Broadband optical cavity absorption spectroscopy in the near-ultraviolet: applications in atmospheric chemistry

A novel spectroscopic method, incoherent broadband cavity enhanced absorption spectroscopy (IBBCEAS), has been modified and extended to measure absorption spectra in the near-ultraviolet with high sensitivity. The near-ultraviolet region extends from 300 to 400 nm and is particularly important in tropospheric photochemistry; absorption of near-UV light can also be exploited for sensitive trace gas measurements of several key atmospheric constituents. In this work, several IBBCEAS instruments were developed to record reference spectra and to measure trace gas concentrations in the laboratory and field. An IBBCEAS instrument was coupled to a flow cell for measuring very weak absorption spectra between 335 and 375 nm. The instrument was validated against the literature absorption spectrum of SO2. Using the instrument, we report new absorption cross-sections of O3, acetone, 2-butanone, and 2-pentanone in this spectral region, where literature data diverge considerably owing to the extremely weak absorption. The instrument was also applied to quantifying low concentrations of the short-lived radical, BrO, in the presence of strong absorption by Br2 and O3. A different IBBCEAS system was adapted to a 4 m3 atmosphere simulation chamber to record the absorption cross-sections of several low vapour pressure compounds, which are otherwise difficult to measure. Absorption cross-sections of benzaldehyde and the more volatile alkyl nitrites agree well with previous spectra; on this basis, the cross-sections of several nitrophenols are reported for the first time. In addition, the instrument was also used to study the optical properties of secondary organic aerosol formed following the photooxidation of isoprene. An extractive IBBCEAS instrument was developed for detecting HONO and NO2 and had a sensitivity of about 10-9 cm-1. This instrument participated in a major international intercomparison of HONO and NO2 measurements held in the EUPHORE simulation chamber in Valencia, Spain, and results from that campaign are also reported here.

Electronic spectroscopy of thiones

The phosphorescence excitation spectra of two thiones, 4-H-1-xanthione (XT) and 4-H-1-pyrane-4-thione (PT), cooled in a supersonic jet were investigated. The vibronic lineshape of the T1z origin of PT measured by cavity ring-down spectroscopy is considered and the excited state rotational constants are calculated. For XT the 3A2(nπ* ) → X1A1 phosphorescence excitation spectrum was investigated in the region 14900-17600 cm-1. The structure observed is shown to be due to the T1← S0 absorption and an assignment in terms of the vibronic structure of the band is proposed. A previous assignment of the S1 ← S0 origin is considered and the transition involved is shown to be most probably due to the absorption of a vibronic tiplet state T1z,v7. An alternative but tentative assignment of the S1,0 ←S0,0 transition is suggested. In the case of PT the phosphorescence excitation spectrum was investigated in the region of the 1A2(ππ*) ← X1A1 absorption band between 27300 and 28800 cm-1. The spectrum exhibits complex features which are typical for the strong vibronic coupling case of two adjacent electronic states. The observed intermediate level structure was attributed to the coupling with a lower lying dark electronic state 1B1(nπ*2), whose origin was estimated to be ~ 825 - 1025 cm-1 below the origin of 1A2(ππ*)0. Consequences of the vibronic coupling on the decay dynamics of 1A2(ππ*) as well as tentative assignments of vibronic transitions 1A2(ππ*)v ← X1A1 are also discussed. In the T1z ← S0 cavity ring-down absorption spectrum of PT, the vibronic lineshape of the T1z origin is analysed. As the T1z line is separated from the T1x,1y lines by a large zero-field splitting it is possible to use an Asyrot-like program to calculate the vibrational-rotational parameters determining the lineshape. It is shown that PT is non-planar in the first excited triplet state and the lineshape is composed of a mixture of A-type and C-type bandshapes. The non-planarity of PT is discussed.

Characterisation and spectroscopy of laser-cooled atoms with an optical nanofibre

In this thesis, a magneto-optical trap setup is used to laser cool and confine a cloud of 85Rb. The cloud typically contains 108 atoms in a 1 mm3 volume at a temperature in the region of the Doppler Limit (146 _K for 85Rb). To study the cold cloud, a subwavelength optical fibre - a nanofibre, or ONF - is positioned inside the cloud. The ONF can be used in two ways. Firstly, it is an efficient fluorescence collection tool for the cold atoms. Loading times, lifetimes and temperatures can be measured by coupling the atomic fluorescence to the evanescent region of the ONF. Secondly, the ONF is used as a probe beam delivery tool using the evanescent field properties of the device, allowing one to perform spectroscopy on few numbers of near-surface atoms. With improvements in optical density of the cloud, this system is an ideal candidate in which to generate electromagnetically induced transparency and slow light. A theoretical study of the van der Waals and Casimir-Polder interactions between an atom and a dielectric surface is also presented in this work in order to understand their effects in the spectroscopy of near-surface atoms.

Identification and analysis of mechanisms involved in a broad-spectrum disease resistant mutant of the winter wheat cv. Guardian

M66 an X-ray induced mutant of winter wheat (Triticum aestivum) cv. Guardian exhibits broad-spectrum resistance to powdery mildew (Blumeria graminis f. sp. tritici), yellow rust (Puccinia striiformis f. sp. tritici), and leaf rust (Puccinia recondita f. sp. tritici), along with partial resistance to stagnonospora nodorum blotch (caused by the necrotroph Stagonosporum nodorum) and septoria tritici blotch (caused by the hemibiotroph Mycosphaerella graminicola) compared to the parent plant ‘Guardian’. Analysis revealed that M66 exhibited no symptoms of infection following artificial inoculation with Bgt in the glasshouse after adult growth stage (GS 45). Resistance in M66 was associated with widespread leaf flecking which developed during tillering. Flecking also occurred in M66 leaves without Bgt challenge; as a result grain yields were reduced by approximately 17% compared to ‘Guardian’ in the absence of disease. At the seedling stage, M66 exhibited partial resistance. M66, along with Tht mutants (Tht 12, Tht13), also exhibit increased tolerance to environmental stresses (abiotic), such as drought and heat stress at seedling and adult growth stages, However, adult M66 exhibited increased susceptibility to the aphid Schizaphis graminum compared to ‘Guardian’. Resistance to Bgt in M66 was characterized with increased and earlier H2O2 accumulation at the site of infection which resulted in increased papilla formation in epidermal cells, compared to ‘Guardian’. Papilla formation was associated with reduced pathogen ingress and haustorium formation, indicating that the primary cause of resistance in M66 was prevention of pathogen penetration. Heat treatment at 46º C prior to challenge with Bgt also induced partial disease resistance to Blumeria graminis f. sp. tritici in ‘Guardian’ and M66 seedlings. This was characterized by a delay in primary infection, due to increased production of ROS species, such as hydrogen peroxide, ROS-scavenging enzymes and Hsp70, resulting in cross-linking of cell wall components prior to inoculation. This actively prevented the fungus from penetrating the epidermal cell wall. Proteomics analysis using 2-D gel electrophoresis identified primary and secondary disease resistance effects in M66 including detection of ROS scavenging enzymes (4, 24 hai), such as ascorbate peroxidase and a superoxidase dismutase isoform (CuZnSOD) in M66 which were absent from ‘Guardian’. Chitinase (PR protein) was also upregulated (24 hai) in M66 compared to ‘Guardian’.Monosomic and ditelosomic analysis of M66 revealed that the mutation in M66 is located on the long arm of chromosome 2B (2BL). Chromosome 2BL is known to have key genes involved in resistance to pathogens such as those causing stripe rust and powdery mildew. The TaMloB1 gene, an orthologue of the barley Mlo gene, is also located on chromosome 2BL. Sanger sequencing of part of the coding sequence revealed no deletions in the TaMloB1 gene between ‘Guardian’ and M66.

Tropospheric aerosol detection over Southern Ireland using a backscatter Raman lidar

Lidar is an optical remote sensing instrument that can measure atmospheric parameters. A Raman lidar instrument (UCLID) was established at University College Cork to contribute to the European lidar network, EARLINET. System performance tests were carried out to ensure strict data quality assurance for submission to the EARLINET database. Procedures include: overlap correction, telecover test, Rayleigh test and zero bin test. Raman backscatter coefficients, extinction coefficients and lidar ratio were measured from April 2010 to May 2011 and February 2012 to June 2012. Statistical analysis of the profiles over these periods provided new information about the typical atmospheric scenarios over Southern Ireland in terms of aerosol load in the lower troposphere, the planetary boundary layer (PBL) height, aerosol optical density (AOD) at 532 nm and lidar ratio values. The arithmetic average of the PBL height was found to be 608 ± 138 m with a median of 615 m, while average AOD at 532 nm for clean marine air masses was 0.119 ± 0.023 and for polluted air masses was 0.170 ± 0.036. The lidar ratio showed a seasonal dependence with lower values found in winter and autumn (20 ± 5 sr) and higher during spring and winter (30 ± 12 sr). Detection of volcanic particles from the eruption of the volcano Eyjafjallajökull in Iceland was measured between 21 April and 7 May 2010. The backscatter coefficient of the ash layer varied between 2.5 Mm-1sr-1 and 3.5 Mm-1sr-1, and estimation of the AOD at 532 nm was found to be between 0.090 and 0.215. Several aerosol loads due to Saharan dust particles were detected in Spring 2011 and 2012. Lidar ratio of the dust layers were determine to be between 45 and 77 sr and AOD at 532 nm during the dust events range between 0.84 to 0.494.

Molecular genetic analysis of DNA alterations in Irish colorectal cancer

Colorectal cancer is the most common cause of death due to malignancy in nonsmokers in the western world. In 1995 there were 1,757 cases of colon cancer in Ireland. Most colon cancer is sporadic, however ten percent of cases occur where there is a previous family history of the disease. In an attempt to understand the tumorigenic pathway in Irish colon cancer patients, a number of genes associated with colorectal cancer development were analysed in Irish sporadic and HNPCC colon cancer patients. The hereditary forms of colon cancer include Familial adenomatous polyposis coli (FAP) and Hereditary Non-Polyposis Colon Cancer (HNPCC). Genetic analysis of the gene responsible for FAP, (the APC gene) has been previously performed on Irish families, however the genetic analysis of HNPCC families is limited. In an attempt to determine the mutation spectrum in Irish HNPCC pedigrees, the hMSH2 and hMLHl mismatch repair genes were screened in 18 Irish HNPCC families. Using SSCP analysis followed by DNA sequencing, five mutations were identified, four novel and a previously reported mutation. In families where a mutation was detected, younger asyptomatic members were screened for the presence of the predisposing mutation (where possible). Detection of mutations is particularly important for the identification of at risk individuals as the early diagnosis of cancer can vastly improve the prognosis. The sensitive and efficient detection of multiple different mutations and polymorphisms in DNA is of prime importance for genetic diagnosis and the identification of disease genes. A novel mutation detection technique has recently been developed in our laboratory. In order to assess the efficacy and application of the methodology in the analysis of cancer associated genes, a protocol for the analysis of the K-ras gene was developed and optimised. Matched normal and tumour DNA from twenty sporadic colon cancer patients was analysed for K-ras mutations using the Glycosylase Mediated Polymorphism Detection technique. Five mutations of the K-ras gene were detected using this technology. Sequencing analysis verified the presence of the mutations and SSCP analysis of the same samples did not identify any additional mutations. The GMPD technology proved to be highly sensitive, accurate and efficient in the identification of K-ras gene mutations. In order to investigate the role of the replication error phenomenon in Irish colon cancer, 3 polyA tract repeat loci were analysed. The repeat loci included a 10 bp intragenic repeat of the TGF-β-RII gene. TGF-β-RII is involved in the TGF-β epithelial cell growth pathway and mutation of the gene is thought to play a role in cell proliferation and tumorigenesis. Due to the presence of a repeat sequence within the gene, TGFB-RII defects are associated with tumours that display the replication error phenomenon. Analysis of the TGF-β-RII 10 bp repeat failed to identify mutations in any colon cancer patients. Analysis of the Bat26 and Bat 40 polyA repeat sequences in the sporadic and HNPCC families revealed that instability is associated with HNPCC tumours harbouring mismatch repair defects and with 20 % of sporadic colon cancer tumours. No correlation between K-ras gene mutations and the RER+ phenotype was detected in sporadic colon cancer tumours.

Analysing energy detector diversity receivers for spectrum sensing

The analysis of energy detector systems is a well studied topic in the literature: numerous models have been derived describing the behaviour of single and multiple antenna architectures operating in a variety of radio environments. However, in many cases of interest, these models are not in a closed form and so their evaluation requires the use of numerical methods. In general, these are computationally expensive, which can cause difficulties in certain scenarios, such as in the optimisation of device parameters on low cost hardware. The problem becomes acute in situations where the signal to noise ratio is small and reliable detection is to be ensured or where the number of samples of the received signal is large. Furthermore, due to the analytic complexity of the models, further insight into the behaviour of various system parameters of interest is not readily apparent. In this thesis, an approximation based approach is taken towards the analysis of such systems. By focusing on the situations where exact analyses become complicated, and making a small number of astute simplifications to the underlying mathematical models, it is possible to derive novel, accurate and compact descriptions of system behaviour. Approximations are derived for the analysis of energy detectors with single and multiple antennae operating on additive white Gaussian noise (AWGN) and independent and identically distributed Rayleigh, Nakagami-m and Rice channels; in the multiple antenna case, approximations are derived for systems with maximal ratio combiner (MRC), equal gain combiner (EGC) and square law combiner (SLC) diversity. In each case, error bounds are derived describing the maximum error resulting from the use of the approximations. In addition, it is demonstrated that the derived approximations require fewer computations of simple functions than any of the exact models available in the literature. Consequently, the regions of applicability of the approximations directly complement the regions of applicability of the available exact models. Further novel approximations for other system parameters of interest, such as sample complexity, minimum detectable signal to noise ratio and diversity gain, are also derived. In the course of the analysis, a novel theorem describing the convergence of the chi square, noncentral chi square and gamma distributions towards the normal distribution is derived. The theorem describes a tight upper bound on the error resulting from the application of the central limit theorem to random variables of the aforementioned distributions and gives a much better description of the resulting error than existing Berry-Esseen type bounds. A second novel theorem, providing an upper bound on the maximum error resulting from the use of the central limit theorem to approximate the noncentral chi square distribution where the noncentrality parameter is a multiple of the number of degrees of freedom, is also derived.