Large eddy simulation of flow and scalar transport in a vegetated channel

Predicting flow and mass transport in vegetated regions has a broad range of applications in ecology and engineering practice. This paper presents large eddy simulation (LES) of turbulent flow and scalar transport within a fully developed open-channel with submerged vegetation. To properly represent the scalar transport, an additional diffusivity was introduced within the canopy to account for the contribution of stem wakes, which were not resolved by the LES, to turbulent diffusion. The LES produced good agreement with the velocity and concentration fields measured in a flume experiment. The simulation revealed a secondary flow distributed symmetrically about the channel centerline, which differed significantly from the circulation in a bare channel. The secondary circulation accelerated the vertical spread of the plume both within and above the canopy layer. Quadrant analysis was used to identify the form and shape of canopy-scale turbulent structures within and above the vegetation canopy. Within the canopy, sweep events contributed more to momentum transfer than ejection events, whereas the opposite occurred above the canopy. The coherent structures were similar to those observed in terrestrial canopies, but smaller in scale due to the constraint of the water surface.     

Mass exchange in a shallow channel flow with a series of groynes: LES study and comparison with laboratory and field experiments

The exchange of dissolved matter between a straight open channel and a series of shallow embayments present at one of its sides is investigated using large eddy simulation (LES). The direct link between the mechanism of mass exchange and the dynamics of coherent structures is demonstrated. It is shown that for the geometrical configuration considered in the present study, the mass exchange process is very non-uniform over the depth in the vicinity of the channel–embayment interface. Most of the contaminant is ejected from the embayments close to the free surface. The amount of contaminant re-entrained into the embayments situated downstream of the one in which contaminant was introduced is quantified. The mass exchange coefficient predicted by LES does not vary significantly with the embayment rank and is in very good agreement with the one predicted by the model proposed by Weitbrecht et al. (J Hydraul Eng 134(2):173–183, 2008) based on the value of a dimensionless morphometric groyne-field parameter. Field experiments were purposely performed in a natural stream with embayments whose length over width ratios were close to the ratio in the LES study. The concentration fields predicted by LES are compared with video-records of colored dye used to visualize the mass exchange in the field experiment. It is shown that, for both LES and the field experiment, the dominant passage frequency of the eddies inside the interfacial mixing layer is well predicted by the analytical model of Sukhodolov and Sukhodolova (in: Cowen et al (eds) Hydraulic measurements & experimental methods. Proceedings of international conference, Lake Placid, USA, pp 172–177, 2007). The model is then used to scale the time in the LES animations and field video-records showing the temporal evolution of the concentration field. The results of the comparison indicate several similarities in the mixing process, despite the differences in the bathymetry and the large difference in the Reynolds number between LES and the field experiment. This proves the usefulness of performing detailed LES and laboratory studies in well-controlled environments to understand mass-exchange processes around river groyne fields.     

Turbulent kinetic energy budgets in a model canopy: comparisons between LES and wind-tunnel experiments

A comparative study of turbulence in a wind-tunnel model canopy is performed, using Large eddy simulation (LES) and experimental data from PIV and hot-wire anemometry measurements. The model canopy is composed of thin cylindrical stalks. In the LES, these are represented using a plant-scale approach, while the scale-dependent Lagrangian dynamic model is used as subgrid-scale model. LES predictions of turbulence statistics and energy spectra are found to be in good agreement with the experimental data. Turbulent kinetic energy (TKE) budgets from the LES simulation are analyzed to provide more information absent in the measurements. Results confirm that sloshing motions at the low levels of the canopy are mainly driven by pressure fluctuations. A difference between the energy flux obtained from the energy spectrum and the SGS dissipation rate is observed, consistent with a spectral bypass mechanism in which the real spectral flux due to cascade is smaller than that implied by the energy-spectrum level, due to direct drain by the canopy.     

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).     

The spatial pattern of nitrogen cycling in the Adirondack Park, New York

Maps of canopy nitrogen obtained through analysis of high-resolution, hyperspectral, remotely sensed images now offer a powerful means to make landscape-scale to regional-scale estimates of forest N cycling and net primary production (NPP). Moreover, recent research has suggested that the spatial variability within maps of canopy N may be driven by environmental gradients in such features as historic forest disturbance, temperature, species composition, moisture, geology, and atmospheric N deposition. Using the wide variation in these six features found within the diverse forest ecosystems of the 2.5 million ha Adirondack Park, New York, USA, we examined linkages among environmental gradients and three measures of N cycling collected during the 2003 growing season: (1) field survey of canopy N, (2) field survey of soil C:N, and (3) canopy N measured through analysis of two 185 x 7.5 km Hyperion hyperspectral images. These three measures of N cycling strongly related to forest type but related poorly to all other environmental gradients. Further analysis revealed that the spatial pattern in N cycling appears to have distinct inter- and intraspecific components of variability. The interspecific component, or the proportional contribution of species functional traits to canopy biomass, explained 93% of spatial variability within the field canopy N survey and 37% of variability within the soil C:N survey. Residual analysis revealed that N deposition accounted for an additional 2% of variability in soil C:N, and N deposition and historical forest disturbance accounted for an additional 2.8% of variability in canopy N. Given our finding that 95.8% of the variability in the field canopy N survey could be attributed to variation in the physical environment, our research suggests that remotely sensed maps of canopy N may be useful not only to assess the spatial variability in N cycling and NPP, but also to unravel the relative importance of their multiple controlling factors.     

Does the canopy mixing layer model apply to highly flexible aquatic vegetation? Insights from numerical modelling

Vegetation is a characteristic feature of shallow aquatic flows such as rivers, lakes and coastal waters. Flow through and above aquatic vegetation canopies is commonly described using a canopy mixing layer analogy which provides a canonical framework for assessing key hydraulic characteristics such as velocity profiles, large-scale coherent turbulent structures and mixing and transport processes for solutes and sediments. This theory is well developed for the case of semi-rigid terrestrial vegetation and has more recently been applied to the case of aquatic vegetation. However, aquatic vegetation often displays key differences in morphology and biomechanics to terrestrial vegetation due to the different environment it inhabits. Here we investigate the effect of plant morphology and biomechanical properties on flow–vegetation interactions through the application of a coupled LES-biomechanical model. We present results from two simulations of aquatic vegetated flows: one assuming a semi-rigid canopy and the other a highly flexible canopy and provide a comparison of the associated flow regimes. Our results show that while both cases display canopy mixing layers, there are also clear differences in the shear layer characteristics and turbulent processes between the two, suggesting that the semi-rigid approximation may not provide a complete representation of flow–vegetation interactions.     

Flows through forest canopies in complex terrain

Recent progress on boundary layer flow within and above tall forest canopies in complex terrain is reviewed from the perspective of developing methods to interpret carbon dioxide fluxes from tower measurements in real terrain. Two examples of complex terrain are considered in detail: a forest edge, which exemplifies nonuniform forests, and hilly terrain, which can lead to drainage currents at night. Dynamical arguments show that, when boundary layer winds approach a forest edge, the mean wind adjusts on a length scale of approximately 3L(c), where L(c) is the canopy drag length scale, which depends inversely on the leaf area density of the forest. Over a further distance that also scales on L(c), turbulence in the flow adjusts, and the mixing and transport in the canopy approaches the homogeneous limit. Even low hills change the neutral flow within and above the forest canopy substantially. When the canopy is tall, pressure gradients drive flow up both the upwind and downwind slopes of the hill, leading to an ejection of air out of the top of the canopy just downwind of the crest. This flow at the crest can then advect scalar out of the top of the forest, leading to large variations in the flux of scalar across the hill. At night, when the air near the ground cools and becomes stably stratified, turbulence within the canopy can collapse, even when the flow above the canopy remains turbulent. This leads to a decoupling of the air motions within the canopy from those above. The air above the canopy can then continue to pass up and over the hill, as it does in the neutral case, but at the same time, air within the canopy drains down the hill slopes as drainage currents. These analyses will help us understand when flux towers are reliably measuring the net ecosystem exchange and suggest ways of correcting the flux tower data in more complex situations.     

Influence of planform geometry and momentum ratio on thermal mixing at a stream confluence with a concordant bed

The effects of planform geometry and momentum flux ratio on thermal mixing at a stream confluence with concordant bed morphology are investigated based on numerical simulations that can capture the dynamics of large-scale turbulence. In two simulations, the bathymetry and asymmetrical planform geometry are obtained from field experiments and the momentum flux ratio is set at values of one and four. These two conditions provide the basis for studying differences in thermal mixing processes at this confluence when the wake mode and the Kelvin–Helmholtz mode dominate the development of coherent structures within the mixing interface (MI). The effects of channel curvature and angle between the two incoming streams on thermal mixing processes are investigated based on simulations conducted with modified planform geometries. Two additional simulations are conducted for the case where the upstream channels are parallel but not aligned with the downstream channel and for the zero-curvature case where the upstream channels are parallel and aligned with the downstream channel. The simulations highlight the influence of large-scale coherent structures within the MI and of streamwise-oriented vortical (SOV) cells on thermal mixing processes within the confluence hydrodynamics zone. Simulation results demonstrate the critical role played by the SOV cells in promoting large-scale thermal mixing for cases when such cells form in the immediate vicinity of the MI and in modifying the shape of the thermal MI within cross sections of the downstream channel—predictions consistent with empirical measurements of thermal mixing at the confluence. The set of numerical simulations reveal that the degree of thermal mixing occurring within the confluence hydrodynamic zone varies dramatically with planform geometry and incoming flow conditions. In some cases thermal mixing at the downstream end of the confluence hydrodynamic zone is limited to the MI and its immediate vicinity, whereas in others substantial thermal mixing has occurred over most of the cross-sectional area of the flow. Overall, the simulations highlight the flow conditions and the controls of these conditions that influence mixing within the immediate vicinity of a confluence.     

The three-dimensionality of obstructed shear flows

Obstructed shear flows (i.e. those over permeable media) are common in the environment. An archetypal example, flow over a submerged vegetation canopy, is investigated here. Like any flow through complex geometry, canopy flows are characterised by strong spatial gradients. The focus of this experimental study is the three-dimensionality of aquatic canopy flow, in particular that of the coherent interfacial vortices that govern mixing into and out of the canopy. It is shown here that the vortices have a finite lateral scale that is comparable to their vertical scale; both are of the order of the drag length scale of the canopy, (C _D a)⁻¹, where a is the frontal area density and C _D is a bulk drag coefficient. The finite lateral extent of the vortices generates strong lateral hydrodynamic gradients, both instantaneously and in the long-term. The instantaneous gradients, which can contribute greatly to the dispersion of dissolved and particulate species, are far more pronounced. Finally, the potential for canopies to generate differential roughness secondary circulation is examined. In the consideration of vertical scalar transport, this circulation can be of the same order as turbulent diffusion.     

A σ-coordinate transport model coupled with rotational boussinesq-type equations

This paper describes a σ-coordinate scalar transport model coupled with a Boussinesq-type hydrodynamic model. The Boussinesq model has the ability to calculate both three-dimensional velocity distributions and the water surface motion. To capture ‘dispersion’ processes in open channel flow, horizontal vorticity effects induced by a bottom shear stress are included in the Boussinesq model. Thus, a reasonable representation of vertical flow structure can be captured in shallow and wavy flow fields. To solve the coupled Boussinesq and scalar transport system, a finite-volume method, based on a Godunov-type scheme with the HLL Riemann solver, is employed. Basic advection and advection–diffusion numerical tests in a non-rectangular domain were carried out and the computed results show good agreement with analytic solutions. With quantitative comparisons of dispersion experiments in an open channel, it is verified that the proposed coupled model is appropriate for both near and far field scalar transport predictions. From numerical simulations in the surf zone, physically reasonable results showing expected vertical variation are obtained.     

A generalized estimating equations approach for capture–recapture closed population models

The estimation of population density animal population parameters, such as capture probability, population size, or population density, is an important issue in many ecological applications. Capture–recapture data may be considered as repeated observations that are often correlated over time. If these correlations are not taken into account then parameter estimates may be biased, possibly producing misleading results. We propose a generalized estimating equations (GEE) approach to account for correlation over time instead of assuming independence as in the traditional closed population capture–recapture studies. We also account for heterogeneity among observed individuals and over-dispersion, modelling capture probabilities as a function of covariates. The GEE versions of all closed population capture–recapture models and their corresponding estimating equations are proposed. We evaluate the effect of accounting for correlation structures on capture–recapture model selection based on the quasi-likelihood information criterion (QIC). An example is used for an illustrative application and for comparison to currently used methodology. A Horvitz–Thompson-like estimator is used to obtain estimates of population size based on conditional arguments. A simulation study is conducted to evaluate the performance of the GEE approach in capture-recapture studies. The GEE approach performs well for estimating population parameters, particularly when capture probabilities are high. The simulation results also reveal that estimated population size varies on the nature of the existing correlation among capture occasions.     

Structure of turbulent plumes from a momentumless source in a smooth bed

The spatial development of a passive scalar plume is studied within the inhomogeneous turbulence of a boundary layer flow in a recirculating laboratory flume with a smooth bed. The source of the scalar is located flush with the bed, and the low-momentum source design is intended to simulate a diffusive-type scalar release. A weakly diffusive fluorescent dye is used as the scalar. Planar laser-induced fluorescence (PLIF) techniques were used to record the structure of the plume at a spatial resolution of 150 μm. The measured structure of the mean concentration field is compared to an analytical solution for shear-free, homogeneous turbulence. The laboratory plume exhibits spatial development in the mean concentration field that deviates from the self-similar behavior predicted by the analytical solution; this deviation is due to the mean shear and inhomogeneity of the turbulence. In particular, the influence of the viscous sublayer on the plume development is seen to be significant. Nonetheless, the analytical solution replicates some of the features seen in the laboratory plume, and the solution suggests methods of reducing the laboratory data even for cases where the results deviate from the analysis. We also examine the spatial development of the root-mean-square (rms) fluctuating concentration field, and use scalar probability density functions to examine the relationship between the mean and fluctuating concentrations.     

Accounting for matching uncertainty in two stage capture–recapture experiments using photographic measurements of natural marks

We propose a Bayesian hierarchical modeling approach for estimating the size of a closed population from data obtained by identifying individuals through photographs of natural markings. We assume that noisy measurements of a set of distinctive features are available for each individual present in a photographic catalogue. To estimate the population size from two catalogues obtained during two different sampling occasions, we embed the standard two-stage $M_t$ capture–recapture model for closed population into a multivariate normal data matching model that identifies the common individuals across the catalogues. In addition to estimating the population size while accounting for the matching process uncertainty, this hierarchical modelling approach allows to identify the common individuals by using the information provided by the capture–recapture model. This way, our model also represents a novel and reliable tool able to reduce the amount of effort researchers have to expend in matching individuals. We illustrate and motivate the proposed approach via a real data set of photo-identification of narwhals. Moreover, we compare our method with a set of possible alternative approaches by using both the empirical data set and a simulation study.     

A Numerical Study for Turbulent Flow and Thermal Influence over Inhomogenous Canopy of Roughness Elements

A large-eddy simulation with transitional structure function(TSF) subgrid model we previously proposed was performed to investigate the turbulent flow with thermal influence over an inhomogeneous canopy, which was represented as alternative large and small roughness elements. The aerodynamic and thermodynamic effects of the presence of a layer of large roughness elements were modelled by adding a drag term to the three-dimensional Navier–Stokes equations and a heat source/sink term to the scalar equation, respectively. The layer of small roughness elements was simply treated using the method as described in paper (Moeng 1984, J. Atmos Sci. 41, 2052–2062) for homogeneous rough surface. The horizontally averaged statistics such as mean vertical profiles of wind velocity, air temperature, et al., are in reasonable agreement with Gao et al.(1989, Boundary layer meteorol. 47, 349–377) field observation (homogeneous canopy). Not surprisingly, the calculated instantaneous velocity and temperature fields show that the roughness elements considerably changed the turbulent structure within the canopy. The adjustment of the mean vertical profiles of velocity and temperature was studied, which was found qualitatively comparable with Belcher et al. (2003, J Fluid Mech. 488, 369–398)’s theoretical results. The urban heat island(UHI) was investigated imposing heat source in the region of large roughness elements. An elevated inversion layer, a phenomenon often observed in the urban area (Sang et al., J Wind Eng. Ind. Aesodyn. 87, 243–258)’s was successfully simulated above the canopy. The cool island(CI) was also investigated imposing heat sink to simply model the evaporation of plant canopy. An inversion layer was found very stable and robust within the canopy.     

Spatial evolution of coherent motions in finite-length vegetation patch flow

A number of experimental studies on submerged canopy flows have focused on fully-developed flow and turbulent characteristics. In many natural rivers, however, aquatic vegetation occurs in patches of finite length. In such vegetated flows, the shear layer is not formed at the upstream edge of the vegetation patch and coherent motions develop downstream. Therefore, more work is neededz to reveal the development process for large-scale coherent structures within vegetation patches. For this work, we considered the effect of a limited length vegetation patch. Turbulence measurements were intensively conducted in open-channel flows with submerged vegetation using Particle Image Velocimetry (PIV). To examine the transition from boundary-layer flow upstream of the vegetation patch to a mixing-layer-type flow within the patch, velocity profiles were measured at 33 positions in a longitudinal direction. A phenomenological model for the development process in the vegetation flow was developed. The model decomposed the entire flow region into four zones. The four zones are the following: (i) the smooth bed zone, (ii) the diverging flow zone, (iii) the developing zone and (iv) the fully-developed zone. The PIV data also confirmed the efficiency of the mixing-layer analogy and provided insight into the spatial evolution of coherent motions.     

The Structure of the Shear Layer in Flows over Rigid and Flexible Canopies

Flume experiments were conducted with rigid and flexible model vegetation to study the structure of coherent vortices (a manifestation of the Kelvin–Helmholtz instability) and vertical transport in shallow vegetated shear flows. The vortex street in a vegetated shear layer creates a pronounced oscillation in the velocity profile, with the velocity near the top of a model canopy varying by a factor of three during vortex passage. In turn, this velocity oscillation drives the coherent waving of flexible canopies. Relative to flows over rigid vegetation, the oscillation in canopy geometry has the effect of decreasing the amount of turbulent vertical momentum transport in the shear layer. Using a waving plant to determine phase in the vortex cycle, each vortex is shown to consist of a strong sweep at its front (during which the canopy is most deflected), followed by a weak ejection at its rear (when the canopy height is at a maximum). Whereas in unobstructed mixing layers the vortices span the entire layer, they encompass only 70% of the flexibly obstructed shear layer studied here.     

CO2 fluxes near a forest edge: a numerical study

In contrast with recent advances on the dynamics of the flow at a forest edge, few studies have considered its role on scalar transport and, in particular, on CO2 transfer. The present study addresses the influence of the abrupt roughness change on forest atmosphere CO2 exchange and contrasts the concentration and flux fields against those of a uniform forested surface. We use an atmospheric boundary layer two-equation closure model that accounts for the flow dynamics and vertical divergence of CO2 sources/sinks within a plant canopy. This paper characterizes the spatial variation of CO2 fluxes as a function of both sources/sinks distribution and the vertical structure of the canopy. Results suggest that the ground source plays a major role in the formation of wave-like vertical CO2 flux behavior downwind of a forest edge, despite the fact that the contribution of foliage sources/sinks changes monotonously. Such a variation is caused by scalar advection in the trunk space and reveals itself as a decrease or increase in vertical fluxes over the forest relative to carbon dioxide exchange of the underlying forest. The effect was more pronounced in model forests where the leaf area is concentrated in the upper part of the canopy. These results can be useful both for interpretation of existing measurements of net ecosystem exchange of CO2 (NEE) from flux towers in limited fetch conditions and in planning future CO2 transport experiments.     

Simulation of Ekman Boundary Layers by Large Eddy Model with Dynamic Mixed Subfilter Closure

Theoretical analysis of boundary layer turbulence has suggested a feasibility of sufficiently accurate turbulence resolving simulations at relatively coarse meshes. However, large eddy simulation (LES) codes, which employ traditional eddy-viscosity turbulence closures, fail to provide adequate turbulence statistics at coarse meshes especially within a surface layer. Manual tuning of parameters in these turbulence closures may correct low order turbulence statistics but severely harms spectra of turbulence kinetic energy (TKE). For more than decade, engineering LES codes successfully employ dynamic turbulence closures. A dynamic Smagorinsky turbulence closure (DSM) has been already tried in environmental LES. The DSM is able to provide adequate turbulence statistics at coarse meshes but it is not completely consistent with the LES equations. This paper investigates applicability of an advanced dynamic mixed turbulence closure (DMM) to simulations of Ekman boundary layers of high Reynolds number flows. The DMM differs from the DSM by explicit calculation of the Leonard term in the turbulence stress tensor. The Horizontal Array Turbulence Study (HATS) field program has revealed that the Leonard term is indeed an important component of the real turbulence stress tensor. This paper presents validation of a new LES code LESNIC. The study shows that the LES code with the DMM provides rather accurate low order turbulence statistics and the TKE spectra at very coarse meshes. These coarse LES maintain more energetic small scale fluctuations of velocity especially within the surface layer. This is critically important for success of simulations. Accurate representation of higher order turbulence statistics, however, requires essentially better LES resolution. The study also shows that LES of the Ekman boundary layer cannot be directly compared with conventionally neutral atmospheric boundary layers. The depth of the boundary layer is an important scaling parameter for turbulence statistics.