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Turbulent flow over urban-like roughness has been numerically studied for various purposes, such as the clarification of turbulent characteristics over rough walls, visualization of turbulent structures around block arrays, and evaluation of urban ventilation and pedestrian winds. In such simulations, a portion of the developing boundary layer is extracted as a numerical domain, assuming periodic boundary conditions in the horizontal direction to reproduce laterally homogeneous rough surfaces. However, the conditions required to drive the airflow by an artificial momentum source uniquely determine the turbulent statistics, which are different from those in developing boundary layers. Therefore, this study presents a new approach for driving the airflow over urban-like block arrays. The new method is based on spatially averaged Navier–Stokes equations to prove the necessity of height-dependent momentum provision. The turbulent flow over a cubical-block array is determined using large-eddy simulations driven by four different momentum sources. Regardless of the driving force, the vertical profiles of the streamwise velocity components are identical. In contrast, slight differences in the vertical Reynolds stress, variances in the velocity components, and turbulence kinetic energy are appropriately reproduced in the new approach. In addition, the budget equations of the turbulent statistics reveal that a change in the vertical Reynolds stress affects the energy production and its redistribution into variance components. The proposed method can contribute to the reproduction of a realistic turbulent flow and provide a theoretical understanding of the momentum provision.

Purpose:Somatic mutations in cancer cells can give rise to novel protein sequences that can be presented by antigen-presenting cells as neoantigens to the host immune system. Tumor neoantigens represent excellent targets for immunotherapy, due to their specific expression in cancer tissue. Despite the widespread use of immunomodulatory drugs and immunotherapies that recharge T and NK cells, there has been no direct evidence that neoantigen-specific T-cell responses are elicited in multiple myeloma.Experimental Design:Using next-generation sequencing data we describe the landscape of neo-antigens in 184 patients with multiple myeloma and successfully validate neoantigen-specific T cells in patients with multiple myeloma and support the feasibility of neoantigen-based therapeutic vaccines for use in cancers with intermediate mutational loads such as multiple myeloma.Results:In this study, we demonstrate an increase in neoantigen load in relapsed patients with multiple myeloma as compared with newly diagnosed patients with multiple myeloma. Moreover, we identify shared neoantigens across multiple patients in three multiple myeloma oncogenic driver genes (KRAS, NRAS, and IRF4). Next, we validate neoantigen T-cell response and clonal expansion in correlation with clinical response in relapsed patients with multiple myeloma. This is the first study to experimentally validate the immunogenicity of predicted neoantigens from next-generation sequencing in relapsed patients with multiple myeloma.Conclusions:Our findings demonstrate that somatic mutations in multiple myeloma can be immunogenic and induce neoantigen-specific T-cell activation that is associated with antitumor activity in vitro and clinical response in vivo. Our results provide the foundation for using neoantigen targeting strategies such as peptide vaccines in future trials for patients with multiple myeloma.

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Physical interactions between T cell receptors (TCRs) and mutation-derived tumour neoantigens (neoAg) presented by major histocompatibility class-I (MHC-I) enable sensitive and specific cytolysis of tumour cells. Adoptive transfer of neoAg-reactive T cells in patients is correlated with response to immunotherapy; however, the structural and cellular mechanisms of neoAg recognition remain poorly understood. We have identified multiple cognate neoAg:TCRs from B16F10, a common murine implantable tumour model of melanoma. We identified a high affinity TCR targeting H2-Db-restricted Hsf2K72N that conferred specific recognition of B16F10 in vitro and in vivo. Structural characterization of the peptide-MHC (pMHC) binary and pMHC:TCR ternary complexes yielded highresolution crystal structures, revealing the formation of a solvent-exposed hydrophobic arch in H2-Db that enables multiple intermolecular contacts between pMHC and the TCR. These features of structural stability strikingly mimic that of a previously published influenza peptide-H2-Db complex and its corresponding TCR, suggesting that there are shared structural motifs between neoantigens and viral peptides that explain their shared immunogenicity.

Introduction: Immunotherapies such as checkpoint blockade, have demonstrated remarkable clinical efficacy yet a large percentage of patients do not respond, potentially due to a paucity of pre-existing immune priming against neoantigens. We developed a personalized genome vaccine (PGV_001) platform to generate neoantigen vaccines targeting each patient’s unique mutanome. Primary objectives of the study were to determine 1) the safety and tolerability; 2) the feasibility of PGV_001 production and administration; and 3) the immunogenicity of PGV_001. Secondary objectives included immunophenotyping vaccine driven cellular and soluble immune milieu in peripheral blood. We previously reported on the clinical efficacy, and here we report, analysis of vaccine-driven immune responses in all treated patients. Methods: The study (Trial Registration NCT02721043) enrolled patients with resected malignancies, including Head and neck squamous cell carcinomas, breast cancer and bladder cancer, or, in the case of multiple myeloma treated with autologous stem cell transplant; all patients determined to have a high risk of disease recurrence (>30% over 5 years). Tumor-derived and germline RNA and DNA was sequenced to predict neoantigens utilizing our custom computation pipeline, OpenVax. Approximately 10 peptides were synthesized per patient, and a mixture of these peptides was administered as 10 subcutaneous and intradermal vaccines over 27 weeks in combination with poly-ICLC and helper Tetanus peptide as adjuvants. Immune responses were analyzed utilizing assays including IFN-gamma ELISPOT, antigen specific T cell expansion followed by flow cytometry, etc. Results: In total 148 neoantigen peptides were manufactured for 15 patients. Overall, 136 PGV_001 doses were administered to 13 patients. Vaccine-specific T cell immunity was observed against multiple vaccine neoepitopes in all 13 subjects. Of the peptides administered, 45% of vaccine antigens (57/126) induced de novo immunity, starting as early as Week8 and often sustaining past last vaccination. Notably, while the vaccine driven T cell immunity was CD4 T cell dominant, most evaluated subjects also displayed vaccine induced polyfunctional CD8-T cell responses. Additional studies are ongoing to define qualities of reactive T cells, evaluate vaccine-induced humoral responses and probe the circulating inflammatory immune milieu. These will be presented. Conclusions: We have established a platform for generating personalized neoantigen vaccines. 100% of the vaccinated patients developed an immune response specific to the vaccine neoantigens predicted by OpenVax. Subjects who received treatment experienced mild Grade 1 or 2 adverse reactions as per the CTEP v 4.0 NCI CTCAE. This vaccine trial reached the primary endpoint of safety, tolerability, feasibility and immunogenicity. Based on the PGV_001 platform two clinical trials, one in patients with glioblastoma multiforme (NCT03223103) in combination with TT fields and second in patients with urothelial carcinoma (NCT03359239) in combination with Atezolizumab have been performed. Data from these trials is under evaluation. Citation Format: Mansi Saxena, Thomas Marron, Julia Kodysh, Alex Rubinsteyn, John Finnigan, Ana Blasquez, Marcia Meseck, Tim O'Donnell, Daniela Delbeau, Mathew Galsky, Deborah Doroshow, Brett Miles, Krzysztof Misiukiewicz, Hanna Irie, Amy Tiersten, Samir Parekh, Marshall Posner, Andrea Wolf, John Mandeli, Rachel Brody, Sacha Gnjatic, Eric Schadt, Philip Friedlander, Nina Bhardwaj. Immunogenicity of PGV_001 neoantigen vaccine in a Phase-I clinical trial, across various types of cancers in adjuvant setting [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr CT270.

International audience; Powerful storms, consisting of strong gusts and winds, damage forests. Therefore, foresters need forest management strategies to reduce the damage risk. This paper focused on the damage patterns within the forest as the final results of multiple tree-wind dynamic interactions in time and space during a storm. Recent developments in computer technology allow for the possibility of simulating the complex and dynamic phenomena of damage during a storm but are extremely time consuming. To simplify the simulations without losing the crucial aspects of wind damage in forests, we introduced a computer simulation model using the agent-based modelling (ABM) technique, which capture the phenomena and interactions of individuals called ‘agents’. We created an ABM for forest wind damage simulation, coupling together an accepted understanding of wind gusts in forests, tree bending moments, and damage propagation. The model was tested with variations in three conditions: trees acclimated and unacclimated to their wind environment; three levels of gust strength; and three tree planting densities. The ABM was able to replicate damage patterns and demonstrate damage propagation within the forest and the effects of forest edges. The difference in the rate of damage in the forest between acclimated and unacclimated edges became similar with an increase in the gust intensity, and a decrease in tree density through a reduction in the shelter effect of the forest. The ABM could be improved in the future by parametrizing the variation in individual tree resistance, and the variation in gust and wind strength, as well as adding more information on local environmental conditions such as topography and soil variation, and storm characteristics such as duration and intensity.

We review developments in the field of boundary-layer flow over complex topography, focussing on the period from 1970 to the present day. The review follows two parallel strands: the impact of hills on flow in the atmospheric boundary layer and gravity-driven flows on hill slopes initiated by heating or cooling of the surface. For each strand we consider the understanding that has resulted from analytic theory before moving to more realistic numerical computation, initially using turbulence closure models and, more recently, eddy-resolving schemes. Next we review the field experiments and the physical models that have contributed to present understanding in both strands. For the period 1970–2000 with hindsight we can link major advances in theory and modelling to the key papers that announced them, but for the last two decades we have cast the net wider to ensure that we have not missed steps that eventually will be seen as critical. Two important new themes are given prominence in the 2000–2020 period. The first is flow over hills covered with tall plant canopies. The presence of a canopy changes the flow in important ways both when the flow is nearly neutral and also when it is stably stratified, forming a link between our two main strands. The second is the use of eddy-resolving models as vehicles to bring together hill flows and gravity-driven flows in a unified description of complex terrain meteorology.

In addition to expanding agricultural land area and intensifying crop yields, increasing the global trade of agricultural products is one mechanism that humanity has adopted to meet the nutritional demands of a growing population. However, climate change will affect the distribution of agricultural production and, therefore, food supply and global markets. Here we quantify the structural changes in the global agricultural trade network under the two contrasting greenhouse gas emissions scenarios by coupling seven Global Gridded Crop Models and five Earth System Models to a global dynamic economic model. Our results suggest that global trade patterns of agricultural commodities may be significantly different from today’s reality with or without carbon mitigation. More specifically, the agricultural trade network becomes more centralised under the high CO2 emissions scenario, with a few regions dominating the markets. Under the carbon mitigation scenario, the trade network is more distributed and more regions are involved as either importers or exporters. Theoretically, the more distributed the structure of a network, the less vulnerable the system is to climatic or institutional shocks. Mitigating CO2 emissions has the co-benefit of creating a more stable agricultural trade system that may be better able to reduce food insecurity.

Canopy wetness is a common condition that influences photosynthesis, the leaching or uptake of solutes, the water status and energy balance of canopies, and the interpretation of eddy covariance and remote sensing data. While often treated as a binary variable, ‘wet’ or ‘dry’, forest canopies are often partially wet, requiring the use of a continuous description of wetness. Minor precipitation events such as dew, that wet a fraction of the canopy, have been found to contribute to dry season foliar water uptake in the Eastern Amazon, and are fundamentally important to the canopy energy balance. However, few studies have reported the spatial and temporal distribution of canopy wetness, or the relative contribution of dew to leaf wetness, for forest ecosystems.In this study, we use two canopy profiles of leaf wetness sensors, coupled with meteorological data, to address fundamental questions about spatial and temporal variation of leaf wetness in an Eastern Amazonian rainforest. We also investigate how well meteorological tower data can predict canopy wetness using two models, one empirical and one that is physically-based.The results show that the canopy is 100% dry only for 34% of the time, otherwise being between 5% and 100% wet. Dew accounts for 20% or 43% of total annual leaf wetness, and 36% or 50% of canopy wetness in dry season, excluding or including dew events that co-occur with rain, respectively. Wetness duration was higher at the top than bottom of the canopy, mainly because of rain events, whilst dew formation was strongly dependent on the local canopy structure and varied horizontally through the canopy. The best empirical model accounted for 55% of the variance in canopy wetness, while the physical model accounted for 48% of the variance. We discuss future modelling improvements of the physical model to increase its predictive capacity.

The spatial variability of the mean flow and turbulence in and above a model canopy is investigated using three-dimensional laser Doppler velocimetry. The mean flow and turbulence are shown to be highly variable in space within the canopy but rapidly converge above the canopy. The coherent variations in the mean flow generate dispersive fluxes contributing almost a fifth to the total flux of momentum, and a greater contribution to the divergence of the flux, within the canopy. The higher-order turbulent statistics are more variable than the mean flow and often strongly correlated in space to variations in the mean flow. The implications of this microscale spatial variability for both field experiments and other laboratory experiments into canopy flow are discussed.

Large-eddy simulation of atmospheric boundary layers interacting with a coupled and resolved plant canopy reveals the influence of atmospheric stability variations from neutral to free convection on canopy turbulence. The design and implementation of a new multilevel canopy model is presented. Instantaneous fields from the simulations show that organized motions on the scale of the atmospheric boundary layer (ABL) depth bring high momentum down to canopy top, locally modulating the vertical shear of the horizontal wind. The evolution of these ABL-scale structures with increasing instability and their impact on vertical profiles of turbulence moments and integral length scales within and above the canopy are discussed. Linkages between atmospheric turbulence and biological control impact horizontal scalar source distributions. Decreasing spatial correlation between momentum and scalar fluxes with increasing instability results from ABL-scale structures spatially segregating momentum and scalar exchange at canopy top. In combination, these results suggest the need for roughness sublayer parameterizations to incorporate an additional length or time scale reflecting the influence of ABL-scale organized motions.

Simple first-order closure remains an attractive way of formulating equations for complex canopy flows when the aim is to find analytic or simple numerical solutions to illustrate fundamental physical processes. Nevertheless, the limitations of such closures must be understood if the resulting models are to illuminate rather than mislead. We propose five conditions that first-order closures must satisfy, then test two widely used closures against them. The first is the eddy diffusivity based on a mixing length. We discuss the origins of this approach, its use in simple canopy flows and extensions to more complex flows. We find that it satisfies most of the conditions and, because the reasons for its failures are well understood, it is a reliable methodology. The second is the velocity-squared closure that relates shear stress to the square of mean velocity. Again we discuss the origins of this closure and show that it is based on incorrect physical principles and fails to satisfy any of the five conditions in complex canopy flows; consequently its use can lead to actively misleading conclusions.

This paper introduces the design of the CSIRO variant of the Global Trade and Environment model (GTEM-C). GTEM-C is a hybrid model that combines the top-down macroeconomic representation of a computable general equilibrium model with the bottom-up engineering details of energy production. The model features detailed accounting for global energy flows that are embedded in traded energy goods, and it offers a unified framework to analyse the energy-carbon-environment nexus. As an illustrative example, we present simulation results on global energy transformation under the Intergovernmental Panel on Climate Change’s representative carbon pathways 4.5 and 8.5. By testing the model’s sensitivity to the relevant parameter, we find that the pace of electrification will significantly contain the spiking of carbon prices because electricity can be produced from carbon-free or less carbon-intensive technologies. The decoupling of energy use and carbon footprint, due to the uptake of clean electricity technologies, such as nuclear, wind, solar, and carbon capture and storage, allows the world to maintain high level of energy consumption, which is essential to economic growth.

Animal products, i.e. meat, milk and eggs, provide an important component in global diets, but livestock dominate agricultural land use by area and are a major source of greenhouse gases. Cultural and personal associations with animal product consumption create barriers to moderating consumption, and hence reduced environmental impacts. Here we review alternatives to conventional animal products, including cultured meat, imitation meat and insects (i.e. entomophagy), and explore the potential change in global agricultural land requirements associated with each alternative. Stylised transformative consumption scenarios where half of current conventional animal products are substituted to provide at least equal protein and calories are considered. The analysis also considers and compares the agricultural land area given shifts between conventional animal product consumption. The results suggest that imitation meat and insects have the highest land use efficiency, but the land use requirements are only slightly greater for eggs and poultry meat. The efficiency of insects and their ability to convert agricultural by-products and food waste into food, suggests further research into insect production is warranted. Cultured meat does not appear to offer substantial benefits over poultry meat or eggs, with similar conversion efficiency, but higher direct energy requirements. Comparison with the land use savings from reduced consumer waste, including over-consumption, suggests greater benefits could be achieved from alternative dietary transformations considered. We conclude that although a diet with lower rates of animal product consumption is likely to create the greatest reduction in agricultural land, a mix of smaller changes in consumer behaviour, such as replacing beef with chicken, reducing food waste and potentially introducing insects more commonly into diets, would also achieve land savings and a more sustainable food system.

Losses at every stage in the food system influence the extent to which nutritional requirements of a growing global population can be sustainably met. Inefficiencies and losses in agricultural production and consumer behaviour all play a role. This paper aims to understand better the magnitude of different losses and to provide insights into how these influence overall food system efficiency. We take a systems view from primary production of agricultural biomass through to human food requirements and consumption. Quantities and losses over ten stages are calculated and compared in terms of dry mass, wet mass, protein and energy. The comparison reveals significant differences between these measurements, and the potential for wet mass figures used in previous studies to be misleading. The results suggest that due to cumulative losses, the proportion of global agricultural dry biomass consumed as food is just 6% (9.0% for energy and 7.6% for protein), and 24.8% of harvest biomass (31.9% for energy and 27.8% for protein). The highest rates of loss are associated with livestock production, although the largest absolute losses of biomass occur prior to harvest. Losses of harvested crops were also found to be substantial, with 44.0% of crop dry matter (36.9% of energy and 50.1% of protein) lost prior to human consumption. If human over-consumption, defined as food consumption in excess of nutritional requirements, is included as an additional inefficiency, 48.4% of harvested crops were found to be lost (53.2% of energy and 42.3% of protein). Over-eating was found to be at least as large a contributor to food system losses as consumer food waste. The findings suggest that influencing consumer behaviour, e.g. to eat less animal products, or to reduce per capita consumption closer to nutrient requirements, offer substantial potential to improve food security for the rising global population in a sustainable manner., Graphical abstract Image 2, Highlights • Food system losses quantified from primary production to human food requirements. • Global agricultural dry biomass consumed as food is 6% (energy 9.0% and protein 7.6%). • 44% of harvested crops dry matter lost prior to human consumption. • Highest loss rate in livestock production, but largest losses before harvest • Over-eating at least as large a contributor to food system losses as consumer waste.

Landscape discontinuities such as forest edges play an important role in determining the characteristics of the atmospheric flow by generating increased turbulence and triggering the formation of coherent tree-scale structures. In a fragmented landscape, consisting of surfaces of different heights and roughness, the multiplicity of edges may lead to complex patterns of flow and turbulence that are potentially difficult to predict. Here, we investigate the effects of different levels of forest fragmentation on the airflow. Five gap spacings (of length approximately 5h, 10h, 15h, 20h, 30h, where h is the canopy height) between forest blocks of length 8.7h, as well as a reference case consisting of a continuous forest after a single edge, were investigated in a wind tunnel. The results reveal a consistent pattern downstream from the first edge of each simulated case, with the streamwise velocity component at tree top increasing and turbulent kinetic energy decreasing as gap size increases, but with overshoots in shear stress and turbulent kinetic energy observed at the forest edges. As the gap spacing increases, the flow appears to change monotonically from a flow over a single edge to a flow over isolated forest blocks. The apparent roughness of the different fragmented configurations also decreases with increasing gap size. No overall enhancement of turbulence is observed at any particular level of fragmentation.

If Ben Franklin lived today, he might say that nothing is certain but death, taxes, and cyberattacks. Our nation's electric grid is under constant cyberattack, according to a survey of electric utilities by Rep. Henry Waxman (D-CA) and Sen. Edward Markey (D-MA).1 The grid was the greatest engineering achievement of the twentieth century,2 but cybersecurity was as unknown to those grid engineers as it was to Ben Franklin. We need to do more to protect our energy infrastructure.

A primary goal of Earth system modelling is to improve understanding of the interactions and feedbacks between human decision making and biophysical processes. The nexus of land use and land cover change (LULCC) and the climate system is an important example. LULCC contributes to global and regional climate change, while climate affects the functioning of terrestrial ecosystems and LULCC. However, at present, LULCC is poorly represented in global circulation models (GCMs). LULCC models that are explicit about human behaviour and decision-making processes have been developed at local to regional scales, but the principles of these approaches have not yet been applied to the global scale level in ways that deal adequately with both direct and indirect feedbacks from the climate system. In this article, we explore current knowledge about LULCC modelling and the interactions between LULCC, GCMs and dynamic global vegetation models (DGVMs). In doing so, we propose new ways forward for improving LULCC representations in Earth system models. We conclude that LULCC models need to better conceptualise the alternatives for upscaling from the local to global scale. This involves better representation of human agency, including processes such as learning, adaptation and agent evolution, formalising the role and emergence of governance structures, institutional arrangements and policy as endogenous processes and better theorising about the role of teleconnections and connectivity across global networks. Our analysis underlines the importance of observational data in global-scale assessments and the need for coordination in synthesising and assimilating available data.

Human appropriation of land for food production has fundamentally altered the Earth system, with impacts on water, soil, air quality, and the climate system. Changes in population, dietary preferences, technology and crop productivity have all played important roles in shaping today’s land use. In this paper, we explore how past and present developments in diets impact on global agricultural land use. We introduce an index for the Human Appropriation of Land for Food (HALF), and use it to isolate the effects of diets on agricultural land areas, including the potential consequences of shifts in consumer food preferences. We find that if the global population adopted consumption patterns equivalent to particular current national per capita rates, agricultural land use area requirements could vary over a 14-fold range. Within these variations, the types of food commodities consumed are more important than the quantity of per-capita consumption in determining the agricultural land requirement, largely due to the impact of animal products and in particular ruminant species. Exploration of the average diets in the USA and India (which lie towards but not at global consumption extremes) provides a framework for understanding land use impacts arising from different food consumption habits. Hypothetically, if the world were to adopt the average Indian diet, 55% less agricultural land would be needed to satisfy demand, while global consumption of the average USA diet would necessitate 178% more land. Waste and over-eating are also shown to be important. The area associated with food waste, including over-consumption, given global adoption of the consumption patterns of the average person in the USA, was found to be twice that required for all food production given an average Indian per capita consumption. Therefore, measures to influence future diets and reduce food waste could substantially contribute towards global food security, as well as providing climate change mitigation options.

We revisit the analytical model for atmospheric boundary-layer flow over a hill covered with a canopy of Finnigan and Belcher (Q J R Meteorol Soc 130:1–29, 2004). Remaining within the overall scope of that analysis we extend in two ways. First we include the impacts of the advection terms within the upper canopy in a simple, but approximate, manner. Second we establish a modification for the associated pressure perturbation. Both extensions allow us to extend the parameter range wherein the analytical framework can be expected to reasonably hold. The within-canopy advection terms act to provide a downstream shift, and decreased magnitude, to the flow perturbations within the canopy as compared to the predictions from the original analysis. Through continuity, similar, but smaller, impacts are seen above the canopy. Together these act to reduce the differences in the streamwise positions of the topographic speed-up seen above and within the canopy. The modified pressure perturbation also acts to decrease the magnitude of the flow perturbations. The predicted topographic influence on the flow is reduced from that given in the original analysis but, importantly, the positions where the topographic influences most strongly affect the flow, and by extension the scalar concentration fields, are also changed. Predictions from the revised analysis are shown to be in good agreement with wind-tunnel data for flow over an isolated narrow ridge covered by a partially dense canopy.

We examine the effects of a one degree Celsius warming globally by 2030 on the distribution of grains sector productivity responses in several major economies. An integrated assessment modelling framework, the Global Integrated Assessment Model is used in our analysis. Our results highlight that at the tails of the distribution of climate change impacts simulated in this study, there is some variation in self-sufficiency and export availability of grains products reported for specific economies. These variations could widen further if distortionary trade policies are added to the current analysis.

Forest canopies are important components of the terrestrial carbon budget, which has motivated a worldwide effort, FLUXNET, to measure CO2 exchange between forests and the atmosphere. These measurements are difficult to interpret and to scale up to estimate exchange across a landscape. Here we review the effects of complex terrain on the mean flow, turbulence, and scalar exchange in canopy flows, as exemplified by adjustment to forest edges and hills, including the effects of stable stratification. We focus on the fundamental fluid mechanics, in which developments in theory, measurements, and modeling, particularly through large-eddy simulation, are identifying important processes and providing scaling arguments. These developments set the stage for the development of predictive models that can be used in combination with measurements to estimate exchange at the landscape scale.

Economic growth and development, along with expanding population, place a continuing pressure on our basic necessities in a world with depleting natural resources, overharvested ecosystems, and volatile commodity markets. These factors pose a range of competing demands relating to: economic and population growth and demographic changes; food, energy and resources security; ecological regime shifts; and climate change mitigation and adaptation. Key indicators of the processes that underlie these competing demands point to continuing food insecurity in low-income countries, exploitation of ecosystems, and depletion of natural resources. This emphasises the need for productivity improvements combined with innovation in institutional and governance structures to help foster global sustainability and ensure food security.

Turbulence within open canopies is shown to undergo a dramatic change in character during the transition from convective to stable conditions. In convective conditions the flow within the canopy is coupled through turbulent exchange to the flow aloft. As the transition proceeds, the within- and above-canopy flows decouple and vertically coherent waves form within the canopy. The intensity of above-canopy turbulence is not a good indicator of flow decoupling. Within-canopy waves can lead to large random error in the measurement of the change of storage and the advection terms in the mass balance equation. More importantly, errors associated with sampling over incomplete wave cycles will inevitably be combined with true advective flux divergences at non-ideal sites. Quantitative estimates of likely errors on storage of heat and CO 2 within the canopy are presented.

AFFILIATIONS: Foken—University of Bayreuth, Bayreuth, Germany; aubineT—Gembloux Agriculture University, Gembloux, Belgium; Finnigan—CSIRO, Canberra, Australia’s Capitol Teritory, Australia; LecLerc—University of Georgia, Griffin, Georgia; mauder—Karlsruhe Institute of Technology, GarmischPartenkirchen, Germany (formerly Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada); Paw u—University of California, Davis, Davis, California CORRESPONDING AUTHOR: Thomas Foken, Department of Micrometeorology, University of Bayreuth, D-95440 Bayreuth, Germany E-mail: thomas.foken@uni-bayreuth.de

New large-eddy simulations of flow over a flexible plant canopy by Dupont et al. (J. Fluid Mech., 2010, this issue, vol. 652, pp. 5–44) have produced apparently paradoxical results. Work over the last three decades had suggested that turbulent eddies could ‘lock onto’ to the waving frequency of uniform cereal canopies. Their new simulations contradict this view, although a resolution may lie in the essentially three-dimensional nature of the instability process that generates the dominant eddies above plant canopies.

An understanding of how topography, including that covered by a plant canopy, influences the flow and turbulence is important in many meteorological and micrometeorological applications. We revisit the framework of Finnigan and Belcher (Q J Roy Meteorol Soc 130:1–29, 2004) for neutral flow over sinusoidal two-dimensional topography covered by a canopy and present a minor modification that enables a formal match between the forms for the flow within and above the canopy, including within the deep canopy. The modification then allows the easy extension of the framework to generalised two-dimensional topography. The revised framework affirms the conclusions of Finnigan and Belcher (op.cit.); above the canopy the flow perturbations are maximised near to where the perturbation pressure is a minimum, whereas deep within the canopy the flow perturbations are maximised when the streamwise gradient of the perturbation pressure is largest. However, the extension to general topography strongly illustrates that it is the pressure perturbation, not the hill shape directly, that controls the magnitude and location of the topographic impacts on the flow. For isolated ridges with a plateau, the flow perturbations above the canopy maximise, not at the ridge crest, but where the hill curvature is largest. Multiple recirculation regions can also exist within the canopy, as determined by the streamwise gradient of the pressure perturbation. These results indicate that knowledge of the terrain over a larger area than hither-to-thought is required to assess whether the use of micrometeorological techniques is appropriate at individual sites.

We compare the turbulence statistics of the canopy/roughness sublayer (RSL) and the inertial sublayer (ISL) above. In the RSL the turbulence is more coherent and more efficient at transporting momentum and scalars and in most ways resembles a turbulent mixing layer rather than a boundary layer. To understand these differences we analyse a large-eddy simulation of the flow above and within a vegetation canopy. The three-dimensional velocity and scalar structure of a characteristic eddy is educed by compositing, using local maxima of static pressure at the canopy top as a trigger. The characteristic eddy consists of an upstream head-down sweep-generating hairpin vortex superimposed on a downstream head-up ejection-generating hairpin. The conjunction of the sweep and ejection produces the pressure maximum between the hairpins, and this is also the location of a coherent scalar microfront. This eddy structure matches that observed in simulations of homogeneous-shear flows and channel flows by several workers and also fits with earlier field and wind-tunnel measurements in canopy flows. It is significantly different from the eddy structure educed over smooth walls by conditional sampling based only on ejections as a trigger. The characteristic eddy was also reconstructed by empirical orthogonal function (EOF) analysis, when only the dominant, sweep-generating head-down hairpin was recovered, prompting a re-evaluation of earlier results based on EOF analysis of wind-tunnel data. A phenomenological model is proposed to explain both the structure of the characteristic eddy and the key differences between turbulence in the canopy/RSL and the ISL above. This model suggests a new scaling length that can be used to collapse turbulence moments over vegetation canopies.

Kowalski correctly points out that the analysis in [Finnigan, J.J., 2006. The storage term in eddy flux calculations. Agric. Forest Meteorol., 136, 108–113] ignores the interplay between the storage terms and the WPL corrections. In this note we develop an expression for the vertical convective velocity that accounts for the effect of both the ‘steady state’ and unsteady ‘storage’ WPL terms on the flux of a trace gas like CO 2 measured with an open path sensor and sonic anemometer. The expression is derived using the mass density rather than the mixing ratio so that the eddy fluxes take the conventional covariance form that is commonly used in turbulence textbooks.

The mean flow and scalar concentration profiles within and above a tall canopy are well known to violate the standard boundary-layer flux-gradient relationships. We present a theory for the scalar concentration profile that is comprised of a canopy exchange model coupled to a modified surface-layer model. The coupling between the two components and the modifications to the surface-layer profiles are formulated through the mixing-layer analogy for the flow at canopy top. This analogy provides an additional length scale—the vorticity thickness—upon which the profiles depend and a set of criteria that allows a reduction in the empiricism associated with earlier forms in the literature. Predictions of the mean scalar concentration profiles are shown to match observations over a wide range of diabatic stabilities for both potential temperature and water vapour.

The origins of the aerodynamic techniques now widely used at sites around the world to measure continuous biosphere-atmosphere exchange of carbon and energy are briefly reviewed. A survey of the current state of this approach concludes that the technique often fails when standard analysis routines are applied to data from single towers in complex flows. In the daytime, problems are signaled by failure to close the surface energy balance because turbulent energy fluxes are routinely underestimated. Complex flows are more prevalent at night when they lead to failure to measure all the respired CO2. At such times, the aerodynamic methodology is commonly supplemented by biological models. A set of papers from a workshop on "Flux Measurements in Difficult Conditions" held at the National Center for Atmospheric Research (NCAR) in January 2006 are introduced next. Two papers review the causes and magnitude of these flow-based problems. Four papers describe intensive field experiments that detail the mechanisms that cause problematic complex flows. These experiments show, inter alia, that the technique of replacing nighttime eddy flux measurements by biological models can also be systematically biased. Finally, two model studies are used both to illustrate the physics behind these complex flows and to motivate an approach to systematic correction of single-tower results.

Double averaged equations for atmospheric boundary layer flows are introduced as natural extensions of single averaged Reynolds equations. We show that in circumstances where double averaged equations are needed, the two fundamental properties of Reynolds averaging are violated. First, we consider double-averaging in free air turbulence, where the aim is to separate coherent motions from background turbulence. We illustrate the different properties of the main operators that have been used and the physical meaning of the terms that result. Second, in canopy flows, the multiply connected nature of the canopy airspace leads to a different set of departures from the standard Reynolds equations. We establish the physical meaning of the extra terms that arise. Finally we briefly discuss the problems, both practical and theoretical, that arise when we use double averaged equations to interpret real data.

The mean flow profile within and above a tall canopy is well known to violate the standard boundary-layer flux–gradient relationships. Here we present a theory for the flow profile that is comprised of a canopy model coupled to a modified surface-layer model. The coupling between the two components and the modifications to the surface-layer profiles are formulated through the mixing layer analogy for the flow at a canopy top. This analogy provides an additional length scale—the vorticity thickness—upon which the flow just above the canopy, within the so-called roughness sublayer, depends. A natural form for the vertical profiles within the roughness sublayer follows that overcomes problems with many earlier forms in the literature. Predictions of the mean flow profiles are shown to match observations over a range of canopy types and stabilities. The unified theory predicts that key parameters, such as the displacement height and roughness length, have a significant dependence on the boundary-layer stability. Assuming one of these parameters a priori leads to the incorrect variation with stability of the others and incorrect predictions of the mean wind speed profile. The roughness sublayer has a greater impact on the mean wind speed in stable than unstable conditions. The presence of a roughness sublayer also allows the surface to exert a greater drag on the boundary layer for an equivalent value of the near-surface wind speed than would otherwise occur. This characteristic would alter predictions of the evolution of the boundary layer and surface states if included within numerical weather prediction models.

Flow in a stably stratified environment is characterized by anisotropic and intermittent turbulence and wavelike motions of varying amplitudes and periods. Understanding turbulence intermittency and wave-turbulence interactions in a stably stratified flow remains a challenging issue in geosciences including planetary atmospheres and oceans. The stable atmospheric boundary layer (SABL) commonly occurs when the ground surface is cooled by longwave radiation emission such as at night over land surfaces, or even daytime over snow and ice surfaces, and when warm air is advected over cold surfaces. Intermittent turbulence intensification in the SABL impacts human activities and weather variability, yet it cannot be generated in state-of-the-art numerical forecast models. This failure is mainly due to a lack of understanding of the physical mechanisms for seemingly random turbulence generation in a stably stratified flow, in which wave-turbulence interaction is a potential mechanism for turbulence intermittency. A workshop on wave-turbulence interactions in the SABL addressed the current understanding and challenges of wave-turbulence interactions and the role of wavelike motions in contributing to anisotropic and intermittent turbulence from the perspectives of theory, observations, and numerical parameterization. There have been a number of reviews on waves, and a few on turbulence in stably stratified flows, but not much on wave-turbulence interactions. This review focuses on the nocturnal SABL; however, the discussions here on intermittent turbulence and wave-turbulence interactions in stably stratified flows underscore important issues in stably stratified geophysical dynamics in general. Fil: Sun, Jielun. National Center for Atmospheric Research; Estados Unidos Fil: Nappo, Carmen J.. CJN Research Meteorology; Estados Unidos Fil: Mahrt, Larry. NorthWest Research Associates; Estados Unidos Fil: Belušić, Danijel. Monash University. School of Earth, Atmosphere and Environment; Australia Fil: Grisogono, Branko. University of Zagreb. Department of Geophysics; Croacia Fil: Stauffer, David R.. Pennsylvania State University. Department of Meteorology; Estados Unidos Fil: Pulido, Manuel Arturo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Modelado e Innovación Tecnológica. Universidad Nacional del Nordeste. Facultad de Ciencias Exactas Naturales y Agrimensura. Instituto de Modelado e Innovación Tecnologica; Argentina. Centre National de la Reserche Scientifique. CONICET. UMI-IFAECI; Argentina Fil: Staquet, Chantal. Laboratoire des Ecoulements Géophysiques et Industriels; Francia Fil: Jiang, Qingfang. Naval Research Laboratory; Estados Unidos Fil: Pouquet, Annick. University of Colorado Boulder. National Center for Atmospheric Research and Laboratory for Atmospheric and Space Physics; Estados Unidos Fil: Yagüe, Carlos. Universidad Complutense de Madrid. Departamento de Geofísica y Meteorología; España Fil: Galperin, Boris. University of South Florida. College of Marine Science. Physical Oceanography; Estados Unidos Fil: Smith, Ronald B.. Yale University. Department of Geology and Geophysics; Estados Unidos Fil: Finnigan, John J.. CSIRO Marine and Atmospheric Research; Australia Fil: Mayor, Shane D.. California State University. Department of Geological and Environmental Sciences; Estados Unidos Fil: Svensson, Gunilla. Stockholm University. Department of Meteorology; Suecia Fil: Grachev, Andrey A.. University of Colorado Boulder. National Oceanic and Atmospheric Administration. Earth System Research Laboratory/Cooperative Institute for Research in Environmental Sciences ; Estados Unidos Fil: Neff, William D.. University of Colorado Boulder. National Oceanic and Atmospheric Administration. Earth System Research Laboratory/Cooperative Institute for Research in Environmental Sciences; Estados Unidos

Formal derivation of the storage term in eddy flux estimates of surface exchange shows that it is just the difference between instantaneous concentration profiles at the tower measured at the beginning and end of the averaging period, T, divided by T. As such, the storage term is likely to be a poorer estimate of the true concentration change in a representative volume around the tower than the time-averaged eddy flux is of exchange from the surface patch. This is because instantaneous profiles are easily biased by a single gust. To avoid this, many workers compute the storage from time-averaged concentration profiles centered on the beginning and the end of the averaging period. Here we show that this procedure underestimates the storage by at least 50% in most conditions with larger errors occurring when the integral time scale of the turbulence is much smaller than the averaging time T. Reducing the averaging time to the minimum required to smooth out the influence of individual gusts does not improve things significantly.

Topography influences many aspects of forest-atmosphere carbon exchange; yet only a small number of studies have considered the role of topography on the structure of turbulence within and above vegetation and its effect on canopy photosynthesis and the measurement of net ecosystem exchange of CO2 (Nee) using flux towers. Here, we focus on the interplay between radiative transfer, flow dynamics for neutral stratification, and ecophysiological controls on CO2 sources and sinks within a canopy on a gentle cosine hill. We examine how topography alters the forest-atmosphere CO2 exchange rate when compared to uniform flat terrain using a newly developed first-order closure model that explicitly accounts for the flow dynamics, radiative transfer, and nonlinear eco physiological processes within a plant canopy. We show that variation in radiation and airflow due to topography causes only a minor departure in horizontally averaged and vertically integrated photosynthesis from their flat terrain values. However, topography perturbs the airflow and concentration fields in and above plant canopies, leading to significant horizontal and vertical advection of CO2. Advection terms in the conservation equation may be neglected in flow over homogeneous, flat terrain, and then Nee = Fc, the vertical turbulent flux of CO2. Model results suggest that vertical and horizontal advection terms are generally of opposite sign and of the same order as the biological sources and sinks. We show that, close to the hilltop, Fc departs by a factor of three compared to its flat terrain counterpart and that the horizontally averaged Fc-at canopy top differs by more than 20% compared to the flat-terrain case.

The use of footprint functions in complex flows has been questioned because of anomalous behaviour reported in recent model studies. We show that the concentration footprint can be identified with the Green's function of the scalar concentration equation or the transition probability of a Lagrangian formulation of the same equation and so is well behaved and bounded by 0 and 1 in both simple and complex flows. The flux footprint in contrast is not a Green's function but a functional of the concentration footprint and is not guaranteed to be similarly well behaved. We show that in simple, homogeneous shear flows, the flux footprint, defined as the vertical eddy flux induced by a unit point source, is bounded by 0 and 1 but that this is not true in more general flow fields. Analysis of recent model studies also shows that the negative flux footprints reported in homogeneous plant canopy flows are an artefact of reducing a canopy with a complex source–sink distribution in the vertical to a single layer but that in canopies on hilly topography, the problems are more fundamental. Finally we compare footprint inversion with the direct mass-balance method of measuring surface exchange. We conclude first that the flux footprint is an appropriate measure of the area influencing both eddy and advective fluxes on a tower but that the concentration footprint is the correct measure when the storage term is important. Second, we deduce that there are serious obstacles to inverting flux footprints in complex terrain.

To convert measurements of windspeed, eddy flux and scalar concentration into estimates of surface scalar exchange, we implicitly or explicitly assimilate the measurements into mathematical statements of the mass balance in a control volume on a representative patch of the surface. The form of this statement depends on the coordinate system in which it is written and the coordinate system should be chosen so that measurements can be used optimally. This requirement imposes a set of conditions on the coordinates. Here we perform a comparative analysis of some candidate coordinate systems, concentrating on the Cartesian and physical streamline systems. We show that over gentle topography there are definite advantages in working in streamline coordinates. Transforming measurements of vector and tensor quantities measured in the reference frame, s i, of the anemometer into the reference frame, e i, of the chosen coordinate system involves using the measured statistics of the wind field to define three Euler rotation angles. We compare the method in most common use, which employs the components of the mean wind vector and the Reynolds stress tensor to define these angles, with the more recent ‘planar-fit’ method that uses instead an ensemble of mean wind vectors to define the rotations. We find that, in real flows, the standard method has a previously unrecognized closure problem that ensures that the third rotation angle defined using the stress tensor or scalar flux vector will always be in error and often give unphysical results. An alternative procedure is recommended. Finally, the relationships between measurements and model outputs are discussed.

We develop an analytical model for atmospheric boundary-layer flow over a hill that is covered with a vegetation canopy. The slope of the hill is assumed to be small enough that the flow above the canopy can be treated within the linear framework of Hunt. Perturbations to the flow within the canopy are driven by the pressure gradient associated with the flow over the hill. In the upper canopy this pressure gradient is balanced by downwards turbulent transport of momentum and the canopy drag. The flow there can be calculated from linearized dynamics, which show that the maximum streamwise winds are where the perturbation pressure is at a minimum, i.e. near the crest of the hill. Deep within the canopy the pressure gradient associated with the flow over the hill is balanced by the canopy drag, here the nonlinear canopy drag. This nonlinear balance shows how the streamwise winds are largest where the perturbation pressure gradient is largest, i.e. on the upwind slope of the hill. In the lee of the hill this nonlinear solution shows how the pressure gradient decelerates the wind deep within the canopy, leading to separation with a region of reversed flow when the canopy is sufficiently deep. Coupling between the out-of-phase flows within and above the canopy means that the maximum velocity is further upwind of the hill crest than in flow over a rough hill, while the extra turbulent mixing caused by the canopy significantly reduces the magnitude of the velocity speed-up over the hill. Finally, we find that there is no formal limit process where the solutions with a canopy yield the well-known solutions for flow over a rough hill. This finding calls into question the very use of a roughness length in accelerating or decelerating turbulent boundary layers. Copyright © 2004 Royal Meteorological Society

Experience of long term flux measurements over tall canopies during the last two decades has revealed that the eddy flux of sensible plus latent heat is typically 30% smaller than the available radiant energy flux. This failure to close the energy balance is less common close to the surface over short roughness but is still sometimes seen, especially in complex topography. These observations cast doubt on the results obtained from long term flux studies where daily and annual net ecosystem exchange is usually the small difference between large positive and negative fluxes over 24 h. In this paper we investigate this problem by examining some fundamental assumptions entailed in analysis of surface exchange by the eddy flux method. In particular, we clarify the form and use of the scalar conservation equation that underlies this analysis and we examine the links between averaging period and rotation of coordinates in the situation where coordinates are aligned with the wind vector. We show that rotating coordinates so that the x axis is aligned with the mean wind vector has the effect of high pass filtering the scalar covariance, wc, such that contributions to the aerodynamic flux from atmospheric motions with periods longer than the averaging period are lost while those of shorter period are distorted. We compare the effect of computing surface exchange by averaging many short periods, in each of which the coordinates are rotated so that the mean vertical velocity is zero (the method currently adopted in most long-term flux studies), with analysis in long-term coordinates and show a systematic underestimation of surface exchange in the former case. This is illustrated with data from three long- term forest field sites where underestimations of sensible and latent heat fluxes of 10-15% averaged over many days are seen. Crucial factors determining the loss of flux are the averaging period T , the measurement height and the content of the scalar cospectrum at periods longer than T. The properties of this cospectrum over tall canopies in both homogeneous and complex terrain are illustrated by measurements at our three sites and we see that over tall canopies on flat ground in convective conditions, or on hilly sites in near neutral flow, the scalar cospectra have much more low frequency content than classical surface-layer spectral forms would predict. We believe that the filtering of this low frequency covari- ance by the averaging-rotation operations in common use is a large contributory factor to the failure to close the energy balance over tall canopies.

Global agroecosystems can contribute to both climate change mitigation and biodiversity conservation, and market mechanisms provide a highly prospective means of achieving these outcomes. However, the ability of markets to motivate the supply of carbon sequestration and biodiversity services from agricultural land is uncertain, especially given the future changes in environmental, economic, and social drivers. We quantified the potential supply of these services from the intensive agricultural land of Australia from 2013 to 2050 under four global outlooks in response to a carbon price and biodiversity payment scheme. Each global outlook specified emissions pathways, climate, food demand, energy price, and carbon price modeled using the Global Integrated Assessment Model (GIAM). Using a simplified version of the Land Use Trade-Offs (LUTO) model, economic returns to agriculture, carbon plantings, and environmental plantings were calculated each year. The supply of carbon sequestration and biodiversity services was then quantified given potential land use change under each global outlook, and the sensitivity of the results to key parameters was assessed. We found that carbon supply curves were similar across global outlooks. Sharp increases in carbon sequestration supply occurred at carbon prices exceeding 50 $ tCO(2)(-1) in 2015 and exceeding 65 $ tCO(2)(-1) in 2050. Based on GIAM-modeled carbon prices, little carbon sequestration was expected at 2015 under any global outlook. However, at 2050 expected carbon supply under each outlook differed markedly, ranging from 0 to 189 MtCO(2) yr(-1). Biodiversity services of 3.32% of the maximum may be achieved in 2050 for a 1 $B investment under median scenario settings. We conclude that a carbon market can motivate supply of substantial carbon sequestration but only modest amounts of biodiversity services from agricultural land. A complementary biodiversity payment can synergistically increase the supply of biodiversity services but will not provide much additional carbon sequestration. The results were sensitive to global drivers, especially the carbon price, and the domestic drivers of adoption hurdle rate and agricultural productivity. The results can inform the design of an effective national policy and institutional portfolio addressing the dual objectives of climate change and biodiversity conservation that is robust to future uncertainty in both national and global drivers. Refereed/Peer-reviewed

We have conducted an Empirical Orthogonal Functionanalysis (EOF) of a three dimensional, 2-pointvelocity covariance field, measured in a wind tunnel. The rate of convergence of the EOF sequence was usedas an objective test for the presence of distinctlarge turbulent structures. We found that in theroughness sublayer (2h > z > 0) the sequence convergedmuch more rapidly than in the lower surface layer(6h > z > 0), 75% of the total velocity variancebeing captured by the first three of 42 eigenmodes;h is the canopy height. The analysis was extended to three dimensions, whereover 50% of the variance and most of the spatialstructure of the covariance fields were captured by aneven smaller fraction of the total number ofeigenmodes. With some relatively weak additionalassumptions we were able to construct the velocityfield of a ‘characteristic eddy’ or large coherentstructure. This consisted of a pair ofcounter-rotating streamwise vortices centred above thecanopy. The sense of rotation of the vortex pair wasopposite to that found in the wall region of boundarylayers but matched that found in plane mixing layers. A strong gust or sweep motion generated between thevortices was responsible for most of the shear stresscarried by the large eddies. The region of significanttransport of streamwise momentum by the characteristiceddy is much smaller than the region of coherence of theeddy's velocity field.

▪ Abstract The single-point statistics of turbulence in the ‘roughness sub-layer’ occupied by the plant canopy and the air layer just above it differ significantly from those in the surface layer. The mean velocity profile is inflected, second moments are strongly inhomogeneous with height, skewnesses are large, and second-moment budgets are far from local equilibrium. Velocity moments scale with single length and time scales throughout the layer rather than depending on height. Large coherent structures control turbulence dynamics. Sweeps rather than ejections dominate eddy fluxes and a typical large eddy consists of a pair of counter-rotating streamwise vortices, the downdraft between the vortex pair generating the sweep. Comparison with the statistics and instability modes of the plane mixing layer shows that the latter rather than the boundary layer is the appropriate model for canopy flow and that the dominant large eddies are the result of an inviscid instability of the inflected mean velocity profile. Aerodynamic drag on the foliage is the cause both of the unstable inflected velocity profile and of a ‘spectral short cut’ mechanism that removes energy from large eddies and diverts it to fine scales, where it is rapidly dissipated, bypassing the inertial eddy-cascade. Total dissipation rates are very large in the canopy as a result of the fine-scale shear layers that develop around the foliage.

We examine the analysis by Lee (1998) of the scalar conservation budget in advective flows. Lee treated the budget in a one-dimensional framework, neglected horizontal derivatives of turbulent quantities and proposed that mean flow advection, simplified to its vertical component, can be used to improve budget closure, when data from only a single tower are available. We conclude: • that the appropriate analysis framework for constructing such budgets is unavoidably two- or three-dimensional because 2D and 3D mean velocity fields always induce streamwise variation in the eddy fluxes of scalars. • that in such flow fields it is generally incorrect to assume that the vertical component of advection w ∂ c /∂z is everywhere much larger than the horizontal component u ∂ c /∂x The vertical component can only provide a good measure of total advective flux divergence in the special circumstance where the tower is located beneath the vertical stagnation streamline of a recirculating flow. By referring to a linear model of scalar transport over a hill we show that the relationship between u ∂ c /∂x and w ∂ c /∂z is entirely dependent on particular flow conditions and that, in general, w ∂ c /∂z cannot even be used to provide a bound on the magnitude of total advection. • that for measurements at heights small compared to the horizontal scale of the advective flow, the horizontal gradient of turbulent flux ∂ u’c’ /∂x can probably be neglected relative to its vertical equivalent ∂ w’c’ /∂z and, • by using simple hydrodynamic models of 2D flows it can be shown that the vertical gradient of mean vertical velocity is approximately constant over tower heights small compared to the horizontal scale of the advective flow. We also comment on the proper choice of coordinate frame for analysis.

Success in scaling the very stable boundary layer has been mixed. One possible reason for this is that wave-turbulence interaction can result in significant energy coupling between turbulence within the planetary boundary layer and the mean flow outside the PBL. Three regimes are described where wave-turbulence interaction forms a significant part of the dynamics. In the first, energy and momentum flows are confined within the PBL and do not preclude local scaling. In the other two, which involve topographically forced waves and propagating waves respectively, energy/momentum transfers across the PBL make success in local scaling unlikely.

An existing second-order closure model is modified to include the effects on mean and turbulent motions of form and viscous drag in vegetative canopies. The additional physical mechanisms represented by the closure are viscous and pressure drag on canopy elements, their role in momentum absorption, in the creation of fine scale turbulent eddies and in enhancing the total viscous dissipation in the canopy airspace. Viscous dissipation is split into a standard 'isotropic’ contribution associated with the spectral eddy cascade and a foliage contribution associated with work against pressure and viscous drag on the foliage. Changes in the turbulent time scale that result from these mechanisms are included in the standard parameterisations of third moments and of the eddy cascade contribution to dissipation. The model is tested against a wind- tunnel 'wheat’ canopy, a corn canopy and a eucalypt canopy, a height range from 50 mm to 12.6 m. Model results show that the parameterisations of foliage interaction used in the closure are sufficiently robust to reproduce second-moment profiles within and above vegetative canopies to a high degree of accuracy without resorting to 'tuning’ of the model constants. The model also shows the natural emergence of two length scales, one associated with the familiar eddy cascade isotropic contribution to total dissipation and the other associated with the length scales of the canopy elements.

To calculate disturbed wind flows in plant canopies, we studied a variant of the K α λk1/2 first-order closure (where K is the eddy viscosity, k is the turbulent kinetic energy calculated from its simplified governing differential equation, and λ is an algebraic length-scale). We compare numerical solutions using this closure (which admits only three empirical constants) with earlier obervations of mean wind, shear stress, and turbulent kinetic energy in three, quite different, uniform canopy flows, and in disturbed canopy flow over a ridge. The closure performs as well as or better than the solutions of others based on modifications of the ‘k-ϵ’ closure, where ϵ is the rate of dissipation of k.