Secondary flow within a river bed and contaminant transport

We have developed a numerical method to simulate the transport of non-sorbing contaminants within the sediment layer of a stream and the leaching of these contaminants in the steam. Typical stream bottom surfaces are uneven with triangularly shaped undulation forms. The flow of the water above such triangular surfaces causes external pressure changes that result in a “pumping effect” and a secondary flow within the sediment. The latter causes a significant contaminant advection within the sediment layer. The flow field in the porous sediment layer is obtained by solving numerically Darcy’s equations. The unsteady mass transfer equation is solved by using a finite-difference method with an up-wind scheme. The effects of parameters, such as channel slope, hydraulic head and dispersion, are studied by quantitatively comparing the numerical results of the total mass flow rate from the contaminant source, the concentration front propagation, and the contaminant mass flow rate into the water column. The “pumping effect,” increases the flow in the vertical direction and, thus, enhances the vertical advective mass transport of the contaminant. This bedform-shape induced flow is largely responsible for the mass transfer of contaminants into the water column. The numerical results also show that the mechanical dispersion inside the sediment bed will significantly increase the contaminant mass flow rate from the source.     

Hydrodynamics and contaminant transport on a degraded bed at a 90-degree channel confluence

Channel confluences at which two channels merge have an important effect on momentum exchange and contaminant diffusion in both natural rivers and artificial canals. In this study, a three-dimensional numerical model, which is based on the Reynolds Averaged Navier–Stokes equations and Reynolds Stress Turbulence model, is applied to simulate and compare flow patterns and contaminant transport processes for different bed morphologies. The results clearly show that the distribution of contaminant concentrations is mainly controlled by the shear layer and two counter-rotating helical cells, which in turn are affected by the discharge ratio and the bed morphology. As the discharge ratio increases, the shear flow moves to the outer bank and the counter-clockwise tributary helical cell caused by flow deflection is enlarged, leading the mixing happens near the outer bank and the mixing layer distorted. The bed morphology can induce shrinkage of the separation zone and increase of the clockwise main channel helical cell, which is initiated by the interaction between the tributary helical cell and the main channel flow and strengthened by the deep scour hole. The bed morphology can also affect the distortion direction of the mixing layer. Both a large discharge ratio and the bed morphology could lead to an increase in mixing intensity.     

Modelling nature-like fishway flow around unsubmerged obstacles using a 2D shallow water model

In the scope to create efficient nature like fish ramps using large-scale roughness elements, the present study is an audit of modelling such complex 3D free surface flows using an industrial 2D code solving shallow water equations. Validation procedure is based upon the comparison between numerous experimental measurements and numerical runs around large-scale roughness patterns disposed on the flume bottom in order to determine what 2D reliable numerical results can be expected. In this paper, we focused on cases of unsubmerged obstacles. The results demonstrate that 2D shallow water modelling using an industrial code such as TELEMAC-2D can be a convenient way for the hydraulic engineer to help design a nature-like fishway. This article emphasizes the limitations due to 2D depth integration of velocities and turbulence modelling and gives the domain of validity of the method.     

Interaction between sorption and biodegradation processes in the contaminant transport

The main goal of this work is to examine in detail the equilibrium and non-equilibrium sorption in a multiple species contaminant transport system undergoing multiplicative Monod biodegradation kinetics, which characterizes a scenario of subsurface contamination by organic contaminants. Mathematically, the problem is given by a nonlinear advection-diffusion-reaction partial differential system coupled by the reaction terms, associated with the biodegradation process. A new operator splitting approach is proposed for treating in a sequential fashion the convective-diffusive and reactive terms. A predictor-multicorrector algorithm with Newton–Raphson and stabilized finite element (streamline-upwind Petrov-Galerkin, SUPG) methods is used in the time and spatial discretizations, respectively. Numerical results illustrate the good applicability of the present approach, corroborating the well-known observation nonlinear physical and biological processes should be inserted in the model that to better predict the contamination scenarios.     

Self-contamination of aquaculture cages in shallow water

Fish farms, which initially colonized quiet and protected natural coastal areas, are now frequently installed in open flow zones, due to the lack of space along coasts and to the emergence of new environmental constraints. For the past two decades, a salmon fish farm has been located inside the roadstead of Cherbourg (France) to benefit from both sea protection and tide currents which regularly refresh the water. In spite of these favourable environmental conditions, periods of non-negligible fish mortalities have been observed to occur without clear evidence of their origin. This motivated the turbidity measurements and the numerical simulations presented in this paper. Firstly, it is shown that high turbidities in the farm site under study are mainly due to the flow acceleration under the cages, which causes the re-suspension of sediments and bio-deposits. Secondly, particles which enter the fishnet can have different origins (external source, bottom, or the net itself). Numerical simulations, based on the Reynolds equations and on the discrete random walk model for particle dispersion, suggest that the rear area of the net can be reached by particles emerging from below the net. It is observed that turbulent dispersion is a key ingredient for such a behaviour, as it can lead particles towards a large recirculation cell behind the net. Dispersion by realistic unsteady vortices has also been analysed by means of a Lattice-Boltzmann model. Though these computations involve smaller Reynolds numbers, they confirm qualitatively the observations of the random walk model. In addition, they suggest that vortex shedding and unsteady recirculation cells near the bottom can force particles from the sand bed to be lifted up and reach the rear of the net.     

Evaluation and application of a three-dimensional water quality model in a shallow lake with complex morphometry

Fundamental hydrodynamic and ecological processes of a lake or reservoir could be adequately depicted by one-dimensional (1D) numerical simulation models. Whereas, lakes with significant horizontal water quality and hydrodynamic gradients due to their complex morphometry, inflow or water level fluctuations require a three-dimensional (3D) hydrodynamics and ecological analyses to accurately simulate their temporal and spatial dynamics. In this study, we applied a 3D hydrodynamic model (ELCOM) coupled with an ecological model (CAEDYM) to simulate water quality parameters in three bays of the morphologically complex Lake Minnetonka. A considerable effort was made in setting up the model and a systematic parameterization approach was adopted to estimate the value of parameters based on their published values. Model calibration covered the entire length of the simulation periods from March 29 to October 20, 2000. Sensitivity analysis identified the top parameters with the largest contributions to the sensitivity of model results. The model was next verified with the same setup and parameter values for the period of April 25 to October 10, 2005 against field data. Spatial and temporal dynamics were well simulated and model output results of water temperature (T), dissolved oxygen (DO), total phosphorus (TP) and one group of algae (Cyanobacteria) represented as chlorophyll a (Chla) compared well with an extensive field data in the bays. The results show that the use of the model along with an accurate bathymetry, a systematic calibration and corroboration (verification) process will help to analyze the hydrodynamics and geochemical processes of the morphologically complex Lake Minnetonka. An example of an ecological application of the model for Lake Minnetonka is presented by examining the effect of spatial heterogeneity on coolwater fish habitat analysis in 3D and under a scenario where horizontal spatial heterogeneity was eliminated (1D). Both analyses captured seasonal fish habitat changes and the total seasonal averages differed moderately. However, the 1D analysis did not capture local and short duration variabilities and missed suitable fish habitat variations of as much as 20%. The experiment highlighted the need for a 3D analysis in depicting ecological hot spots such as unsuitable fish habitats in Lake Minnetonka.     

Automatic sensitivity analysis of a finite volume model for two-dimensional shallow water flows

Given a numerical model for solving two-dimensional shallow water equations, we are interested in the robustness of the simulation by identifying the rate of change of the water depths and discharges with respect to a change in the bottom friction coefficients. Such a sensitivity analysis can be carried out by computing the corresponding derivatives. Automatic differentiation (AD) is an efficient numerical method, free of approximation errors, to evaluate derivatives of the objective function specified by the computer program, Rubar20 for example. In this paper AD software tool Tapenade is used to compute forward derivatives. Numerical tests were done to show the robustness of the model and to demonstrate the efficiency of these AD-derivatives.     

Modeling the buoyant flow of heated water discharged from surface and submerged side outfalls in shallow and deep water with a cross flow

In this study, a three-dimensional model was used to numerically study the buoyant flow, along with its mixing characteristics, of heated water discharged from the surface and submerged side outfalls in shallow and deep water with a cross flow. Hydraulic experimental data were used to evaluate the applicability of the model. The simulation results agree well with the experimental results, particularly, the jet trajectories, the dimensions of the recirculating zone, and the distribution of the dimensionless excess temperature. The level of accuracy of the simulation results of the present study is nearly identical to that of the results conducted by McGuirk and Rodi (1978). If the heated water is discharged into shallow water where the momentum flux ratio and the discharge densimetric Froude number are high, the submerged discharge method is better than the surface discharge method in terms of the scale of the recirculating zone and the minimum dilution. In deep water, where the momentum flux ratio and discharge densimetric Froude number are low, however, the submerged discharge method had few advantages. In shallow water, the discharge jet is deflected by the ambient cross flow, while forcing the ambient flow to bend towards the far bank for the full depth. For a submerged discharge in shallow water, the recirculating zone is the largest in the lowest layer but becomes smaller in the upper layer. As the water depth increases, the ambient flow goes over the jet and diminishes the blocking effect, thereby decreasing the bending of the jet.     

Modeling linkages between sediment resuspension and water quality in a shallow,eutrophic, wind-exposed lake

The interactions between bed sediments and the water column in shallow, eutrophic lakes have tremendous implications for the fate and transport of nutrients in those water bodies. This has resulted in the development of water quality models for lakes incorporating the processes of sediment resuspension. Reliable resuspension models are thus needed to accurately represent this phenomenon. In this paper, three different sediment-resuspension models are combined with a hydrodynamic and water quality model, dynamic lake model-water quality (DLM-WQ), and the resulting models are used to simulate nutrient distributions in the highly eutrophic Salton Sea, California, USA. One of the resuspension formulas is based upon sediment characteristics as well as the bed shear stress exerted by wind-induced waves and currents, while the other two are standard, power-law-type formulas for cohesive sediments with two different exponents. The outputs for water quality variables, such as temperature, chlorophyll a, dissolved oxygen and nutrients, obtained from the three resulting models and from an earlier DLM-WQ run with a simple empirical sediment-resuspension model are compared with measured data. The level of agreement between the simulations and the measured data is assessed by using both statistical and graphical model evaluation methods, including measures of residual errors, sample autocorrelations, t-tests, and box plots. Based on these assessments, DLM-WQ with an extended version of the García and Parker [García, M.H., Parker, G., 1993. Experiments on the entrainment of sediment into suspension by a dense bottom current. J. Geophys. Res.-Oceans 98, 4793–4807] relationship gave the best results for water quality in the Salton Sea, confirming that the use of formulas with more information on the sediment characteristics yields more accurate results. To the best of our knowledge, this is the first effort to combine water quality models for lakes and reservoirs with a sediment-resuspension model which was originally intended for open-channel flows. The simulations confirm that sediment resuspension is the most dominant process in the Salton Sea's nutrient cycling. The effect of proposed physical changes to the Salton Sea on water quality characteristics is also addressed.     

Nested numerical scheme in a polar coordinate shallow water model for the coast of Bangladesh

This study is concerned with the development of storm surge model to predict water level accurately due to surge associated with a cyclone along the coast of Bangladesh. Considering the funnel shape of the Bay of Bengal, coastal bending and the existence of off-shore islands, a vertically integrated model in cylindrical polar coordinate system is developed using nested numerical scheme. A fine mesh scheme capable of incorporating coastal bending and offshore islands properly in the numerical scheme is nested into a coarse mesh scheme covering up to 15° N latitude of the Bay of Bengal. The developed model is used to estimate water levels at different coastal and island stations associated with a few storms that hit the coast of Bangladesh. The computed surge levels compared well with observed ones and predicted surge levels investigated with different approaches.     

Lunar influence on distribution of a calanoid copepod in the water column of a shallow,temperate estuary

Moonlight had a significant influence on the distribution of the copepodPseudodiaptomus hessei in the water column. Copepod samples were taken between March 1986 and March 1987 in the Sundays River estuary. South Africa. Late copepodid stages and adults showed vertical differences in abundance on moonlit nights, with more animals in bottom waters, but not on dark nights. Numbers of adults present in the water column were markedly lower on full moon nights compared with new moon nights. The strongest decrease in abundance was displayed by ovigerous females. These observed distribution patterns support published predation hypotheses.     

湖北省湖泊大型底栖动物群落结构及水质生物学评价

大型底栖动物是湖泊生态系统的重要生物类群,在生态系统物质循环和能量流动中起着重要作用。底栖动物具有生命周期长、迁移能力较弱、对环境变化反应敏感等特点,可有效指示湖泊生态系统的健康状况。湖北省是我国淡水湖泊分布最密集的区域之一,湖泊总面积为3025 km2。近年来,伴随着工农业、养殖业及城市化的快速发展,富营养化已成为本地区湖泊面临的一个主要环境问题,并可能直接影响大型底栖动物的群落结构。目前关于本地区湖泊大型底栖动物群落的研究还较少,为此本研究对湖北省27个浅水湖泊底栖动物进行了调查,并对水质状况进行生物学评价。共采集到底栖动物40种,隶属于4门7纲18科,其中寡毛类5种,摇蚊幼虫16种,软体动物双壳类4种、腹足类8种。霍甫水丝蚓（Limnodrilus hoffmeisteri）、苏氏尾鳃蚓（Branchiura sowerbyi）、花翅前突摇蚊（Procladius choreus）、中国长足摇蚊（Tanypus chinensis）、多巴小摇蚊（Microchironomus tabarui）及铜锈环棱螺（Bellamya aeruginosa）是本地区湖泊最常见的种类。所调查湖泊底栖动物平均密度为32~1243 ind·m-2,其中12个湖泊密度低于200 ind·m-2,摇蚊幼虫和寡毛类对密度的贡献较大,以摇蚊幼虫占优势的湖泊有19个。底栖动物平均生物量为0.034~460.7 g·m-2,生物量低于50 g·m-2的湖泊数量最多（19个）,软体动物占优势的湖泊有16个,摇蚊幼虫和寡毛类占优势的湖泊数量共11个。各湖泊底栖动物物种数为3~14种,Margalef指数为0.71~2.33,Simpson指数为0.69~0.85,Shannon-Wiener为0.78~2.13,Spearman相关性分析结果显示物种丰富度和三种多样性指数与湖泊面积呈显著正相关。BI（Hilsenhoff生物指数）评价结果显示共11个湖泊为一般和轻度污染（6.01~7.44）,中度污染湖泊数量为13个（7.57~8.47）,长湖（8.52）、上津湖（8.65）和玉湖（8.50）处于重污染状态。     

Analytical solutions of nonlinear and variable-parameter transport equations for verification of numerical solvers

All numerical codes developed to solve the advection–diffusion-reaction (ADR) equation need to be verified before they are moved to the operational phase. In this paper, we initially provide four new one-dimensional analytical solutions designed to help code verification; these solutions are able to handle the challenges of the scalar transport equation including nonlinearity and spatiotemporal variability of the velocity and dispersion coefficient, and of the source term. Then, we present a solution of Burgers’ equation in a novel setup. Proposed solutions satisfy the continuity of mass for the ambient flow, which is a crucial factor for coupled hydrodynamics-transport solvers. By the end of the paper, we solve hypothetical test problems for each of the solutions numerically, and we use the derived analytical solutions for code verification. Finally, we provide assessments of results accuracy based on well-known model skill metrics.     

塔里木河下游应急输水前后胡杨年轮生长差异

1972年塔里木河下游大西海子水库建成,下游365km河道彻底断流。为拯救沿河植被,2000年5月启动了塔里木河下游应急输水工程,迄今已经完成了7次应急输水。文章通过对塔里木河中游英巴扎和下游输水河畔英苏、喀尔达依、阿拉干断面胡杨(Populus euphratica)一级枝年轮取样调查,运用统计方法比较不同离河距离输水前后胡杨生长量差异的大小,分析了下游应急输水河畔胡杨种群对输水的响应。结果表明:1)英苏断面和喀尔达依断面在离河0~1000m输水前后胡杨生长量差异极显著。阿拉干断面在离河0~300m输水前后胡杨生长量差异极显著,离河300~700m生长量差异显著,700~1000m生长量差异不显著。由输水前后胡杨年轮生长量均值差可得,同一断面不同离河距胡杨年均生长量随离河距增大而降低。2)输水后下游3个调查断面在离河0~300m胡杨生长量增长由大到小顺序为:喀尔达依>英苏>阿拉干;离河300~700m由大到小顺序为:喀尔达依>阿拉干>英苏。3)以中游胡杨同年生长量作为参照对下游胡杨生长量进行相关比较的结果表明:应急输水前输水河畔各离河距离胡杨生长量均小于中游参照河段的生长量。应急输水后,输水河畔离河0~300m生长量已超过中游的生长量;离河300~700m输水河畔的生长量接近中游生长量;离河700~1000m生长量小于中游参照河段生长量,应急输水明显地促进了胡杨生长。     

Effects of visible light radiation on macrophyte litter degradation and nutrient release in water samples from a eutrophic shallow lake

Visible light is a major fraction of the solar spectrum; however, information on visible light radiation of macrophyte detritus is lacking. In this study, we conducted a microcosm experiment to assess the effects of visible light radiation on degradation of two litter species: Potamogeton malaianus (P. malaianus) and Phragmites australis (Ph. australis). This research represents an investigation of mass loss, microbial activity and nutrients released over a period of 168 days. Overall, we found that visible light radiation had significant effects on litter decomposition, but it did not affect the microbial activities which degrade cellulose and lignin. The decomposition rate order of the three components in P. malaianus and Ph. australis in treatments was: cellulose?>?hemicellulose?>?lignin. The visible light radiation mainly affected the degradation of lignin, which is the primary compound in litter susceptible to photodegradation. The exposure to visible light radiation up to 17.6?Wm^?2 stimulated the dissolved organic carbon release and reduced the molecular weight to less reactive. Meanwhile, no obvious difference in nutrient contents (TP, TN, NO₃–N, NO₂–N, and NH₃–N) was observed among different visible light intensities. The results of this study contribute to better understanding of the photochemical behaviour of macrophyte litter in shallow lakes.     

Development of a new antifouling method for a marine cooling water system

Variations in meristic characters occur within and between samples of milkfish Chanos chanos (Forsskal) collected on June 1977 from five localities in Philippine waters. The unbranched anal and ventral fin rays are the most plastic, and vertebral number is the most stable of nine meristic characters examined. The number of ventral fin rays is the only meristic feature which differed consistently enough to suggest distinct population groups: South China Sea, comprising samples from Ilocos and Panay Island; Pacific Ocean from Bicol; and Celebes Sea, from Zamboanga and Davao. A discriminant analysis which incorporated generalized distance (Mahanalobis D²) and percent overlap of a reduced set of characters indicated several morphometric subgroups of milkfish in Philippine waters, although geographic subgroups were not clearly demonstrated.SEAFDEC Contribution No. 218     

In situ thermal dynamics of shallow water corals is affected by tidal patterns and irradiance

We studied the diel variation of in situ coral temperature, irradiance and photosynthetic performance of hemispherical colonies of Porites lobata and branching colonies of Porites cylindrica during different bulk water temperature and tidal scenarios on the shallow reef flat of Heron Island, Great Barrier Reef, Australia. Our study presents in situ evidence that coral tissue surface temperatures can exceed that of the surrounding water under environmental conditions typically occurring during low tide in shallow reef or lagoon environments. Such heating may be a regular occurrence on shallow reef flats, triggered by the combined effects of high irradiance and low water flow characteristic of low Spring tides. At these times, solar heating of corals coincides with times of maximum water temperature and high irradiance, where the slow flow and consequent thick boundary layers impede heat exchange between corals and the surrounding water. Despite similar light-absorbing properties, the heating effect was more pronounced for the hemispherical P. lobata than for the branching P. cylindrica. This is consistent with previous laboratory experiments showing the evidence of interspecific variation in coral thermal environment and may result from morphologically influenced variation in convective heat transfer and/or thermal properties of the skeleton. Maximum coral surface warming did not coincide with maximum irradiance, but with maximum water temperature, well into the low-tide period with extremely low water flow in the partially drained reef flat, just prior to flushing by the rising tide. The timing of low tide thus influences the thermal exposure and photophysiological performance of corals, and the timing of tidally driven coral surface warming could potentially have different physiological impacts in the morning or in the afternoon.     

Microphytobenthos of the Dogger Bank: a comparison between shallow and deep areas using phytopigment composition of the sediment

The surface sediment characteristics related to benthic microalgae primary production were studied at the Dogger Bank, North Sea, in order to evaluate the potential role of microphytobenthos as a food source for the macrobenthic fauna. Twenty-one stations were sampled in July 2001 and May 2002, with water depth ranging from 16.3 to 68.5 m. High-performance liquid chromatography pigment analyses revealed that concentrations of chlorophyll a, chlorophyll c and fucoxanthin are mainly associated with benthic diatom flora at most parts of the Dogger Bank. High percentage of phytopigments (>50%) was firmly attached to sand grains at the stations shallower than 40 m water depth. The deeper stations were characterized by a phytopigment composition originating from pelagic phytoplankton settled on the sea floor. Qualitative microscopy showed that the benthic microflora on top of the Bank mainly consists of small diatoms (5–10 μm), such as e.g., Diploneis spp., living attached to the sand grains. The results are discussed concerning possible implications for ecology and biogeochemistry of the Dogger Bank area.     

A non-negative and high-resolution finite volume method for the depth-integrated solute transport equation using an unstructured triangular mesh

This paper proposes a new high-resolution finite volume method for solving the two-dimensional (2D) solute transport equation using an unstructured mesh. A new simple r-factor algorithm is introduced into the Total Variation Diminishing flux limiter to achieve a more efficient yet accurate high-resolution scheme for solving the advection term. To avoid the physically-meaningless negative solutions resulted from using the Green–Gauss theorem, a nonlinear two-point flux approximation scheme is adopted to deal with the anisotropic diffusion term. The developed method can be readily coupled with a two-dimensional finite-volume-based flow models under unstructured triangular mesh. By integrating with the ELCIRC flow model, the proposed method was verified using three idealized benchmark cases (i.e., advection of a circle-shaped solute field, advection in a cyclogenesis flow field and transport of a initially square-shaped solute plume), and further applied to simulate the non-reactive solute transport process driven by irregular tides in the Deep Bay, eastern Pearl River Estuary of China. These cases are also simulated by models using other existing methods, including different r-factor for advection term and the Green–Gauss theorem for diffusion term. The comparison between the results from the new method and those from other existing methods demonstrated the new method could describe advection induced concentration shock and discontinuities, and anisotropic diffusion at high resolution without providing spurious oscillations and negative values.     

Relationship between bottom characteristics and benthic organisms in the shallow water of Oppa Bay,Miyagi

An investigation was conducted to examine the species composition, abundance and biomass of benthic macrofaunal invertebrates in Oppa Bay, Miyagi Prefecture, Japan, in August 1984. Among 212 species identified, nearly half (105) were Polychaetes. Usually five species, Ampharete sp. 1, Neosabellides sp. 1, Nephtys polybranchia, Chaetozone sp. 1, and Lumbrineris longifolia were numerically dominant. The faunal features of dominant species were clearly divided into two areas using two indicator species, Amphalete sp. 1 and Neosabellides sp. 1. The former species decreased in numbers in the area from the river to the bay mouth, while the latter increased. Sediments consisted of sand at the river mouth and in the northern bay; and of silt-clay in the central bay, bay mouth and southern part of the bay. Gradients of species diversity (H) were expressed as a function of distance by linear regression. The relationship was positive (r=0.812) from the river to the bay mouth accompanied by increasing depth; and negative (r=-0.906) from northern to southern parts of the bay in proportion to the increase of silt-clay in sediments.