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.

Holocene and Pleistocene grainstone deposits surrounding Ocean Cay located on the western margin of Great Bahama Bank provide key evidence for the comprehension of patterns, processes and petrophysical heterogeneity of carbonate grainstone shoals. New datasets consisting of high-resolution remote sensing data, acoustic Doppler current measurements, sub-bottom profiles, and sedimentological and petrophysical analyses offer an opportunity to elucidate the various factors in the deposition of a grainstone shoal complex and assess of how much of the sedimentary fabric and early diagenetic overprint influences the petrophysical characteristics of similar ancient deposits. The Holocene shoal complex investigated here includes the Cat Cay ooid shoal and the Ocean Cay tidal deltas, which collectively form a 1-3 km wide, 35 km long sand belt around Ocean Cay. These factors controlling the distribution, preservation and modification of these sediments are the antecedent Pleistocene topography, bathymetry, and hydrodynamics at this margin. High-resolution seismic data reveal that the laterally continuous and thick Cat Cay ooid shoal north of Ocean Cay is situated on top of a flat Pleistocene surface and located platformward of a Pleistocene rock ridge. This finding challenges the assumption of previous studies that an antecedent high is needed for ooid shoal initiation. In contrast, south of Ocean Cay, skeletal-rich tidal deltas occur east of rocky Pleistocene islands and formed over an irregular Pleistocene surface that is slightly shallower than the flat surface north of Ocean Cay. In addition to the antecedent topography, differences in shoal morphology and sediment attributes between the north and south areas around Ocean Cay are related to linkages among fluid flow patterns, shoal morphology and granulometry. The hydrodynamic data document the influence of tidal flows in modifying the shape of bars creating sinuous and parabolic forms during flood and ebb reversing flows. Spatial distribution of grain size and sorting is affected because high flow velocities (up to 100 cm sec-1) inside tidal channels and inlets can erode and remobilized sediments mixing skeletal grains, peloids and ooids. Dominance of flood tide across this Holocene shoal complex allowed tidal deltas to form bankward of inlets between rock islands. Tidal channels and inter-bar troughs can focus tidal flow during flood tide creating lobes platformward instead of previously assumptions on the effect of storm and formation of spillover lobes bankward. Cores from the subsurface at Ocean Cay show that the architecture of the Pleistocene grainstone facies is similar to the Holocene shoal configuration of bars, channels, and bioturbated stabilized areas. Cross-bedded oolitic/peloidal and bioturbated skeletal/peloidal facies exhibit facies-dependent petrophysical heterogeneity, and reveal depositional and early diagenetic controls on petrophysical properties. Porosity and permeability in the grainstones at Ocean Cay are high, up to 47% and up to 11500 mD, respectively. Early diagenesis modifies the pore geometry of the rock, thus reducing permeability. A comparison of petrographic and petrophysical properties of the Pleistocene shoal with those from the Pennsylvanian ooid shoals reveals that were strongly influenced by the original fabric and early near-surface diagenesis. The integration of data from both the modern and ancient carbonate systems provides a better understanding of the factors controlling shoal morphology, facies architecture, and rock properties. The results of this study can be used as a guide for interpreting heterogeneity and reservoir properties of analogous facies within ancient ooid shoals.

Modern anthropogenic forcing of atmospheric chemistry poses the question of how the Earth System will respond as thousands of gigatons of greenhouse gas are rapidly added to the atmosphere. A similar, albeit nonanthropogenic, situation occurred during the early Paleogene, when catastrophic release of carbon to the atmosphere triggered abrupt increase in global temperatures. The best documented of these events is the Paleocene-Eocene Thermal Maximum (PETM, ~55 Ma) when the magnitude of carbon addition to the oceans and atmosphere was similar to those expected for the future. This event initiated global warming, changes in hydrological cycles, biotic extinction and migrations. A recently proposed hypothesis concerning changes in marine ecosystems suggests that this global warming strongly influenced the shallow-water biosphere, triggering extinctions and turnover in the Larger Foraminifera (LF) community and the demise of corals. The successions from the Adriatic Carbonate Platform (SW Slovenia) represent an ideal location to test the hypothesis of a possible causal link between the PETM and evolution of shallow-water organisms because they record continuous sedimentation from the Late Paleocene to the Early Eocene and are characterized by a rich biota, especially LF, fundamental for detailed biostratigraphic studies. In order to reconstruct paleoenvironmental conditions during deposition, I focused on sedimentological analysis and paleoecological study of benthic assemblages. During the Late Paleocene-earliest Eocene, sedimentation occurred on a shallow-water carbonate ramp system characterized by enhanced nutrient levels. LF represent the common constituent of the benthic assemblages that thrived in this setting throughout the Late Paleocene to the Early Eocene. With detailed biostratigraphic and chemostratigraphic analyses documenting the most complete record to date available for the PETM event in a shallow-water marine environment, I correlated chemostratigraphically for the first time the evolution of LF with the δ¹³C curves. This correlation demonstrated that no major turnover in the LF communities occurred synchronous with the PETM; thus the evolution of LF was mainly controlled by endogenous biotic forces. The study of Late Thanetian metric-sized microbialite-coral mounds which developed in the middle part of the ramp, documented the first Cenozoic occurrence of microbially-cemented mounds. The development of these mounds, with temporary dominance of microbial communities over corals, suggest environmentally-triggered “phase shifts” related to frequent fluctuations of nutrient/turbidity levels during recurrent wet phases which preceding the extreme greenhouse conditions of the PETM. The paleoecological study of the coral community in the microbialites-coral mounds, the study of corals from Early Eocene platform from SW France, and a critical, extensive literature research of Late Paleocene – Early Eocene coral occurrences from the Tethys, the Atlantic, the Caribbean realms suggested that these corals types, even if not forming extensive reefs, are common in the biofacies as small isolated colonies, piles of rubble or small patch-reefs. These corals might have developed ‘alternative’ life strategies to cope with harsh conditions (high/fluctuating nutrients/turbidity, extreme temperatures, perturbation of aragonite saturation state) during the greenhouse times of the early Paleogene, representing a good fossil analogue to modern corals thriving close to their thresholds for survival. These results demonstrate the complexity of the biological responses to extreme conditions, not only in terms of temperature but also nutrient supply, physical disturbance and their temporal variability and oscillating character. / Die anthropogene Beeinflussung der Chemie der Atmosphäre in der modernen Zeit wirft die Frage nach dem Schicksal des Systems Erde auf, wenn tausende von Tonnen an Treibhausgasen in kurzer Zeit in die Atmosphäre einströmen. Im Känozoikum trat bereits eine ähnliche Situation während des frühen Paläogens auf, als eine katastrophale Freisetzung von Kohlenstoff in die Atmosphäre einen plötzlichen Anstieg der globalen Temperatur hervorrief. Das am besten dokumentierte dieser Ereignisse stellt das Paläozän-Eozäne Temperatur Maximum (PETM, ~55 Ma) dar, bei welchem die Größenordnung der Kohlenstoffzufuhr in Ozeanen und Atmosphäre jener ähnelte, die in der Zukunft zu erwarten ist. Das damalige Ereignis initiierte eine globale Erwärmung, Veränderungen hydrologischer Kreisläufe, biotische Auslöschung und Abwanderungen. Eine kürzlich veröffentlichte Hypothese zu Veränderungen in marinen Ökosystemen postuliert, dass diese globale Erwärmung die Biosphäre der Flachwässer stark beeinflusste, indem sie Aussterben und Fluktuation innerhalb der Gemeinschaft der Großforaminiferen (GF) sowie den Niedergang einiger Korallen bewirkte. Die Abfolgen der Adriatischen Karbonatplattform (SW-Slovenien) stellen einen idealen Ort dar, um die Hypothese des kausalen Zusammenhangs zwischen dem PETM und der Evolution der Flachwasserorganismen zu überprüfen, da sie aufgrund ihrer kontinuierlichen Sedimentation vom Spätpaläozän bis zum Früheozän und ihres Reichtums an Biota, insbesondere an GF, fundamentale Voraussetzungen für eine detaillierte biostratigraphische Studie erfüllen. Um die Paläoumweltbedingungen während der Sedimentablagerung zu rekonstruieren, wurde der Schwerpunkt dieser Arbeit auf eine sedimentologische Analyse und eine paäoökologische Studie benthischer Vergesellschaftungen gesetzt. Während dem Spätpaläozan bis zum frühesten Eozän fand die Sedimentation auf einem Flachwasser-Rampensystem statt, welches durch ein erhöhtes Nährstoffangebot gekennzeichnet war. GF stellen jenen häufigen und verbreiteten Bestandteil der benthischen Vergesellschaftungen dar, welcher in dieser Umgebung durch das Spätpaläozän hindurch bis ins Früheozän gedeihen konnte. Mit den in dieser Arbeit vorgestellten detaillierten bio- und chemostratigraphischen Analysen, deren Dokumentation den zur Zeit vollständigsten Datensatz für das PETM-Ereignis in einem flachmarinen Milieu repräsentieren, wurde die Evolution der GF zum ersten Mal mit δ¹³C -Kurven chemostratigraphisch korreliert. Diese Korrelation zeigte, dass in den GF-Gemeinschaften keine großmaßstäbliche Fluktuation zeitgleich mit dem PETM auftrat, und dass daher die Evolution der GF hauptsächlich durch endogene biotische Einflüsse kontrolliert worden sein muss. Die Studie mikrobiell-überkrustete Korallenhügel im Größenbereich zwischen einigen Metern und einigen Zehnermetern, die sich im Spätthanetium im mittleren Teil der Rampe entwickelten, dokumentiert das erste Auftreten mikrobiell-zementierter Erhebungen während des Känozoikums. Die Entwicklung dieser Erhebungen, mit einer zeitweiligen Dominanz der mikrobiellen Gemeinschaften gegenüber den Korallen, spricht für ein Auftreten Umwelt-gesteuerter "Phasenverschiebungen" im Zusammenhang mit häufigen Wechseln von Nahrungsangebot und Trübung während wiederkehrender nasser Phasen, welche dem extremen Treibhaus der PETM vorausgingen. Die paläoökologische Studie der Korallen-Gemeinschaften in den mikrobiell-überkrusteten Korallenhügeln, die Studie der Korallen der früheozänen Plattform in SW-Frankreich sowie eine kritische, ausgedehnte Literaturrecherche zum Auftreten spätpaläozäner bis früheozäner Korallen in der Tethys, im Atlantik und in der Karibik sprechen dafür, dass diese Korallentypen – selbst wenn sie nicht ausgedehnte Riffe formen – in der Biofazies häufig als kleine isolierte Kolonien, Berge von Geröll oder kleine Kuppelriffe auftreten. Diese Korallen könnten 'alternative' Überlebensstrategien entwickelt haben, um mit den rauen Bedingungen (hohes/wechselndes Nahrungsangebot, schwache/starke Trübung, schwankende Temperaturen, häufige physikalische Störungen) fertig zu werden, die während den Zeiten des paläogenen Treibhauses vorherrschten, und stellen damit ein gutes fossiles Analog zu modernen Korallen dar, welche nahe an ihrer Überlebensgrenze gedeihen. Diese Ergebnisse zeigen die Komplexität der biologischen Reaktionen auf extreme Bedingungen, nicht nur im Hinblick auf Temperaturen, sondern auch hinsichtlich Nahrungsangebot, physikalische Beeinträchtigungen sowie deren zeitliche Schwankungen und deren oszillierenden Charakter.

The dynamics of the world's oceans occur at a vast range of length scales. Although there are theories that aid in understanding the dynamics at planetary scales and microscales, the motions in between are still not yet well understood. This work discusses a numerical model to study barotropic wind-driven gyre flow that is capable of resolving dynamics at the synoptic, O(1000 km), mesoscale, O(100 km) and submesoscales O(10 km). The Quasi-Geostrophic (QG) model has been used predominantly to study ocean circulations but it is limited as it can only describe motions at synoptic scales and mesoscales. The Rotating Shallow Water (SW) model that can describe dynamics at a wider range of horizontal length scales and can better describe motions at the submesoscales. Numerical methods that are capable of high-resolution simulations are discussed for both QG and SW models and the numerical results are compared. To achieve high accuracy and resolve an optimal range of length scales, spectral methods are applied to solve the governing equations and a third-order Adams-Bashforth method is used for the temporal discretization. Several simulations of both models are computed by varying the strength of dissipation. The simulations either tend to a laminar steady state, or a turbulent flow with dynamics occurring at a wide range of length and time scales. The laminar results show similar behaviours in both models, thus QG and SW tend to agree when describing slow, large-scale flows. The turbulent simulations begin to differ as QG breaks down when faster and smaller scale motions occur. Essential differences in the underlying assumptions between the QG and SW models are highlighted using the results from the numerical simulations.

Underwater communication is an important research of applied underwater acoustic since sound wave is the only effective way of transmitting messages under water. Underwater communication has always been a complicated problem especially in the shallow water environment due to the influence of multipath propagation. In the past, research on underwater communication had been done mostly by numerical simulation or laboratory experiments instead of doing in real oceanic areas. As a result, several research teams such as the Institute of Oceanography in Taiwan University, the Naval Research Laboratory and the acoustic laboratory of National Sun Yat-sen University Institute of Applied Marine Physics and Undersea Technology had executed a one-week real oceanic area experiment of underwater networking, communication, and acoustical tomography in Sizih Bay Marine Test Field. The experiment adopted 9 sets of underwater modem distributed within the range of 30 square kilometer to transmit, receive signals and collect CTD data. This research adopted part of the data gained from the experiment mentioned above to progress the feasibility test of acoustic tomography on current estimate to shallow water environment. By transmitting and receiving signals between stations, This research study the travel time difference between transmitting signals forward and backward caused by the flow field when using high frequency source in shallow water environment. This research estimated the average current speed and compared it to the weather buoy data from the Harbor and Marine Technology Center. This research discovered that most of the estimated results correspond to the weather buoy's ADCP data. Finally, this research adopted the method which does not require complex mathematics operation to estimate the two-dimensional flow field, and probe into what influence the angle between stations would bring to the deviation of estimating flow speed by using the Monte Carlo method.

The purpose of this study explores the sound propagation in very shallow water to understand the environment quality of the Si-Tzi Marine Test Field. Very shallow water acoustics characterized by that sound wave will have a dramatic interaction between the bottoms and the propagation of wave and bottom with a high degree of correlation. Those types of environment are concentrated in the west coast of Taiwan. Analysis of actual acoustic data from the ocean obtain and to use "OASES" simulation that an applied acoustic tool. Expect to understand the phenomenon of water acoustic propagation in the very shallow. The Si-Tzi marine test field had detailed environmental information by previously study. In experiment process, the hydrophone "iTC-6050c" receiving broadband sound source "UW350" signal. The use of personal computer with DAQ card for data acquisition and control. The source in the research vessel was moored 20 m below sea, at the same time to launch three consecutive single (frequency signal 350 Hz, 800 Hz, and 1250 Hz). Reception of signals in order to drift the way. Measured at different frequencies in very shallow water of the transmission loss. The results showed that the results of the current measurement and simulation in line with the follow-up study will be measured "transmission loss" to do to Inversion for geoacoustic parameters in very shallow water. Then obtained "geoacoustic parameters" Comparison of sea-bed surface sampling results. Confirmation "geoacoustic inversion technique" is correct.

Shallow water acoustics is one of the most challenging areas of underwater acoustics; it deals with strong sea bottom and surface interactions, multipath propagation, and it often involves complex variability in the water column. The sea bottom is the dominant environmental influence in shallow water. An accurate solution to the Helmholtz equation in a shallow water waveguide requires accurate seabed acoustic parameters (including seabed sound speed and attenuation) to define the bottom boundary condition. Direct measurement of these bottom acoustic parameters is excessively time consuming, expensive, and spatially limited. Thus, inverted geo-acoustic parameters from acoustic field measurements are desirable. Because of the lack of convincing experimental data, the frequency dependence of attenuation in sandy bottoms at low frequencies is still an open question in the ocean acoustics community. In this thesis, geo-acoustic parameters are inverted by matching different characteristics of a measured sound field with those of a simulated sound field. The inverted seabed acoustic parameters are obtained from long range broadband acoustic measurements in the Yellow Sea '96 experiment and the Shallow Water '06 experiment using the data-derived mode shape, measured modal attenuation coefficients, measured modal arrival times, measured modal amplitude ratios, measured spatial coherence, and transmission loss data. These inverted results can be used to test the validity of many seabed geo-acoustic models (including Hamilton model and Biot-Stoll model) in sandy bottoms at low frequencies. Based on the experimental results in this thesis, the non-linear frequency dependence of seabed effective attenuation is justified.

Shallow-water hydrothermal vents occur world-wide in regions of volcanic activity. The vents located at Tutum Bay, Ambitle Island, Papua New Guinea are unique in that the vent fluids and surrounding sediments contain some of the highest concentrations of arsenic in a natural system. This study addresses the effects of the vent system on the benthic communities, focusing on the eukaryotes, macrofauna, meiofauna and bacteria. Samples were collected in November 2003 and May/June 2005. Analysis of the 2003 macrofaunal samples indicated that pH, rather than arsenic was influencing the benthic community, and that the hydrothermal influence occurred at a greater distance than expected. Results of more intensive sampling carried out in 2005 are the primary focus of this dissertation. The pore water and sediment characteristics revealed distinct physical habitats corresponding with distance from the vent. There was a trend of decreasing temperature and arsenic concentration and increasing salinity and pH with distance from the vent. The vent sediment was poorly sorted volcanic gravel, while sediments along the transect showed a gradient from fine, well sorted volcanic sands to coarser carbonate sands farther away. The macrofauna showed a trend of increasing diversity with distance from the vent and similar taxa were present in both the 2003 and 2005 samples. The vent community was dominated by the polychaete Capitella cf. capitata. The inner transect from 30 m to 140 m had low diversity. Dominant taxa included thalassinid shrimp and the amphipod Platyischnopus sp.A. The 180 m to 300 m sites had significantly higher diversity. The Danlum Bay reference site had relatively higher diversity than the nearshore transect sites and was dominated by deposit feeding polychaetes. Macrofaunal community structure was influenced by the sediment characteristics, notably by CaCO3 content, sorting and median grain size. The meiofaunal community also showed changes with distance from the vent. Chromadorid nematodes were dominant at the vent site and were a major component of the meiofauna at most sites, along with copepods. The meiofaunal community at the reference site showed greater similarity to the vent community and both sites had low abundances. Nematodes were more abundant than copepods near the vent, but copepods were more abundant farther offshore and at the reference site. Meiofaunal community structure was influenced primarily by the pore water temperature and salinity. Biological interactions with the macrofaunal community through physical disturbance and predation may also influence the meiofaunal community.  The molecular analysis of eukaryotic and bacterial diversity also revealed changes with distance from the vent. The 0 m and reference sites grouped together due to the presence of fungal sequences and the 140 m and 300 m sites grouped together due to a common molluscan sequence. Metazoans and fungi dominated the eukaryote sequences. The most abundant eukaryotic OTUs included fungi matching Paecilomyces sp. and Cladosporium cladosporioides and metazoans matching Viscosia viscosa (Nematoda) and Astarte castanea represented by 24 phyla and was dominated by Actinobacteria and γ-Proteobacteria. More bacterial phyla were present near the vent, while more overall OTUs were found at the intermediate sites along the transect. The most distant site had much lower diversity dominated by Firmicutes. The macrofaunal community had the strongest correlation with environmental variables. Comparison between the meiofauna and the metazoan sequences showed the proportion of nematodes found in both datasets were comparable, but the meiofauna analysis found a higher proportion of arthropods, while the molecular results were disproportionally high for platyhelminthes. Overall, the vents increased the complexity of the system by creating unique habitats. The extreme environment created by the hydrothermal activity maintained the surrounding habitat at an early successional stage colonized by a few opportunistic species. There was a gradation in the benthic communities away from the vent towards a more carbonate based climax community. The low pH environment had an effect on the sediment composition, which in turn influenced the benthic community. These findings can serve as a model for studying the potential effects of ocean acidification and climate change on benthic communities and marine biocomplexity.

Waves and circulation processes interact in daily wind and tide driven flows as well as in more extreme events such as hurricanes. Currents and water levels affect wave propagation and the location of wave-breaking zones, while wave forces induce setup and currents. Despite this interaction, waves and circulation processes are modeled separately using different approaches. Circulation processes are represented by the shallow water equations, which conserve mass and momentum. This approach for wind-generated waves is impractical for large geographic scales due to the fine resolution that would be required. Therefore, wind-waves are instead represented in a spectral sense, governed by the action balance equation, which propagates action density through both geographic and spectral space. Even though wind-waves and circulation are modeled separately, it is important to account for their interactions by coupling their respective models. In this dissertation we use discontinuous-Galerkin (DG) methods to couple spectral wave and circulation models to model wave-current interactions. We first develop, implement, verify and validate a DG spectral wave model, which allows for the implementation of unstructured meshes in geographic space and the utility of adaptive, higher-order approximations in both geographic and spectral space. We then couple the DG spectral wave model to an existing DG circulation model, which is run on the same geographic mesh and allows for higher order information to be passed between the two models. We verify and validate coupled wave/circulation model as well as analyzing the error of the coupled wave/circulation model. / text