The kinetic effects in an inductively coupled plasma (ICP) due to thermal motion of particles modified by self-consistent magnetic fields are studied by using a particle-in-cell (PIC) simulation. In the low pressure, low frequency regime, electron mean free paths are large relative to device size and the trajectories are strongly curved by the induced radio frequency (RF) magnetic field. This causes problems for linear theories, which ignore the influence of the magnetic field on the particles, and are therefore unable to recover effects accumulated along each nonlinear path.<p>The tools to perform high-performance parallel PIC simulations of inductively coupled plasmas were developed to allow rapid scanning of a broad range of the input parameters, such as wave amplitude, frequency, and plasma temperature. Different behavioural regimes are identified by observing the resultant variations in the skin depth, surface impedance, and ponderomotive force (PMF). At low electron-neutral collision rates, these are shown to include the local collisionless regime, the anomalous skin effect regime, and the nonlinear regime.<p>The local collisionless regime occurs at high driving frequencies and is characterized by plasma behaviour independent of both the driving frequency and amplitude: a short skin depth, low energy absorption, and strong PMF. The anomalous skin effect regime occurs at low frequencies and low amplitudes: the plasma varies with driving frequency, but not driving amplitude, the skin depth increases with frequency, the plasma is much more absorptive in the anomalous regime than in the local regime, and the PMF increases with frequency. The nonlinear regime occurs at low frequencies and high amplitudes: the plasma varies with driving amplitude, but not frequency, the skin depth decreases with amplitude, there is low energy absorption, and the PMF increases with wave amplitude.<p>The simulation runs in four modes: linear collisionless, linear collisional, nonlinear collisionless, and nonlinear collisional. The linear modes, in which the particles ignore the magnetic field, are used to validate the results against theory, while the nonlinear modes are used to test actual plasma behaviour. In linear collisionless mode, the plasma was found to exhibit only the local collisionless and anomalous skin effect regimes, as expected by theories. In nonlinear collisionless mode, the plasma exhibits the nonlinear regime in addition to the regimes found in linear mode. Finally, the nonlinear regime disappears in nonlinear collisionless mode because the curved paths caused by the magnetic field are disrupted by collisions.<p>Finally, the regime boundaries are investigated as a function of temperature. Since the plasma properties vary continuously, a boundary exists where two regimes share the same characteristics. From linear theories, it is known that the division between the local collisionless and anomalous skin effect regimes moves to higher frequencies as the plasma temperature is increased. When nonlinear fields are present, this still occurs, but in conjunction with the boundary between the local collisionless and nonlinear regimes moving to higher wave amplitudes. Temperature also effects the boundary between the anomalous skin effect and nonlinear regimes, causing the minimum frequency of the anomalous skin effect regime to be reduced at low wave amplitudes.

The mechanism of three important aldol reactions and a biomimetic transamination is investigated using a combination of experimental kinetic isotope effects (KIEs), standard theoretical calculations and dynamics trajectory simulations. This powerful mechanistic probe is found to be invaluable in understanding intricate details of the mechanism of these reactions. The successful application of variational transition state theory including multidimensional tunneling to theoretically predict isotope effects, described in this dissertation, represents a significant advance in our research methodology. The role of dynamic effects in aldol reactions is examined in great detail. The study of the proline catalyzed aldol reaction has revealed an intriguing new dynamic effect - quasiclassical corner cutting - where reactive trajectories cut the corner between reactant and product valleys and avoid the saddle point. This phenomenon affects the KIEs observed in this reaction in a way that is not predictable by transition state theory. The study of the Roush allylboration of aldehydes presents an example where recrossing affects experimental observations. The comparative study of the allylboration of two electronically different aldehydes, which are predicted to have different amounts of recrossing, suggests a complex interplay of tunneling and recrossing affecting the observed KIEs. The Mukaiyama aldol reaction has been investigated and the results unequivocally rule out the key carbon-carbon bond forming step as rate-limiting. This raises several interesting mechanistic scenarios - an electron transfer mechanism with two different rate-limiting steps for the two components, emerges as the most probable possibility. Finally, labeling studies of the base catalyzed 1,3- proton transfer reaction of fluorinated imines point to a stepwise process involving an azomethine ylide intermediate. It is found that dynamic effects play a role in determining the product ratio in this reaction.

This dissertation details work aimed at better understanding topographic effects in earthquake ground motions. The experiment, conducted in Central-Eastern Utah, used frequent and predictable seismicity produced by underground longwall coal mining as a source of low-intensity ground motions. Locally-dense arrays of seismometers deployed over various topographic features were used to passively monitor seismic energy produced by mining-induced implosions and/or stress redistribution in the subsurface. The research consisted of two separate studies: an initial feasibility experiment (Phase I) followed by a larger-scale main study (Phase II). Over 50 distinct, small-magnitude (M[subscript 'L'] < 1.6) seismic events were identified in each phase. These events were analyzed for topographic effects in the time domain using the Peak Ground Velocity (PGV), and in the frequency domain using the Standard Spectral Ratio (SSR) method, the Median Reference Method (MRM), and the Horizontal-to-Vertical Spectral Ratio (HVSR) method. The polarities of the horizontal ground motions were also visualized using directional analyses. The various analysis methods were compared to assess their ability to estimate amplification factors and determine the topographic frequencies of interest for each feature instrumented. The MRM was found to provide the most consistent, and presumably accurate, estimates of the amplification factor and frequency range for topographic effects. Results from this study clearly indicated that topographic amplification of ground motions does in fact occur. These amplifications were very frequency dependent, and the frequency range was correctly estimated in many, but not all, cases using simplified, analytical methods based on the geotechnical and geometrical properties of the topography. Amplifications in this study were found to generally range from 2 to 3 times a reference/baseline site condition, with some complex 3D features experiencing amplifications as high as 10. Maximum amplifications occurred near the crest of topographic features with slope angles greater than approximately 15 degrees, and the amplifications were generally oriented in the direction of steepest topographic relief, with some dependency on wave propagation direction. / text

Nonlinear magneto-optical effects, originated from atomic coherence, are studied both theoretically and experimentally in thermal Rb vapor. The analytical description of the fundamental properties of coherent media are based on the simplified three- and four-level systems, and then verified using numerical simulations and experimental measurements. In particular, we analyze the modification of the long-lived atomic coherence due to various physical effects, such as reabsorption of spontaneous radiation, collisions with a buffer gas atoms, etc. We also discuss the importance of the high-order nonlinearities in the description of the polarization rotation for the elliptically polarized light. The effect of self-rotation of the elliptical polarization is also analyzed. Practical applications of nonlinear magneto-optical effects are considered in precision metrology and magnetometery, and for the generation of non-classical states of electromagnetic field.

There is growing evidence of carry-over effects in migratory birds. Aerial insectivores are declining across North America; therefore, to determine the cause of these declines, we must have a holistic view of their annual cycle. I use geolocators to map the annual movements of tree swallows breeding in Nova Scotia, Canada, determine if reproduction has carry-over effects on migration, and examine the effects of geolocators. Geolocators revealed that tree swallows began migration in July and had an extended stopover in the northeastern United States. They wintered in Florida or Cuba, returning from spring migration in late April. This study revealed that later breeding swallows began migration later than earlier breeding swallows, but all birds arrived on the wintering grounds around the same time, due to differences in stopover length. No short-term effects of geolocators were found, although the sample size was small, and thus these results must be interpreted cautiously.

Statistical models like Transition State Theory (TST) and Rice-Ramsperger-Kassel-Marcus (RRKM) Theory have generally been successful in predicting the rates and selectivities of chemical reactions. However, these statistical models can fail to explain experimental results of ordinary organic reactions. For these reactions, consideration of nonstatistical dynamic effects or the detailed motion and momenta of the atoms is necessary to account for the experimental observations. Dynamic effects have been found to be important in a growing number of reactions and the nature of these effects can be varied. One of the most interesting reactions investigated is the ozonolysis of vinyl ethers. Ozonolysis of a homologous series of vinyl ethers in solution exhibit experimental product ratios wherein the selectivity among cleavage pathways increases with the size of the alkyl group to an extent that is far less than RRKM theory would predict. Trajectory studies account for the observed selectivities and support a mechanism involving a competition between cleavage of the primary ozonide and intramolecular vibrational energy redistribution. A recent theoretical study from our group predicted that a highly asynchronous organocatalytic Diels-Alder (DA) reaction, which is concerted in the potential energy surface, is stepwise in the free energy surface. Kinetic isotope effects (KIEs) were measured for three DA reactions. We envision that the entropic barrier may have several experimental consequences such as unusual isotope effects due to extensive recrossing. Preliminary results for the organocatalytic reaction show an intramolecular KIE close to unity that cannot be reconciled with statistical theories. This is in contrast with Lewis-acid catalyzed and thermal DA reactions, which exhibit substantial "normal" intramolecular KIEs that are in accord with TST predictions. Finally, the Baeyer-Villiger oxidation of cylohexanone in water was investigated. KIEs were measured for the oxidation of cyclohexanone with peracetic acid and trifluoroperacetic acid. When using peracetic acid as the oxidant, the alkyl migration was determined to be the rate-determining step based on significant intermolecular KIEs on the carbonyl and alpha-methylene carbons. A change in the rate-determining step is seen when trifluoroperacetic acid is used. Only the carbonyl carbon exhibits a significant isotope effect. Theoretical predictions provide an experimental picture of the transition states and qualitatively support these conclusions.

This thesis contributes to the under-researched field of political selection, namely one’s re-selection onto the party list after one has been elected in the previous term. The theoretical rationale is to introduce a broader concept of political selection to a field mostly focused on political recruitment, one’s first point of entry into Politics. We show that the framework developed to study political recruitment can be adapted to study any kind of political selection that involves a broad pool of aspirants from which successful candidates must be selected. To this end, we utilise a panel dataset containing data on 387 Czech legislators covering the period between 1996 and 2013. Using fixed- and random-effects panel models, we show that voting along the party line and preferential vote share at time t are strong predictors of getting a better party-list rank at t+1. Legislative experience, however, is negatively associated with how well one fares at the re-selection process. We also provide evidence that it is left-wing parties rather than their right-wing counterparts that discriminate against women at the re-selection stage. The study thus contributes, directly or otherwise, to debates on women’s representation, political careers and re-election.

Throughout history, objects of art have been damaged and sometimes destroyed in earthquakes. Even though the importance of providing seismically adequate design for nonstructural components has received attention over the past decade, art objects in museums, either on display or in storage, require further research. The research reported in this study was undertaken to investigate the seismic vulnerability of art objects. Data for this research was gathered from three museums in Montreal. / The seismic behaviour of three unrestrained display cases, storage shelves, and a 6m long dinosaur skeleton model structure was investigated according to the seismic hazard for Montreal and representative museum floor motions were simulated for that purpose. Particular attention was paid to the support conditions, the effects of modified floor surface conditions, the sliding and rocking response of unrestrained display cases, the location (floor elevation) of the display case and/or storage shelves, art object mass, and the dynamic properties of the display cases/storage shelves. The seismic vulnerability of art objects was evaluated based on the seismic response of the display cases/storage shelves at the level of art object display. The display cases were investigated experimentally using shake table testing. Computer analyses were used to simulate the seismic behaviour of storage shelves, and the seismic sensitivity of the dinosaur structure was determined via free vibration acceleration measurements. The floor contact conditions and floor elevation had a crucial effect on the unrestrained display cases, causing them to slide or rock vigorously. The distribution of content mass had a large impact on the response of the shelving system. As a result of experimental and analytical analyses, recommendations and/or simple mitigation techniques are provided to reduce the seismic vulnerability of objects of art.

Ionising radiation can cause damage to DNA that can result in gene mutations contributing to carcinogenesis. Radiation-protection policy currently estimates cancer risks from exposures to radiation in terms of excess risk per unit dose. At very low radiation dose-rates, where not all cells are absorbing radiation energy, this formula carries the inherent assumption that risk is limited to those cells receiving direct energy depositions. Numerous studies have now called this assumption into question. Such low dose-rates are in the relevant range that the public receives from natural background and man-made sources, and, if this fundamental assumption proves unfounded, current estimations of radiation-induced cancer risk at low doses will be incorrect. Accurate predictions of stochastic cancer risks from low-dose radiation exposures are crucial to evaluating the safety of radiation-based technologies for industry, power generation and the increasing use of radiation for medical diagnostic and screening purposes. This thesis explores phenomena known as radiation-induced bystander effects. The term bystander effects, as used here, describes biological responses to ionising radiation (hitherto observed in vitro) in cells not directly traversed by an ionising track, due to intercellular signals received from neighbouring cells that did receive energy depositions. This study aimed to determine whether radiation effects are communicated between irradiated and unirradiated cells in vivo, and if so, whether this effect alters current estimations of cancer risk following low-dose radiation exposures. In order to answer these questions, an in vivo experimental system for studying bystander effects in mice was developed. The method was based on the adoptive transfer of irradiated splenocytes into unirradiated hosts with simultaneous identification of irradiated donor cells, and biological endpoints in unirradiated bystander cells in situ using fluorescence microscopy and image analysis. Splenocytes from donor mice were radiolabelled with 3H-thymidine or received an acute X-ray dose. The irradiated donor cells, labelled with a fluorescent probe, were then adoptively transferred into unirradiated recipient mice via the tail vein, whilst control mice received sham-irradiated donor cells. A proportion of the cells lodged in the recipient mouse spleens where they remained for a period before the tissues were cryopreserved. The locations of donor cells were identified in frozen spleen sections by the fluorescent probe, and the levels of apoptosis and proliferation were simultaneously evaluated in situ in the surrounding unirradiated bystander cells using fluorescence-based assays. Transgenic pKZ1 recipient mice were also used to quantify chromosomal inversions in bystander cells. Since three-dimensional spatial relationships were preserved, responses could be measured in the local area surrounding irradiated cells as well as further afield. Following the development of the irradiated-cell adoptive transfer protocol and validation of the sensitivity and reproducibility of the biological assays in situ, a series of experiments was performed. In the initial experiments, 500,000 radiolabelled cells (0.33 mBq.cell-1) were injected into recipient mice and the spleen tissues were isolated 22 h later. No changes in apoptosis or proliferation were detected in local bystander spleen cells or throughout the spleen, compared to mice receiving sham-radiolabelled donor cells. In subsequent experiments, the effects of a number of experimental conditions were explored including the injection of tenfold more donor cells, analysis of spleen tissues after three days lodging in vivo, radiolabelling of donor cells with 100-fold higher 3H dose-rate and irradiation of donor cells ex vivo with 0.1 or 1 Gy X-rays. In each case, no changes in apoptosis or proliferation were observed. The in vivo method described here was designed to simulate the conditions of a bystander scenario from low dose-rate exposures relevant to public radiation protection. Contrary to the many reports of bystander effects in vitro, experiments using this sensitive method for examining the in vivo responses of unirradiated cells to neighbouring low-dose irradiated cells, have so far shown no changes in bystander cells in the spleen. This adoptive transfer method is the first in vivo method for examining the effects of known irradiated cells exposed to low radiation doses at low dose-rates, on neighbouring cells in situ that are truly unirradiated. Both the irradiated and bystander cells are normal, non-transformed primary spleen cells functioning in their natural environment. This in vivo experimental system allows the examination of tens of thousands of bystander cells and has shown a remarkable sensitivity, with statistical power to rule out changes in apoptosis &lt10% from the control. The relevance of in vitro bystander findings is unclear. Many reported bystander effects are more analogous to the systemic communication of abscopal effects from highly irradiated tissues. Disagreement between experimental systems and difficulty in reproducing key results between laboratories further complicate the translation of bystander data in vitro to human risk-estimation. The radiation protection community has expressed its need for in vivo validation of the bystander phenomenon before it can be included into the appraisal of carcinogenic risk. This adoptive transfer method is now available to study a range of bystander endpoints and potential signalling mechanisms in vivo, and provides a way to translate the wealth of data previously collected in vitro into findings directly relevant to human risk-estimation.

Every year hundreds of cetaceans strand on New Zealand beaches. Options for dealing with disposal of their carcasses are few, creating significant problems for the Department of Conservation (DOC). More often than not their carcasses are buried in beaches at or just above high water mark, near where the animals have stranded. The primary objective of this thesis is to determine the effects of cetacean burial on beach sediments, and evaluate potential health and safety risks associated with this practice. A secondary objective of this thesis is to appraise the appropriateness of one location DOC has repeatedly transported cetacean carcasses to and buried within beach sediments, Motutapu Island in Waitemata Harbour. The chemical effects of cetacean burial over a six-month period are reported for two sites at which animals were buried in 2008, Muriwai and Pakiri beaches; the biological effects of this burial are reported for one of these sites, Muriwai Beach, 12 months post burial. Intertidal faunal and floral inventories are provided for six sites around Motutapu Island, and these then compared and contrasted with inventories compiled from an additional 290 intertidal sites between Whangarei Heads and Tauranga Harbour, North Island East Coast, to appraise the relative uniqueness of intertidal species diversity around Motutapu Island. At both Muriwai and Pakiri beaches, nitrogen and phosphate concentrations in surface sands changed considerably following cetacean burial, although over six months the effect was localized and elevated concentrations of these two chemicals that could be attributed to a buried carcass did not extend more than 40 m from the site of whale burial. Deep-core profiles revealed nitrogen and phosphate concentrations at and in the immediate vicinity of cetacean burial approximately six months after burial to be markedly elevated to the level of the water table, but elevated concentrations attributable to the buried carcass were not observed greater than 25 m from the site of burial. Elevated concentrations of nitrogen and phosphates in beaches persist in surface sediments for at least six months post burial. Twelve months post cetacean burial no significant difference in species richness or abundance were apparent in intertidal communities extending along transects proximal to and some distance from the Muriwai Beach carcass; there is no evidence for any significant short-term (to 12 months) biological effects of cetacean burial in beaches. Of those shores on Motutapu Island accessible by earth-moving equipment and large vessels capable of dealing with and transporting large cetacean carcasses, Station Bay appeared to be the most appropriate site for whale burial. However its small size and relatively high biological value (fairly high species richness for comparable shores between Whangarei Heads and Tauranga) renders it an inappropriate long-term option for whale burial. Other shores on Motutapu Island host some of the highest species richness of all shores surveyed between Whangarei Heads and Tauranga Harbour, rendering them entirely inappropriate locations for burying cetaceans, over and above other variables that may influence disposal location identification (such as archaeological sites, dwellings and accessibility). Motutapu Island is not considered an appropriate location for cetacean burial within beaches. Alternative disposal strategies need to be explored for dealing with cetaceans that strand on Auckland east coast beaches. Although burial is the most convenient and most economical strategy to dispose of cetacean carcass, especially in mass stranding events or when cetaceans are of large size, and the biological effects of this practice are not considered significant (for the one whale that could be studied), persistent enrichment of beach sediments with organic matter could result in prolonged persistence of pathogens in beaches, causing unforeseen risks to human health and safety. Recommendations are made to minimize possible threats to public following burial of cetaceans in beaches, until the potential health risks of burial are more fully understood.