The propagation of radiowaves through ionospheric irregularities can lead to random amplitude and phase fluctuations of the signal, otherwise known as scintillation, which can severely impact the performance of Global Navigation Satellite System (GNSS) and communication systems. Research into high latitude scintillation, through statistical analysis and inverse modeling, was completed to provide insight into the temporal and spatial distribution, and irregularity parameters, which can ultimately support the development of impact mitigation techniques, and deepen our understanding of the underlying physics. The work in this dissertation focused on the statistical analysis of Global Positioning System (GPS) scintillation data, data inversion, two-dimensional (2D) and three-dimensional (3D) scintillation modeling. The statistical analysis revealed distinct trends in the distribution of scintillation, while demonstrating that for GPS signals, phase scintillation occurs most frequently and can be treated as stochastic Total Electron Content (TEC); findings which have significant implications for impact mitigation. For the first of two inversion studies, scintillation data associated with a series of Polar Cap Patches (PCPs), which are common large-scale high latitude structures, was inverted to gain insight into the composition of the underlying irregularities. The results of this study suggest that the irregularities can be modeled as rods interbedded with sheets, which is knowledge that is crucial for the anchoring of models used to develop system mitigation techniques. The final study presents the results of modeling and inversion work to identify the conditions under which a 2D analytic version of the 3D numerical Satellite-beacon Ionospheric-scintillation global model of the upper atmosphere (SIGMA) model can be used to perform modeling in high latitude regions. During the study, it was found that the analytic model tends to diverge for electron density variance times irregularity layer thickness values exceeding 2, matched reasonably well for correlation length to thickness ratios up to 0.2, and was incompatible when ratios approached 0.35. An elevation angle limitation was also identified for the 2D model, and inflated values for the electron density variance were observed overall, which are thought to result from the weak scatter limits of the analytic model. These inflated values were particularly acute in the auroral zone during elevated conditions and suggest that the analytic model used in the study is not well suited for modeling the highly elongated irregularities associated with auroral precipitation. / Doctor of Philosophy / The ionosphere is a region of the earth's atmosphere extending from approximately 90 to 1000 km in altitude. Radio wave signals which travel through irregularities in the ionosphere can be distorted in a way that can lead to random amplitude and phase fluctuations of the signal, otherwise known as scintillation, which can severely degrade the performance of navigation and communication systems. Research into high latitude scintillation, through statistical analysis, and data and model matching, was completed to provide insight into the time and space distribution, and irregularity parameters, in order to ultimately deepen our understanding of the physics and to help develop better models. The work in this dissertation focused on the statistical analysis of GPS scintillation data, data and model matching, and 2D and 3D irregularity modeling. The statistical analysis revealed distinct trends in the distribution of scintillation, while demonstrating that for GPS signals, phase scintillation occurs most frequently but the impacts can be corrected if measured; findings which have significant implications for impact mitigation. For the first of two model and data matching studies, scintillation data associated with a series of common large-scale high latitude structures called PCPs, was matched to a model to gain insight into the composition of the underlying irregularities. The results of this study suggest that the irregularities can be modeled as vertical rods oriented along the magnetic field interbedded within flat sheets, which is knowledge that is crucial for having confidence in the models used to develop system mitigation techniques. The final study presents the results of modeling and data matching work to identify the conditions under which a 2D or 3D model can be used to perform irregularity modeling in the high latitude regions. During the study, it was found that the 2D model tends to diverge from the 3D model for significant variations in the ionosphere, and when irregularity rods are highly elongated. A signal propagation path elevation angle limitation was also identified for the 2D model, and inflated values for the predicted ionospheric variations were observed overall, which are thought to result from limits of the 2D model compared to the more general 3D version. These inflated values were particularly acute in the auroral region during elevated conditions and suggest that the 2D model used in the study is not well suited for modeling the highly elongated irregularities associated with aurora effects.

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Cytochromes P450 (P450s) are a superfamily of heme-thiolate monooxygenases. They catalyse a wide variety of reactions on a vast number of substrates and are of particular interest for biocatalyst development due to their ability to oxidise non-activated C-H bonds. Fusion of a P450 to a suitable redox partner protein produces a catalytically self-sufficient enzyme and removes the need to produce electron transfer proteins separately. The well-studied bacterial protein P450cam (Pseudomonas putida) has been fused to the reductase (RhFRed) from the natural fusion protein P450-RhF (Rhodococcus sp.). The P450cam-RhFRed system catalyses the oxidation of camphor and several non-natural substrates and served as the basis for P450cam re-engineering in this current project, with the aim of expanding the substrate scope towards a more mammalian-like activity. The P450cam active site was partitioned into seven paired amino acids and each pair randomised in turn to generate seven sub-libraries of P450cam variants. These were screened for activity using a specially developed colony screen for detection of the blue pigment indigo. In total 94 new variants were identified and then pooled for secondary screening on a number of new substrates, identifying potentially novel activities within the ‘indigo positive’ population. In a separate ‘chimeragenesis’ approach substrate recognition sites (SRSs) within P450cam were targeted for exchange with equivalent portions from a number of human P450s. The B’ helix and F-G loop regions from CYPs 1A2, 2C8, 2D6 and 3A4 were grafted onto the P450cam structure and several of the B’ helix swaps were produced as soluble proteins. The P450cam-2C8-B’-RhFRed chimera gave a Soret peak at 420 nm in the Fe(II)-CO state although an additional substitution next to the proximal cysteine appeared to restore a P450-like state. SRS-exchange therefore offered some insight into structural modularity in P450s, providing a basis for further biocatalyst development.

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Pas de résumé / Propagation of nonlinear acoustic waves in inhomogeneous media is an important problem inmany research domains of modern theoretical and applied acoustics. For example, studies onpropagation of high amplitude N-waves in turbulent atmosphere are relevant to the sonic boomproblem which involves high interest due to development of new civil supersonic aircrafts. Inrelation to sonic boom problem, many studies on spark-generated N-wave propagation through aturbulent layer were carried out in model laboratory-scale experiments which are more controlledand reproducible than field measurements. Propagation of high intensity focused ultrasound intissue (HIFU) is intensively studied for medical applications. HIFU is a basis of new surgicaldevices for noninvasive thermal and mechanical ablation of tumors.In this thesis, the problem of characterization of high amplitude N-waves generated in air byan electric spark was studied using combined acoustical and optical methods. The fine structureof shocks was deduced from the shadowgraphy images with a resolution that cannot be obtainedusing condenser microphones. It was shown that the combination of optical and acoustical methodsallows complete characterization of the N-waves.N-wave propagation through a layer of thermal turbulence was further studied in a laboratoryexperiment. The evolution of statistical distributions and average values of the most importantN-wave parameters was investigated at different propagation distances. Experimental results werecompared to data obtained in another experiment known in literature, where N-wave was propagatedthrough kinematic turbulence. It was shown that in the case of almost the same widths ofthe turbulent layers, values of the characteristic scales and rms of refractive index fluctuations, thekinematic turbulence leads to stronger distortions of the peak pressure and the shock rise time ofthe N-wave and to 2-3 greater probabilities to observe intense focusing in caustics.Effects of nonlinear propagation and random focusing on the statistics of N-wave amplitudewere studied theoretically using the KZK equation and the phase screen model. The phase screenwas characterized by the correlation length and the refraction length – the distance where firstcaustics occur. Probability distributions, mean values and standard deviations of the N-wave peakpressure were obtained from the numerical solutions and were presented as functions of the propagationdistance and the nonlinear length. Statistical results from the KZK model were comparedwith analytical predictions of the nonlinear geometrical acoustics approach (NGA). It was shown,that NGA approach is valid only up to the distance of one third of refraction length of the screen.Strong nonlinear effects were shown to suppress amplitude fluctuations. The effect of the scale ofinhomogeneities on amplitude statistics was also investigated.The problem of focusing of ultrasound beam through inhomogeneous medium is importantfor medical diagnostics and nondestructive testing problems. The inhomogeneities of biologicaltissue or of industrial materials can destroy beam focusing. In the thesis, distortions of a weaklynonlinear diagnostic beam focused through a phase layer of special configuration were consideredexperimentally and theoretically. Feasibility of selective destruction of focusing of differentharmonics in the beam was predicted in the modeling and confirmed in experiment.The most modern HIFU devices rely on using two-dimensional multi-element phased arrayswith elements randomly distributed over a segment of a spherical surface. Numerical experimentis an important tool to characterize pressure fields created by HIFU radiators. Intensity levels atthe focus of HIFU radiators can reach several tens of thousands of W/cm2, causing nonlinearpropagation effects and formation of shocks [...]

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