A finite element method to solve a population dynamics stage-structured model of intertidal barnacles

Many marine organisms are fixed or highly sedentary as adults but the adult population may be strongly dependent on the oceanic transport of planktonic larvae. In order to assess interactions between oceanographic and biological processes that determine the population dynamics of marine organisms with a sessile adult phase restricted to the coastline and a planktonic larval phase, we present a stage-structured finite element model for the barnacle Balanus glandula that inhabits the rocky intertidal zone of central California, USA.     

Simulation of cumulative effects of nearshore restoration projects on estuarine hydrodynamics

Many nearshore restoration projects are currently underway at coastal locations where human influence and development have disrupted natural habitat and coastal ecological systems. The objectives of these projects in general are to restore the lost estuarine functions to the tidal marshland. Often these projects are conducted with little understanding of the potential effects of other nearby projects within the ecosystem, and similarly, it is easy to neglect the effect of the local project on the larger estuarine scale. In this paper, a modeling study is presented to evaluate the hydrodynamic responses of multiple restoration projects and their cumulative effect in the Snohomish River estuary in Washington, USA. The concept of absolute mean tidal transport is introduced and used to measure the cumulative effect of the proposed restoration projects on the estuarine hydrodynamics. The results show that the hydrodynamic responses due to multiple restoration projects are additive in the estuary, and the effect is nonlinear. The hydrodynamic response under restoration conditions depends on the size of the restoration area and the geometric configuration of the existing river channels. Within a complex braided estuary such as the Snohomish, the influence of a specific restoration project is not only experienced locally, but also found to significantly affect tidal transport in all distributary branches within the system.     

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.     

Application of a three-dimensional eutrophication model for the Beijing Guanting Reservoir, China

The Beijing Guanting Reservoir (BGR) is located northwest of Beijing and has been an important water supply reservoir ever since the construction of a dam near the town of Guanting in 1954. As a result of excessive nutrients and organic carbon loadings from the drainage basin over the last several decades, the BGR suffers from eutrophication as well as other contamination problems and has not been used as a drinking water supply reservoir since 1997. As a management step to restore the reservoir's water quality, a numerical model was developed based on the environmental fluid dynamics code (EFDC) framework. The model simulated three phytoplankton species based on the observed cyanobacteria, green algae, and diatom concentrations in 2004 for the Yongding arm of the reservoir, which is separated from the rest of the reservoir by a sand bar. The model was calibrated with vertical temperature profiles as well as the observed chlorophyll a and nutrients concentrations in the water column. The calibrated model was further applied to investigate management scenarios, which include reduction in external loadings of nutrients with constructed wetlands, biomanipulation, and transferring water from CeTian Reservoir. All three scenarios can reduce the peak chlorophyll a levels in the reservoir. The background nutrients were high, and reducing the external nutrients was effective only after a reduction in background nutrients after phytoplankton growth. The biomanipulation and water transfer scenarios could also delay the occurrence of the peak chlorophyll a. Because the model was developed based on one year of data, the model can only reveal the short-term effects of applying the management scenarios. Future studies will consider the long-term processes, such as diagenesis, when data are available to predict the long-term effects of the scenarios.     

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.     

Application of a three-dimensional model for assessing effects of small clear-cuttings on radiation and soil temperature

A three-dimensional model Mixfor-3D of soil–vegetation–atmosphere transfer (SVAT) was developed and applied to estimate possible effects of tree clear-cutting on radiation and soil temperature regimes of a forest ecosystem. The Mixfor-3D model consists of several closely coupled 3D sub-models describing: forest stand structure; radiative transfer in a forest canopy; turbulent transfer of sensible heat, H₂O and CO₂ between ground surface and the atmospheric surface layer; evapotranspiration of ground surface vegetation and soil; heat and moisture transfer in soil. The model operates with the horizontal grid resolution, 2 m × 2 m; vertical resolution, 1 m and primary time step, 1 h.     

Integrated modeling of flood flows and tidal hydrodynamics over a coastal floodplain

The interactions of physical processes between estuaries and upstream river floodplains are of great importance to the fish habitats and ecosystems in coastal regions. Traditionally, a hydraulic analysis of floodplains has used one- or two-dimensional models. While this approach may be sufficient for planning the engineering design for flood protection, it is inadequate when floodwaters inundate the floodplain in a complex manner. Similarly, typical estuarine and coastal modeling studies do not consider the effect of upstream river floodplains because of the technical challenge of modeling wetting and drying processes in floodplains and higher bottom elevations in the upstream river domain. While various multi-scale model frameworks have been proposed for modeling the coastal oceans, estuaries, and rivers with a combination of different models, this paper presents a modeling approach for simulating the hydrodynamics in the estuary and river floodplains, which provides a smooth transition between the two regimes using an unstructured-grid, coastal ocean model. This approach was applied to the Skagit River estuary and its upstream river floodplain of Puget Sound along the northwest coast of North America. The model was calibrated with observed data for water levels and velocities under low-flow and high-flood conditions. This study successfully demonstrated that a three-dimensional estuarine and coastal ocean model with an unstructured-grid framework and wetting-drying capability can be extended much further upstream to simulate the inundation processes and the dynamic interactions between the estuarine and river floodplain regimes.     

Simulation of small bird populations. I. Development of a stochastic model

A computer model was developed to simulate the fate of small populations of birds. It uses general and easily available data as input. Monte-Carlo techniques are used and a survival probability is calculated for every population member four times per simulated year. The model allows for density-dependence in winter survival and also in fecundity.Simulation results are used to compile standard age-specific life-tables for all complete cohorts generated. A mean life-table is also made. The survivor functions, both accumulated and mean, are contrasted with control functions and tested for significance.The model has been applied to classical population data in ornithology, namely those for the great tit and the tawny owl in Wytham Woods (Oxford, UK). There was a fair agreement between simulation results and field data.     

Evaluating the hydrodynamics of a round jet in a vegetated crossflow through large eddy simulation

Environmental Fluid Mechanics - Vegetation plays an important role on the turbulence structures of the effluent spreading in an open channel, which are insufficiently studied. This paper employs a...     

Simulation of NO and N2O emissions from a spruce forest during a freeze/thaw event using an N-flux submodel from the PnET-N-DNDC model integrated to CoupModel

The amount of nitrogen gases (N₂O, NO and N₂) emitted from forest soils depends on interactions between soil properties, climatic factors and soil management. To increase the understanding of nitrogen processes in soil ecosystems, two dynamic models, CoupModel (coupled heat and mass transfer model for soil–plant–atmosphere systems) and the denitrification–decomposition (DNDC) model were selected. Both are dynamic models with different submodels for soil, vegetation, hydrology and climate system. CoupModel has a higher degree of detail on soil physical and abiotic components, whereas the DNDC model contains details of microbiological processes involved in production of nitrogen gases. To improve the previous simple submodel of nitrogen emission in CoupModel, we included a submodel corresponding to the forest version of DNDC containing photosynthesis/evapotranspiration-nitrogen (PnET-N-DNDC model).     

Simulation of herbicide impacts on a plant community: comparing model predictions of the plant community model IBC-grass to empirical data

Background

Semi-natural plant communities such as field boundaries play an important ecological role in agricultural landscapes, e.g., provision of refuge for plant and other species, food web support or habitat connectivity. To prevent undesired effects of herbicide applications on these communities and their structure, the registration and application are regulated by risk assessment schemes in many industrialized countries. Standardized individual-level greenhouse experiments are conducted on a selection of crop and wild plant species to characterize the effects of herbicide loads potentially reaching off-field areas on non-target plants. Uncertainties regarding the protectiveness of such approaches to risk assessment might be addressed by assessment factors that are often under discussion. As an alternative approach, plant community models can be used to predict potential effects on plant communities of interest based on extrapolation of the individual-level effects measured in the standardized greenhouse experiments. In this study, we analyzed the reliability and adequacy of the plant community model IBC-grass (individual-based plant community model for grasslands) by comparing model predictions with empirically measured effects at the plant community level.

Results

We showed that the effects predicted by the model IBC-grass were in accordance with the empirical data. Based on the species-specific dose responses (calculated from empirical effects in monocultures measured 4 weeks after application), the model was able to realistically predict short-term herbicide impacts on communities when compared to empirical data.

Conclusion

The results presented in this study demonstrate an approach how the current standard greenhouse experiments—measuring herbicide impacts on individual-level—can be coupled with the model IBC-grass to estimate effects on plant community level. In this way, it can be used as a tool in ecological risk assessment.

     

On interacting bee/mite populations: a stochastic model with analysis using cumulant truncation

Parasitism by the Varroa mite has had recent drastic impact on both managed and feral bee colonies. This paper proposes a stochastic population dynamics model for interacting African bee colony and Varroa mite populations. Cumulant truncation procedures are used to obtain approximate transient cumulant functions, unconstrained by the usual assumption of bivariate Normality, for an assumed large-scale model. The apparent size of the variance and skewness functions suggest the importance of the proposed truncation procedure which retains some higher-order cumulants, but determining the accuracy of the approximations is problematical. A smaller-scale bee/Varroa mite model is hence proposed and investigated. The accuracy for the means is exceptional, for the second-order cumulants is moderate, and for some third-order cumulants is poor. Notwithstanding the poor accuracy of a skewness approximation, the saddlepoint approximations for the marginal transient population size distributions are excellent. The cumulant truncation methodology is very general, and research is continuing in its application to this new class of host-parasite models.     

三维电极对水中染料降解脱色处理

研究了在传统二维电解槽的铁板电极之间填充锰砂并鼓气搅拌，得到三相三维电极流化床反应器，对比两种反应器对酸性大红3R染色模拟废水降解脱色作用，考察了槽电压、支持电解质质量浓度、反应时间等因素对两种反应器处理染料脱色率的影响。实验表明，这些因素对酸性大红3R的降解脱色均有不同程度的影响，在相同条件下，三相三维电极流化床反应器比二维电极电解槽的处理脱色速度快和处理效率高，在不同处理时间内，脱色率可提高30％～50％。紫外-可见光吸收光谱分析表明，该方法不仅能对酸性大红3R的生色基团进行降解脱色，且对萘环不饱和共轭体系也具有破坏降解作用。     

The clearance rate of microzooplankton as the key element for describing estimated non-linear dilution plots demonstrated by a model

The objective of this study was to determine whether the clearance rate of grazers (as an individual response) was sensitive enough to describe non-linear plots estimated by dilution experiments for measuring the instant grazing rate of microzooplankton. The study was based on an initial analysis of a non-linear feeding pattern based on the food concentration dependence of clearance rate of microzooplankton. In contrast to the traditional assumption of a linear functional response, I assumed that the microzooplankton functional response was non-linear and that the dependence of the clearance rate can be sub-divided into four intervals of food concentration (Sections I–IV) as follows: in Section I clearance rate is zero; Section II is a transitional interval in which the clearance rate increases from zero to a maximum value; in Section III, the clearance rate is maximal and constant, and in Section IV, the clearance rate decreases from its maximum value due to saturated ingestion rate. A set of derived differential equations describes the phytoplankton growth rate in each section, leading to the possibility of comparing predicted non-linear dilution plots with observed non-linear dilution data, using only the specific solutions for Sections III and IV. One should evaluate the quality of fit provided by the non-linear and linear models, rather than uncritically accepting only the linear model for observed non-linear dilution data, using calculated expected non-linear and linear dilution plots as alternative hypotheses. It can be demonstrated that the non-linear model provided a better fit to estimated non-linear dilution data from the Red Sea, Rhode River Estuary (USA) and Kiel Fjord (Germany) than the standard linear model. Published dilution experiments which had a non-linear shape were also selected as illustrative examples to demonstrate the superior fit of the non-linear model.     

Sulphur isotope mass balance of dissolved sulphate ion in a freshwater dam reservoir

We show that sulphur isotopic composition can be a useful tool to discriminate between various sources of sulphate and a tool for better understanding of the sulphur cycling and mass balance. Our investigations, carried out in a dam reservoir, demonstrate differences in sulphur biogeochemistry between different seasons, caused by recharge water supply in spring and intensive sulphate reduction in summer. In the riverine-affected part of the reservoir δ³⁴S(SO₄ ²⁻) varied from 4.7 to 5.9‰ in spring, and from 4.1 to 4.6‰ in summer. In the lacustrine-affected part δ³⁴S(SO₄²⁻) varied from 4.0 to 5.0‰ in spring, and from 4.5 to 5.4‰ in summer. Diurnal variations of δ³⁴S(SO₄ ²⁻) were negligible as compared to seasonal variations.     

南亚热带两座不同水文动态的水库浮游植物的功能类群演替比较

南屏、竹仙洞水库是珠海市拱北水厂的水源地,也是对澳门供水的主要水库。于2010年4月-2011年3月对这两座水库逐月采样,依据Padisák等（2009）功能类群方法对水样中浮游植物进行分类,不同的功能类群以不同的字母或字母与数字组合来命名。并结合水库的水文、水质及浮游植物生境特征,分析优势功能类群的演替动态及其主要环境影响因子。结果表明：南屏水库浮游植物功能类群演替具有明显的时间异质性。泽丝藻（Limnothrix sp.）、假鱼腥藻（Pseudanabaena sp.）等丝状蓝藻代表的S1功能类群与薄甲藻（Glenodinium sp.）代表的Y功能类群在6、7月份相对稳定水体中共同占优势,是南屏水库丰水期浮游植物演替的一个重要特征;而枯水期则主要以小环藻（Cyclotella sp.）、针杆藻（Synedra sp.）、颗粒直链藻（Aulacoseira granulata）等适应混合水体的C＋D＋P功能类群为优势群落。竹仙洞水库中几乎全年以C＋D＋P功能类群占优势,推测是因为竹仙洞水库水力滞留时间较短,利于耐冲刷的功能类群的生长。通过PCA（主成分分析）和RDA（冗余分析）探讨浮游植物功能类群演替与环境因子之间的关系,结果显示水力滞留时间、降雨量和正磷是影响南屏水库浮游植物功能类群演替的重要因子,而竹仙洞水库则是水力滞留时间和降雨量。两座水库的水力滞留时间差异明显,从而造成两座水库浮游植物功能类群组成及演替趋势的不同。     

Experimental study on the discharge characteristics of viscous debris flow with grid-type dam

Environmental Fluid Mechanics - Experimental tests were conducted on a rectangular flume with different grid-type dam grid sizes, channel slopes and debris flow bulk density. We use the Bernoulli...     

应用HYDRUS-1D模型模拟农田土壤水渗漏及硝态氮淋失特征

在定位试验基础上,应用HYDRUS-1D模型对黄淮海平原典型土壤(黄潮土)中土壤水渗漏及硝态氮淋失动态进行了模拟分析。结果表明:在传统水氮管理模式下,黄潮土2m土体深处的土壤水渗漏和硝态氮淋失非常严重,2个轮作期内,土壤水渗漏总量占地表总入水量的23.7%,硝态氮淋失总量占总输入N量的15.9%,冬小麦生长季的硝态氮淋失量大于夏玉米生长季;改良灌溉和改良施肥模式下产生的硝态氮淋失量比传统灌溉和传统施肥模式减少74.7%,节约灌溉水211.5mm、节省施N423.5kg·hm-2。     

Laboratory study investigating the regeneration potential of iron particles by and the hydrodynamics of a dam-break generated flow from an infinite reservoir into a channel with an adverse slope

To determine the feasibility of using a dam-break generated flow from the sea into a storm-drain to aid in the regeneration of iron particles that control the production of H₂S in the storm-drain, a laboratory experimental investigation is carried out to measure the regeneration potential and the detailed hydrodynamics of the dam-break generated flow that causes the regeneration. The experiments are carried out using a reservoir of essentially infinite size, the sea, and a channel of limited width and adverse slope 1:20, the storm-drain. The regeneration experiments confirmed the ability of the dam-break generated flow to aid in the regeneration of the iron particles, however the regeneration potential varies from good to poor with distance away from the gate into the channel. The detailed measurements of the hydrodynamics highlighted that the dam-break generated flow from an infinite reservoir diverges little during the first uprush, has much smaller velocities during the first backwash and includes significant free surface waves. An initially wet channel bed reduces the flux into the channel. Close to the gate the flow depth increases more quickly but the velocity, and therefore the regeneration potential, is smaller.