The biodiversity of two distinct marine environments was observed to describe the biogeocomplexity of these extreme ecological systems. A shallow-water hydrothermal vent in Papua New Guinea served as a study of a thermophilic ecosystem influenced by arsenic rich vent fluids while a 60 m deep offshore primarily anoxic karst sink served as a study of an anaerobic sulfur-influenced habitat. Both environments support unique biological communities that are influenced by the physical and chemical pressures imposed on them by the harsh conditions of these systems. In Tutum Bay, Ambitle Isle, Papua New Guinea, a transect was created from a shallow hydrothermal vent that extended 120 m away from the vent. Previous studies have shown that the geochemistry of the system is heavily influenced by arsenic which is toxic to most organisms. In this study, macro- and meiofauna were collected and scored and combined with bacterial sequence data collected along the length of the transect. It was found that near vent sites harbored biological communities more similar than sites further from the vent. Many species were found only at sites near the hydrothermal vent. Near-vent communities were less diverse than those away from the vent, and biodiversity generally increased as distance from the vent increased. Distinct correlations between thermophilic organisms and temperature were observed. The metabolic repertoire of the microbial communities suggests that many strategies are used to obtain energy and carbon. The relative abundance of bacteria containing genes to reduce arsenic was comparable to those able to reduce sulfur compounds. Primary production appeared to be a mix of chemo- and phototrophy. Food webs and association analysis suggest a complex interplay between macrofaunal, meiofaunal and bacterial communities. While the system is heavily influenced by arsenic, no specific correlation between the relative abundance of arsenic metabolizing organisms and the amount of arsenic in the system could be drawn. This is likely due to the fact that most of the arsenic produced by the system is readily adsorbed onto iron oxyhydroxides, reducing the arsenic's bioavailability. The anoxic conditions at Jewfish sink provide a different hurdle than the hot arsenic conditions found in Papua New Guinea. The anoxic conditions are shared by other pit features found in karst geography, but the metabolic processes between Jewfish sink and these other karst habitats are different. The blue holes and black holes of the Bahamas are some of the most well-studied of these karstic pits. In these features, which are large circular pits with diameters of over 300 m, light and sulfur are used as a means of energy acquisition. Jewfish sink, having an opening only 6 m in diameter, is light restricted compared to these systems. As a result, the strategy of organisms dwelling in the anoxic conditions of the sink is different than those found at the well-studied holes in the Bahamas. Geochemical measurements were recorded over two time periods spanning a combined total of 6 years. The anoxic bottom waters of Jewfish sink remain stable and contained high levels of sulfide throughout most of the seasons studies. Sequence analysis of prokaryotes within the sink showed that sulfur reducers had the highest relative abundance compared to other functional guilds. To monitor the changes of the microbial communities within the sink, bacterial communities were examined at 4 depths within the sink at 9 different intervals over a period of 685 days. Denaturing Gradient Gel Electrophoresis (DGGE) was used to fingerprint 16s rRNA bacterial communities and dissimilatory sulfite reducing communities by targeting the 16s rRNA bacterial gene and the dsr gene associated with dissimilatory sulfite reducing bacteria and archaea. The lowest depth studied within the sink (40 m) remained stable chemically and biologically until a turnover event occurred within the second winter of the study. This turnover event disrupted the biological communities at 40 m and led to a reestablished community comprised of different species that those found prior to the event. Upper waters within the sink show that clines establish themselves seasonally and partition zones that confine bacterial communities that are more similar to each other within these zones while excluding bacterial communities that are outside of these zones. Oxygenated water was shown to not contain prokaryotes containing the dsr gene. As the oxycline changed seasonally, dissimilatory sulfite reducing prokaryotes containing the dsr gene remained in the anoxic zone and required time to reestablish themselves whenever oxygenated water displaced them.

This study evaluated the impacts of shallow and deep open drains on groundwater levels and drain performance under varying climate scenarios and irrigation application rates. The MIKE SHE model used for this study is an advanced and fully spatially distributed hydrological model. Three drain depths, climates and irrigation application rates were considered. The drains depths included 0, 1 and 2 m deep drains. The annual rainfall and meteorological data were collected from study area from 1976 to 2004 and analysed to identify the typical wet, average and dry years within the record. Similarly three irrigation application rates included 0, 10 and 16 ML/ha-annum. All together twenty seven scenarios (3 drains depths, 3 climates and 3 irrigation application rates) were simulated. The observed soil physical and hydrological data were used to calibrate and validate the model. Mean square error (R[superscript]2) of the simulated and observed water table data varied from 0.7 to 0.87. Once validated the MIKE SHE model was used to evaluate the effectiveness of 1 and 2 metre deep drains. The simulated water table depth, unsaturated zone deficit, exchange between unsaturated and saturated zones, drain outflow and overland flow were used to analyse their performance. The modeling results showed that the waterlogging was extensive and prolonged during winter months under the no drainage and no irrigation scenario. In the wet climate scenario, the duration of water logging was longer than in the average climate scenario during the winter months. In the dry climate scenario no waterlogging occurred during the high rainfall period. The water table reached soil surface during the winter season in the case of wet and average climate. For the dry climate, the water table was about 0.9 metres below soil surface during winter. / One and 2 metre deep drains lowered the water table up to 0.9 and 1.8 metres in winter for the wet climate when there was no irrigation application. One metre deep drains proved effective in controlling water table during wet and average climate without application of irrigation water. One metre deep drains were more effective in controlling waterlogging a in wet, average and dry years when the irrigation application rate was 10 ML/ha-annum. With 16 ML/ha-annum irrigation application, 1 metre deep drains did not perform as efficiently as 2 metre deep drains in controlling the water table and waterlogging. In the dry climate scenario, without irrigation application, 1 metre deep drains were not required as there was not enough flux from rainfall and irrigation to raise the water table and create waterlogging risks. Two metre deep drains lowered the water table to greater depths in the wet, average and dry climate scenarios respectively when no irrigation was applied. They managed water table better in wet and average climate with 10 and 16 ML/ha-annum irrigation application rate. Again in the dry climate, without irrigation application 2 metre deep drains were not required as there was a minimal risk of waterlogging. The recharge to the groundwater table in the no drainage case was far greater than for the 1 and 2 metre deep drainage scenarios. The recharge was higher in case of 1 metre deep drains than 2 metre deep drains in wet and average climate during winter season. / There was no recharge to ground water with 1 and 2 metre deep drains under the dry climate scenarios and summer season without irrigation application as there was not enough water to move from the ground surface to the unsaturated and saturated zones. When 10 ML/ha-annum irrigation rate was applied during wet, average and dry climate respectively, 1 metre deep drains proved enough drainage to manage the recharge into the groundwater table with a dry climate. For the wet and average climate scenarios, given a 10 ML/ha-annum irrigation application rate, 2 metre deep drains managed recharge better than 1 metre deep drains. Two metres deep drains with a 10 ML/ha-annum irrigation application rate led to excessive drainage of water from the saturated zone in the dry climate scenario. Two metres deep drains managed recharge better with a 16 ML/ha-annum irrigation application rate in the wet and average climate scenarios than the 1 metre deep drains. Two metres deep drains again led to excessive drainage of water from the saturated zone in dry climate. In brief, 1 metre deep drains performed efficiently in the wet and average climate scenarios with and without a 10 ML/ha-annum irrigation application rate. One metre deep drains are not required for the dry climate scenario. Two metre deep drains performed efficiently in the wet and average climate scenarios with 16 ML/ha-annum irrigation application rate. Two metre deep drains are not required for the dry climate scenario.

Lake Waikare is a large, shallow eutrophic lake devoid of submerged macrophytes. I investigated potential methods for re-establishing submerged macrophytes in the lake. Specifically, I subjected charophyte (Chara corallina) plantlets to two treatments of exposure in the lake (in areas exposed and sheltered from wind) to test for survival and growth under these conditions, and inside and outside fish exclosures to test for growth and survival in the presence of fish. While plantlets grew outside the exclosures in winter, their accumulated biomass over 21 days was less than protected plantlets. In winter, the accumulated biomass was lower outside than inside exclosures (by ~40%) at the sheltered site and was lower outside than inside exclosures (by 43%) at the exposed site. Overall, growth rates in winter were higher at the sheltered site (compared to the exposed site) by ~7%. In summer, charophyte accumulated biomass inside the exclosures increased by 85%, while at the sheltered site accumulated biomass increased by 58%. Outside the exclosures in summer the plantlets were completely removed at both sites. Overall, growth rates where higher at the exposed site than the sheltered site by 31%. Fish were responsible for the partial removal of plantlets in winter and total removal of plantlets in summer, and therefore affect the survival and growth of charophytes in Lake Waikare. The embayment at the sheltered site provides the best location in winter for re-establishment of charophytes from oospores because better growth rates were obtained there, and its sheltered location provides protection from severe wave action found at the exposed site. Oospores did not germinate after being submersed in the lake for 90 days due to heavy sedimentation. To induce an improvement in the present light climate, Alum was tested to determine its effectiveness and longevity for settling lake sediments to allow charophytes to establish and grow. Examining the settling rates of Lake Waikare sediments and water treated with Alum over a range of suspended sediment concentrations and time intervals, sediments settled faster with Alum than without for at least 15 days (at 200 g l^1 suspended sediment concentration) and it remained active to 60 days but at reduced effectiveness. At the other concentrations tested (100 g l^1 and 300 g l^1 suspended sediment concentration), Alum responses were insignificant. An improved light climate achieved by fish removal or Alum treatment will likely not be sufficient to permit the re-establishment of submerged macrophytes due to the turbid, algal-dominated state of the lake. The present nutrient and sediment levels, wave climate and fish influence must be mitigated so charophyte plantlets can be established.

Nous étudions dans ce document des problèmes mathématiques de la mécanique des fluides. Ce travail s'articule principalement autour de deux thèmes : les modèles bi-couches à surface libre ou à toit rigide, l'analyse de problèmes définis dans des domaines à frontière libre.

On aborde des questions liées à l'étude de quelques aspects de la modélisation mathématique en mécanique des fluides et des structures. Cette étude s'articule principalement autour de deux thèmes : le couplage fluid-structure, l'analyse de problèmes d'écoulements peu profonds à surface libre.

<p>Development of a predictive model for the distribution of diagenetic alterations and related evolution of reservoir quality of sandstones was achieved by integrating the knowledge of diagenesis to sequence stratigraphy. This approach allows a better elucidation of the distribution of eogenetic alterations within sequence stratigraphy, because changes in the relative sea level induce changes to: (i) pore water chemistry, (ii) residence time of sediments under certain near-surface geochemical conditions, (iii) variations in the detrital composition, and (iv) amounts and type of organic matter.</p><p>This thesis revealed that eogenetic alterations, which are linked to sequence stratigraphy and have an impact on reservoir quality evolution, include formation of: (i) pseudomatrix and mechanically infiltrated clays in fluvial sandstones of the lowstand and highstand systems tracts (LST and HST, respectively), (ii) kaolinite in tide-dominated deltaic and foreshore-shoreface sandstones of HST, Gilbert-type deltaic sandstones of LST and fluvial deltaic sandstones of LST, (iii) kaolinite and mechanically infiltrated clays in sandstones lying below sequence boundary, (iv) K-feldspar overgrowths in fluvial deltaic LST, (v) glaucony towards the top of fluvial deltaic LST immediately below and at transgressive surface (TS) and in foreshore and shoreface transgressive systems tracts (TST) below parasequence boundaries (PB) and maximum flooding surface (MFS), (vi) framboidal pyrite and extensive cementation by calcite and dolomite in foreshore and shoreface and tide-dominated deltaic TST, and shoreface and tidal flat HST bioclastic-rich arenites particularly in the vicinity of PB, TS and MFS, (vii) pervasive cementation by iron oxide in shoreface-offshore and shoreface sandstones of TST immediately below the MFS, (viii) zeolites and palygroskite in shoreface sandstones of TST and HST, particularly above PB, and (ix) cementation by siderite in Gilbert-type deltaic sandstones of LST, tide-dominated deltaic and foreshore-shoreface sandstones of HST and in tide-dominated deltaic sandstones of TST, particularly at MFS. Moreover, this thesis revealed that the distribution of eogenetic alterations strongly control, and thus provide information for constraining the distribution patterns of mesogenetic alterations, such as illitization of mechanically infiltrated clays and dickitization of kaolinite, and hence of related reservoir quality evolution of sandstones during progressive burial.</p>

<p>This thesis constrains the distribution of diagenetic alterations and their impact on reservoir-quality and heterogeneity evolution pathways in relation to depositional environments and sequence stratigraphy (systems tracts and key sequence stratigraphic surfaces) of four selected paralic and shallow marine siliciclastic successions. </p><p>Typical eogenetic alterations encountered include the dissolution and kaolinitization of framework silicates, which are closely associated to shoreface facies of forced regressive systems tract (FRWST), lowstand systems tract (LST), upper part of the highstand systems tract (HST), and below the sequence boundary (SB). These alterations are attributed to incursion of meteoric water owing to rapid and considerable fall in the relative sea level. Extensive carbonate cementation is most evident below marine and maximum flooding surfaces (MFS), whereas dissolution of carbonate cement and detrital dolomite occur in LST, HST and below SB. Parameters controlling the patterns and texture (microcrystalline vs. poikilotopic) of calcite cement have been constrained within sequence stratigraphic framework of the sandstones. Coarse crystalline to poikilotopic calcite textures of meteoric water origin are thus closely linked to the FRWST, LST and upper part of the HST sandstones and occur mainly as stratabound concretions, whereas microcrystalline calcite, which was precipitated from marine porewaters, occurs as continuously cemented layers in the transgressive systems tract (TST) and lower part of the HST sandstones.</p><p>Eogenetic alterations impose, in turn, profound control on the distribution pattern of mesogenetic alterations, and hence on reservoir quality evolution (destruction vs. preservation) pathways of sandstones. Eogenetic infiltrated clays, which occur in the tidal estuarine TST and HST sandstones, have helped preserving porosity in deeply buried sandstone reservoirs (≈ 5 km) through inhibition of extensive cementation by quartz overgrowths. Other essential findings of this thesis include deciphering the control on the formation of authigenic illite and chlorite by ultra-thin (≤ 1 µm thick), grain-coating clay mineral substrate. </p>

Shallow foundations are extensively used to support structures of all sizes and derive their support from near surface soils. Thus, they are typically embedded up to a few meters into the soil profile. Designers of shallow foundations are required to meet two limit states: overall failure of the soil beneath the foundation (bearing capacity) and excessive settlement. Existing bearing capacity design methods use an assumed shearing plane within the soil and perfectly plastic soil behavior to estimate the ultimate resistance available. The immediate settlement of a shallow foundation is typically approximated using an elasticity-based method that does not account for actual, nonlinear soil behavior. A load test database was developed from footing load tests reported in the literature to assess the accuracy and uncertainty in existing design methodologies for calculating bearing capacity and immediate settlement. The assessment of uncertainty in bearing capacity and immediate settlement was accomplished through the application of a hyperbolic bearing pressure-displacement model, and the adaptation of the Duncan-Chang soil constitutive model to footing displacements. The prediction of bearing capacity using the general bearing capacity formula was compared to the bearing capacity extrapolated from the load test database using a hyperbolic bearing pressure-displacement model. On average the general bearing capacity formula under-predicts the bearing capacity and exhibits a significant amount of variability. The comparison was used to develop resistance statistics that were implemented to produce resistance factors for an LRFD based design approach using AASHTO load statistics. The Duncan-Chang model was adapted to predict bearing pressure displacement curves for footings in the load test database and used to estimate governing soil parameters. Bearing pressure-displacement curves fitted to the observed curves were used to back calculate soil stiffness. The soil stiffness was used with an elasticity-based displacement prediction method to evaluate the accuracy of the method. Finally, the back-calculated modulus from the fitted Duncan-Chang model was used to assess the accuracy and uncertainty associated with the elasticity-based K-factor, a correlation based stiffness parameter. In general the comparisons indicate that the current design procedures over-predict the bearing pressure associated with a given displacement and exhibit a significant amount of uncertainty. / Graduation date: 2012

River dynamic behaviour is affected by variations both in the water phase and in the transported sediment phase. A change in the water regime may lead to significant morphological changes in the bed profile, which in turn may strongly influence the flow conditions. Transcritical flows over mobile beds are particularly challenging to model due to the rapid variation in space and time of the solid transport, and to the specific treatment required for boundary conditions. The one-dimensional numerical model presented in this dissertation divides the flow in two fully coupled layers: a water layer and a water-sediment transport layer. This model was initially designed to depict dam-break flows, which does not require a specific treatment of boundary conditions. An extension of the two-layer approach is proposed in order to properly take into account boundary conditions. The treatment of boundary conditions commonly relies on characteristics. Within a two-layer model, which embodies five governing equations, an appropriate eigenstructure analysis is developed based on numerical estimations. This novel approach results in a new characterization of the critical stage by defining a specific two-layer Froude number. The model is compared to the classical Saint-Venant – Exner approach and favourably applied to several typical situations: uniform flow, which allows a straightforward calibration of the model parameters; regressive erosion around a mild-to-steep slope transition; evolution of a mobile bed under a hydraulic jump; and scour hole formation downstream of a fixed bed.

In case of exceptional floods induced by the failure of a dam, huge amounts of sediments may be eroded. This results in large-scale modifications of the valley morphology and may drastically increase the resulting damages. The objective of the research is to advance the understanding of sediment transport under dam-break flows. For such highly erosive and transient floods, it is crucial to account explicitly for sediment inertia, and therefore traditional “clear-water” modelling approaches are largely inappropriate. The present approach relies on a two-layer idealisation of the flow behaviour. Separating a clear-water flow region from the underlying sediment bed, the transported sediments are confined in a flow layer of finite thickness, endowed with its proper inertia, density and velocity. The thesis also pinpoints granular dilatancy as an essential mechanism of interaction between the layers. When passing from a solid-like to a fluid-like behaviour as they are entrained by the flow, the eroded sediment grains dilate along the vertical, and this generates vertical exchanges of mass and momentum that should be accounted for. The thesis proceeds first with experimental investigations. Laboratory dam-break waves are reproduced in a dedicated flume, exploring different bed configurations and sediment densities. Imaging observations are used to support the proposed phenomenological description of the flow. Within a shallow-water framework, theoretical and numerical endeavours are then developed to investigate the implications on the flow dynamics of the two essential contributions of the proposed description, i.e. the two-layer flow behaviour, and the effects of granular dilatancy.