A new view of dispersion in well-mixed estuaries

A two-dimensional simulation of Delaware estuary hydrodynamics has been constructed. This simulation has been achieved through a rational estimate of the character of natural turbulence. Non-homogeneous velocities, on the cross-section, are employed in two-dimensional, laterally homogeneous species mass balances. In turn, concentration profiles are interpreted in the form of classical, one-dimensional dispersion coefficients. Variation of dispersion as a function of both freshwater inflow and longitudinal distance was generated. Variation of dispersion in time within a tidal cycle was found to be insignificant while no significant variation from one tidal cycle to the next has been detected.The modeling process involves the solution of tractable equations by implicit numerical methods and is capable of being excited by a wide range of input conditions.A study of the sensitivity of dispersion due to vertical mass diffusion revealed that longitudinal mixing characteristics are inversely proportional to vertical eddy diffusivity and analysis of the numerical results showed the dispersion coefficient is essentially insensitive to variation of longitudinal mass diffusivity. This leads to the conclusion that turbulent diffusivity of mass in the longitudinal direction may be taken as constant for most purposes in the study of a two-dimensional species mass balance model.A field program was carried out near the Delaware Memorial Bridge to collect velocity profiles. Substantial portions of the scheme have been verified (i.e. one- and two-dimensional tidal dynamic models) through the use of these data.     

Large-eddy simulation of turbulent flow and dispersion over a complex urban street canyon

Turbulent flow and dispersion characteristics over a complex urban street canyon are investigated by large-eddy simulation using a modified version of the Fire Dynamics Simulator. Two kinds of subgrid scale (SGS) models, the constant coefficient Smagorinsky model and the Vreman model, are assessed. Turbulent statistics, particularly turbulent stresses and wake patterns, are compared between the two SGS models for three different wind directions. We found that while the role of the SGS model is small on average, the local or instantaneous contribution to total stress near the surface or edge of the buildings is not negligible. By yielding a smaller eddy viscosity near solid surfaces, the Vreman model appears to be more appropriate for the simulation of a flow in a complex urban street canyon. Depending on wind direction, wind fields, turbulence statistics, and dispersion patterns show very different characteristics. Particularly, tall buildings near the street canyon predominantly generate turbulence, leading to homogenization of the mean flow inside the street canyon. Furthermore, the release position of pollutants sensitively determines subsequent dispersion characteristics.     

LES validation of urban flow,part II: eddy statistics and flow structures

Time-dependent three-dimensional numerical simulations such as large-eddy simulation (LES) play an important role in fundamental research and practical applications in meteorology and wind engineering. Whether these simulations provide a sufficiently accurate picture of the time-dependent structure of the flow, however, is often not determined in enough detail. We propose an application-specific validation procedure for LES that focuses on the time dependent nature of mechanically induced shear-layer turbulence to derive information about strengths and limitations of the model. The validation procedure is tested for LES of turbulent flow in a complex city, for which reference data from wind-tunnel experiments are available. An initial comparison of mean flow statistics and frequency distributions was presented in part I. Part II focuses on comparing eddy statistics and flow structures. Analyses of integral time scales and auto-spectral energy densities show that the tested LES reproduces the temporal characteristics of energy-dominant and flux-carrying eddies accurately. Quadrant analysis of the vertical turbulent momentum flux reveals strong similarities between instantaneous ejection-sweep patterns in the LES and the laboratory flow, also showing comparable occurrence statistics of rare but strong flux events. A further comparison of wavelet-coefficient frequency distributions and associated high-order statistics reveals a strong agreement of location-dependent intermittency patterns induced by resolved eddies in the energy-production range. The validation concept enables wide-ranging conclusions to be drawn about the skill of turbulence-resolving simulations than the traditional approach of comparing only mean flow and turbulence statistics. Based on the accuracy levels determined, it can be stated that the tested LES is sufficiently accurate for its purpose of generating realistic urban wind fields that can be used to drive simpler dispersion models.     

The Modelling of Turbulence from Traffic in Urban Dispersion Models — Part II: Evaluation Against Laboratory and Full-Scale Concentration Measurements in Street Canyons

The paper addresses the problem of the parameterisation of traffic induced turbulent motion in urban dispersion models. Results from a variety of full-scale and wind-tunnel studies are analysed and interpreted within a modelling framework based on scaling considerations. The combined effects of traffic and wind induced dispersive motions are quantified for different traffic situations (variable traffic densities, vehicle velocities and vehicle types) and incorporated into the developed parameterisations. A new dispersive velocity scale is formulated and recommendations regarding its application in urban dispersion models are given. The necessity of accounting for traffic induced air motions in predictions of street-canyon pollution levels is demonstrated. Further research is needed to verify the empirical constants in the proposed parameterisations and to generalize the developed approach for a broader range of urban building configurations, meteorological conditions, and traffic situations.     

A stochastic Lagrangian micromixing model for the dispersion of reactive scalars in turbulent flows: role of concentration fluctuations and improvements to the conserved scalar theory under non-homogeneous conditions

Several reaction schemes, based on the conserved scalar theory, are implemented within a stochastic Lagrangian micromixing model to simulate the dispersion of reactive scalars in turbulent flows. In particular, the formulation of the reaction-dominated limit (RDL) reaction scheme is here extended to improve the model performance under non-homogeneous conditions (NHRDL scheme). The validation of the stochastic model is obtained by comparison with the available measurements of reactive pollutant concentrations in a grid-generated turbulent flow. This test case describes the dispersion of two atmospheric reactant species (NO and O₃) and their reaction product (NO₂) in an unbounded turbulent flow. Model inter-comparisons are also assessed, by considering the results of state-of-the-art models for pollutant dispersion. The present validation shows that RDL reaction scheme provides a systematic overestimation (relative error of ca. 85% around the centreline) in computing the local reactant consumption/production rate, whereas the NHRDL scheme drastically reduces this gap (relative error lower than 5% around the centreline). In terms of NO₂ production (or reactant consumption), neglecting concentration fluctuations determines overestimations of the product mean of around 100% and a NO₂ local production of one order of magnitude higher than the reference simulation. In terms of standard deviations, the concentration fluctuations of both the passive and reactive scalars are generally of the same order of magnitude or up to 1 or 2 orders of magnitudes higher than the corresponding ensemble mean values, except for the background reactant close to the plume edges. The study highlights the importance of modelling pollutant reactions depending on the instantaneous instead of the mean concentrations of the reactants, thus quantifying the role of the turbulent fluctuations of concentration, in terms of scalar statistics (mean, standard deviation, intensity of fluctuations, skewness and kurtosis of concentration, segregation coefficient, simulated reaction rate). This stochastic particle method represents an efficient numerical technique to solve the convection–diffusion equation for reactive scalars and involves several application fields: micro-scale air quality (urban and street-canyon scales), accidental releases, impact of odours, water quality and fluid flow industrial processes (e.g. combustion).     

Deterministic particle tracking simulation of pollutant discharges in rivers and estuaries

A two-dimensional deterministic particle tracking model, in which the anisotropic-dispersive process is described by a particle strength exchange scheme, is established for the simulation of pollutant transport in vertically well-mixed rivers and estuaries. By simulating two benchmark problems with analytic solutions, the PSE scheme is shown to be accurate even if the anisotropic ratio of dispersion coefficients is very high. Further simulations of two specific problems concerning the optimal effluent discharge location and procedure are presented. The major conclusion is that in a tidal estuary with a relatively large fresh-water flow, setting the discharge position at the mixing center and making the discharge rate proportional to flow speed may minimize the peaks of concentration.     

Lagrangian models of dispersion in marine environment

Turbulent dispersion can be studied successfully by using Lagrangian particle models. In general, the prediction of correct concentration fields is a complex issue when the turbulent field is inhomogeneous and non-stationary. Two classes of Lagrangian dispersion models have been considered in this work, which are based on the Wiener process and the so called “well-mixed” criterion. In order to test the performances of these models and shed light on the underlying physical processes and modeling assumptions, four different numerical models have been compared and tested by means of their long time behavior by considering several study cases concerning idealized marine environment. Furthermore, the coupling of the community model Princeton Ocean Model (POM) with the Lagrangian model LASEMOD (LAgrangian SEa MODel) is used to investigate the temporal and spatial evolution of a passive pollutant released in the vicinity of the coast in the Tyrrhenian Sea basin. The simulation shows with reasonable accuracy the time evolution of both the hydrodynamic and the concentration fields and provides a useful insight into the evaluation of the environmental impact of pollutant releases along the coast.     

A numerical (LES) investigation of a shallow-water, mid-latitude, tidally-driven boundary layer

We investigate turbulent mixing in a tidally driven, mid-latitude, shallow-water basin. The study is carried out numerically at a laboratory-scale, using large-eddy simulation. We compared the results of the simulation with those of a correspondent purely oscillatory flow (Stokes boundary layer). The effect of rotation on the flow dynamics is twofold. First, rotation gives rise to a mean spanwise flow that concurs to redistribute the turbulent energy among the Reynolds stresses, in particular between the horizontal directions, thus increasing the mixing across the water column and thickening the layer where developed turbulence is observable. Second, the presence of the horizontal component of the background vorticity (latitude effect) breaks the symmetry between the two semi-cycles of the oscillation, since turbulence results suppressed/enhanced during the first/second semi-cycle. These two effects significantly modify the turbulent characteristics with respect to the purely oscillating flow, although the mechanisms that generates turbulence present similar features. The qualitative agreement between our results and some measurements carried out in two sites with characteristics similar to the case analyzed suggests that the outcomes here provided may be of general use for the analysis of mid-latitude, neutrally stratified, shallow-water basins mainly driven by semi-diurnal tidal currents.     

Prediction of mass and momentum transport in turbulent plane wall jets over smooth and transitionally rough surfaces

This paper is concerned with the prediction of mass and momentum transport in turbulent wall jets developing over smooth and transitionally rough plane walls. The ability to accurately predict the resulting wall shear stresses and vertical profiles of the Reynolds stresses in these flows is prerequisite to the accurate prediction of bed scour, sediment re-suspension and transport by turbulent diffusion. The computations were performed by solving the Reynolds-averaged forms of the equations describing conservation of mass, momentum and concentration. The unknown correlations that arise from the averaging process (the Reynolds stresses in the case of the momentum equation, and the turbulent mass fluxes in the case of concentration) were obtained from the solution of modeled differential equations that describe their conservation. Since these models are somewhat more complex than those typically used in practice, their benefits are demonstrated by comparisons with results obtained from simpler, eddy-viscosity based closures. Comparisons with experimental data show that results of acceptable accuracy can be obtained only by using the appropriate combination of models for the turbulent fluxes of mass and momentum that properly account for the reduction of the Reynolds stresses due to wall damping effects, and for the modification of the mass transfer rates due to interactions with the mean rates of strain.     

Ecological metrics of biomass removed by three methods of purse-seine fishing for tunas in the eastern tropical Pacific Ocean

An ecosystem approach to fisheries management is a widely recognized goal, but describing and measuring the effects of a fishery on an ecosystem is difficult. Ecological information on the entire catch (all animals removed, whether retained or discarded) of both species targeted by the fishery and nontarget species (i.e., bycatch) is required. We used data from the well-documented purse-seine fishery for tunas (Thunnus albacares, T. obesus, and Katsuwonus pelamis) in the eastern tropical Pacific Ocean to examine the fishery's ecological effects. Purse-seine fishing in the eastern tropical Pacific is conducted in 3 ways that differ in the amount and composition of target species and bycatch. The choice of method depends on whether the tunas are swimming alone (unassociated sets), associated with dolphins (dolphin sets), or associated with floating objects (floating-object sets). Among the fishing methods, we compared catch on the basis of weight, number of individuals, trophic level, replacement time, and diversity. Floating-object sets removed 2-3 times as much biomass as the other 2 methods, depending on how removal was measured. Results of previous studies suggest the ecological effects of floating-object sets are thousands of times greater than the effects of other methods, but these results were derived from only numbers of discarded animals. Management of the fishery has been driven to a substantial extent by a focus on reducing bycatch, although discards are currently 4.8% of total catch by weight, compared with global averages of 7.5% for tuna longline fishing and 30.0% for midwater trawling. An ecosystem approach to fisheries management requires that ecological effects of fishing on all animals removed by a fishery, not just bycatch or discarded catch, be measured with a variety of metrics.     

Three-Dimensional Modelling of Concentration Fluctuations in Complicated Geometry

The strong fluctuating component in the measured concentration time series of a dispersing gaseous pollutant in the atmospheric boundary layer, and the hazard level associated to short-term concentration levels, demonstrate the necessity of calculating the magnitude of turbulent fluctuations of concentration using computational simulation models. Moreover the computation of concentration fluctuations in cases of dispersion in realistic situations, such as built-up areas or street canyons, is of special practical interest for hazard assessment purposes. In this paper, the formulation and evaluation of a model for concentration fluctuations, based on a transport equation, are presented. The model is applicable in cases of complex geometry. It is included in the framework of a computational code, developed for simulating the dispersion of buoyant pollutants over complex geometries. The experimental data used for the model evaluation concerned the dispersion of a passive gas in a street canyon between 4 identical rectangular buildings performed in a wind tunnel. The experimental concentration fluctuations data have been derived from measured high frequency concentrations. The concentration fluctuations model is evaluated by comparing the model's predictions with the observations in the form of scatter plots, quantile-quantile plots, contour plots and statistical indices as the fractional bias, the geometrical mean variance and the factor-of-two percentage. From the above comparisons it is concluded that the overall model performance in the present complex geometry case is satisfactory. The discrepancies between model predictions and observations are attributed to inaccuracies in prescribing the actual wind tunnel boundary conditions to the computational code.     

模拟酸雨及其活化Al~（3＋）构成的复合污染对中小型土壤动物的毒杀效果

酸雨可引起土壤中铝离子的活化而造成铝毒问题,因此酸雨及其活化的金属铝离子势必造成对土壤中小型动物的复合污染与影响。为此,通过室内模拟试验,研究3种优势土壤动物直接暴露在4种不同酸度的模拟酸雨和4种不同铝离子浓度梯度组合而构成的复合污染处理条件下的死亡率,以探明酸雨通过降低土壤酸度同时活化Al3＋对土壤动物的叠加影响效应。研究结果表明：弹尾目、线虫、蜱螨目等土壤动物直接暴露在酸水和铝离子的复合溶液中,其死亡率总体上均会随着酸水pH值的降低和Al3＋离子浓度的升高而增加。通过单因素和双因素方差分析还发现,不同类群的土壤动物对模拟酸雨pH和溶液中Al3＋含量的敏感性各不相同,其中酸水和铝离子复合胁迫对线虫和蜱螨目动物死亡率的影响并没有表现出明显的交互作用,但对弹尾目土壤动物死亡率存在显著的交互作用影响。     

Testing Accuracy of Finite Element and Random Walk Schemes in Prediction of Pollutant Dispersion in Coastal Waters

Distribution of pollutants in coastal waters is usually represented by depth averaged twodimensional convection-dispersion equation. Under very specific conditions this equation can be solved analytically. Although such a solution is restricted to simplified situations it provides a very useful case for testing the performance of various numerical solution techniques currently available for the simulation of convective-dispersion of pollutants in natural water systems. In this paper the analytical solution of the convective dispersion equation is used as a benchmark against which the accuracy of other techniques are assessed. These assessments are based on quantitative comparisons between the results of the solution of two-dimensional convection-dispersion equation by the deterministic finite element and stochastic random walk methods. Both Eulerian and Lagrangian frameworks are employed to obtain the finite element solution of the convection-dispersion problem. It has been shown that the Lagrange–Galerkin finite element scheme yields the most accurate results for the case under study. However, computational costs of the Lagrange–Galerkin method can be relatively high and under certain conditions it may be reasonable to use a less accurate but cost effective random walk scheme to make water quality management decisions.     

Topographic heterogeneity influences fish use of an experimentally restored tidal marsh.

Ecological theory predicts that incorporating habitat heterogeneity into restoration sites should enhance diversity and key functions, yet research is limited on how topographic heterogeneity affects higher trophic levels. Our large (8-ha) southern California restoration experiment tested effects of tidal creek networks and pools on trophic structure of salt marsh habitat and high-tide use by two regionally dominant fish species, California killifish (Fundulus parvipinnis) and longjaw mudsucker (Gillichthys mirabilis). We expected tidal creeks to function as "conduits" that would enhance connectivity between subtidal and intertidal habitat and pools to serve as microhabitat "oases" for fishes. Pools did provide abundant invertebrate prey and were a preferred microhabitat for F. parvipinnis, even when the entire marsh was inundated (catch rates were 61% higher in pools). However, G. mirabilis showed no preference for pools. At a larger scale, effects of tidal creek networks were also mixed. Areas containing creeks had 12% higher catch rates of G. mirabilis, but lower catch rates and feeding rates of F. parvipinnis. Collectively, the results indicate that restoring multiple forms of heterogeneity is required to provide opportunities for multiple target consumers.     

Fragmentation drives tropical forest fragments to early successional states: A modelling study for Brazilian Atlantic forests

Land use leads to massive habitat destruction and fragmentation in tropical forests. Despite its global dimensions the effects of fragmentation on ecosystem dynamics are not well understood due to the complexity of the problem. We present a simulation analysis performed by the individual-based model FORMIND. The model was applied to the Brazilian Atlantic Forest, one of the world's biodiversity hot spots, at the Plateau of São Paulo. This study investigates the long-term effects of fragmentation processes on structure and dynamics of different sized remnant tropical forest fragments (1-100 ha) at community and plant functional type (PFT) level. We disentangle the interplay of single effects of different key fragmentation processes (edge mortality, increased mortality of large trees, local seed loss and external seed rain) using simulation experiments in a full factorial design.Our analysis reveals that particularly small forest fragments below 25 ha suffer substantial structural changes, biomass and biodiversity loss in the long term. At community level biomass is reduced up to 60%. Two thirds of the mid- and late-successional species groups, especially shade-tolerant (late successional climax) species groups are prone of extinction in small fragments. The shade-tolerant species groups were most strongly affected; its tree number was reduced more than 60% mainly by increased edge mortality. This process proved to be the most powerful of those investigated, explaining alone more than 80% of the changes observed for this group. External seed rain was able to compensate approximately 30% of the observed fragmentation effects for shade-tolerant species.Our results suggest that tropical forest fragments will suffer strong structural changes in the long term, leading to tree species impoverishment. They may reach a new equilibrium with a substantially reduced subset of the initial species pool, and are driven towards an earlier successional state. The natural regeneration potential of a landscape scattered with forest fragments appears to be limited, as external seed rain is not able to fully compensate for the observed fragmentation-induced changes. Our findings suggest basic recommendations for the management of fragmented tropical forest landscapes.     

酸雨对外来植物入侵的影响

酸雨和外来种入侵都是全球关注的问题。结合外来入侵植物的生态适应特性以及酸雨的危害特征,系统分析了酸雨对外来植物入侵产生的影响。酸雨对外来植物入侵的影响是复杂多样的。酸雨导致群落冠层稀疏,群落透光率增加,加之氮沉降后土壤、水体氮素的增加,有利于生长力强的外来喜阳植物入侵;酸雨加速土壤酸化,促使基本离子淋失以及A1毒等危害植物的生长发育,植物的内源激素以及化感作用发生改变,适应力和耐受力强的外来植物在与本地植物竞争中处于相对优势而成为入侵种;酸雨以及外来植物入侵改变了土壤微生物群落结构,影响本地植物的生长而促使外来植物的入侵。     

Use of Fully Biodegradable Panels to Reduce Derelict Pot Threats to Marine Fauna

Fishing pots (i.e., traps) are designed to catch fish or crustaceans and are used globally. Lost pots are a concern for a variety of fisheries, and there are reports that 10 – 70% of deployed pots are lost annually. Derelict fishing pots can be a source of mortality for target and bycatch species for several years. Because continual removal of derelict gear can be impractical over large spatial extents, modifications are needed to disarm gear once it is lost. We tested a fully biodegradable panel with a cull or escape ring designed for placement on the sides of a crab pot that completely degrades into environmentally neutral constituents after approximately 1 year. This panel is relatively inexpensive, easy to install, and can be used in multiple fisheries. We used the blue crab (Callinectes sapidus) fishery as a test case because it is a large pot fishery and blue crab pots are similar to traps used in other pot fisheries. We had commercial fishers deploy pots with panels alongside standard pots in Chesapeake Bay (U.S.A.) to assess potential effects of our experimental pots on blue crab catch. We compared the number, biomass, and size of crabs captured between standard and experimental pots and evaluated differences in catch over a crabbing season (March–November) at five locations. There was no evidence that biodegradable panels adversely affected catch. In all locations and time periods, legal catches were comparable in abundance, biomass, and size between experimental and standard pots. Properly designed biodegradable panels appear to be a viable solution to mitigate adverse effects of derelict pots. Uso de Paneles Completamente Biodegradables para Reducir las Amenazas de Vasijas Abandonadas para la Fauna Marina     

Patchiness and bistability in the comprehensive cyanobacterial model (CCM)

We analyzed spatiotemporal dynamics of cyanobacteria using a four-component mathematical model with nutrients, unicellular algae, colonial algae and herbivorous zooplankton. One of the astonishing abilities of cyanobacteria is the morphological change from the unicellular type to the colonial or filamentous type in response to grazing activities of zooplankton, the phenomenon known as phenotypic plasticity. Our model, referred to as comprehensive cyanobacterial model (CCM), includes the effects of phenotypic plasticity. Depending on parameter values, CCM exhibits not only bistability but also limit cycle oscillations without showing the paradox of enrichment, which has been a controversy among mathematical ecologists. Further, CCM is modified to reaction–advection–diffusion equations, the simulation results of which indicate that the ratio of the lateral diffusivity to the turbulent velocity significantly affects the appearance of patchiness patterns.     

Spatial characteristics of turbulent organized structures within the roughness sublayer over idealized urban surface with obstacle-height variability

Environmental Fluid Mechanics - The effects of obstacle-height variability on spatial characteristics of turbulent organized structures were investigated with the use of a large-eddy simulation...