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.     

Spatio-temporal modeling of striped-bass egg, larval movement, and fate in the San Francisco Bay-Delta

Most models developed for the movement and fate of eggs and larvae of aquatic species are based on a particle tracking approach. Although this method has many advantages due to its high flexibility, particle tracking may become computationally intensive for complex geometries and when large numbers of particles are needed to simulate the population properly. In continuous models based on advection and dispersion mechanisms, the computational burden is independent of the size of the population. We developed a continuous fate and transport model for striped bass eggs and larvae in the San Francisco Bay-Delta. The model predicts the concentration of eggs and larvae at any location over time. The method of moments was used to account for the effect of temperature and age on the transition of eggs to larvae and larvae to juveniles. Egg and larval mortality were represented as functions of temperature, and eggs also experienced settling mortality. The fate and transport model used the same one-dimensional spatial grid as the existing Delta Simulation Model II (DSM2) hydrodynamics model. DSM2 output of flow rates, water depths, and cross-sectional areas were inputted into the fate and transport model to determine transport. The model was applied to striped bass eggs and larvae data collected during years 1990-1994; agreement between the modeled and the measured data was acceptable in most cases. Exploratory simulations were performed to demonstrate how the model could be used to evaluate the effects on egg and larval survival and total juvenile production of water diversions for supply and agricultural use and changes in the long-term mean water temperature. The model can be further used to examine the impact of various operation strategies in the San Francisco Bay-Delta, where diversion losses of early life stages of fishes remain a major management issue.     

An individual-based stochastic hazard model of eastern king prawn (Melicertus plebejus) migration with spatially and temporally varying fishing effort

This paper describes an individual-based stochastic model of eastern king prawn migration along the eastern Australian coast. Migration is treated as one-dimensional diffusion with drift. Capture of a prawn is seen as a failure event driven by movement through a spatially and temporally variable fishing mortality hazard. This hazard is combined with a uniform natural mortality hazard. We use a Monte Carlo method to estimate parameters by comparing expected numbers of tag-returns predicted from the model with previously published tag-release data. As the previous study used a discrete compartmental model, with compartments corresponding to zones of constant fishing effort, we used the same zones and fishing effort in our comparison. The marginal distribution of yield in each zone per single recruit is determined, providing more information compared with the deterministic approach to yield-per-recruit. Using our model we also derive the constant fishing mortality rate equivalent to a spatially variable fishing mortality rate in its impact on the proportion of prawns surviving the migration to reach spawning grounds. Determination of this proportion could contribute significantly to a sustainability assessment of the fishery. It is demonstrated using the AIC that better fits to the data of the previous study and greater parsimony are obtained using our model than were found in the deterministic compartmental analysis of that study. This improvement results from the ability of our model to account separately for average speed of movement and average dispersal rate, whereas in the previous deterministic compartmental model, movement is governed by just one parameter. Our individual-based model includes a parameter that explicitly accounts for dispersal of prawns in migration, so it can distinguish between speed effects and dispersal effects in the data. It also models both types of mortality as processes distinct from those of movement. This enables it to better separate movement and mortality effects compared to the compartmental approach, in which movement and mortality are treated as similar departure processes from a compartment. This separation reduces confounding of movement and mortality effects when parameters are estimated.     

Suspended particulate matter dynamics in a particle framework

Suspended particulate matter (SPM) dynamics in ocean models are usually treated with an advection–diffusion equation for one or more sediment size classes coupled to the hydrodynamical part of the model. Numerical solution of these additional partial differential equations unavoidably introduces numerical diffusion, i.e. in the case of sharp gradients the possible occurrence of artificial oscillations and non-positivity. A Lagrangian particle-tracking model has been developed to simulate short-term SPM dynamics. Modelling individual sediment particles allows a straightforward physical interpretation of the processes. The tracking of large numbers of individual and independent particles (up to 25 million in total in a single sediment class) can be achieved on high performance computer clusters, due to efficient parallelisation of particle tracking. The movement of the particles is described by a stochastic differential equation, which is consistent with the advection–diffusion equation. Here, the concentration profile is represented by a set of independent moving particles, which are advected according to the 3D velocity field, while the diffusive displacements of the particles are sampled from a random distribution, which is related to the eddy diffusivity field. To account for erosion a new parameterisation is proposed. Three numerical particle tracking schemes (EULER, MILSTEIN and HEUN) are presented and validated in idealised test cases. Finally, the particle tracking algorithms are applied to a realistic scenario, a severe winter storm in the East Frisian Wadden Sea (southern North Sea). The comparison with observations and an Eulerian SPM transport model seems to indicate a somewhat better fidelity of the Lagrangian approach.     

Mapping risk for nest predation on a barrier island

Barrier islands and coastal beach systems provide nesting habitat for marine and estuarine turtles. Densely settled coastal areas may subsidize nest predators. Our purpose was to inform conservation by providing a greater understanding of habitat-based risk factors for nest predation, for an estuarine turtle. We expected that habitat conditions at predated nests would differ from random locations at two spatial extents. We developed and validated an island-wide model for the distribution of predated Diamondback terrapin nests using locations of 198 predated nests collected during exhaustive searches at Fisherman Island National Wildlife Refuge, USA. We used aerial photographs to identify all areas of possible nesting habitat and searched each and surrounding environments for nests, collecting location and random-point microhabitat data. We built models for the probability of finding a predated nest using an equal number of random points and validated them with a reserve set (N?=?67). Five variables in 9 a priori models were used and the best selected model (AIC weight 0.98) reflected positive associations with sand patches near marshes and roadways. Model validation had an average capture rate of predated nests of 84.14 % (26.17–97.38 %, Q1 77.53 %, median 88.07 %, Q3 95.08 %). Microhabitat selection results suggest that nests placed at the edges of sand patches adjacent to upland shrub/forest and marsh systems are vulnerable to predation. Forests and marshes provide cover and alternative resources for predators and roadways provide access; a suggestion is to focus nest protection efforts on the edges of dunes, near dense vegetation and roads.     

Including model uncertainty in estimating variances in multiple capture studies

We present bootstrap-based methods which incorporate model uncertainty in estimating variances in multiple capture studies. Each of our three methods has a specific set of properties, and we discuss when each method should be used. Our first method can be used in any multiple capture setting, but it gives an estimate of the variance conditional on the number of observed animals. Our other two methods yield estimates of the unconditional variance; they require good estimates of part or all of the specific probability model, respectively. Smoothed estimated cell probabilities are utilized by the latter method. We contrast the three methods on a real-life data set, and then conduct simulations for a simple setting. Finally, we detail the use of our methodology for specific settings and discuss adaptations for tag-return studies.     

Use of Spatial Capture‐Recapture Modeling and DNA Data to Estimate Densities of Elusive Animals

Abstract: Assessment of abundance, survival, recruitment rates, and density (i.e., population assessment) is especially challenging for elusive species most in need of protection (e.g., rare carnivores). Individual identification methods, such as DNA sampling, provide ways of studying such species efficiently and noninvasively. Additionally, statistical methods that correct for undetected animals and account for locations where animals are captured are available to efficiently estimate density and other demographic parameters. We collected hair samples of European wildcat (Felis silvestris) from cheek‐rub lure sticks, extracted DNA from the samples, and identified each animals’ genotype. To estimate the density of wildcats, we used Bayesian inference in a spatial capture‐recapture model. We used WinBUGS to fit a model that accounted for differences in detection probability among individuals and seasons and between two lure arrays. We detected 21 individual wildcats (including possible hybrids) 47 times. Wildcat density was estimated at 0.29/km² (SE 0.06), and 95% of the activity of wildcats was estimated to occur within 1.83 km from their home‐range center. Lures located systematically were associated with a greater number of detections than lures placed in a cell on the basis of expert opinion. Detection probability of individual cats was greatest in late March. Our model is a generalized linear mixed model; hence, it can be easily extended, for instance, to incorporate trap‐ and individual‐level covariates. We believe that the combined use of noninvasive sampling techniques and spatial capture‐recapture models will improve population assessments, especially for rare and elusive animals.     

A stochastic model for the use of a country park

The subject of this theoretical study is a country park with a very delicate natural environment, located near large urban areas, as a result of which it receives a heavy inflow of visitors.The problem is that of determining the best organization of the park to achieve a distribution of visitors which is compatible with the protection of the natural environment. Therefore a mathematical model is sought which describes the distribution of visitors in relation to the various zones within the park.In this paper the mathematical model and its subsequent calibration are described.     

Numerical modelling of horizontal sediment-laden jets

Sediment-laden turbulent flows are commonly encountered in natural and engineered environments. It is well known that turbulence generates fluctuations to the particle motion, resulting in modulation of the particle settling velocity. A novel stochastic particle tracking model is developed to predict the particle settling out and deposition from a sediment-laden jet. Particle velocity fluctuations in the jet flow are modelled from a Lagrangian velocity autocorrelation function that incorporates the physical mechanism leading to a reduction of settling velocity. The model is first applied to study the settling velocity modulation in a homogeneous turbulence field. Consistent with basic experiments using grid-generated turbulence and computational fluid dynamics (CFD) calculations, the model predicts that the apparent settling velocity can be reduced by as much as 30 % of the stillwater settling velocity. Using analytical solution for the jet mean flow and semi-empirical RMS turbulent velocity fluctuation and dissipation rate profiles derived from CFD predictions, model predictions of the sediment deposition and cross-sectional concentration profiles of horizontal sediment-laden jets are in excellent agreement with data. Unlike CFD calculations of sediment fall out and deposition from a jet flow, the present method does not require any a priori adjustment of particle settling velocity.     

Modeling and experiments of polydisperse particle clouds

A model for polydisperse particle clouds has been developed in this study. We extended the monodisperse particle cloud model of Lai et al. (Environ Fluid Mech 13(5):435–463, 2013) to the case of polydisperse particles. The particle cloud is first considered to be a thermal or buoyant vortex ring, with the thermal induced velocity field modeled by an expanding spherical Hill’s vortex. The buoyancy of the composite thermal is assumed to be the sum of buoyancy contributed by the all particles inside the thermal. Individual particles (of different particle properties) in the cloud are then tracked by the particle tracking equation using the computed induced velocity field. The turbulent dispersion effect is also accounted for by using a random walk model. Experiments of polydisperse particle clouds were carried out to validate the model. The agreement between model predictions and experiments was reasonable. We further validate our model by comparing it with the LES study of Wang et al. (J Hydraul Eng ASCE 141(7):06015006, 2014). The limitations of our model are then discussed with reference to the comparison. Overall, although some flow details are not captured by our model, the simplicity and generality of the model makes it useful in engineering applications.     

A Conservation Gap Analysis of Brazil''s Amazonian Vegetation

Vegetation types lacking protection in the existing conservation units of the nine states in the Brazilian Legal Amazon were identified, and locations were noted where these vegetation types could be protected. Maps of vegetation, protected areas, and semi-protected areas, such as Amerindian and forestry reserves, were digitized and overlaid using a geographic information system. There are 28 natural vegetation types in the Brazilian Legal Amazon. Locations of new areas for protection were selected using a minimum criterion of protecting at least one example of each vegetation type in each state (here called "vegetation zones"). There are 111 vegetation zones in the Legal Amazon, of which only 37 (33%) have some portion of their area protected. There are few protected areas in the most heavily deforested states along the southeastern fringe of the forest. In Maranhão, where 60% of the original forest had been lost by 1990, only one of 10 vegetation types is protected. Negotiating agreements with indigenous tribes, and to a lesser extent with extractivists who harvest nontimber products from the forest, represents a major opportunity to increase significantly the area and representativeness of the conservation units. Additional conservation units need to be established quickly before rapidly increasing deforestation and land prices preclude this opportunity; otherwise, some vegetation types may virtually disappear.     

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.     

Identification of distinct movement patterns in Pacific leatherback turtle populations influenced by ocean conditions

Interactions with fisheries are believed to be a major cause of mortality for adult leatherback turtles (Dermochelys coriacea), which is of particular concern in the Pacific Ocean, where they have been rapidly declining. In order to identify where these interactions are occurring and how they may be reduced, it is essential first to understand the movements and behavior of leatherback turtles. There are two regional nesting populations in the East Pacific (EP) and West Pacific (WP), comprising multiple nesting sites. We synthesized tracking data from the two populations and compared their movement patterns. A switching state-space model was applied to 135 Argos satellite tracks to account for observation error, and to distinguish between migratory and area-restricted search behaviors. The tracking data, from the largest leatherback data set ever assembled, indicated that there was a high degree of spatial segregation between EP and WP leatherbacks. Area-restricted search behavior mainly occurred in the southeast Pacific for the EP leatherbacks, whereas the WP leatherbacks had several different search areas in the California Current, central North Pacific, South China Sea, off eastern Indonesia, and off southeastern Australia. We also extracted remotely sensed oceanographic data and applied a generalized linear mixed model to determine if leatherbacks exhibited different behavior in relation to environmental variables. For the WP population, the probability of area-restricted search behavior was positively correlated with chlorophyll-a concentration. This response was less strong in the EP population, but these turtles had a higher probability of search behavior where there was greater Ekman upwelling, which may increase the transport of nutrients and consequently prey availability. These divergent responses to oceanographic conditions have implications for leatherback vulnerability to fisheries interactions and to the effects of climate change. The occurrence of leatherback turtles within both coastal and pelagic areas means they have a high risk of exposure to many different fisheries, which may be very distant from their nesting sites. The EP leatherbacks have more limited foraging grounds than the WP leatherbacks, which could make them more susceptible to any temperature or prey changes that occur in response to climate change.     

Analysis of capture efficiency in suspension feeding: Application of nonparametric binary regression

Suspension feeding is an important mechanism by which many marine organisms obtain food. A nonparametric method for analyzing experimental results on capture efficiency in suspension feeding is described. This approach can be used to estimate capture efficiency along the length of a cilium and to compare the capture efficiencies of two different cilia. The method is applied to experimental data on feeding by larvae of the clamMerenaria merenaria (Linné), to examine changes in capture efficiency through time, and to assess the effect of particle electrostatic charge on capture efficiency.     

Gap Analysis of Conserved Genetic Resources for Forest Trees

Abstract:  We developed a gap analysis approach to evaluate whether the genetic resources conserved in situ in protected areas are adequate for conifers in western Oregon and Washington (U.S.A.). We developed geographic information system layers that detail the location of protected areas and the distribution and abundance of each tree species (noble fir [ Abies procera Rehd.] and Douglas-fir [ Pseudotsuga menzeisii Mirb.]). Distribution and abundance were inferred from available spatial data showing modeled potential and actual vegetation. We stratified the distribution of each species into units for genetic analysis using seed and breeding zones and ecoregions. Most strata contained at least 5000 reproductive-age individuals in protected areas, indicating that genetic resources were well protected in situ throughout most of the study region. Strict in situ protection was limited, however, for noble fir in the Willapa Hills of southwestern Washington. An in situ genetic resource gap arguably occurred for Douglas-fir in the southern Puget lowlands, but this gap was filled by extensive ex situ genetic resources from the same region. The gap analysis method was an effective tool for evaluating the genetic resources of forest trees across a large region.     

Use of demand for and spatial flow of ecosystem services to identify priority areas

Policies and research increasingly focus on the protection of ecosystem services (ESs) through priority‐area conservation. Priority areas for ESs should be identified based on ES capacity and ES demand and account for the connections between areas of ES capacity and demand (flow) resulting in areas of unique demand–supply connections (flow zones). We tested ways to account for ES demand and flow zones to identify priority areas in the European Union. We mapped the capacity and demand of a global (carbon sequestration), a regional (flood regulation), and 3 local ESs (air quality, pollination, and urban leisure). We used Zonation software to identify priority areas for ESs based on 6 tests: with and without accounting for ES demand and 4 tests that accounted for the effect of ES flow zone. There was only 37.1% overlap between the 25% of priority areas that encompassed the most ESs with and without accounting for ES demand. The level of ESs maintained in the priority areas increased from 23.2% to 57.9% after accounting for ES demand, especially for ESs with a small flow zone. Accounting for flow zone had a small effect on the location of priority areas and level of ESs maintained but resulted in fewer flow zones without ES maintained relative to ignoring flow zones. Accounting for demand and flow zones enhanced representation and distribution of ESs with local to regional flow zones without large trade‐offs relative to the global ES. We found that ignoring ES demand led to the identification of priority areas in remote regions where benefits from ES capacity to society were small. Incorporating ESs in conservation planning should therefore always account for ES demand to identify an effective priority network for ESs.     

Predicting functional response and size selectivity of juvenile Notonecta maculata foraging on Daphnia magna

A mechanistic model was developed to assess the impact of predation of juvenile Notonecta maculata on size structured Daphnia magna populations and to provide a framework for quantifying the backswimmers uptake of food. Results of experiments and model predictions clearly demonstrate selective predation of backswimmers when fed with a choice of daphnid size classes, with patterns of selectivity differing across N. maculata instars. The model describes the foraging process empirically on the base of a general predation cycle including four conditional events instead of using classic functional response curves. For model parameterisation components of predation, namely probability of encounter, attack and success as well as time spent on handling prey was directly observed by means of video tracking experiments. Since attack rate, capture success and handling time appeared to be a function of prey size differing between Notonecta instars, the model takes into account ontogenic changes in both predator and prey characteristics. Independent data of functional response and size selectivity experiments were used for model validation and proved the model outcome to be consistent with observations.     

The nitrate time bomb: a numerical way to investigate nitrate storage and lag time in the unsaturated zone

Nitrate pollution in groundwater, which is mainly from agricultural activities, remains an international problem. It threatens the environment, economics and human health. There is a rising trend in nitrate concentrations in many UK groundwater bodies. Research has shown it can take decades for leached nitrate from the soil to discharge into groundwater and surface water due to the ‘store’ of nitrate and its potentially long travel time in the unsaturated and saturated zones. However, this time lag is rarely considered in current water nitrate management and policy development. The aim of this study was to develop a catchment-scale integrated numerical method to investigate the nitrate lag time in the groundwater system, and the Eden Valley, UK, was selected as a case study area. The method involves three models, namely the nitrate time bomb—a process-based model to simulate the nitrate transport in the unsaturated zone (USZ), GISGroundwater—a GISGroundwater flow model, and N-FM—a model to simulate the nitrate transport in the saturated zone. This study answers the scientific questions of when the nitrate currently in the groundwater was loaded into the unsaturated zones and eventually reached the water table; is the rising groundwater nitrate concentration in the study area caused by historic nitrate load; what caused the uneven distribution of groundwater nitrate concentration in the study area; and whether the historic peak nitrate loading has reached the water table in the area. The groundwater nitrate in the area was mainly from the 1980s to 2000s, whilst the groundwater nitrate in most of the source protection zones leached into the system during 1940s–1970s; the large and spatially variable thickness of the USZ is one of the major reasons for unevenly distributed groundwater nitrate concentrations in the study area; the peak nitrate loading around 1983 has affected most of the study area. For areas around the Bowscar, Beacon Edge, Low Plains, Nord Vue, Dale Springs, Gamblesby, Bankwood Springs, and Cliburn, the peak nitrate loading will arrive at the water table in the next 34 years; statistical analysis shows that 8.7 % of the Penrith Sandstone and 7.3 % of the St Bees Sandstone have not been affected by peak nitrate. This research can improve the scientific understanding of nitrate processes in the groundwater system and support the effective management of groundwater nitrate pollution for the study area. With a limited number of parameters, the method and models developed in this study are readily transferable to other areas.     

Predicting aquaculture-derived benthic organic enrichment: Model validation

A sediment trap validation study was conducted near the commercial sea bass and sea bream fish farm in order to assess the predictive capability of a particle tracking deposition model. The validation procedure consisted of two distinct phases. First, the deposition of particulate waste (i.e. fecal pellets and excess feed) was measured near a single net pen containing 19 tons of sea bass. Afterwards, the model quality was determined by statistical comparison of predicted and observed values.Goodness of fit analysis indicates that the model successfully accounts for more than 75% of variance in the observed deposition. At 5% significance level, predictions do not underestimate or overestimate observations and there is no bias. Mean absolute relative error of ±48.9% compares favorably to other published deposition models. Obtained results affirm the reliability of particle tracking techniques in modeling the aquaculture-derived benthic organic enrichment.     

Ag@AgCl催化剂的制备及可见光降解三聚氰胺

在超声波辅助作用下制备了Ag@AgCl可见光催化剂,采用紫外可见分光光度计、扫描电镜(SEM)对该催化剂进行了表征,该催化剂在可见光区有较强的吸收,粒径在微米级.以三聚氰胺为模型化合物测试其可见光催化性能.研究发现,该催化剂在可见光照下,不仅可以使三聚氰胺发生脱氨基反应,而且能使其环结构破坏,但却不能催化氰脲酸降解.通过除氧实验、空穴捕获、顺磁共振等实验测试,对其可能的催化降解机理进行了探讨.