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Located in the south-west region of Spencer Gulf, South Australia, a multi-million dollar aquaculture industry based on the ranching of southern bluefin tuna (Thunnus maccoyii) contributes significantly to the regional economy. The interaction between aquaculture activities and the environment is of significant interest to industry stakeholders, management authorities and the broader science community. No studies, to the best of my knowledge, have investigated the relationships between the hydrodynamics and biogeochemistry of the system and the ability of the benthic ecosystem to deal with the increased loads of organic material from aquaculture activities. This thesis uses a multi-disciplinary approach combined with modern statistical techniques to explore the linkages between hydrodynamics, sediment geochemistry, sedimentary nutrient cycling and the aquaculture industry. Modelling results have identified that swell entering the mouth of Spencer Gulf from directly south causes the greatest swell heights in the central tuna farming zone. Winds from the north-east through to south-east generate the greatest wind-wave heights in the central tuna farming zone. This is directly related to the available fetch. The energy contained in the locally generated wind waves was the same order of magnitude as that of the dissipated oceanic swells. Yet the incoming swell poses the greatest risk to aquaculture activities as the increased wave length causes swell energy to penetrate to the seafloor. The results of this work suggest that the sediment geochemistry is tightly coupled to both the hydrodynamic regime and the buildup of silt originating from aquaculture activities. In the more exposed regions of the tuna farming zone, periodic resuspension events caused by swell propagating into the area from the Southern Ocean, resuspend fine unconsolidated sediments into the lower 10 m of the water column. This material is then advected through the region by the residual (low-frequency) currents until it settles out in areas of lower energy. This process has created two distinct provinces within the region that can either be classified as depositional or erosional. The combined effect of wave action and tidal currents have generated a heterogeneous distribution of biogeochemical properties within the sediments. Denitrification rates were measured in these heterogeneous sediments using a novel technique based on Bayesian statistics to explicitly account for the spatial variability of the sediment biogeochemistry. The denitrification rates were found to be generally low, largely due to the lack of organic matter entering the sediments. However, adjacent to aquaculture activities, the high organic loads stimulate sedimentary denitrification, with rates reaching values of up to three orders of magnitude greater than the control sites. Denitrification efficiencies were high adjacent to the aquaculture activities, with up to 95% of the dissolved inorganic nitrogen produced from the breakdown of organic matter in the sediments being removed. Variability in the denitrification efficiencies was related to the textural characteristics of the sediments, with high efficiencies in finer sediments. It is proposed that this is due to the lower permeability of these sediments restricting the advective exchange of porewater nutrients.

Forward modelling of seismic waves is an essential tool in the determination of the underlying structure of the Earth using inversion techniques. Despite recent advances in computer power and memory resources, full 3-D elastic wave modelling continues to place a heavy burden on a typical personal computer. 2.5-D modelling reduces the computational burden while maintaining 3-D wavefield characteristics. In this thesis I present 2.5-D frequency-domain equations of motion for elastic wave modelling in anisotropic media. The reduced set of equations for vertical transversely isotropic media and tilted transversely isotropic media are presented separately. Using the spectral-element method, I develop the equations of motion into readily implemented sub-equations by identifying simple 1-D and 2-D patterns. Some aspects of my computational implementation are unique, in particular the use of a system of dynamically growing binary trees to serve as a system matrix. Using this system, the matrix is automatically stored in compressed row format. I investigate the use of both distributed memory and shared memory super-computers for 3-D modelling and compare the resource use of various matrix solvers. In this thesis I adapt recently developed Perfectly Matched Layer formulations to the 2.5-D elastic case, and find them to be adequate in most situations. I investigate the possiblity of instability in the absorbing layers. Observation of 2.5-D modelling results in the frequency wavenumber domain uncovers polelike behaviour at critical wavenumbers within the spectrum. I demonstrate how this behaviour threatens the accuracy of the inverse Fourier transformed frequency-domain solution. However for inhomogeneous media, under certain conditions the only medium that exhibits pole-like behaviour is the medium containing the source. Further study of the phenomenon shows that in homogeneous, transversely isotropic media, the critical wavenumber values are not dependent on the receiver position, but rather can be predicted using the maximum phase velocities of the media. The recommended strategy for wavenumber sampling is to use dense even spacing of values, to adequately capture the behaviour close to the critical wavenumbers. A further recommendation it to introduce slight attenuation through the use of complex velocities (or elastic constants) to eliminate any pole-like behaviour at the critical values. / http://proxy.library.adelaide.edu.au/login?url= http://library.adelaide.edu.au/cgi-bin/Pwebrecon.cgi?BBID=1385923 / Thesis (Ph.D.) -- University of Adelaide, School of Chemistry and Physics, 2010

The benefits of the Oceans and Seas have been exploited by societies for many centuries; the marine offshore and naval sectors have been the predominant users of the waters. It has been overlooked until recently, that significant amounts of energy can be harnessed by waves, providing an additional abundant resource for renewable energy generation. The increasing energy needs of current societies have led to the consideration of waves as an exploitable renewable resource. During the past decades, advancements have been made towards commercialising wave energy converters (WECs), though significant knowledge gap exists on the accurate estimation of the potential energy that can be harnessed. In order, to enhance our understanding of opportunities within wave energy highly resolved long-term resource assessment of potential sites are necessary, which will allow for not only a detailed energy estimation methodology but also information on extreme waves that are expected to affect the survivability and reliability of future wave energy converters. This research work aims to contribute the necessary knowledge to the estimation of wave energy resources from both highly energetic and milder sea environment, exhibiting the opportunities that lay within these environments. A numerical model SWAN (Simulating WAves Nearshore), based on spectral wave formulation has been utilised for wave hindcasting which was driven by high resolution temporal and spatially varying wind data. The capabilities of the model, allow a detailed representation of several coastal areas, which are not usually accurately resolved by larger ocean models. The outcome of this research provides long-term data and characterisation of the wave environment and its extremes for the Scottish region. Moreover, investigation on the applicability of wave energy in the Mediterranean Sea, an area which was often overlooked, showed that wave energy is more versatile than expected. The outcomes provide robust estimations of extreme wave values for coastal waters, alongside valuable information about the usage of numerical modelling and WECs to establish energy pattern production. Several key tuning factors and inputs such as boundary wind conditions and computational domain parameters are tested. This was done in a systematic way in order to establish a customized solution and detect parameters that may hinder the process and lead to erroneous results. The uncertainty of power production by WECs is reduced by the introduction of utilization rates based on the long-term data, which include annual and seasonal variability. This will assist to minimize assumptions for energy estimates and financial returns in business plans. Finally, the importance of continuous improvements in resource assessment is stressed in order to enhance our understanding of the wave environment.

<p>The wave field in the Baltic Sea has been modelled for a two-year period with the spectral wave model HYPAS. There is a large seasonal variation in the field and a minor annual one, both reflect the wind variation in the area. Since the Baltic Sea is fetch limited, the dominant wind direction is important for the maximum wave heights.</p><p>By studying the modelled wave energy density in combination with bottom type maps, the effect of the wave field on the sediment surface is examined. Up to half the bottoms in the Baltic Sea are affected ~25% of the time. A statistical relation between wave energy density and bottom types is found for the Gulf of Riga, but in the rest of the area the sediment maps were to coarse. It is, due to this, not possible to say if the result is valid for the whole area or if it is site specific.</p><p>During resuspension events the remineralisation is increased since deposited organic material is reintroduced into the watermass and there exposed to higher levels of oxygen. This process could act as an increased regional source of nitrogen in nutrient budgets and thus influence the conditions for nitrogen fixation and perhaps explain some of the geographical differences in the nitrogen fixation rates.</p>

The wave field in the Baltic Sea has been modelled for a two-year period with the spectral wave model HYPAS. There is a large seasonal variation in the field and a minor annual one, both reflect the wind variation in the area. Since the Baltic Sea is fetch limited, the dominant wind direction is important for the maximum wave heights. By studying the modelled wave energy density in combination with bottom type maps, the effect of the wave field on the sediment surface is examined. Up to half the bottoms in the Baltic Sea are affected ~25% of the time. A statistical relation between wave energy density and bottom types is found for the Gulf of Riga, but in the rest of the area the sediment maps were to coarse. It is, due to this, not possible to say if the result is valid for the whole area or if it is site specific. During resuspension events the remineralisation is increased since deposited organic material is reintroduced into the watermass and there exposed to higher levels of oxygen. This process could act as an increased regional source of nitrogen in nutrient budgets and thus influence the conditions for nitrogen fixation and perhaps explain some of the geographical differences in the nitrogen fixation rates.

L'étude et la gestion des risques littoraux sont plébiscitées par notre société au vu des enjeux économiques et écologiques qui y sont impliqués. Ces risques sont généralement réponse à des conditions environnementales extrêmes. L'étude de ces phénomènes physiques repose sur la compréhension de ces conditions rarement (voire nullement) observées.Dans un milieu littoral, la principale source d'énergie physique est véhiculée par les vagues. Cette énergie est responsable des risques littoraux comme l'érosion et la submersion qui évoluent à des échelles de temps différentes (événementielle ou long-terme). Le travail réalisé, situé à l'interface de l'analyse statistique, de la géophysique et de l'informatique, vise à apporter des méthodologies et outils aux décideurs en charge de la gestion de tels risques.En pratique, nous nous intéressons à mettre en place des méthodes qui prennent en compte non seulement un site ponctuel mais traitent les problématiques de façon spatiale. Ce besoin provient de la nature même des phénomènes environnementaux qui sont spatiaux, tels les champs de vagues.L'étude des réalisations extrêmes de ces processus repose sur la disponibilité d'un jeu de données représentatif à la fois dans l'espace et dans le temps, permettant de projeter l'information au-delà de ce qui a déjà été observé. Dans le cas particulier des champs de vagues, nous avons recours à la simulation numérique sur calculateur haute performance (HPC) pour réaliser un tel jeu de données. Le résultat de ce premier travail offre de nombreuses possibilités d'applications.En particulier, nous proposons à partir de ce jeu de données deux méthodologies statistiques qui ont pour but respectif de répondre aux problématiques de risques littoraux long-termes (érosion) et à celles relatives aux risques événementiels (submersion). La première s'appuie sur l'application de modèles stochastiques dit max-stables, particulièrement adapté à l'étude des événements extrêmes. En plus de l'information marginale, ces modèles permettent de prendre en compte la structure de dépendance spatiale des valeurs extrêmes. Nos résultats montrent l'intérêt de cette méthode au devant de la négligence de la dépendance spatiale de ces phénomènes pour le calcul d'indices de risque.La seconde approche est une méthode semi-paramétrique dont le but est de simuler des champs spatio-temporels d'états-de-mer extrêmes. Ces champs, interprétés comme des tempêtes, sont des amplifications contrôlées et bi-variés d'épisodes extrêmes déjà observés. Ils forment donc des tempêtes encore plus extrêmes. Les tempêtes simulées à une intensité contrôlée alimentent des modèles physiques événementiels à la côte, permettant d'aider les décideurs à l'anticipation de ces risques encore non observés.Enfin et depuis la construction de ces scenarii extrêmes, nous abordons la notion de pré-calcul dans le but d'apporter en quasi-temps réel au décideur et en tant de crise une prévision sur le risque littoral.L’ensemble de ce travail s'inscrit dans le cadre d'un besoin industriel d’aide à la modélisation physique : chainage de modèles numériques et statistiques. La dimension industrielle de cette thèse est largement consacrée à la conception et au développement d’un prototype de plateforme de modélisation permettant l’utilisation systématique d’un calculateur HPC pour les simulations et le chainage de modèles de façon générique.Autour de problématiques liées à la gestion du risque littoral, cette thèse démontre l'apport d'un travail de recherche à l'interface de plusieurs disciplines. Elle y répond en conciliant et proposant des méthodes de pointe prenant racine dans chacune de ces disciplines. / Studies and management of coastal hazards are of high concerns in our society, since they engage highly valuable economical and ecological stakes. Coastal hazards are generally responding to extreme environmental conditions. The study of these physical phenomena relies on the understanding of such environmental conditions, which are rarely (or even never) observed.In coastal areas, waves are the main source of energy. This energy is responsible of coastal hazards developed at different time-scales, like the submersion or the erosion.The presented work, taking place at the interface between Statistical Analysis, Geophysics and Computer Sciences, aiming at bringing forward tools and methods serving decision makers in charge of the management of such risks.In practice, the proposed solutions answer to the questionings with a consideration of the space dimension rather than only punctual aspects. This approach is more natural considering that environmental phenomena are generally spatial, as the sea-waves fields.The study of extreme realisations of such processes is based on the availability of a representative data set, both in time and space dimensions, allowing to extrapolating information beyond the actual observations. In particular for sea-waves fields, we use numerical simulation on high performance computational clusters (HPC) to product such a data set. The outcome of this work offers many application possibilities.Most notably, we propose from this data set two statistical methodologies, having respective goals of dealing with littoral hazards long-terms questionings (e.g., erosion) and event-scale questionings (e.g., submersion).The first one is based on the application of stochastic models so-called max-stable models, particularly adapted to the study of extreme values in a spatial context. Indeed, additionally to the marginal information, max-stable models allow to take into account the spatial dependence structures of the observed extreme processes. Our results show the interest of this method against the ones neglecting the spatial dependence of these phenomena for risk indices computation.The second approach is a semi-parametric method aiming at simulating extreme waves space-time processes. Those processes, interpreted as storms, are controlled and bi-variate uplifting of already observed extreme episodes. In other words, we create most severe storms than the one already observed. These processes simulated at a controlled intensity may feed littoral physical models in order to describe a very extreme event in both space and time dimensions. They allow helping decision-makers in the anticipation of hazards not yet observed.Finally and from the construction of these extreme scenarios, we introduce a pre-computing paradigm in the goal of providing the decision-makers with a real-time and accurate information in case of a sudden coastal crisis, without performing any physical simulation.This work fits into a growing industrial demand of modelling help. Most notably a need related to the chaining of numerical and statistical models. Consequently, the industrial dimension of this PhD.~is mostly dedicated to the design and development of a prototype modelling platform. This platform aims at systematically using HPC resources to run simulations and easing the chaining of models.Embracing solutions towards questionings related to the management of coastal hazard, this thesis demonstrates the benefits of a research work placed at the interface between several domains. This thesis answers such questionings by providing end-users with cutting-edge methods stemming from each of those domains.