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We investigate the atmospheric diurnal variability inside and above the Amazonian rainforest for a representative day during the dry season. To this end, we combine high‐resolution large‐eddy simulations that are constrained and evaluated against a comprehensive observation set, including CO2 concentrations, gathered during GoAmazon2014/15. We design systematic numerical experiments to quantify whether a multilayer approach in solving the explicit canopy improves our canopy‐atmosphere representation. We particularly focus on the relationship between photosynthesis and plant transpiration, and their distribution at leaf and canopy scales. We found the variability of photosynthesis drivers like vapor pressure deficit and leaf temperature to be about 3 times larger for sunlit leaves compared to shaded leaves. This leads to a large spread on leaf stomatal conductance values with minimum and maximum values varying more than 100%. Regarding the turbulent structure, we find wind‐driven stripe‐like shapes at the canopy top and structures resembling convective cells at the canopy. Wind‐related variables provide the best spatiotemporal agreement between model and observations. The potential temperature and heat flux profiles agree with an observed decoupling near the canopy top interface, although with less variability and cold biases of up to 3 K. The increasing complexity on the biophysical processes leads to the largest disagreements for evaporation, CO2 plant assimilation and soil efflux. The model is able to capture the correct dependences and trends with the magnitudes still differing. We finally discuss the need to revise leaf and soil models and to complete the observations at leaf and canopy levels. Plain Language Summary: Most atmospheric models currently represent the vegetated canopy as one slab layer at the lowest level of the model. This oversimplification leads to limitations in our understanding on how the canopy and the atmosphere interact, as well as when comparing and interpreting model output with real world observations largely influenced by the presence of a canopy. In this study we implemented a more realistic multilayer canopy scheme in a turbulence‐resolving atmospheric model. We focused and analyzed the features and changes that appear in atmospheric variables due to the presence of a three‐dimensional canopy. To do so we designed several numerical experiments to understand how to best represent the relevant physical and biological processes. We quantified the variability of light, humidity and temperature at leaf‐level, and discussed the large variability the features appearing in the lowest atmosphere by the presence of the canopy. We also compare our model simulations with a complete set of atmospheric observations taken inside and above the Amazonian rainforest, and find an overall good agreement. We finally propose future ways to improve the canopy scheme and, in general, simulations including a vegetated canopy. Key Points: We implemented a 1D multilayer canopy scheme at every gridpoint in the Dutch Atmospheric Large Eddy Simulation resolving leaf, canopy and boundary layer scales as a continuumThe model is compared against a data set gathered during the Amazonian dry season, showing that wind and temperature are better represented than humidityWe present the first Large Eddy Simulations validation of in‐canopy CO2 processes [ABSTRACT FROM AUTHOR]

The explicit coupling at meter and second scales of vegetation's responses to the atmospheric‐boundary layer dynamics drives a dynamic heterogeneity that influences canopy‐top fluxes and cloud formation. Focusing on a representative day during the Amazonian dry season, we investigate the diurnal cycle of energy, moisture and carbon dioxide at the canopy top, and the transition from clear to cloudy conditions. To this end, we compare results from a large‐eddy simulation technique, a high‐resolution global weather model, and a complete observational data set collected during the GoAmazon14/15 campaign. The overall model‐observation comparisons of radiation and canopy‐top fluxes, turbulence, and cloud dynamics are very satisfactory, with all the modeled variables lying within the standard deviation of the monthly aggregated observations. Our analysis indicates that the timing of the change in the daylight carbon exchange, from a sink to a source, remains uncertain and is probably related to the stomata closure caused by the increase in vapor pressure deficit during the afternoon. We demonstrate quantitatively that heat and moisture transport from the subcloud layer into the cloud layer are misrepresented by the global model, yielding low values of specific humidity and thermal instability above the cloud base. Finally, the numerical simulations and observational data are adequate settings for benchmarking more comprehensive studies of plant responses, microphysics, and radiation. Plain Language Summary: Clouds and forest in the Amazonian rainforest region are closely related. We investigated the final month of the Amazonian dry season in order to study interactions between the rainforest and the overlying atmosphere, placing particular emphasis on studying small spatiotemporal effects, such as that of cloud shading on photosynthesis. We employed three different methods: a cloud‐turbulence resolving model, a global weather model, and a complete set of canopy‐top and atmospheric observations. We holistically studied these relationships by systematically analyzing the characteristics of incoming solar radiation, evapotranspiration, and cloud cover and thickness. This comparison enabled us to make two relevant findings related to these diurnal carbon and cloud cycles. First, we observed that photosynthesis is offset by the soil carbon dioxide efflux earlier than the two models calculations. With respect to cloud formation and intensification, we showed quantitatively that the inefficiently modeled moisture transport leads to less active shallow convection, which may be insufficient to trigger deep convection. This systematic study paves the way for more comprehensive studies that would include more complex descriptions of microphysics processes and radiation, as well as chemistry and aerosol formation. Key Points: Explicit interactions between carbon uptake and clouds on subdaily and subkilometer scales are modeled and validatedNEE observations show an early afternoon shift from a CO2 sink to a source, whereas in the model results, the CO2 uptake is longerObservations and DALES results show enhancement of moisture transport at cloud base that favors triggering afternoon deep convection [ABSTRACT FROM AUTHOR]

Understanding the interactions between the land surface and the atmosphere is key to model boundary-layer meteorology and cloud formation, as well as carbon cycling and crop yield. In this study we explore these interactions in the exchange of water, heat, and CO2 in a cropland--atmosphere system at the diurnal and local scale. We thereto couple an atmospheric mixed-layer model (MXL) to two land-surface schemes, developed from two different perspectives: while one land-surface scheme (A-gs) simulates vegetation from an atmospheric point of view, the other (GECROS) simulates vegetation from a carbon-storage point of view. We calculate surface fluxes of heat, moisture and carbon, as well as the resulting atmospheric state and boundary-layer dynamics, over a maize field in the Netherlands, for a day on which we have a rich set of observations available. Particular emphasis is placed on understanding the role of upper atmosphere conditions like subsidence, in comparison to the role of surface forcings like soil moisture. We show that the atmospheric-oriented model (MXL-A-gs) outperforms the carbon storage-oriented model (MXL-GECROS) on this diurnal scale. This performance strongly depends on the sensitivity of the modelled stomatal conductance to water stress, which is implemented differently in each model. This sensitivity also influences the magnitude of the surface fluxes of CO2, water and heat (surface control), and subsequently impacts the boundary-layer growth and entrainment fluxes (upper atmosphere control), which alter the atmospheric state. These findings suggest that observed CO2 mole fractions in the boundary layer can reflect strong influences of both the surface and upper atmospheric conditions, and the interpretation of CO2 mole fraction variations depends on the assumed land-surface coupling. We illustrate this with a sensitivity analysis where increased subsidence, typical for periods of drought, can induce a change of 12 ppm in atmospheric CO2 mole fractions, solely by decreasing the boundary-layer volume. The effect of such high subsidence on the Bowen ratio is of the same magnitude as induced by the depletion of soil moisture that would typically occur during a corresponding drought event. Correctly including such two-way land-surface interactions on the diurnal scale can thus potentially improve our understanding and interpretation of observed variations in atmospheric CO2, as well as improve crop yield forecasts by better describing the water loss and carbon gain. [ABSTRACT FROM AUTHOR]

Based on the prognostic equations of mixed-layer theory assuming a zeroth order jump at the entrainment zone, analytical solutions for the boundary-layer height evolution are derived with different degrees of accuracy. First, an exact implicit expression for the boundary-layer height for a situation without moisture is analytically derived without assuming any additional relationships or specific initial conditions. It is shown that to expand the solution to include moisture, only minor approximations have to be made. Second, for relatively large boundary-layer heights, the implicit representation is simplified to an explicit function. Third, a hybrid expression is proposed as a reasonable representation for the boundary-layer height evolution during the entire day. Subsequently, the analysis is extended to present the evolution of any boundary-layer averaged scalar, either inert or under idealized chemistry, as an analytical function of time and boundary-layer height. Finally, the analytical solutions are evaluated. This evaluation includes a sensitivity analysis of the boundary-layer height for the entrainment ratio, the free tropospheric lapse rate of the potential temperature, the time-integrated surface flux and the initial boundary-layer height and potential temperature jump. [ABSTRACT FROM AUTHOR]

We investigated the impact of aerosol heat absorption on convective atmospheric boundary-layer (CBL) dynamics. Numerical experiments using a large-eddy simulation model enabled us to study the changes in the structure of a dry and shearless CBL in depth-equilibrium for different vertical profiles of aerosol heating rates. Our results indicated that aerosol heat absorption decreased the depth of the CBL due to a combination of factors: (i) surface shadowing, reducing the sensible heat flux at the surface and, (ii) the development of a deeper inversion layer, stabilizing the upper CBL depending on the vertical aerosol distribution. Steady-state analytical solutions for CBL depth and potential temperature jump, derived using zero-order mixed-layer theory, agreed well with the large-eddy simulations. An analysis of the entrainment zone heat budget showed that, although the entrainment flux was controlled by the reduction in surface flux, the entrainment zone became deeper and less stably stratified. Therefore, the vertical profile of the aerosol heating rate promoted changes in both the structure and evolution of the CBL. More specifically, when absorbing aerosols were present only at the top of the CBL, we found that stratification at lower levels was the mechanism responsible for a reduction in the vertical velocity and a steeper decay of the turbulent kinetic energy throughout the CBL. The increase in the depth of the inversion layer also modified the potential temperature variance. When aerosols were present we observed that the potential temperature variance became significant already around $$0.7z_i$$ (where $$z_i$$ is the CBL height) but less intense at the entrainment zone due to the smoother potential temperature vertical gradient. [ABSTRACT FROM AUTHOR]

Compared to dry boundary layers, dispersion in cloud-topped boundary layers has received less attention. In this LES based numerical study we investigate the dispersion of a passive tracer in the form of Lagrangian particles for four kinds of atmospheric boundary layers: 1) a dry convective boundary layer (for reference), 2) a "smoke" cloud boundary layer in which the turbulence is driven by radiative cooling, 3) a stratocumulus topped boundary layer and 4) a shallow cumulus topped boundary layer. We show that the dispersion characteristics of the smoke cloud boundary layer as well as the stratocumulus situation can be well understood by borrowing concepts from previous studies of dispersion in the dry convective boundary layer. A general result is that the presence of clouds enhances mixing and dispersion - a notion that is not always reflected well in traditional parameterization models, in which clouds usually suppress dispersion by diminishing solar irradiance. The dispersion characteristics of a cumulus cloud layer turn out to be markedly different from the other three cases and the results can not be explained by only considering the well-known top-hat velocity distribution. To understand the surprising characteristics in the shallow cumulus layer, this case has been examined in more detail by 1) determining the velocity distribution conditioned on the distance to the nearest cloud and 2) accounting for the wavelike behaviour associated with the stratified dry environment. [ABSTRACT FROM AUTHOR]

The role of turbulence in the dispersion of atmospheric pollutants that react with linear (decay) and nonlinear (second-order) chemical reactions is examined. The most relevant processes that drive the reactivity of species emitted in a surface area or released by a point source are studied by deriving the dimensionless scaling numbers from equations for the atmospheric turbulent reacting flow. The first number is the ratio of the time scale of turbulence to the time scale of the chemical reaction, namely the Damköhler number. The second number is the ratio of the concentrations of the species present in the chemical transformations. In this paper, model results and experimental studies of turbulent reacting flows in the atmospheric boundary layer are presented to show the modifications and control exerted by turbulence on the atmospheric chemistry as a function of these numbers and processes. We also discuss how the chemical transformation is affected when species are in a state of chemical equilibrium. By studying the plume dispersion of a reactant, that decays with a simple chemical reaction, one can analyse the dependence of concentration fluctuations on the Damköhler number. The study is extended to plumes that react nonlinearly. In such reacting systems, the large gradients and segregation of species result in a significant reduction in the reaction rates. Because of this modification, the chemistry of species related to NOx and HOx can be very different from the chemistry in conditions where the species are uniformly mixed. The lack of complete observational evidence is hampering our understanding of these processes and our evaluation of numerical modelling results. Finally, we discuss briefly how to represent, in the form of a parameterization, the effect that turbulence can have on the reactivity of species emitted by a point source or an area source. [ABSTRACT FROM AUTHOR]

We investigate the interaction between the ammonium nitrate aerosol ( N A O 3 ) abundance and convective boundary-layer (CBL) dynamics by means of a large-eddy simulation (LES) framework. In our LES model the CBL dynamics is solved coupled with radiation, chemistry, and surface exchange. Concerning the aerosol coupling we assume a simplified representation that accounts for black carbon, aerosol water and inorganic aerosols, focusing on the semi-volatile ammonium nitrate aerosol within the CBL. The aerosol absorption and scattering of shortwave radiation is also taken into consideration. We use a data set of observations taken at the Cabauw Experimental Site for Atmospheric Research during the IMPACT/EUCAARI (European Integrated Project on Aerosol, Cloud, Climate, and Air Quality Interactions) campaign to successfully evaluate our LES approach. We highlight that our LES framework reproduces the observations of the ratio between gas-phase nitrate and total nitrate at the surface, with a diurnally-averaged overestimation of only ≈12%. We show that the dependence between gas-aerosol conversion of nitrate and CBL (thermo)dynamics produces highly non-linear concentration and turbulent flux vertical profiles. The flux profiles maximize at around 1/3 of the CBL. Close to the surface, we show that the outgassing of N A O 3 affects the dry deposition of nitrate. This outgassing is responsible for the high deposition velocities obtained from the concentration and flux measurements during observational campaigns. To account for the influence of CBL (thermo)dynamics on gas-aerosol conversion we propose an effective turbulent exchange coefficient based on an analysis of the flux budget equation of aerosol nitrate calculated by our LES. The implementation of this effective turbulent exchange coefficient in a 1D model leads to a better agreement with the LES results and with surface observations. [ABSTRACT FROM AUTHOR]

The effects of plant responses to cumulus (Cu) cloud shading are studied from free convective to shear-driven boundary-layer conditions. By using a large-eddy simulation (LES) coupled to a plant physiology embedded land-surface submodel, we study the vegetation–cloud feedbacks for a wide range (44) of atmospheric and plant stomatal conditions. The stomatal relaxation time is prescribed as an instantaneous, symmetrical (10, 15 and 20 min) and asymmetrical (5 min closing, 10 min opening) response, and the background wind ranges from 0 to 20 m s −1 . We show that in free convective, non-shading (i.e. transparent) cloud conditions the near-surface updraft region is marked by an enhanced CO 2 assimilation rate ( A n ; 7%) and increased latent (LE; 9%) and sensible heat ( H ; 19%) fluxes. When we introduce Cu shading, we find an enhancement in plant transpiration and CO 2 assimilation rates under optically thin clouds due to an increase in diffuse radiation. However, these effects vanish when a background wind is present and the Cu are advected. Optically thick clouds reduce the assimilation rate and surface fluxes under all simulated wind conditions. With increasing background wind, the shaded surface area is enlarged due to Cu tilting. The consequent decrease in surface fluxes by a reduction in incoming radiation, is partly offset due to an enhancement in the surface exchange and turbulent mixing as a result of stronger wind speeds. Different and non-linear processes control the H and LE response to shading. H is mainly radiation driven, whereas plant responses dampen the shading effects on LE. As a result, the regional averaged (48 km 2 ) reduction in H and LE are found to be 18% and 5%, respectively, compared to non-shading cloud conditions. Surprisingly, a nearly uniform regional net radiation reduction of 11% is found, with only a deviation between all 35 Cu shading cases of 0.5% (i.e. 1.2 W m −2 ) at the moment of maximum cloud cover. By comparing four representative simulations that are equal in net available energy, but differ in interactive and prescribed surface energy fluxes, we find a relative reduction in cloud cover between 5 and 10% during the maximum cloud cover period when the dynamic surface heterogeneity is neglected. We conclude that the local and spatial dynamic surface heterogeneity influences Cu development, while the Cu–vegetation coupling becomes progressively weaker with increasing stomatal relaxation time and background wind. [ABSTRACT FROM AUTHOR]

We investigate diurnal variability of the atmospheric ammonia (NH 3) budget over unfertilized grassland by combining observations with a conceptual atmospheric boundary layer model. Our combined approach of diurnal observations and modeling enables us to identify the contribution of the four governing processes to the NH 3 diurnal cycle: surface-atmosphere exchange, entrainment, advection and chemical gas-aerosol transformations. The observations contain new NH 3 flux and molar fraction measurements obtained using the Differential Optical Absorption Spectroscopy (DOAS) remote sensing technique, eliminating problems related to inlet tubing. Using strict filter criteria, 22 days with clear-sky summer conditions are selected. From this selection, we analyze a single representative day characterized by prototypical convective boundary layer conditions, using the boundary layer model constrained by meteorological observations. We design two numerical experiments to study the NH 3 diurnal variability and the individual contributions of the processes governing the ammonia budget. These experiments only differ in their representation of the NH 3 surface exchange. First, a fitted function through the observed NH 3 flux is prescribed to the model. In the second numerical experiment, the surface flux is solved following the DEPosition of Acidifying Compounds (DEPAC) parameterization. With a prescribed surface flux, the modeled NH 3 molar fraction closely fits the observations. Two regimes are identified in the NH 3 diurnal cycle: the morning, where boundary layer dynamics dominate the budget through entrainment, and the afternoon, where multiple processes are of importance. A similarly close fit to the observed molar fraction is achieved in the second experiment, but we identify a mismatch between the observed and parameterized NH 3 surface flux. As a result, the model requires an unrealistic budget representation to achieve this close fit, e.g. high free tropospheric NH 3. Our findings on the NH 3 budget, based on integrating modeling and observations, paves the way for future research on the NH 3 surface-atmosphere exchange at the subdaily scales. [ABSTRACT FROM AUTHOR]