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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]

The atmospheric oxidation of biogenic volatile organic compounds (BVOC) by OH radicals over tropical rainforests impacts local particle production and the lifetime of globally distributed chemically and radiatively active gases. For the pristine Amazon rainforest during the dry season, we empirically determined the diurnal OH radical variability at the forest-atmosphere interface region between 80 and 325 m from 07:00 to 15:00 LT using BVOC measurements. A dynamic time warping approach was applied showing that median averaged mixing times between 80 to 325 m decrease from 105 to 15 min over this time period. The inferred OH concentrations show evidence for an early morning OH peak (07:00–08:00 LT) and an OH maximum (14:00 LT) reaching 2.2 (0.2, 3.8) × 106 molecules cm−3 controlled by the coupling between BVOC emission fluxes, nocturnal NOx accumulation, convective turbulence, air chemistry and photolysis rates. The results were evaluated with a turbulence resolving transport (DALES), a regional scale (WRF-Chem) and a global (EMAC) atmospheric chemistry model. [ABSTRACT FROM AUTHOR]

Global reanalyzes like ERA5 accurately capture atmospheric processes at spatial scales of O(10) $\mathcal{O}(10)$ km or larger. By downscaling ERA5 with large‐eddy simulation (LES), LES can provide details about processes at spatio‐temporal scales down to meters and seconds. Here, we present an open‐source Python package named the "Large‐eddy simulation and Single‐column model—Large‐Scale Dynamics," or (LS)2D in short, designed to simplify the downscaling of ERA5 with doubly‐periodic LES. A validation with observations, for several sensitivity experiments consisting of month‐long LESs over Cabauw (the Netherlands), demonstrates both its usefulness and limitations. The day‐to‐day variability in the weather is well captured by (LS)2D and LES, but the setup under‐performs in conditions with broken or near overcast clouds. As a novel application of this modeling system, we used (LS)2D to study surface solar irradiance variability, as this quantity directly links land‐surface processes, turbulent transport, and clouds, to radiation. At a horizontal resolution of 25 m, the setup reproduces satisfactorily the solar irradiance variability down to a timescale of seconds. This demonstrates that the coupled LES‐ERA5 setup is a useful tool that can provide details on the physics of turbulence and clouds, but can only improve on its host reanalysis when applied to meteorological suitable conditions. Plain Language Summary: Modern global weather models are accurate in predicting atmospheric processes at scales of around 10 km or larger, but are less good at predicting smaller scale processes, like for example, the interaction between solar radiation, individual clouds, and the resulting clouds shadows that are cast onto the land surface. High spatio‐temporal resolution research models are able to capture these smaller scale processes, but require a coupling to a weather model to account for the day‐to‐day variability in our weather. In this paper, we present a framework to couple large to small scale models, and demonstrate both the benefits and challenges of using this coupled model setup. The coupled setup excels in capturing the aforementioned high frequency interactions between small clouds and surface solar radiation. However, the chaotic nature of broken to overcast clouds is proven difficult to represent. The coupled model setup is published as open‐source code, and is therefore freely available to the research community. Key Points: We developed an open‐source Python package named (LS)2D, designed to downscale the ERA5 reanalysis with turbulence and cloud‐resolving large‐eddy simulation (LESs)One month long experiments with (LS)2D and MicroHH over the Netherlands demonstrate both the skill and limitations of the coupled setupCapturing high‐frequency interactions between clouds and surface solar irradiance requires high resolution (O $\mathcal{O}$(10) m) LES [ABSTRACT FROM AUTHOR]

The atmospheric oxidation of biogenic volatile organic compounds (BVOC) by OH radicals over tropical rainforests impacts local particle production and the lifetime of globally distributed chemically and radiatively active gases. For the pristine Amazon rainforest during the dry season, we empirically determined the diurnal OH radical variability at the forest-atmosphere interface region between 80 and 325 m from 07:00 to 15:00 LT using BVOC measurements. A dynamic time warping approach was applied showing that median averaged mixing times between 80 to 325 m decrease from 105 to 15 min over this time period. The inferred OH concentrations show evidence for an early morning OH peak (07:00–08:00 LT) and an OH maximum (14:00 LT) reaching 2.2 (0.2, 3.8) × 106 molecules cm−3 controlled by the coupling between BVOC emission fluxes, nocturnal NOx accumulation, convective turbulence, air chemistry and photolysis rates. The results were evaluated with a turbulence resolving transport (DALES), a regional scale (WRF-Chem) and a global (EMAC) atmospheric chemistry model. [ABSTRACT FROM AUTHOR]

The atmospheric oxidation of biogenic volatile organic compounds (BVOC) by OH radicals over tropical rainforests impacts local particle production and the lifetime of globally distributed chemically and radiatively active gases. For the pristine Amazon rainforest during the dry season, we empirically determined the diurnal OH radical variability at the forest-atmosphere interface region between 80 and 325 m from 07:00 to 15:00 LT using BVOC measurements. A dynamic time warping approach was applied showing that median averaged mixing times between 80 to 325 m decrease from 105 to 15 min over this time period. The inferred OH concentrations show evidence for an early morning OH peak (07:00–08:00 LT) and an OH maximum (14:00 LT) reaching 2.2 (0.2, 3.8) × 106 molecules cm−3 controlled by the coupling between BVOC emission fluxes, nocturnal NOx accumulation, convective turbulence, air chemistry and photolysis rates. The results were evaluated with a turbulence resolving transport (DALES), a regional scale (WRF-Chem) and a global (EMAC) atmospheric chemistry model. [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]

Abstract: The convective boundary layer (CBL) is characterised by narrow vigorous thermals (updraft motions) surrounded by relatively large subsidence motions. In such a flow, reactants are normally segregated and their chemical transformations depend on the ability of atmospheric turbulence to mix them. This process is particularly important when the time-scale of the chemical transformation is similar to the turbulent characteristic time scale. For large atmospheric models, the segregation occurs at scales smaller than the grid length. As a result, instantaneous and homogeneous mixing of the reactants is normally assumed. This paper is aimed at the study of this assumption and to apply a parameterisation of an effective reaction rate accounting for the inefficient mixing due to convective turbulence in the CBL. We simulate a growing CBL with two models that use different physical assumptions. The first one, the so-called mixed-layer model, assumes an instantaneous and homogeneous mixing of the reactants in the boundary layer (BL). The second one, a three-dimensional large eddy simulation (LES) model, explicitly solves atmospheric turbulent motions and describes the heterogeneity of the mixing due to the turbulent characteristics of the CBL. By comparing their results in a simple case, i.e. a second-order chemical reaction, we show that the heterogeneous mixing due to convective turbulence has an important impact on the chemical transformations by slowing down the reaction rate. By introducing effective reaction rates through a parameterisation which accounts for this inefficient mixing, the mixed-layer model results improve significantly. We extend our study to a chemical mechanism that accounts for the ozone formation and depletion in the CBL. We show that the reaction rate can be slowed down or increased depending on whether the reactants are transported in opposite directions or not. We propose coefficients to be used to calculate the effective reaction rates in large-scale or mixed-layer models. [Copyright &y& Elsevier]

The development and maintenance of the atmospheric boundary layer (ABL) plays a key role in the distribution of atmospheric constituents, especially in a polluted urban area. In particular, the ABL has a direct impact on the concentration and transformation of pollutants. In this work, in order to analyze the different mechanisms which control the boundary layer growth, we have simulated by means of the non-hydrostatic model MM5 several boundary layer observed in the city of Barcelona (Spain). Sensitivity analysis of the modelled ABL is carried out by using various descriptions of the planetary boundary layer (PBL). Direct and continuous measurements of the boundary layer depth taken by a lidar are used to evaluate the results obtained by the model. [Copyright &y& Elsevier]

The leaf photosynthesis models developed by Farquhar et al. (1980, https://doi.org/10.1007/BF00386231) (FvCB) and Goudriaan et al. (1985, https://doi.org/10.1007/978‐1‐4899‐3665‐3%5f10) (G85) are both used in Earth system and weather models to quantify ecosystem carbon assimilation. Despite their common role, a systematic comparison between these two photosynthesis models is currently lacking in scientific literature. In this technical report we compared the two models in a systematic way. Hereto we performed a comparative analysis of the model structures as well as the modeled responses of photosynthesis to light and CO2 at leaf level. To facilitate future model comparison, we also constructed a lookup table that presents FvCB model parameters fitted to CO2‐response curves from G85 in a wide natural range in photosynthetic capacity at standardized temperature. The structure of the FvCB model differs fundamentally from the G85 model as the FvCB model considers rate‐limiting processes due to Rubisco capacity, electron transport and triose phosphate utilization in parallel, whereas the G85 model considers Rubisco activity and triose phosphate utilization limitation to act in series scaled with quantum use efficiency. The models also differ fundamentally in terms of the parametrization of dark respiration. Still, both models calculate near‐similar responses of photosynthesis to changes in light and CO2 across a wide range in photosynthetic capacity with only two free parameters each. Our work thereby highlights functional similarities between these model approaches despite fundamental differences in model structure. Hence, standardized parameter sets that yield similar photosynthesis responses to light and CO2 may facilitate intercomparison of Earth system and weather models. Plain Language Summary: In Earth system and weather models the exchange of CO2 between the vegetation and the atmosphere is primarily determined by photosynthesis at leaf level. Two commonly applied representations of leaf photosynthesis are based on the models of Farquhar et al. (1980, https://doi.org/10.1007/BF00386231) (FvCB) and Goudriaan et al. (1985, https://doi.org/10.1007/978‐1‐4899‐3665‐3%5f10) (G85). A systematic comparison between the two model approaches is currently lacking in scientific literature. The objective of our technical report is to provide such a comparison and thereby to contribute to an exchange of ideas, data and applications between users of the respective models. We found that the two models calculate a similar response of net photosynthesis to light and CO2, despite having considerable differences in their model structure and representation of physiological processes. The main difference in model structure is that the limitations to photosynthesis in the FvCB model are applied in parallel, whereas in the G85 model they are in series. We also present a lookup table to express parameters from the G85 model in terms of their equivalent FvCB parameters. This technical report thereby contributes to the comparison of models used across the Earth system and weather modeling communities. Key Points: We compare two leaf photosynthesis models, based on different biophysical assumptions, that are both used in Earth system and weather modelingThe two models calculate a near‐similar response of net photosynthesis to light and CO2 despite having considerable differences in their structure and process representation. This finding is significant across a wide range of naturally occurring photosynthetic capacities in vegetationThrough a flowchart, a comparison of photosynthetic response to light and CO2 and a parameter conversion table, we aim to enable more communication and exchange of data between users of the two models within the Earth system and weather modeling communities [ABSTRACT FROM AUTHOR]

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 studied the effects of shading by shallow cumulus (shallow Cu) and the subsequent effect of inducing heterogeneous conditions at the surface on boundary-layer characteristics. We placed special emphasis on quantifying the changes in the characteristic length and time scales associated with thermals, shallow Cu and induced thermal circulation structures. A series of systematic numerical experiments, inspired by Amazonian thermodynamic conditions, was performed using a large-eddy simulation model coupled to a land-surface model. We used four different experiments to disentangle the effects of shallow Cu on the surface and the response of clouds to these surface changes. The experiments include a 'clear case', 'transparent clouds', 'shading clouds' and a case with a prescribed uniform domain and reduced surface heat flux. We also performed a sensitivity study on the effect of introducing a weak background flow. Length and time scales were calculated using autocorrelation and two-dimensional spectral analysis, and we found that shading controlled by shallow Cu locally lowers surface temperatures and consequently reduces the sensible and latent heat fluxes, thus inducing spatial and temporal variability in these fluxes. The length scale of this surface heterogeneity is not sufficiently large to generate circulations that are superimposed on the boundary-layer scale, but the heterogeneity does disturb boundary-layer dynamics and generates a flow opposite to the normal thermal circulation. Besides this effect, shallow Cu shading reduces turbulent kinetic energy and lowers the convective velocity scale, thus reducing the mass flux. This hampers the thermal lifetime, resulting in a decrease in the shallow Cu residence time (from 11 to 7 min). This reduction in lifetime, combined with a decrease in mass flux, leads to smaller clouds. This is partially compensated for by a decrease in thermal cell size due to a reduction in turbulent kinetic energy. As a result, inter-cloud distance is reduced, leading to a larger population of smaller clouds, while maintaining cloud cover similar to the non-shading clouds experiment. Introducing a $$1\,\hbox {m}\, \hbox {s}^{-1}$$ background wind speed increases the thermal size in the sub-cloud layer, but the diagnosed surface-cloud coupling, quantified by characteristic time and length scales, remains. [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]

In this study, the canopy effects on the vertical ozone exchange within and above Californian orchard are investigated. We examined the comprehensive dataset obtained from the Canopy Horizontal Array Turbulence Study (CHATS). CHATS typifies a rural central Californian site, with O3 mixing ratios of less than 60 ppb and moderate NOx mixing ratios. The CHATS campaign covered a complete irrigation cycle, with our analysis including periods before and after irrigation. Lower O3 mixing ratios were found following irrigation, together with increased wind speeds, decreased air temperatures and increased specific humidity. Friction velocity, sensible heat and gas fluxes above the canopy were estimated using variations on the fluxgradient method, including a method which accounts for the roughness sublayer (RSL). These methods were compared to fluxes derived from observed eddy diffusivities of heat and friction velocity. We found that the use of the RSL parameterization, which accounts for the canopy-induced turbulent mixing above the canopy, resulted in a stronger momentum, heat, and ozone exchange fluxes above this orchard, compared to the method which omits the RSL. This was quantified by the increased friction velocity, heat flux and ozone deposition flux of up to 12, 29, and 35% at 2.5 m above the canopy, respectively. Within the canopy, vertical fluxes, as derived from local gradients and eddy diffusivity of heat, were compared to fluxes calculated using the Lagrangian inverse theory. Both methods showed a presence of vertical flux divergence of friction velocity, heat and ozone, suggesting that turbulent mixing was inefficient in homogenizing the effects driven by local sources and sinks on vertical exchange of those quantities. This weak mixing within the canopy was also corroborated in the eddy diffusivities of friction velocity and heat, which were calculated directly from the observations. Finally, the influence of water stress on the O3 budget was examined by comparing the results prior and after the irrigation. Although the analysis is limited to the local conditions, our in situ measurements indicated differences in the O3 mixing ratio prior and after irrigation during CHATS. We attribute these O3 mixing ratio changes to enhanced biological emission of volatile organic compounds (VOCs), driven by water stress. [ABSTRACT FROM AUTHOR]

One‐dimensional radiative transfer solvers are computationally much more efficient than full three‐dimensional radiative transfer solvers but do not account for the horizontal propagation of radiation and thus produce unrealistic surface irradiance fields in models that resolve clouds. Here, we study the impact of using a 3‐D radiative transfer solver on the direct and diffuse solar irradiance beneath clouds and the subsequent effect on the surface fluxes. We couple a relatively fast 3‐D radiative transfer approximation (TenStream solver) to the Dutch Atmosphere Large‐Eddy Simulation (DALES) model and perform simulations of a convective boundary layer over grassland with either 1‐D or 3‐D radiative transfer. Based on a single case study, simulations with 3‐D radiative transfer develop larger and thicker clouds, which we attribute mainly to the displaced clouds shadows. With increasing cloud thickness, the surface fluxes decrease in cloud shadows with both radiation schemes but increase beneath clouds with 3‐D radiative transfer. We find that with 3‐D radiative transfer, the horizontal length scales dominating the spatial variability of the surface fluxes are over twice as large as with 1‐D radiative transfer. The liquid water path and vertical wind velocity in the boundary layer are also dominated by larger length scales, suggesting that 3‐D radiative transfer may lead to larger convective thermals. Our case study demonstrates that 3‐D radiative effects can significantly impact dynamic heterogeneities induced by cloud shading. This may change our view on the coupling between boundary‐layer clouds and the surface and should be further tested for generalizability in future studies. Plain Language Summary: Solar radiation warms the surface and provides energy for evaporation and biological processes, resulting in the release of heat and moisture to the atmosphere. This upward transport of warm and moist air eventually leads to the formation of clouds, which then alter the spatial distribution of solar radiation at the surface by partly reflecting and absorbing the incoming sunlight. Most previous studies that simulated these complex interactions between clouds, solar radiation, and the surface used 1‐D radiation models. These are faster than 3‐D radiation models but produce unrealistic surface solar radiation fields by only considering the vertical propagation of radiation. In this study, we use a relatively fast 3‐D radiation model to simulate the formation of clouds and the surface heat and moisture fluxes. In our simulations, 3‐D radiation results in thicker and wider clouds than 1‐D radiation, predominantly because clouds no longer shade the surface beneath them when radiation propagates under an angle. Unlike in simulations with 1‐D radiation, we find higher surface fluxes below clouds than under clear‐sky and higher surface fluxes with increasing cloud thickness in simulations with 3‐D radiation. Our results show that 3‐D radiation may strongly impact the coupling between clouds and the land surface. Key Points: We couple a 3‐D radiative transfer solver to a LES with an interactive vegetated surfaceDisplaced cloud shadows with 3‐D radiative transfer result in thicker and larger cloudsHeterogeneities in the surface heat fluxes are larger with 3‐D than with 1‐D radiative transfer [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]

In this observational study, the role of tree phenology on the atmospheric turbulence parameterization over 10-m-tall and relatively sparse deciduous vegetation is quantified. Observations from the Canopy Horizontal Array Turbulence Study (CHATS) field experiment are analyzed to establish the dependence of the turbulent exchange of momentum, heat, and moisture, as well as kinetic energy on canopy phenological evolution through widely used parameterization models based on 1) dimensionless gradients or 2) turbulent kinetic energy (TKE) in the roughness sublayer. Observed vertical turbulent fluxes and gradients of mean wind, temperature, and humidity, as well as velocity variances, are used in combination with empirical dimensionless functions to calculate the turbulent exchange coefficient. The analysis shows that changes in canopy phenology influence the turbulent exchange of all quantities analyzed in this study. The turbulent exchange coefficients of those quantities are twice as large near the canopy top for a leafless canopy than for a full-leaf canopy under unstable and near-neutral conditions. This turbulent exchange coefficient difference is related to the differing penetration depths of the turbulent eddies organized at the canopy top, which increase for a canopy without leaves. The TKE and dissipation analysis under near-neutral atmospheric conditions additionally shows that TKE exchange increases for a leafless canopy because of reduced TKE dissipation efficiency relative to that when the canopy is in full-leaf stage. The study closes with discussion surrounding the implications of these findings for parameterizations used in large-scale models. [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]