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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]

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]

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]