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The Ria de Aveiro, a mesotidal lagoon located on the Northwestern Portuguese coast, is characterized by large areas of intertidal flats and a web of narrow channels. The lagoon has a large area of mostly abandoned salt pans, whose progressive degradation is caused by the lack of maintenance and by the strong currents which erode their protective walls. The shallow water model ELCIRC was implemented and calibrated for the Ria de Aveiro in order to study its hydrodynamics, with special emphasis on the effect of the destruction of the salt pans protective walls. The calibration was performed by adjusting the bottom friction coefficient, through the comparison between measured and computed time series of surface water elevations at several stations within thelagoon. Harmonic analyses of these data were performed in order to evaluate the models accuracy. An assessment of root mean square errors and skill showed that a good calibration was achieved.Once calibrated, ELCIRC was used to characterize the hydrodynamics of the entire lagoon and the channels around the salt pans under different scenarios (present athymetry and a projection of the bathymetry resultingfrom the walls destruction). An extreme destruction of the salt pan walls would result in a significant increase of the inundation area in Ria de Aveiro, as well as in changes of the global and local hydrodynamic regimes. In summary, this study reveals how the increase of the flooded area in estuarine lagoons can affect tidalpropagation, including the increase of tidal currents, tidal prism and tidal asymmetry. The long-term implications of the salt pans inundation are discussed based on the results.

Due to the increasing sand demand for construction and beach nourishment, offshore extraction is being considered as an alternative source. Long term morphological changes caused by such an extraction must be predicted because they can affect the sediments budget and potentially promote coastal erosion. Numerical models are powerful tools that can help in the evaluation of environmental impacts induced by this activity. They should, however, be used with caution, the validation of a particular model being an important task. The objective of this study is to describe the hydrodynamics in the area surrounding a sandpit through the use of numerical models, namely ELCIRC for the tidal flow and SWAN for the waves. The sandpit under study is located offshore Vale do Lobo, an important beach and golf resort located on the Southern Portuguese coast. A wave climate analysis was done in order to assess mean wave conditions and to choose extreme events to propagate with SWAN. Four wave conditions were identified as representative. The numerical results obtained show that the tidal flow and the orbital wave velocities within the pit and neighbouring areas are modified by the presence of the pit. The excavation influences the tidal flow in an area of approximately 3000 * 3000 m2 around it. In this area the maximum velocity increase is of 2%, occurring in the nearby surroundings of the pit, and the maximum decrease is of 16%, in the pit deepest zone. The orbital velocities for the storm wave conditions show a decrease of 15% within the pit and its influence extends up to the 4 m contour, not reaching the shore.

The 2D horizontal morphodynamic modeling system MORSYS2D simulates bottom topography evolution in coastal zones. Sand fluxes are computed with different practical formulas, either for current dominated (e.g, Ackers & White, van Rijn) or combined wave-current flows (e.g., Soulsby van Rijn). Although sensitivity analyses of bottom topography changes in terms of the transport formulas used have already been done, a comparison of the sediment fluxes computed with the different formulations, considering the same flow conditions and using the parameterizations considered in the model (e.g, bottom roughness, bottom stress) is lacking. With that purpose, we have conceptualized a suitable range of wave and current conditions above a sand bed composed of uniform sediment that is characteristic of the conditions encountered in estuaries, tidal inlets and continental shelves, and applied the several flux formulations. To assess the differences obtained, the average value and the standard deviation were computed for each flow condition. This exercise enabled us to identify, for different parameter ranges, the transport formulations which are consistent with one another and those that deviate the most from the mean. This information is useful in practical applications by defining conditions for optimal formula performance.

Morphodynamic modeling systems increasingly appear as valuable tools to understand the dynamics of coastal systems, including mixed-energy tidal inlets, driven by the combined action of tides and waves. This study aims at: 1) applying and validating a morphodynamic modeling system to a rapidly evolving tidal inlet and 2) verifying both qualitatively and quantitavely the ability of the morphodynamic modeling system to simulate the development of the inlet's main features. The MORSYS2D morphodynamic modeling system is applied to the Ancão Inlet (South Portugal), just after its relocation in August 1997. The relocation and the first stages of the inlet development were monitored in the scope of the EU project INDIA, which provided a large database of tidal, wave and bathymetric data. The first step of the present study consists on a fine calibration of the morphodynamic modeling system using the INDIA data. The model/data comparison shows that the modeling system was able to reproduce well wave heights, elevations and current velocities, with root mean square errors of 0.25 m, 0.065 m and 0.12 m/s, respectively. The morphological evolution of Ancão Inlet is then simulated over the period August 1997-January 1999, starting at the inlet relocation. Model predictions were compared to the bathymetric surveys available over the simulated period. Model/data comparison demonstrates that the model is able to reproduce the development of the main features of the Ancão Inlet. From a quantitative viewpoint, the model was also able to reproduce the development of the inlet's cross-section, characterized by faster growths during fair weather conditions. Finally, this study also provides additional insight regarding on the dynamics of mixed-energy (tide, waves) tidal inlets.

Sandy beaches can be found in fetch-limited environments that are protected from ocean generated waves, as estuaries, lagoons, and backbarriers, and where fetch characteristics allow local wind-generated waves to develop and maintain a beach. The morphodynamics of these low-energy beaches present a peculiar behaviour and general open-ocean models are inappropriate for their study. The main objective of this work is the development of a fetch-limited beach classification scheme based on the relative importance of wave, tidal and river flow forcing. This objective was pursue through the study of the evolutionary pattern of two fetch-limited beaches located in two different Portuguese systems, Alfeite (in Tagus Estuary) and Ancão backbarrier (in RiaFormosa barrier system). Results show that both beaches display a typical fetch-limited profile, with a narrow reflective beach face and a wide dissipative tidal flat, and that profile shape exhibits small changes without a seasonal pattern typical of ocean beaches. At Alfeite, profile changes are restricted to the beach face and result from low-frequency extreme events (strong wind generated waves, Hs>0.5m). At Ancão, although major morphologic changes are also related to the beach face, which is typical behaviour of wave dominated beaches,sediment transport, mainly driven by tidal currents, extends through the entire profile. A tentative fetch-limited beach classification, based on the relative importance of wave and tide effects, is presented.

Profile characteristics of low energy sandy beaches include narrow foreshores that are often steep, with reflective swash zones. Seaward of the foreshore a low gradient terrace is generally present, acting as a wave energy filter. Low magnitude changes are usually associated to this type of environments, either cross- or longshore. To examine the short- (between months) and medium-term (from months to years) morphological changes at Ancão backbarrier (Ria Formosa), data from monthly cross-shore surveys was used. The degree of morphological mobility was given by the volumetric variability within specific morphologic units (foreshore, tidal flat and sand spit) and through the analysis of three cross-shore sections. Results show low medium-term variability, not seasonally distributed, and without a direct connection to changes on average wind intensity. The three morphologies are not interdependent and do not show a clear relation on sediment exchanges between them. Low intensity short-term changes are however present, which seem to be related with net sediment adjustments. Although the morphology and beach slope changes do not indicate a linear pattern of sediment exchange across the profile, cross-shore transport seems to dominate the small scale short-term process, mainly at the foreshore, being related with changes in wind direction (erosion associated to S-SE directions). At the medium- to long-term scale of evolution (years to decades) beach morphodynamics is probably more related with other forcing factors (e.g. inlet position, currents intensity and direction) rather than wind conditions.

This work describes the application of hydrodynamic (ELCIRC) and transport (VELA and VELApart) models to the Ria Formosa lagoon (Portugal) to study the impact of the relocation of the Ancão Inlet. Located in the south of Portugal, this lagoon is a mesotidal barrier island system that communicates with the sea through 6 inlets. The Old Ancão Inlet was artificially closed and the New Ancão Inlet was relocated into a westward position. This work investigates the hydrodynamic patterns and the potential pathways of tracers in Ria Formosa in two distinct configurations: before and after the Ancão Inlet relocation. The hydrodynamic model was successfully calibrated and validated against elevation, velocity and inlet discharges data, accurately reproducing the tidal propagation. The inlet relocation increases the magnitude of tidal currents, residual velocities and the tidal prism across the bar, suggesting a better stability. The tracers transport simulations suggest enhanced water exchanges through the Ancão Inlet and smaller residence times in the western part of Ria Formosa with the present configuration. Overall, it is concluded that the Ancão Inlet relocation had a positive contribution towards increasing the water renewal of the western part of the lagoon, thus decreasing its vulnerability to pollution

Estuaries are unique systems with an unquestionable economical, ecological and recreational value which has motivated a large amount of research work. Out of the research focus emerge the estuarine margins and more particularly the estuarine beaches, especially in what concerns their macro-scale evolution. This work aims tounderstand the origin and evolution of Tagus estuary beaches. To meet this objective, a detailed geomorphological characterization of peri-estuarine margins, complemented with geological and sedimentological data, was performed. This study was coupled with the analysis of meteorological andhydrodynamic processes that control the estuarine sedimentary dynamics; particular attention was given to local waves through the application of a wind-wave generated model calibrated with field data.The origin of Tagus estuarine beaches is related with the Holocene transgression, which promoted the drowning of the present-day upper estuarine depression and generated a wide and shallow fetch-limited basin. From the transgressive maximum onwards the estuary initiated an infilling process dominated by fluvial fine-graineddeposition within the estuarine basin, whereas sand input was retained in a bay-head delta. At the same time,fetch-limited waves promoted the erosion of estuarine margins, initiating beach development, related to the growth of sand spits anchored in Plio-Pleistocene reliefs. This process depended on wave energy and also on mean wave power direction, which controlled the spit growing pattern. At present, beach evolution reflects thedisturbance of sediment budget due to the increase of human intervention in estuarine margins.

A one-dimensional vertical (1-DV) numerical model that predicts mean sediment transport rates has been recently updated with state-of-the-art methods and tested against available field observations. Model calibration has been done through a comparison analysis between formulations regarding three main parameters: bed roughness, reference concentration and sediment vertical mixing coefficient. The objective was to find the optimal combination of formulae based on the agreement of the model results with field data. Though important discrepancies were found between different predictors, with differences reaching, in some cases, two orders of magnitude, the best combinations of predictors allowed a very good agreement between model predictions and observations.

Ecological models can be useful tools for understanding the dynamics of the estuarine and coastal ecosystems. However, the application of these models in real systems requires the specification of many empirical input parameters, which are in general difficult to quantify for a specific site. This study presents a sensitivity analysis on the input parameters of the model ECO-SELFE applied to the Ria de Aveiro. ECO-SELFE is a threedimensional, unstructured grid, fully-coupled hydrodynamic-ecological model. The sensitivity analysis is based on a previous analysis using the zero-dimensional ecological model, where one parameter was varied with the others being held constant. Results show that phytoplankton growth rate and zooplankton excretion and mortality rates are the parameters that influence the results the most. The degree of influence of these parameters depends on the local concentrations of zooplankton and phytoplankton. These two ecological variables are also most affected by the variations in the input parameters.

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The hydrodynamics and sediment dynamics of a low energy estuarine beach was analysed. The beach is subjected to local wind waves generated in an area of restricted fetch, wake waves generated by catamarans and a semi diurnal meso-tidal regime. Only storm events of short duration modify the beach profile, which, once the normal hydrodynamic conditions are restored, naturally recovers its initial shape. The beach is characterised by having a steep upper slope until mean sea level, followed, seaward, by a low gradient terrace, and a bimodal sediment distribution. To investigate the hydro sedimentologic beach behaviour, wind, topo-hydrographic and sedimentologic data were used as input and validation of process based numerical modelling. Wave generation and transformation in an area of restricted fetch, nearshore circulation, sediment transport and morphological evolution were simulated for average annual conditions and storm conditions. The statistical analysis of a six-year wind data series allowed to derive the average wind regime, based on which, the average annual wave regime and the average annual longshore sediment budget, 14.5x103 m3year-1, were calculated. The contribution of the individual components of the representative wave regime, discretised by directional sector and height class of incidence, was evaluated as well as the spatial distribution of the longshore sediment transport in the active part of the beach profile. The characteristics of the wave groups generated by the passage of catamarans at different speeds were estimated and their action on the beach morphology was simulated. Although when the catamarans travel at 20 knots speed the average annual wake wave energy dissipated at the beach is 2.5 times higher than the average annual wind wave energy, the erosion effect on the beach profile is still not relevant for the present traffic. In opposition, short duration storm events generate the formation of an erosion scarp at the upper part of the beach face. The numerical modelling of this phenomenon allowed to acknowledge on the protective effect that the low gradient terrace has on the beach face.

A presente tese tem como objetivo melhorar a gestão dos sistemas de distribuição de água através da utilização de métodos probabilísticos e estatísticos para analisar os dados de contadores inteligentes. Assim, é proposta uma metodologia para avaliação da incerteza em medições de caudal dinâmicas, baseada apenas nas próprias medições, no método de bootstrap por blocos e no ajustamento de um modelo adequado aos dados em estudo. De seguida, é desenvolvida uma metodologia de amostragem probabilística estratificada dos clientes para identificação de uma amostra representativa onde deverão ser instalados contadores inteligentes, sendo os estratos definidos pelos grupos obtidos numa análise de clusters baseada em dados de faturação. É ainda apresentada uma metodologia para a decomposição¸ de séries temporais de caudal em consumo autorizado, consumo não autorizado, roturas e perdas, utilizando técnicas de suavização de séries temporais e análise do espetro singular (singular sprectum analysis). Por último, são testados alguns métodos robustos e de analise funcional para deteção de valores anómalos em series temporais de caudal.

A compreensão dos impactes das alterações climáticas é fundamental para agestão a longo do prazo dos ecossistemas estuarinos. Esta compreensão sópoderá ser efectiva considerando a variabilidade climática natural e o papelrelativo das intervenções antropogénicas nestes ecossistemas. Assim, apresente dissertação analisa a influência das alterações climáticas e pressõesantropogénicas na qualidade da água e dinâmica ecológica da Ria de Aveirocom base numa abordagem integrada, que combinou a análise de sériestemporais dos últimos 25 anos e a modelação numérica de elevada resoluçãode cenários futuros de alterações climáticas e intervenções antropogénicas.A componente de modelação de qualidade da água e ecológica foi melhoradaa vários níveis. A análise de sensibilidade do modelo 3D hidrodinâmicoecológicoECO-SELFE aplicado à Ria de Aveiro e a revisão das constantes desemi-saturação para absorção de nutrientes pelo fitoplâncton contribuírampara a precisão e robustez das aplicações. A concentração do fitoplâncton foisignificativamente influenciada pelas taxas de crescimento do fitoplâncton e demortalidade e excreção do zooplâncton, e apresentou uma sensibilidadereduzida à variação das constantes de semi-saturação na gama identificadapara as diatomáceas. O acoplamento do ECO-SELFE a um modelo de campopróximo e a integração do ciclo do oxigénio aumentaram a sua capacidade derepresentação dos processos e das escalas espaciais relevantes. A validaçãodo ECO-SELFE foi realizada com base num conjunto de campanhasespecíficas realizadas no canal de Mira. Os padrões espaciais e temporaisobservados para as várias variáveis (clorofila a, nutrientes, oxigénio dissolvido,salinidade, temperatura da água, correntes e níveis) foram simulados comerros menores ou semelhantes aos obtidos neste tipo de aplicações.A análise dos padrões de variabilidade espacial e temporal da qualidade daágua e ecológica na Ria de Aveiro a diferentes escalas, efectuada com basenos dados históricos de 1985 a 2010 complementados pelas campanhasrealizadas, sugeriu uma influência combinada da variabilidade climática e dasacções antropogénicas. Os cenários futuros de alterações climáticas eintervenções antropogénicas simulados evidenciaram uma influência maissignificativa das alterações climáticas quando comparadas com os efeitos dasacções antropogénicas analisadas. As variações mais significativas sãoprevistas para os cenários de subida do nível do mar, seguidos dos cenáriosde alterações dos regimes hidrológicos, evidenciando o papel da circulação(maré e caudal fluvial) no estabelecimento da qualidade da água e dinâmicaecológica na laguna. Para os cenários de subida do nível do mar são previstosdecréscimos significativos da clorofila a e dos nutrientes a jusante e nas zonasintermédias do canal, e um aumento significativo da salinidade a montante.Estas alterações poderão favorecer modificações da composição e distribuiçãodas comunidades, afectando a cadeia alimentar e causando uma progressãopara montante de espécies marinhas. Os resultados sugerem ainda que osefeitos poderão ser mais significativos em estuários pouco profundos.

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A temática dos derrames de hidrocarbonetos continua a ser um assunto de extremaimportância dados os graves impactes continuadamente causados no meio marinho. O desenvolvimentode ferramentas para auxilio às autoridades responsáveis pela gestão costeirano combate e mitigação deste tipo de acidentes é prioritário nos planos estratégicos governamentais.Neste trabalho propõe-se um novo sistema integrado de análise de hidrocarbonetos desenvolvidopara aplicação a derrames em zonas costeiras, portuárias e oceânicas. Desenvolveuseuma nova metodologia baseada na sinergia da modelação numérica com a detecção remotapor satélites. Este sistema integra uma componente de modelação numérica flexível(2D/3D) e um novo algoritmo de segmentação de manchas de hidrocarbonetos observadasem imagens SAR. O algoritmo de detecção remota foi concebido para validar os resultadosdo sistema de modelos. O sistema de modelação baseia-se numa abordagem Euleriana-Lagrangeana para a resolução dos processos de evolução dos hidrocarbonetos, utilizandomalhas não-estruturadas para a representação dos domínios de estudo numa perspectivamulti-escala. O modelo de hidrocarbonetos inclui a maioria dos processos relevantes numderrame à superfície e na coluna de água e inclui um novo algoritmo para a retenção costeiraque considera a dinâmica intertidal para aplicação a domínios praias, lagunas e estuários.Realizaram-se diversas aplicações sintéticas e reais que comprovaram a precisão, robustez,fiabilidade e flexibilidade do sistema integrado, com custos computacionais e níveisde complexidade variável. A aplicação do sistema ao caso Prestige permitiu demonstrarque a sinergia entre a modelação numérica e a detecção remota é uma mais-valia para aprevisão de derrames de hidrocarbonetos no mar e serviu como base para uma análise qualitativada influência da precisão da previsão do vento como agente forçador.Futuramente, o sistema poderá ser aplicado na optimização de planos de contingência,sustentando análises de risco, e em sistemas de alerta e aviso para acidentes de poluição.

As margens estuarinas são constituídas por diversos elementos morfo-sedimentares, interdependentes entre si através de processos hidrodinâmicos, sedimentares, morfológicos e ecológicos. Estas características conferem à zona marginal do estuário uma sensibilidade particular a desequilíbrios entre o suporte morfológico e sedimentar e à acção dos agentes hidrodinâmicos, climáticos e antrópicos. A presente tese contempla o estudo da evolução morfo-sedimentar de margens estuarinas, procurando identificar as condições genéticas, caracterizar e quantificar os processos evolutivos actuais e passados. A área em estudo situa-se na margem sul do estuário interno do Tejo, entre Alcochete e Cacilhas, incluindo a restinga do Alfeite e a baía do Seixal. Efectuou-se a caracterização hidrodinâmica, morfológica e sedimentar da região em estudo e a avaliação dos padrões evolutivos à mesoescala e microescala. O estuário do Tejo é caracterizado por extensas zonas intertidais constituídas por rasos de maré e sapais. Estas áreas são alimentadas por sedimento em suspensão de origem fluvial, redistribuído pelas correntes de maré. Contrastando com o predomínio da sedimentação essencialmente silto-argilosa, surgem na margem sul praias e restingas de natureza arenosa que indicam a actividade de ondas de geração local. A morfologia da restinga do Alfeite evidencia a actividade de ondas, quer na sua formação, quer na sua evolução temporal. A sua instalação, há cerca de 500 anos atrás, terá correspondido a um episódio de mobilização considerável de material grosseiro proveniente de fontes sedimentares próximas - as rochas detríticas miocénicas e pliocénicas. A instalação da restinga proporcionou a manutenção de um ambiente de baixa energia, constituído por rasos de maré e sapais (baía do Seixal). O clima de agitação local está sobretudo relacionado com as nortadas, devido às maiores distâncias de fetch associadas e à intensidade mais elevada dos ventos daquele quadrante. O clima de agitação médio, obtido através de um modelo de previsão da agitação, caracteriza-se por alturas significativas de onda entre 0,2 e 0,4 m e por períodos de zero ascendente de 2 s. Em condições extremas a altura significativa de onda pode atingir 1,3 m. As ondas de geração local no estuário interno têm capacidade para causar a ressuspensão, transporte e acumulação de areias na margem sul, virada às direcções de fetch mais longo. Identificaram-se dois domínios principais de transporte longitudinal, envolvendo um caudal sólido semelhante de 20 000 - 30 000 m3/ano. Estes resultados concordam como as direcções de desenvolvimento e de progradação das restingas de areia. O padrão de dispersão de material sedimentar concorda também com a localização de fontes sedimentares potenciais. A restinga do Alfeite mostra uma variação morfológica evidente nos últimos 150 anos, dominada pelos processos de erosão e envolvendo a redução da área da praia em cerca de 15 ha. As modificações mais importantes ocorreram no período 1930-1979, com uma taxa de erosão média de 0,3 ha/ano, que coincidiu com intensa intervenção antrópica no sistema envolvendo alteração dos balanços sedimentares locais. As taxas de erosão obtidas através da análise evolutiva à mesoescala concordam com os volumes sedimentares avaliados para a deriva litoral local. O padrão evolutivo à microescala da praia do Alfeite mostra igualmente um comportamento particular de resposta a alterações hidrodinâmicas locais e à acção antrópica. O padrão de evolução à mesoescala e microescala da baía do Seixal sugere uma diferença acentuada entre o comportamento das zonas subtidal e intertidal inferior, com alguma dominância dos processos erosivos (com uma taxa de erosão média de 1-2 cm/ano), e o da zona supratidal com taxas de sedimentação relativamente elevadas (1cm/ano). O modelo morfo-sedimentar proposto para a baía do Seixal é essencialmente um modelo de redistribuição de sedimentos entre os rasos de maré superiores e sapais e os canais; resulta a selecção natural entre siltes grosseiros e areia e uma fracção mais fina com componente orgânica importante. À macroescala, o modelo evolutivo proposto será interrompido por episódios de entrada excepcional de material, principalmente através da rede hidrográfica local, associados a eventos extremos. As margens estuarinas são particularmente sensíveis a alterações extremas dos balanços sedimentares locais, sendo clara a interdependência entre a evolução morfológica e a interferência antrópica no sistema.

Os estuários são sistemas ricos em recursos naturais e de grande fragilidade ecológica. O seu uso, como suporte de múltiplas actividades, faz com que seja necessário definir planos de gestão destinados a compatibilizar tais utilizações, salvaguardando o equilíbrio ecológico e a saúde pública. Reviram-se os conceitos de estuário, suas características e tipos. Identificaram-se princípios e metodologias para a sua gestão, que requerem o uso de instrumentos, dentre os quais são objecto central do presente estudo os sistemas de indicadores ambientais. O modelo de enquadramento adoptado foi o de Pressão Estado Resposta. As aplicações do conceito de indicador ambiental a estuários são recentes e limitadas, devido à especificidade destes sistemas, em particular, da coexistência de escalas de tempo distintas no controlo dos processos hidrodinâmicos e das suas características bio-geo-químicas. A caracterização ambiental dum estuário requer a aplicação de uma metodologia que inclui, além de informação de contexto, a identificação das zonas homogéneas, definidas com base em critérios morfológicos, de salinidade e de gestão, e das escalas de tempo relevantes, para definir os domínios de integração espacial e temporal das variáveis observadas, que conduzem aos valores significativos. A estes é removida a dimensão, sendo normalizados por aplicação de operadores algébricos e gráficos, inferindo-se a conformidade com a qualidade ambiental a partir dos valores dos indicadores normalizados. A metodologia inclui a definição de classes de qualidade. A metodologia foi ensaiada no estuário do Tejo. A sua caracterização, cobrindo as temáticas da eutrofização e estado de oxigenação, da qualidade estética e da contaminação bacteriológica e por xenobióticos, demonstrou a exequibilidade do método. Os resultados, se bem que de interesse relativo por recorrerem a dados heterogéneos e, por vezes, sem actualidade, revelam um estuário com baixa susceptibilidade à poluição, onde o incumprimento das normas de emissão pelas fontes poluentes era dominante. Porém, o estado do estuário revelou-se, em grande parte da sua extensão, bom ou excelente relativamente a alguns parâmetros, embora tenham sido identificadas situações de não conformidade. A metodologia é, assim, exequível, mesmo quando aplicada a um estuário complexo como o Tejo, e capaz de diferenciar situações de qualidade ambiental distintas. Constitui um instrumento de gestão útil para o apoio ao planeamento de programas de monitorização, para a sistematização da informação e para a comunicação clara com os responsáveis pelas decisões e com o público.

Eulerian-Lagrangian methods (ELMs) are increasingly used to simulate groundwater and surface water transport and water quality, largely due to their ability to use large time steps and to formally decouple processes with distinct time scales. Yet, two severe limitations remain: (1) ELMs do not inherently conserve mass, AND (2) in multiple dimensions, robust implementations of "higher-order" ELMs are expensive. Our research focused on the understanding of the main sources of errors in ELMs. We analyzed systematically the impact and relative importance of tracking errors, integration errors and forcing by non-conservative flow fields, on measures of mass conservation, overall accuracy and stability. From this analysis, we propose new methodologies and general guidelines towards mass conservative, globally accurate and stable multi- dimensional ELM transport simulations in estuarine and coastal regions. We performed a pioneering study of the influence of tracking errors, demonstrating their very strong negative impact on mass conservation, overall accuracy and stability. Low-order tracking methods are strongly discouraged in the presence of complex flow fields, typical of estuaries, because they are too inaccurate to allow overall mass balance and phase preservation, and they lead to potential instability. We show that the evaluation of the integrals at the feet of the characteristic lines is an important source of mass and overall errors, which can be controlled through grid refinement. To avoid such errors, we develop a new method that combines the flexibility and local mass properties of control volume finite element methods (CVFE), with a new quadrature integration technique. Subdivision quadrature overcomes stability constrains of traditional quadratures and allows for easy implementation in multiple dimensions. We find subdivision quadrature CVFE-ELMs to be an attractive alternative to current finite element ELMs in estuaries and coasts. Non-conservative flow fields are the primary concern for estuarine and coastal applications because ELMs cannot mitigate their effect without jeopardizing overall accuracy. We found bathymetric gradients and complex geometry to be the main sources for flow mass errors, and grid refinement to be inadequate to eliminate them. Consequently, mass imbalances in ELM solutions cannot be removed by grid refinement. Control volume finite elements and conservative-equation-based formulations are equally ineffective in the presence of a non-conservative flow. The problem needs to be addressed at the source, i.e., the circulation models that generate the flows. A detailed analysis of residence times illustrates the importance of improving numerical models, and provides new insights on the variability of residence times in estuarine systems. A new methodology is proposed, which emphasizes the importance of local analysis of residence times to understand the fluxing properties of a complex system, while providing an alternative approach to traditional bulk evaluations of residence times. Key Words: Flow mass conservation. Transport Mass conservation. Transport equation. Eulerian-Lagrangian methods. Finite Volumes. Finite elements. Accuracy Analysis. Residence Times.

The thesis deals with the numerical modelling of random wave propagation in the nearshore region. The mathematical modelling is based on the mild - slope equation.The mild - slope equation has been considered in a linear elliptic form in order to take into account wave refraction, diffraction, and reflections, and therefore to allow for the applicability of the model without constraints even to areas like harbours where reflections play an important role. Owing to the fact that we are dealing with a boundary value problem, the mathematical methods for solving the linear system of equations generated after discretising the governing equation and the boundary conditions imposed are fundamental to developing an efficient numerical model. A range of mathematical methods for solving the linear elliptic form of the mild-slope equation as well as a range of appropriate radiation boundary conditions are analysed, implemented and compared. Comparisons with available results, experimental and numerical, for different cases of study, validate the model for monochromatic waves.To overcome the difficulty of applying the linear elliptic model over large areas, a multigrid technique was deployed in a numerical model of a non-linear transformed form of the mild-slope equation in order to accelerate convergence. This technique was applied to a range of iterative solvers and satisfactory results were obtained.A numerical model of a hyperbolic form of the mild-slope equation, an initial value problem, was also developed and extended in order to test a range of radiation boundary conditions. Results show that "sponge layers" provide the best means of dealing with radiation type boundary conditions.The elliptic model was then further developed by extending it to random waves using the concept of superposition of spectral components. The importance of frequency and directional spreading was investigated. Based on the energy balance equation the phenomenon of breaking of irregular waves in the surf zone was incorporated, using two different approaches, in the model which was applied to cases that had been experimentally studied before. The results from this part of the work are unique and demonstrate the practical usefulness of the model.

STERNA é um sistema de modelos matemáticos para a simulação de processos hidrodinâmicos e de qualidade da água em estuários não-estratificados. Este sistema é constituído pelo modelo hidrodinâmico MOHID, previamente existente, e por um modelo de transporte e por um conjunto de módulos de qualidade da água, desenvolvidos no decurso deste estudo. As equações de conservação da massa e de conservação da quantidade de movimento, do modelo hidrodinâmico, e a equação de advecção-difusão, do modelo de transporte, são resolvidas pelo método das diferenças finitas, a partir de uma formulação bidimensional (2D), integrada na vertical.Descreve-se a aplicação do sistema STERNA ao estuário do Tejo. Os resultados são comparados com observações efectuadas em campanhas do "Estudo Ambiental do Estuário do Tejo". Estas observações compreendem: a) séries temporais de correntes, salinidade, temperatura e sedimentos em suspensão, com cerca de 24 horas de duração; b) séries de valores mensais de salinidade, temperatura, clorofila-a, fosfato, amónia, nitrato, CBO e oxigénio dissolvido, com 4 anos de duração. Verifica-se, para a generalidade dos parâmetros, uma concordância satisfatória entre observações e resultados dos modelos.Os dados de campo e o sistema de modelos proposto servem de suporte a uma análise das características do ambiente no estuário do Tejo. Discutem-se, em particular: as trocas de maré entre o estuário e o exterior; a importância da estratificação de densidade; os fluxos de calor através da superfície; os mecanismos de formação da zona de turvação máxima; os factores responsáveis pela limitação da produção primária fitoplanctónica; os processos envolvidos no ciclo do fósforo e do azoto; e a ocorrência de défices de oxigénio. Conclui-se pela importância de uma abordagem integrada no estudo dos processos estuarinos.Palavras-chave: Modelos matemáticos; método das diferenças finitas; hidrodinâmica de estuários; qualidade da água; estuário do Tejo.

Although three-dimensional (3D) modeling of coastal and estuarine flows is becoming common, several limitations remain related to our ability both to describe and to numerically simulate the correct physics. Two key limitations concern vertical resolution: the lack of flexibility of current methods for vertical discretization prevents the optimal use of computational resources, and guidelines for vertical nodal placement are not available.The major contribution of this thesis is the development, analysis and test of an approach that allows for an unprecedented flexibility in the vertical refinement of the domain. This approach, which we refer to as localized sigma coordinates (LSC), is the first to allow the number of nodes per vertical to vary horizontaly, and can therefore be considered a natural extension to the use of unstructured grids in the horizontal.To take advantege of the LSC, we perform the first systematic study for the vertical discretization in barotropic tidal flow simulations. The resulting optimal grid can reduce the errors relative to a uniform grid by over an order of magnitude and compares favorably with non-uniform grids previously proposed. A criterion to guide the horizontal distribution of the total number of nodes is proposed and discussed in the context of simple one- and two-dimensional models, and is then extended to three dimensions. Accounting for advection in three dimenions forces modifications to the criterion, but the overall concept proved to be useful: using a variable number of nodes per vertical reduces the maximum velocity errors by a factor of two.As part of our analysis of the LSC, we investigate the evaluation of the horizontal gradients in sigma-coordinate shallow water models. We show that horizontal gradients should be computed in sigma rather than z-coordinates, and that the so-called hydrostatic inconsistency typically associated with sigma coordinates does not correspond to a numerical inconsistency. The large errors associated with the evaluation of horizontal gradients can be by-passed through appropriate horizontal resolution, and a procedure to define this resolution is proposed based on results from a truncation error analysis.An application to the Tagus estuary demonstrates the enhanced accuracy provided by the LSC, and provides new insights into the estuarys 3D barotropic circulation. Strong residual currents (depth-averaged eulerian residual velocities of up to 0.5 m/s) are generated by advective accelerations and have a major impact on the mixing characteristics at the mouth of the estuary. The assymetry between ebbing and flooding promotes exchanges between marine and estuarine waters, while he interaction between tidal and residual flows leads to strong chaotic stirring.The good performance of the LSC in a complex application establishes this method as an attractive alternative to the traditional sigma- and z-coordinates.

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