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© 2013. American Geophysical Union. All Rights Reserved. This investigation was partially supported by projects CGL-2008-05093/CLI and CGL-2011-29677-C02 and was accomplished within the collaboration agreement 09/490 between CIEMAT and NCAR as well as the collaboration agreement 09/153 between CIEMAT and UCM. NCAR is sponsored by the National Science Foundation. We would like to thank the Navarra government and the ECMWF for facilitating the access to its data sets. We also would like to thank the reviewers for their constructive comments which helped to increase the value of the contents of the manuscript., The performance of the Weather Research and Forecasting (WRF) model to reproduce the surface wind circulations over complex terrain is examined. The atmospheric evolution is simulated using two versions of the WRF model during an over 13year period (1992 to 2005) over a complex terrain region located in the northeast of the Iberian Peninsula. A high horizontal resolution of 2km is used to provide an accurate representation of the terrain features. The multiyear evaluation focuses on the analysis of the accuracy displayed by the WRF simulations to reproduce the wind field of the six typical wind patterns (WPs) identified over the area in a previous observational work. Each pattern contains a high number of days which allows one to reach solid conclusions regarding the model performance. The accuracy of the simulations to reproduce the wind field under representative synoptic situations, or pressure patterns (PPs), of the Iberian Peninsula is also inspected in order to diagnose errors as a function of the large-scale situation. The evaluation is accomplished using daily averages in order to inspect the ability of WRF to reproduce the surface flow as a result of the interaction between the synoptic scale and the regional topography. Results indicate that model errors can originate from problems in the initial and lateral boundary conditions, misrepresentations at the synoptic scale, or the realism of the topographic features., Ministerio de Economía y Competitividad (MINECO), Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), España, National Center for Atmospheric Research (NCAR), Universidad Complutense de Madrid (UCM), National Science Foundation (NSF), Depto. de Física de la Tierra y Astrofísica, Fac. de Ciencias Físicas, TRUE, pub

Global reanalyzes like ERA5 accurately capture atmospheric processes at spatial scales of urn:x-wiley:19422466:media:jame21967:jame21967-math-0001 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.

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.

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_10) (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.

The leaf photosynthesis models developed by Farquhar et al. (1980) (FvCB) and Goudriaan et al. (1985) (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.

Understanding evaporation in arid regions is essential for climate change assessment and optimizing water resources management under a changing climate. This thesis analyses the physical processes that govern local evaporation in a representative salt flat setting at the Altiplano region of the Atacama Desert. Such physical processes are analyzed from climatic to sub-diurnal scales. Moreover, regional (>100 km) to local (<1 km) scales are integrated, through the analysis of the ocean-desert circulation and its influences on the atmospheric boundary layer and surface fluxes. Firstly, findings show that wind-driven turbulence is the primary evaporation controller at the sub-diurnal scale, whereas radiation plays a major role at the seasonal scale. Secondly, at the local scale, surface fluxes are mainly controlled by mechanical turbulence, which is only present in the afternoon due to a regional-scale flow resulting from the thermal contrast between the cool Pacific Ocean and the warm Atacama Desert. Thirdly, the regional flow that triggers evaporation in the Altiplano origins from the marine boundary layer, whose stability regime dominates the formation of fog and the inland moisture transport. Finally, the role of surface heterogeneity on turbulent fluxes measurements is quantified at the sub-kilometer scale, where footprint and MOST functions play an important role. This thesis contributes to untangling and linking processes driving evaporation from local to regional-scale and from sub-diurnal to inter-annual scale, across confined saline lakes in arid regions.

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 flux-gradient 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 co

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

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‐Dor 3‐D radiative transfer. Based ona 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 radiativetransfer. 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, suggestingthat 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 furthertested for generalizability in future studies.

Motivation: Ethiopia is one of the Sub-Saharan countries that are strongly influenced by climate fluctuations. These meteorological changes directly affect agriculture and consequently cause disturbances on the regional and local economy. To pinpoint a few crucial issues: (1) the agricultural sector in Ethiopia accounts for 80% of the employment and contributes 45% of the GDP. A relevant factor in relation to this PhD thesis is that the country’s agriculture is by 95% rainfed agronomy. (2) The Ethiopian landscape is composed of complex terrains of the East African mountain system – the Ethiopian Highlands (40% of the Ethiopia’s landmass is elevated more than 1500 m above sea level). This complex orography modulates weather and climate at scales ranging from local to regional. In the region, weather dynamics are mainly driven by both synoptic (e.g. Intertropical Convergence Zone – ITCZ) and mesoscale flows (e.g. lake and mountain breezes). These weather scales ultimately influence the way crops grow. The aim of this study was to evaluate how weather and crop growth vary in a complex terrain and heterogeneous landscape. I focus on the Gamo Highlands, south-west Ethiopia, a mountainous region with two large Rift-Valley lakes in Ethiopia. The crop of interest was potato – a crop that has become popular in Ethiopia, significantly contributing to food security and income, but sensitive to climatic variations. As a research method, I deployed a high-resolution weather and crop modelling approach to describe how the growth and yield of the potato crop depend on the variations in weather. For observation-based studies and for testing the models’ performance, six automatic weather stations were installed and field crop experiments were conducted near the stations. More specifically, this thesis addresses the role of meteorological crop drivers (e.g. the incoming shortwave radiation (SW↓), maximum temperature (Tmax), minimum temperature (Tmin) and precipitation (PPT)) and edap

The interactions between biogenic volatile organic compounds (BVOCs), like isoprene and monoterpenes, and anthropogenic emissions of nitrogen and sulfur oxides lead to high concentrations of secondary organic aerosol (SOA) in the southeastern United States. To improve our understanding of SOA formation, we study the diurnal evolution of SOA in a land–atmosphere coupling context based on comprehensive surface and upper air observations from a characteristic day during the 2013 Southern Oxidant and Aerosol Study (SOAS) campaign. We use a mixed layer model (MXLCH-SOA) that is updated with new chemical pathways and an interactive land surface scheme that describes both biogeochemical and biogeophysical couplings between the land surface and the atmospheric boundary layer (ABL) to gain insight into the drivers of the daytime evolution of biogenic SOA.MXLCH-SOA reproduces observed BVOC and surface heat fluxes, gas-phase chemistry, and ABL dynamics well, with the exception of isoprene and monoterpene mixing ratios measured close to the land surface. This is likely due to the fact that these species do not have uniform profiles throughout the atmospheric surface layer due to their fast reaction with OH and incomplete mixing near the surface. The flat daytime evolution of the SOA concentration is caused by the dampening of the increase due to locally formed SOA by entrainment of SOA-depleted air from the residual layer. SOA formation from isoprene through the intermediate species isoprene epoxydiols (IEPOXs) and isoprene hydroxyhydroperoxides (ISOPOOHs) is in good agreement with the observations, with a mean isoprene SOA yield of 1.8 %.However, SOA from monoterpenes, oxidised by OH and O3, dominates the locally produced SOA (69 %), with a mean monoterpene SOA yield of 10.7 %. Isoprene SOA is produced primarily through OH oxidation via ISOPOOH and IEPOX (31 %). Entrainment of aged SOA from the residual layer likely contributes to the observed more oxidised oxygenated organic

The effects of increases in carbon dioxide and temperature on the vegetation‐atmosphere‐cloud interaction are studied with a bottom‐up approach. Using the 3‐D large‐eddy simulation technique coupled with a CO2‐sensitive dynamic plant physiological submodel, we aimed to spatially and temporally understand the surface and vegetation forcing on the coupled land‐atmosphere interactions in future scenarios. Four simulations were designed: a control simulation for current conditions, an enhanced carbon dioxide simulation (current +200 ppm), an elevated temperature simulation (current +2 K), and a simulation covering the combination of both elevations in temperature and CO2. With elevations in carbon dioxide, plant transpiration is reduced due to stomatal closure, resulting in reduced latent‐ and increased sensible heat fluxes. Although no effects on cloud cover were found in this simulation, the in‐cloud moisture flux was enhanced. Elevations in temperature yielded opposite results with reduced sensible and increased latent heat fluxes, which reduced the turbulent kinetic energy and buoyancy rates, thereby negatively impacting cloud formation. Our future climate mimicking simulation shows minimal changes in the regional energy balance due to offsetting effects between increased temperature and [CO2], while plant photosynthesis increased and transpiration decreased. The atmospheric boundary layer was drier, even though surface fluxes were very similar current conditions, thereby hampering cloud formation and development. Our results highlight the necessity of small scales and interactions, which require a bottom‐up approach to be able to accurately capture the nonlinear plant‐atmosphere interactions.

We investigated sharp disruptions of local turbulence and scalar transport due to the arrival of sea‐breeze fronts (SBFs). To this end, we employed a comprehensive 10‐year observational database from the Cabauw Experimental Site for Atmospheric Research (CESAR, the Netherlands). Sea‐breeze (SB) days were selected using a five‐filter algorithm, which accounts for large‐scale conditions and a clear mesoscale‐frontal signal associated with the land–sea contrast. Among those days (102 in all, 8.3%), based on the value of the sensible‐heat flux at the onset of SB, we identified three atmospheric boundary‐layer (ABL) regimes: convective, transition and stable. In the convective regime, the thermally driven convective boundary layer is only slightly altered by a small enhancement of the shear when the SBF arrives. Regarding the transition regime, we found that the ABL afternoon transition is accelerated. This was quantified by estimating the contributions of shear and buoyancy to the turbulent kinetic energy. Other relevant disruptions are the sharp reduction in ABL depth (∼250 m/hr) and the sudden increase in average wind speed (> 2 m/s). In the stable regime, the arrival of the SB leads to disturbances in the wind profile at the surface layer. We observed a deviation of more than 1 m/s in the observed surface‐layer wind profile compared with the profile calculated using Monin–Obukhov Similarity Theory (MOST). Our findings furthermore reveal the determinant role of the SB direction in the transport of water vapour, CO2 and 222Rn. The return of continental air masses driven by the SB circulation generates sharp CO2 increases (up to 14 ppm in half an hour) in a few SB events. We suggest that the variability in 222Rn evolution may also be influenced by other non‐local processes such as the large‐scale footprint from more remote sources.

The Gamo Highlands in Ethiopia are characterized by complex topography and lakes. These modulate the mesoscale and synoptic scale weather systems. In this study, we analyzed the temporal and spatial variations in weather as function of topography and season and their impact on potato crop growth. To determine how crop growth varies with elevation, we installed a network of six automatic weather stations along two transects. It covers a 30-km radius and 1800-m elevation difference. We conducted a potato field experiment near the weather stations. We used the weather observations as input for a crop model, GECROS. Data analysis showed large differences between weather in February and May. February is more dominated by mesoscale circulations. The averaged February diurnal patter shows a strong east to southeast lake breezes and, at night, weak localized flows driven by mountain density flows. In contrast, in May, the synoptic flow dominates, interacting with the mesoscale flows. The GECROS model satisfactorily predicted the elevational gradient in crop yield. Model sensitivity experiments showed that belg-averaged precipitation distribution gave the highest yield, followed by exchanging May weather observations with April.

This thesis deals with the representation of the exchange of energy, momentum and chemically reactive compounds between the land, covered by high vegetation, and the lowest part of the atmosphere, named as atmospheric boundary layer (ABL). The study presented in this thesis introduces the roughness sublayer (RSL), the layer just above the tall vegetation canopy in which the atmospheric flow is directly affected by the presence of roughness elements, as an important part of the ABL system. Our focus is on the exchange of the thermodynamic, as well as the chemical properties of the boundary layer. Our methodology combines observational analysis using high resolution meteorological and chemistry measurements from the Canopy Horizontal Array Turbulence Study (CHATS) and modelling framework of the soil-vegetation-atmospheric boundary layer system. The systematic investigation in this thesis showed the relevance of the RSL for the turbulent exchange processes between the atmosphere and the land surface characterized by high vegetation. More specifically, we explained and discussed how the turbulence parameterization within the roughness sublayer is strongly dependent on canopy-phenology (canopy leaf state) and atmospheric-stability changes, and provided parameterization formulations for . Our modelling analysis further showed that the CHATS boundary-layer dynamics are mainly affected and controlled by the large-scale processes (advection and subsidence), while the effect of the canopy and the roughness sublayer were relatively small. Near the canopy top however, the the canopy had a significant impact on the modelled boundary layer state variables (wind speed, potential temperature and specific humidity) and the corresponding turbulent transfer coefficients (drag coefficients for momentum and scalars), as supported by the observations. With respect to the exchange of reactive compounds, we diagnosed twice-larger magnitude of the ozone deposition fluxes when the roughness

The representation of a neutral atmospheric flow over roughness elements simulating a vegetation canopy is compared between two large-eddy simulation models, wind-tunnel data and recently updated empirical flux-gradient relationships. Special attention is devoted to the dynamics in the roughness sublayer above the canopy layer, where turbulence is most intense. By demonstrating that the flow properties are consistent across these different approaches, confidence in the individual independent representations is bolstered. Systematic sensitivity analyses with the Dutch Atmospheric Large-Eddy Simulation model show that the transition in the one-sided plant-area density from the canopy layer to unobstructed air potentially alters the flow in the canopy and roughness sublayer. Anomalously induced fluctuations can be fully suppressed by spreading the transition over four steps. Finer vertical resolutions only serve to reduce the magnitude of these fluctuations, but do not prevent them. To capture the general dynamics of the flow, a resolution of 10 % of the canopy height is found to suffice, while a finer resolution still improves the representation of the turbulent kinetic energy. Finally, quadrant analyses indicate that momentum transport is dominated by the mean velocity components within each quadrant. Consequently, a mass-flux approach can be applied to represent the momentum flux.

Forests impact regional hydrology and climate directly by regulating water and heat fluxes. Indirect effects through cloud formation and precipitation can be important in facilitating continental-scale moisture recycling but are poorly understood at regional scales. In particular, the impact of temperate forest on clouds is largely unknown. Here we provide observational evidence for a strong increase in cloud cover over large forest regions in western Europe based on analysis of 10 years of 15 min resolution data from geostationary satellites. In addition, we show that widespread windthrow by cyclone Klaus in the Landes forest led to a significant decrease in local cloud cover in subsequent years. Strong cloud development along the downwind edges of larger forest areas are consistent with a forest-breeze mesoscale circulation. Our results highlight the need to include impacts on cloud formation when evaluating the water and climate services of temperate forests, in particular around densely populated areas.

Guided by a holistic approach, the combined effects of direct and diffuse radiation on the atmospheric boundarylayer dynamics over vegetated land are investigated on a daily scale. Three numerical experiments are designed thatare aimed at disentangling the role of diffuse and direct radiation below shallow cumulus at the surface and onboundary layer dynamics. A large-eddy simulation (LES) model coupled to a land surface model is used,including a mechanistically immediate response of plants to radiation, temperature, and water vapor deficitchanges. The partitioning in direct and diffuse radiation created by clouds and farther inside the canopy is explicitlyaccounted for. LES results are conditionally averaged as a function of the cloud optical depth. The findings showlarger photosynthesis under thin clouds than under clear sky, due to an increase in diffuse radiation and a slightdecrease in direct radiation. The reduced canopy resistance is the main driver for the enhanced carbon uptake byvegetation, while the carbon gradient and aerodynamic effects at the surface are secondary.Because of the couplingof CO2 and water vapor exchange through plant stomata, evapotranspiration is also enhanced under thin clouds,albeit to a lesser extent. This effect of diffuse radiation increases the water use efficiency and evaporative fractionunder clouds. The dynamic perturbations of the surface fluxes by clouds do not affect general boundary layer orcloud characteristics because of the limited time and space where these perturbations occur. It is concluded that anaccurate radiation partitioning calculation is necessary to obtain reliable estimations on local surface processes.