henslowii) and Grasshopper Sparrows (A. savannarum). I conducted >10,000 bird surveys at sites located throughout eastern Kansas, home to North America’s largest remaining tracts of tallgrass prairie, during the breeding seasons of 2015 and 2016. I assessed the relative importance of different landscape attributes in determining occurrence and within-season site-fidelity of Henslow’s Sparrows using dynamic occupancy models. The species was rare, inhabited <1% of sites, and appeared and disappeared from sites within and between seasons. Henslow’s Sparrows only settled in unburned prairie early in spring, but later in the season, inhabited burned areas and responded to landscape structure at larger scales (50-ha area early in spring vs. 200-ha during mid-season). Sparrows usually settled in unfragmented prairie, strongly favored Conservation Reserve Program (CRP) fields embedded within rangeland, avoided trees, and disappeared from hayfields after mowing. Having identified fragmentation as an important determinant of Henslow’s Sparrow occurrence, I used N-mixture models to test whether abundance of the more common Grasshopper Sparrow was driven by total habitat area or core habitat area (i.e. grasslands >60 m from woodlands, croplands, or urbanized areas). Among 50-ha landscapes containing the same total grassland area, sparrows favored landscapes with more core habitat, and like Henslow’s Sparrows, avoided trees; in landscapes containing ~50–70% grassland, abundance decreased more than threefold if half the grassland area was near an edge, and the landscape contained trees. Effective conservation requires ensuring that habitat is suitable at spatial scales larger than that of the territory or home range. Protecting prairie remnants from agricultural conversion and woody encroachment, promoting CRP enrollment, and maintaining portions of undisturbed prairie in working rangelands each year are critical to protecting threatened grassland species. Both Henslow’s Sparrows and Grasshopper Sparrows were influenced by habitat fragmentation, underscoring the importance of landscape features in driving habitat selection by migratory birds. As habitat loss threatens animal populations worldwide, conservation efforts focused on protecting and restoring core habitat could help mitigate declines of sensitive species.

The inductively coupled plasma - mass spectrometer (ICP-MS) is the analytical instrument of choice for trace element detection and quantification. Despite the popularity of ICP-MS, significant degradation in sensitivity and precision occurs as the result of matrix and instrument-induced effects. The sources of these effects are not well understood, characterized, or correlated to particular plasma operating condition settings or matrix compositions and involve both neutral and charged species. The purpose of this study is to characterize the behavior of metastable Ar (I) atom and Ca (II) ion through the measurement of Doppler velocities and fluorescence line width "temperatures." For the characterization of Ar (I), axial and radial velocity and temperature profiles were collected as a function of nebulizer rate, incident ICP power and matrix composition to establish a behavioral baseline for neutral species in the first vacuum stage expansion of an ICP-MS. Velocities were determined from the Doppler shift of laser-induced Ar (I) fluorescence compared to stationary population wavelength reference. Unambiguous evidence of a thick Mach disk forming 10-12 mm downstream and persisting through 17-18 mm downstream, under standard ICP conditions, conflicts with the widely held view of a thin Mach disk located between 15-17 mm downstream. Characterization of Ca (II) ion focused on the effect of changing ICP conditions and matrix composition on calcium ion Doppler velocity and temperature profiles in the first vacuum stage expansion. Evidence of the plasma potential acceleration of ions through the interface was found as a higher Ca (II) terminal velocity than that of Ar (I) under standard ICP conditions. Additionally, the effect of a lithium matrix on Ca (II) velocity and temperature profiles was generally opposite than on Ar (I) velocity and temperature profiles.