Characterization And Modeling Of Atmospheric Flow Within And Above Plant Canopies

The turbulent flow within and above plant canopies is responsible for the exchange of momentum, heat, gases and particles between vegetation and the atmosphere. Turbulence is also responsible for the mixing of air inside the canopy, playing an important role in chemical and biophysical processes occurring in the plants environment. In the last fifty years, research has significantly advanced the un- derstanding of and ability to model the flow field within and above the canopy, but important issues remain unsolved. In this work, we focus on (i) the estimation of turbulent mixing timescales within the canopy from field data; and (ii) the development of new computationally efficient modeling approaches for the coupled canopy-atmosphere flow field.The turbulent mixing timescale represents how quickly turbulence creates a well- mixed environment within the canopy. When the mixing timescale is much smaller than the timescale of other relevant processes (e.g. chemical reactions, deposition), the system can be assumed to be well-mixed and detailed modeling of turbulence is not critical to predict the system evolution. Conversely, if the mixing timescale is comparable or larger than the other timescales, turbulence becomes a controlling factor for the concentration of the variables involved; hence, turbulence needs to be taken into account when studying and modeling such processes. In this work, we used a combination of ozone concentration and high-frequency velocity data measured within and above the canopy in the Amazon rainforest to characterize turbulent mixing. The eddy diffusivity parameter (used as a proxy for mixing efficiency) was applied in a simple theoretical model of one-dimensional diffusion, providing an estimate of turbulent mixing timescales as a function of height within the canopy and time-of-day. Results showed that, during the day, the Amazon rainforest is characterized by well-mixed conditions with mixing timescales smaller than thirty minutes in the upper-half of the canopy, and partially mixed conditions in the lower half of the canopy. During the night, most of the canopy (except for the upper 20%) is either partially or poorly mixed, resulting in mixing timescales of up to several hours. For the specific case of ozone, the mixing timescales observed during the day are much lower than the chemical and deposition timescales, whereas chemical processes and turbulence have comparable timescales during the night. In addition, the high day-to-day variability in mixing conditions and the fast increase in mixing during the morning transition period indicate that turbulence within the canopy needs to be properly investigated and modeled in many studies involving plant-atmosphere interactions.Motivated by the findings described above, this work proposes and tests a new approach for modeling canopy flows. Typically, vertical profiles of flow statistics are needed to represent canopy-atmosphere exchanges in chemical and biophysical processes happening within the canopy. Current single-column models provide only steady-state (equilibrium) profiles, and rely on closure assumptions that do not represent the dominant non-local turbulent fluxes present in canopy flows. We overcome these issues by adapting the one-dimensional turbulent (ODT) model to represent atmospheric flows from the ground up to the top of the atmospheric boundary layer (ABL). The ODT model numerically resolves the one-dimensional diffusion equation along a vertical line (representing a horizontally homogeneous ABL column), and the presence of three-dimensional turbulence is added through the effect of stochastic eddies. Simulations of ABL without canopy were performed for different atmospheric stabilities and a diurnal cycle, to test the capabilities of this modeling approach in representing unsteady flows with strong non-local transport. In addition, four different types of canopies were simulated, one of them including the transport of scalar with a point source located inside the canopy. The comparison of all simulations with theory and field data provided satisfactory results. The main advantages of using ODT compared to typical 1D canopy-flow models are the ability to represent the coupled canopy-ABL flow with one single modeling approach, the presence of non-local turbulent fluxes, the ability to simulate transient conditions, the straightforward representation of multiple scalar fields, and the presence of only one adjustable parameter (as opposed to the several adjustable constants and boundary conditions needed for other modeling approaches).The results obtained with ODT as a stand-alone model motivated its use as a surface parameterization for Large-Eddy Simulation (LES). In this two-way coupling between LES and ODT, the former is used to simulate the ABL in a case where a canopy is present but cannot be resolved by the LES (i.e., the LES first vertical grid point is above the canopy). ODT is used to represent the flow field between the ground and the first LES grid point, including the region within and just above the canopy. In this work, we tested the ODT-LES model for three different types of canopies and obtained promising results. Although more work is needed in order to improve first and second-order statistics within the canopy (i.e. in the ODT domain), the results obtained for the flow statistics in the LES domain and for the third order statistics in the ODT domain demonstrate that the ODT-LES model is capable of capturing some important features of the canopy-atmosphere interaction. This new surface superparameterization approach using ODT provides a new alternative for simulations that require complex interactions between the flow field and near-surface processes (e.g. sand and snow drift, waves over water surfaces) and can potentially be extended to other large-scale models, such as mesoscale and global circulation models.

The last 30 years has seen the development of increasingly sophisticated models that quantify canopy carbon exchange. These models are now essential parts of larger models for prediction and simulation of crop production, climate change, and regional and global carbon dynamics. There is thus an urgent need for increasing expertise in developing, use and understanding of these models. This in turn calls for an advanced, yet easily accessible textbook that summarizes the “canopy science” and introduces the present and the future scientists to the theoretical background of the current canopy models. This book presents current knowledge of functioning of plant canopies, models and strategies employed to simulate canopy function, and the significance of canopy architecture, physiology and dynamics in ecosystems, landscape and biosphere.

This report is comprised of two studies. The first study focuses on plant canopies in pinyon-juniper woodland, ponderosa pine woodland, and waste sites at Los Alamos National Laboratory which involved five basic areas of research: (1) application of hemispherical photography and other gap fraction techniques to study solar radiation regimes and canopy architecture, coupled with application of time-domain reflectometry to study soil moisture; (2) detailed characterization of canopy architecture using stand mapping and allometry; (3) development of an integrated geographical information system (GIS) database for relating canopy architecture with ecological, hydrological, and system modeling approaches; (4) development of geometric models that simulate complex sky obstruction, incoming solar radiation for complex topographic surfaces, and the coupling of incoming solar radiation with energy and water balance, with simulations of incoming solar radiation for selected native vegetation and experimental waste cover design sites; and (5) evaluation of the strengths and limitations of the various field sampling techniques. The second study describes an approach to develop software that takes advantage of new generation computers to model insolation on complex topographic surfaces. SOLARFLUX is a GIS-based (ARC/INFO, GRID) computer program that models incoming solar radiation based on surface orientation (slope and aspect), solar angle (azimuth and zenith) as it shifts over time, shadows caused by topographic features, and atmospheric conditions. This manual serves as the comprehensive guide to SOLARFLUX. Included are discussions on modelling insolation on complex surfaces, the theoretical approach, program setup and operation, and a set of applications illustrating characteristics of topographic insolation modelling.

This report is comprised of two studies. The first study focuses on plant canopies in pinyon-juniper woodland, ponderosa pine woodland, and waste sites at Los Alamos National Laboratory which involved five basic areas of research: (1) application of hemispherical photography and other gap fraction techniques to study solar radiation regimes and canopy architecture, coupled with application of time-domain reflectometry to study soil moisture; (2) detailed characterization of canopy architecture using stand mapping and allometry; (3) development of an integrated geographical information system (GIS) database for relating canopy architecture with ecological, hydrological, and system modeling approaches; (4) development of geometric models that simulate complex sky obstruction, incoming solar radiation for complex topographic surfaces, and the coupling of incoming solar radiation with energy and water balance, with simulations of incoming solar radiation for selected native vegetation and experimental waste cover design sites; and (5) evaluation of the strengths and limitations of the various field sampling techniques. The second study describes an approach to develop software that takes advantage of new generation computers to model insolation on complex topographic surfaces. SOLARFLUX is a GIS-based (ARC/INFO, GRID) computer program that models incoming solar radiation based on surface orientation (slope and aspect), solar angle (azimuth and zenith) as it shifts over time, shadows caused by topographic features, and atmospheric conditions. This manual serves as the comprehensive guide to SOLARFLUX. Included are discussions on modelling insolation on complex surfaces, the theoretical approach, program setup and operation, and a set of applications illustrating characteristics of topographic insolation modelling.

The work is dedicated to the investigation of the interaction between an Atmospheric Boundary Layer and a canopy (representing a forest cover). We have focused our attention to the complex problem of the generation and transformation of turbulent vortices over homogeneous, heterogeneous and sparse canopy. This problem has been studied using Large Eddy Simulation (LES) approach and High Performance Computing (HPC) technique.The numerical results reproduced correctly all the main characteristics of this flow, as reported in the literature: the formation of a first generation of coherent structures aligned transversally with the wind flow direction, the reorganization and the deformation of these vortex tubes into horse-shoe structures. The results obtained with the introduction of a discontinuity in the canopy (reproducing a clearing or a fuel break in a forest) are compared with the experimental data collected in a wind tunnel. In this case, the results confirmed the existence of a strong turbulence activity inside the canopy at a distance equal to 8 times the height of the canopy, referenced in the literature as the Enhance Gust Zone (EGZ) characterized by a local peak of the skewness factor. Then, the process of passive scalar transport from a forest canopy into a clear atmosphere is studied for two cases, i.e., when the concentration held by the forest canopy is either constant or variable. While this difference has little influence on the concentration patterns, results show that it has an important influence on the concentration magnitude as well as on the dynamics of the total concentration in the atmosphere.

This volume arises from an International Symposium on Flow and Transport in the Natural Environment held in Canberra, Australia, in September 1987. The meeting was hosted by the CSIRO Division of Environmental Mechanics (now the Centre for Environmental Mechanics) to mark the opening of the second stage of its headquarters, the F.C. Pye Field Environment Laboratory, twenty-one years after the opening of the first stage. Those twenty-one years have seen much progress in our understanding of the physics of the natural environment and the occasion provided an ideal opportunity to review advances in our knowledge of flow and transport phenomena, particularly with regard to flow and transport in soils, plants and the atmosphere. The contents of this volume are based very closely on the Symposium's program. Undoubtedly, our choices of topics were idiosyncratic, but we believe that those we have selected exhibit progress, innovation, and much scope for practical application. Rather than being encyclopaedic, we have sought to deal with thirteen selected topics in depth.

Starting with the description of meteorological variables in forest canopies and its parameter variations, a numerical three-dimentional model is developed. Its applicability is demonstrated, first, by wind sheltering effects of hedges and, second, by the effects of deforestation on local climate in complex terrain. Scientists in ecology, agricultural botany and meteorology, but also urban and regional lanners will profit from this study finding the most effective solution for their specific problems.

This work combines numerical, experimental, and theoretical methods to investigate the dispersion of particles inside and above plant canopies. The large-eddy simulation (LES) approach is used to reproduce turbulence statistics and three-dimensional (3-D) particle dispersion within the canopy roughness sublayer (the region of flow significantly modified by the presence of the canopy, extending from ground to about three canopy heights). The Eulerian description of conservation laws of fluid momentum and particle concentration implies that the continuous concentration field is advected by the continuous flow field. Within the canopy, modifications are required for the filtered momentum and concentration equations, because spatial filtering of flow variables and concentration field is inapplicable to a control volume consisting of both fluid and solid elements. In this work, the canopy region is viewed as a space occupied by air only. The sink of airflow momentum induced by forces acting on the surfaces of canopy elements is parameterized as a non-conservative virtual body force that dissipates the kinetic energy of the air. This virtual body force must reflect the characteristic of the surface forces exerted by canopy elements within the control volume, and is parameterized as a "drag force" following standard practice in LES studies. Specifically, the "drag force" is calculated as a product of a drag coefficient, the projected leaf area density, and the square of velocity. Using a constant drag coefficient, this model allows first-order accuracy in reproducing the vertically integrated sink of momentum within the canopy layer for airflows of high Reynolds number. The corresponding LES results of first- and second-order turbulence statistics are in good agreement with experimental data obtained in the field interior, within and just above mature maize canopies. However, the distribution of momentum sink among weak (low velocity) and strong (high velocity) events has not been well reproduced, inferred from the significant underestition of streamwise and vertical velocity skewness as well as the fractions of vertical momentum flux transported by strong events. Using a velocity-dependent drag coefficient that accounts for the effect of plant reconfiguration (bending of canopy elements due to the aerodynamic drag force), the "drag force" model leads to LES results of streamwise and vertical velocity skewness as well as the fractions of vertical momentum flux transported by strong events in better agreement with field experimental data. Specifically, modeling the impact of reconfiguration allows strong events to penetrate into deeper canopy regions, reducing the underprediction of streamwise and vertical velocity skewness as well as the vertical momentum flux transported by strong events from 60%, 60%, and 40% to 5%, 20%, and 5%, respectively. On the other hand, the vertically integrated sink of momentum within the canopy layer has been kept approximately the same, so do first- and second-order turbulence statistics.The link between plant reconfiguration and turbulence dynamics within the canopy roughness sublayer is further investigated. The "reconfiguration drag model" using velocity-dependent drag coefficient is revised to incorporate a theoretical model of the force balance on individual crosswind blades. In the LES, the dimension and degree of the reconfiguration of canopy elements affect the magnitude and position of peak streamwise velocity skewness within the canopy as well as the fractions of vertical momentum flux transported by strong events. The streamwise velocity skewness is shown to be related to the penetration of strong events into the canopy, which is associated with the passage of canopy-scale coherent eddies. With the profile of mean vertical momentum flux constrained by field experimental data, changing the model of drag coefficient induces negligible changes in the vertically integrated "drag force" within the canopy layer. Consequently, first- and second-order turbulence statistics remain approximately the same. However, enhancing the rate of decrease of drag coefficient with increasing velocity increases the streamwise and vertical velocity skewness, the fractions of vertical momentum flux transported by strong events, as well as the ratio between vertical momentum flux transported by relatively strong head-down "sweeps" and relatively weak head-up "ejections". Note that "sweeps" and "ejections" are defined based on streamwise and vertical velocity fluctuations, and are different from their classical definitions. These results confirmed the inadequacy of describing the effects of canopy-scale coherent structures using just first- and second-order turbulence statistics.The filtered concentration equation is applied to the dispersion of particles within the canopy roughness sublayer, assuming that a virtual continuous concentration field is advected by a virtual continuous velocity field. A canopy deposition model is used to model the sink of particle concentration associated with the impaction, sedimentation, retention, and re-entrainment of particles on the surfaces of canopy elements. LES results of mean particle concentration field and mean ground deposition rate were evaluated against data obtained during an artificial continuous point-source release experiment. Accounting for the effect of reconfiguration by using a velocity dependent drag coefficient leads to better agreement between LES results and field experimental data of the mean particle concentration field, suggesting the importance of reproducing the distribution of momentum sink among weak and strong events for reproducing the dispersion of particles. LES results obtained using a velocity-dependent drag coefficient are analyzed to estimate essential properties for the occurrence of plant disease epidemics, i.e., the fraction of particles that escape the canopy (escape fraction) and the growth of the particle plume in the vertical direction. The most interesting finding is that an existing analytical function can be used to model the crosswind-integrated mean concentration field above the canopy normalized by the escape fraction for particles released from the field interior.Our LES results suggest that the escape fractions of particles released close to the canopy leading edge are greater than those released in the field interior, especially for particles released in the bottom half of the canopy. Effects of the canopy leading edge on the escape fraction can be tracked to the effects on the fractions of particles removed by deposition on modeled "canopy elements" and on the ground. The rate of deposition on canopy elements can be suppressed by enhanced modeled retention and re-entrainment of particles in the region of strong mean wind, while the rate of deposition on the ground can be suppressed by non-negligible mean vertical advection with respect to vertical turbulent transport. Away from the source, the vertical growth of the plume above the canopy-leading-edge area is slower than that above the field interior, due to greater shear of mean streamwise velocity in the internal boundary layer (IBL) than that in the fully-developed canopy roughness sublayer above the canopy.Spore dispersal downwind from the source field is investigated by representing the infected field as a prescribed constant mean concentration at a reference height near the canopy top. This "source-in-the-mean" model neglects the spatial heterogeneity of infections, release rates, and escape fractions, allowing a first-order accuracy in reproducing the effective source strength of a severely infected field. For dispersion of particles emitted from finite area sources in the atmospheric boundary layer (ABL), pre-existing theoretical models proposed for neutral conditions are extended to unstable conditions. The major effects of buoyancy are accounted for by modifying the profile of vertical velocity variance and considering the ratio between friction and convection velocities. Theoretical predictions of mean concentration profile, plume height, and horizontal transport above the source as well as ground deposition rate downstream from the source are in good agreement with LES results for the plume within the atmospheric surface layer.

With major implications for applied physics, engineering, and the natural and social sciences, the rapidly growing area of environmental fluid dynamics focuses on the interactions of human activities, environment, and fluid motion. A landmark for the field, the two-volume Handbook of Environmental Fluid Dynamics presents the basic principles, fundamental flow processes, modeling techniques, and measurement methods used in the study of environmental motions. It also offers critical discussions of environmental sustainability related to engineering. The handbook features 81 chapters written by 135 renowned researchers from around the world. Covering environmental, policy, biological, and chemical aspects, it tackles important cross-disciplinary topics such as sustainability, ecology, pollution, micrometeorology, and limnology. Volume One: Overview and Fundamentals provides a comprehensive overview of the basic principles. It starts with general topics that emphasize the relevance of environmental fluid dynamics research in society, public policy, infrastructure, quality of life, security, and the law. It then discusses established and emerging focus areas. The volume also examines the sub-mesoscale flow processes and phenomena that form the building blocks of environmental motions, with emphasis on turbulent motions and their role in heat, momentum, and species transport. As communities face existential challenges posed by climate change, rapid urbanization, and scarcity of water and energy, the study of environmental fluid dynamics becomes increasingly relevant. This volume is a valuable resource for students, researchers, and policymakers working to better understand the fundamentals of environmental motions and how they affect and are influenced by anthropogenic activities. See also Handbook of Environmental Fluid Dynamics, Two-Volume Set and Volume Two: Systems, Pollution, Modeling, and Measurements.