A wide array of species, from ants to humans, live or forage in groups. Shoaling – the formation of groups by fish – confers protection from predation and enhances foraging. However, little is known about the detailed characteristics or the dynamics of shoaling. Shoaling is a complex social interaction and a better understanding of its mechanisms and limitations would permit the study of natural and induced changes on social behavior generally in fish. Here, I present data on the shoaling characteristics of zebrafish (Danio rerio). Novel tracking techniques are used to extract detailed trajectories of all members of a free-swimming shoal of zebrafish. Multiple measures of shoaling – such as distributions of nearest neighbor distances, shoal polarizations, and speeds – are calculated, to better describe the subtleties of the behavior including, for the first time, the high resolution spatio-temporal dynamics of shoaling. In addition, a novel criterion is introduced to determine when and how individual fish or sub-groups leave the shoal. Comparisons are presented between the shoaling characteristics of three populations of zebrafish (LFWT, SFWT, AB) and between days and hours of repeated exposure to the same testing environment, demonstrating the gradual effects of habituation on shoaling. In addition, the effects of manipulating the number of fish in the shoal, hunger levels, and predation threat are also examined, lending empirical support to ecological theories on the adaptive functions of the behavior. Finally, the data are compared to two leading theoretical models of shoaling and a novel simulation approach is suggested. The data strongly suggest that various aspects of shoaling in zebrafish are constantly changing, complex, and flexible, representing a dynamic form of social cognition. The study of these characteristics sheds much-needed light on complex social interactions in this popular genetic model organism, which may eventually lead to a better understanding of social behaviors in other species, including our own.

A wide array of species, from ants to humans, live or forage in groups. Shoaling – the formation of groups by fish – confers protection from predation and enhances foraging. However, little is known about the detailed characteristics or the dynamics of shoaling. Shoaling is a complex social interaction and a better understanding of its mechanisms and limitations would permit the study of natural and induced changes on social behavior generally in fish. Here, I present data on the shoaling characteristics of zebrafish (Danio rerio). Novel tracking techniques are used to extract detailed trajectories of all members of a free-swimming shoal of zebrafish. Multiple measures of shoaling – such as distributions of nearest neighbor distances, shoal polarizations, and speeds – are calculated, to better describe the subtleties of the behavior including, for the first time, the high resolution spatio-temporal dynamics of shoaling. In addition, a novel criterion is introduced to determine when and how individual fish or sub-groups leave the shoal. Comparisons are presented between the shoaling characteristics of three populations of zebrafish (LFWT, SFWT, AB) and between days and hours of repeated exposure to the same testing environment, demonstrating the gradual effects of habituation on shoaling. In addition, the effects of manipulating the number of fish in the shoal, hunger levels, and predation threat are also examined, lending empirical support to ecological theories on the adaptive functions of the behavior. Finally, the data are compared to two leading theoretical models of shoaling and a novel simulation approach is suggested. The data strongly suggest that various aspects of shoaling in zebrafish are constantly changing, complex, and flexible, representing a dynamic form of social cognition. The study of these characteristics sheds much-needed light on complex social interactions in this popular genetic model organism, which may eventually lead to a better understanding of social behaviors in other species, including our own.

No description available.

Abstract Internal waves have been identified as one of the most active mechanisms producing vertical mixing in continental slope and shelf waters. The major contribution of mixing are due to internal tides, however, shorter period internal waves are unlikely to be the main source of energy for mixing, especially on the inner part of the continental shelf. In this study, we observe the vertical mixing of huge internal waves in the Dongsha Atoll South China Sea. These solitary waves were originate near the Luzon Strait, propagated westward across the basin, evolving into internal solitary wave trains and dissipated at the western shallow continental shelf. The wave energy and phase speed reduced significantly during the shoaling process. Internal waves and their likely related induced mixing phenomena are analyzed based on multiple cruises of observations consisted of CTD hydrographic measurements, water samples and moored thermister strings. Data analyses show that the mixing processes are related to depths of water and the interfacial of wave. For depression wave in the deep water zone, upper layer water may push downward producing vertical mixing beyond the thermocline. The mixing usually dilutes the nutrients in the upper layer of water column. Statistics suggest that the N:P ratio is 12:1 which is lower than the standard value (16:1) indicating the region is nitrogen deficit, similar to most of the surface water in South China Sea. The depression solitons in deep water may evolved to a packet of elevation waves in the shallow water area at ¡§turning point¡¨ of approximately equal depth of upper and lower layers. The mixing of shallow water internal waves can entrain cold nutrient rich water from the lower layer into the frequently nutrient depleted subsurface layer to enhance the local coral reef ecosystem. For example, CTD profiles (2008.5.7) before and after the passage of internal wave show large differences. The vertical density distribution has dramatic change. The column was stratified in two layers in normal condition. The internal waves perturbed the water column into stepwise multi-layer density distribution. The water at 50 m showed temperature decrease by 6 ¢J, salinity increase by 23 psu, density increase by 1.8 , fluorescence decrease by 0.065 £gg/L etc. The MODIS chlorophyll images confirm the high concentration fertilized by the internal wave pumping near the NE region of the Dongsha Atoll.

No description available.

The primary aim of this study was to investigate the sedimentation processes within Buffalo Bay, particularly within and adjacent to the Whitianga tidal inlet, in order to ascertain reasons for the shoaling at both the inlet, and the identified shallow zone around Pandora Rock. Comparison of historic bathymetries suggests the ebb delta and ebb discharge channel of the Whitianga tidal inlet are rapidly accreting and the ebb tidal discharge channel is gradually migrating northeast towards Whakapenui Point. Accretion rates of up to 25 cm y-1 were calculated in the ebb delta and inlet discharge channel area between 1979 and 1995 and aerial photo comparisons suggest the ebb delta area had increased by 400 % between 1990 and 2002. Results of the hydrodynamic and sediment transport modelling suggest the rapid accretion in the ebb delta vicinity is likely to be caused by a combination of catchment estuary inputs, which are deposited on the ebb tide as the ebb flow decelerates over the ebb delta, and inputs that have been moved south along Buffalo Beach by flood currents and an eddy that forms landward of the ebb tidal discharge. Residual tidal velocities further suggest a deposition zone in the ebb delta vicinity resulting from opposing currents and the deceleration of currents. Hydrodynamic modelling results indicate the isolated shallow zone around Pandora rock appears to be caused by a transient eddy in the southern section of Buffalo Bay. The eddy is formed by the ebb tidal discharge from the inlet. Accretion probably occurs in the centre of the eddy which moves north as the ebb tide progresses. Results obtained from a current meter and sediment trap deployed in northern Buffalo Bay suggest suspended sediment transport is minimal in northern Buffalo Bay, only occurring with large wave activity. Results of the hydrodynamic and sediment transport modelling further demonstrate that this area experiences low flow velocities, and has little interaction with the rest of Buffalo Bay. The minimal sediment input to this area, combined with the occasional erosion of the seafloor, primarily by wave activity, is thought to have resulted in long term erosion of northwestern Buffalo Bay between 1938 and 1979. Although the beach and nearshore is eroding, it is likely the addition of sediment would act to stabilise this section of eroding beach. Renourishment material could be provided by the ebb delta, the southern tip of Buffalo Bay or the isolated sandbar northeast of the inlet entrance.

Determining the largest breaking wave height which can occur in water of finite depth is a fundamental reference quantity for the design of coastal structures. Current design guidelines are based on investigations which predominantly used monochromatic waves, thereby neglecting group effects which are inherent to the free propagation of waves in deep water. The Coastal Engineering Manual (CEM) states that wave grouping and its consequences is of significant concern, with breakwater armour damage being generally attributed to higher waves associated with wave groups. However, the CEM also acknowledges that there is little guidance and few formulae for use in practical engineering. This thesis describes a laboratory-based investigation into the effect of wave groupiness on wave shoaling, breaking and surf zone processes. New optical-based techniques for data abstraction, developed within this study, have allowed examination of the interaction between deep water intra-wave group processes and shallow water shoaling processes. The applicability of existing methods for predicting breaking wave height and position is evaluated, along with the implications of groupiness on engineering design in the nearshore. The effect of wave groupiness on overtopping and hazard on emerged rock platforms is similarly assessed. Wave group testing has revealed that the spatial phasing of intra-group processes during shoaling can result in considerably different shoaling and breaking regimes. Under certain regimes, wave breaking occurred further shoreward and in a more plunging manner than under other regimes. Within the mid to inner surf zone, waves were also observed to propagate into shallower water before breaking than is predicted by existing design guidelines. This could result in under-prediction of wave height by up to 100%. Expressions are developed for the prediction of maximum wave heights and surface elevation on plane slopes. These expressions implicitly include non-linear group effects and group-induced water-level variations within the surf zone, and are found to provide conservative upper envelopes for the range of data observed within the current testing regimes. Predictive schemes are similarly developed for overtopping hazard on emerged rock platforms based on critical wave and water-level conditions. Variations in maximum overtopping flow values due to intra-wave group processes of up to +/-35% were found. These group effects were found to reduce by up to 30% the threshold wave conditions before the initiation of hazard.

Dans ce manuscrit, nous nous inéressons à l'étude du mouvement des vagues soumises uniquement à leur poids par le biais d'équations asymptotiques. Nous commençons par rappeler la dérivation des principaux modèles généralement utilisés (Boussinesq, Green-Naghdi,...). Nous introduisons également un nouveau modèle exprimé en amplitude-flux qui correspond à une variante des équations de Nwogu. Dans le second chapitre, nous démontrons un résultat d'existence en temps long pour ces nouvelles équations et nous étudions l'existence d'ondes solitaires pour les équations de Boussinesq. Ce travail permet notamment de calculer avec une grande précision ces solutions exactes. Le troisième chapitre détaille les différences non linéaires que l'on retrouve entre les différentes équations de Boussinesq (modèles en flux-amplitude comparés aux modèles en vitesse-amplitude). Enfin, les deux derniers chapitres introduisent un nouveau paradigme pour trouver des schémas numériques adaptés aux modèles asymptotiques. L'idée est d'appliquer une analyse asymptotique aux équations d'Euler discrétisées. Ce nouveau paradigme est appliqué aux équations de Peregrine, de Nwogu et de Green-Naghdi. Plusieurs cas tests sont proposés dans ces deux chapitres. / In this work, we are interested in the evolution of water waves under the gravity force using asymptotics models. We start by recalling the derivation of most used models (Boussinesq, Green-Naghdi,...) and we introduce a new model expressed amplitude-flux, which is an alternative version of the Nwogu equations. In the second chapter, we prove a long time existence result for the new model and we investigate the existence of solitary waves for the Boussinesq models. This work allow us to compute these solutions with a good precision. The third chapter highlights the nonlinear differences between the Boussinesq equations (amplitude-flux models versus amplitude-velocity models). Finally, the two last chapter introduce a new paradigm in order to find numerical schemes adapted to asymptotics models. The idea is to apply an asymptotic analysis to a discretized Euler system. This new paradigm is applied to Peregrine equations, Nwogu equations and Green-Naghdi equations. Test cases are presented in these two chapters

An understanding of extreme waves is important in the design and analysis of offshore structures, such as oil and gas platforms. With the increase of interest in the shipping of LNG, the design of import and export terminals in coastal water of slowly varying intermediate depth requires accurate analysis of steep wave shoaling. In this thesis, data from laboratory experiments involving random wave simulations on very gentle slopes have been analysed in terms of a model of large wave events, and the results interpreted by observation of the shape and magnitude of the large wave events. The auto-correlation function of the free surface elevation time histories, called NewWave, has been calculated from the wave spectrum and shown to fit very well up to the point where waves start to break (when compared to the ‘linear’ surface elevation time history). It has been shown that NewWave is an appropriate model for the shape of the ‘linear’ part of large waves provided kd > 0.5. A Stokes-like expansion for NewWave analysis has been demonstrated to match the average shape of the largest waves, accounting for the dominant vertical asymmetry. Furthermore, an appropriate local wave period derived from NewWave has been inserted into a Miche-based limiting criterion, using the linear dispersion equation, to obtain estimates for the limiting wave height. Overall, the analysis confirms the Miche-type criterion applies to limiting wave height for waves passing over very mild bed slopes. A derivation of general Green-Naghdi (GN) theory, which incorporates non-linear terms in its formulation, is also presented. This approach satisfies the boundary conditions exactly and approximates the field equations. The derived 2-dimensional vertical GN Level 1 model, capable of simulating steep waves on varying water depth, is validated against solitary waves and their interactions, and solitary waves on varying water depth and gives good qualitative agreement against the KdV equation. The developed and validated numerical model is used to simulate focussed wave groups on both constant depth and gentle slope. In general, the behaviour of waves simulated by the numerical model is very similar to that observed in the experimental data. There is evidence of vertical asymmetry as the water depth is reduced, owing to the non-linearity. Although the main physics is still controlled by linear dispersion, the higher order harmonics become increasingly important for shoaling waves. The numerical results also show a slope-induced wave set-up that keeps on increasing in amplitude as the wave group travels on the gentle slope.

In the Maritime Works Engineering department of Saipem, studies have been carried out to design an extension to an existing LNG export facility. The scope of work comprises the design of a jetty on piles. For this purpose, wave propagation and ship mooring computations have been performed, as well as shore protection and abutment studies. These studies were preceded by meteocean site data and bathymetry analysis.