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As human encroachment increases in the Amazon rain forest, it is important to determine how anthropogenic emissions of reactive gases affect regional atmospheric chemistry. In the present study, we investigate the extent to which urban air plumes modify the levels of ozone (O3) and nitrogen oxides (NOX) in the downwind rain forest. The median mixing ratios of the background O3, NOX, and NOX oxidation products (NOZ) were 20 (15 parts per billion on a volume basis, ppbv), 0.6 ppbv (0.6 ppbv), and 1.0 ppbv (0.5 ppbv) during the dry (wet) season at the study site. Compared to the background environment, air plumes from the city of Manaus had enhanced median mixing ratios for O3 and NOZ by 30–50% and 40–90%, respectively. However, the enhancements of NOX in the air plumes were less than 20%, indicating that the majority of NOX was chemically converted to O3 and NOZ during transport. Results from a photochemical model showed that an injection of 8 ppbv of NOX into the rain forest can cause up to 260% and 150% increases in O3 and hydroxyl radical (OH) levels compared to the background conditions, indicating the likely extent that NOX can modify the air quality and oxidative capacity in the Amazon rain forest. Slopes of the O3-temperature linear relationships increased with NOX levels from 3.7 to 6.5 ppbv per degree Kelvin during the dry season and 1.7–5.5 ppbv per degree Kelvin during the wet season. Average rates of change of the slope with respect to NOZ were approximately 1.8 and 2.3 times higher than those with respect to NOX for the dry and wet seasons. One key conclusion of this study is that NOZ substantially contributed to the O3 formation in response to temperature under enhanced NOX conditions in the forested environment.

A framework to describe transport and deposition of ultrafine particles (UFP) within forests using large eddy simulation (LES) is presented. Comparison with measurements collected within and above a Scots pine stand in Southern Finland are used to explore the plausibility of the simulations. The numerical model is then employed to quantify the effects of canopy morphology (leaf area index and leaf area density), turbulence intensity, and particle size on the partitioning between upper canopy and subcanopy deposition and the overall deposition velocities. Results show a complex interplay between canopy morphology and turbulence, which is reflected on the particle flux profiles within the canopy. However, mean particle concentration profiles, total deposition, and deposition velocities at the canopy top are insensitive to the leaf area density profile but show dependence mostly on leaf area index, turbulence levels, and particle size. Finally, with the goal of understanding the sensitivity of the deposition velocity to all these parameters, an analytical model is developed that shows good agreement with LES results (within ± 20 % ) for all conditions simulated here.

The Amazon rain forest is a major global isoprene source, but little is known about its seasonal ambient concentration patterns. To investigate the environmental and phenological controls over isoprene seasonality, we measured isoprene mixing ratios, concurrent meteorological data, and leaf area indices from April 2014 to January 2015 above a rain forest in the central Amazon, Brazil. Daytime median isoprene mixing ratios varied throughout the year by a factor of two. The isoprene seasonal pattern was not solely driven by sunlight and temperature. Leaf age and quantity also contributed to the seasonal variations of isoprene concentrations, suggesting leaf phenology was a crucial variable needed to correctly estimate isoprene emissions. A zero-dimensional model incorporating the estimated emissions, atmospheric boundary layer dynamics, and air chemistry was used to assess the contributions of each process on the variability of isoprene. Surface deposition was an important sink mechanism and accounted for 78% of the nighttime loss of isoprene. Also, chemical reactions destroyed isoprene and during 6:00 to 18:00 h local time 56, 77, 69, and 69% of the emitted isoprene was chemically consumed in June, September, December, and January, respectively. Entrainment fluxes from the residual layer contributed 34% to the early-morning above-canopy isoprene mixing ratios. Sensitivity analysis showed that hydroxyl radical (HO) recycling and segregation of isoprene–HO played relatively lesser roles (up to 16%) in regulating ambient isoprene levels. Nitric oxide (NO) levels dominated isoprene chemical reaction pathways associated with consumption and production of HO under low-NO and high volatile organic compound (VOC) conditions. While surface deposition and oxidative processes altered isoprene levels, the relative importance of these factors varied seasonally with leaf phenology playing a more important role.

The suitability of Kerstein's One-Dimensional Turbulence (ODT) model in the representation of atmospheric boundary layer (ABL) flows within and above plant canopies is investigated. The ODT model was adapted to represent a filtered version of flow and scalar fields, equipped with a Smagorinsky-like sub-grid scale model, a wall model, and a parameterization of the canopy effects on the flow. In the filtered ODT, the entire vertical extension of the ABL is modeled and the “resolved” vertical turbulent transport is represented by stochastic eddies that effectively mix fluid parcels across a path length, representing non-local turbulent fluxes that are a critical feature of the canopy roughness sublayer. Simulations for different canopies and stability conditions are performed and vertical profiles of turbulence and scalar statistics are compared with observational and large-eddy simulation data. This new filtered version of the ODT model yields grid-independent results. Model performance for plant canopies is consistent with previous results from ODT for all cases tested without any case-specific parameter adjustment, generating reasonable agreement in profiles of mean velocity, temperature and water vapor mixing ratio, as well as vertical fluxes of momentum and sensible and latent heat, despite the underestimation of all velocity variances. Non-local transport is intrinsic to the formulation of ODT, which represents a significant advantage compared to other reduced-model approaches employed for canopy flows.

In this study a stochastic wall model based on the “large-eddy” version of the One-Dimensional Turbulence (ODT) model was developed for Large-Eddy Simulation (LES) of smooth and rough channel flows, with the primary goal of providing a refined turbulent flow field near the wall. This LES-ODT coupling was tested with the dynamic Smagorinsky and the scale-dependent Lagrangian dynamic subgrid-scale models. When compared to the same LES with a wall model based on a local law-of-the-wall, LES-ODT improved the one-dimensional energy spectra for all three velocity components close to the wall for both subgrid-scale models tested. More importantly, improving the LES wall model had a more positive effect in the near-wall spectra than improving the subgrid-scale model from the traditional dynamic to the scale-dependent Lagrangian dynamic model. For smooth channels, LES-ODT results compared well with DNS of R e λ = 590 and 5200; however, the variance modeled by the ODT presents discrepancies for all three velocity components, an issue inherent to ODT. Finally, the simulation of a channel flow with additional roughness modeled by a drag force was compared to data of atmospheric flow through a maize field, providing evidence of the potential for this approach to directly simulate complex near-wall phenomena. Given its high computational cost, the main use of the LES-ODT coupling is in studies that require a refinement of the near-wall region without the need to refine the entire LES domain.

In this work, we investigate the ozone dynamics during the occurrence of both downdrafts associated with mesoscale convective storms and non-classical low-level jets. Extensive data sets, comprised of air chemistry and meteorological observations made in the Amazon region of Brazil over the course of 2014–15, are analyzed to address several questions. A first objective is to investigate the atmospheric thermodynamic and dynamic conditions associated with storm-generated ozone enhancements in the Amazon region. A second objective is to determine the magnitude and the frequency of ground-level ozone enhancements related to low-level jets. Ozone enhancements are analyzed as a function of wind shear, low-level jet maximum wind speed, and altitude of jet core. Strong and sudden increases in ozone levels are associated with simultaneous changes in variables such as horizontal wind speed, convective available potential energy, turbulence intensity and vertical velocity skewness. Rapid increases in vertical velocity skewness give support to the hypothesis that the ozone enhancements are directly related to downdrafts. Low-level jets associated with advancing density currents are often present during and after storm downdrafts that transport ozone-enriched air from aloft to the surface.

Traffic-related pollutant concentrations are typically much higher in near-roadway microenvironments, and pedestrian and resident exposures to air pollutants can be substantially increased by the short periods of time spent on and near roadways. The design of the built environment plays a critical role in the dispersion of pollutants at street level; after normalizing for traffic, differences of a factor of ~5 have been observed between urban neighborhoods with different built environment characteristics. We examined the effects of different built environment designs on the concentrations of street-level ultrafine particles (UFP) at the scale of several blocks using the Quick Urban and Industrial Complex (QUIC) numerical modeling system. The model was capable of reasonably reproducing the complex ensemble mean 3D air flow patterns and pollutant concentrations in urban areas at fine spatial scale. We evaluated the effects of several built environment designs, changing building heights and spacing while holding total built environment volumes constant. We found that ground-level open space reduces street-level pollutant concentrations. Holding volume/surface area constant, tall buildings clustered together with larger open spaces between buildings resulted in substantially lower pollutant concentrations than buildings in rows. Buildings arranged on a ‘checkerboard’ grid with smaller contiguous open spaces, a configuration with some open space on one of the sides of the roadway at all locations, resulted in the lowest average concentrations for almost all wind directions. Rows usually prohibit mixing for perpendicular and oblique wind directions, even when there are large spaces between them, and clustered buildings have some areas where buildings border both sides of the roadways, inhibiting mixing. The model results suggest that pollutant concentrations drop off rapidly with height in the first 10 m or so above the roadways. In addition, the simulated vertical concentration profiles show a moderate elevated peak at the roof levels of the shorter buildings within the area. Model limitations and suggestions both for urban design are both discussed.

Inland deposition of sea salt aerosol (SSA) particles emitted over the ocean is studied via numerical and theoretical models. The focus is on the large particles that contribute most to the total mass deposition. Large eddy simulations of idealized sea wind are used to investigate the development of the particle plume over land for different particle sizes and to validate some of the assumptions in the theoretical model. An existing theoretical modeling framework for particle dispersion in the atmospheric boundary layer is adapted to the problem of SSA deposition and it is shown to be adequate for the large particles of interest here. The decay of monodisperse SSA particle deposition flux with distance from the shoreline is shown to have a power-law behavior far from the shoreline. A complete model for predicting mass deposition as a function of distance is formulated and shown to present reasonable agreement with existing data.

Flowers emit mixtures of scents that mediate plant-insect interactions such as attracting insect pollinators. Because of their volatile nature, however, floral scents readily react with ozone, nitrate radical, and hydroxyl radical. The result of such reactions is the degradation and the chemical modification of scent plumes downwind of floral sources. Large Eddy Simulations (LES) are developed to investigate dispersion and chemical degradation and modification of floral scents due to reactions with ozone, hydroxyl radical, and nitrate radical within the atmospheric surface layer. Impacts on foraging insects are investigated by utilizing a random walk model to simulate insect search behavior. Results indicate that even moderate air pollutant levels (e.g., ozone mixing ratios greater than 60 parts per billion on a per volume basis, ppbv) substantially degrade floral volatiles and alter the chemical composition of released floral scents. As a result, insect success rates of locating plumes of floral scents were reduced and foraging times increased in polluted air masses due to considerable degradation and changes in the composition of floral scents. Results also indicate that plant-pollinator interactions could be sensitive to changes in floral scent composition, especially if insects are unable to adapt to the modified scentscape. The increase in foraging time could have severe cascading and pernicious impacts on the fitness of foraging insects by reducing the time devoted to other necessary tasks.

Large-eddy simulation (LES) has proven to be a valuable tool for high-fidelity modeling of environmental and geophysical turbulent flows. An important application of LES is to study the transport of effluents (e.g. oils from a subsea blowout) in the ocean mixed layer (OML). Oil plumes being transported in the OML experience the action of shear-generated turbulence, Langmuir circulations, Ekman transport and submesoscale quasi-geostrophic eddies. To resolve such turbulent processes, grid sizes of a few meters are desirable while horizontal domain sizes of LES are typically restricted from hundreds of meters to a few kilometers, for LES to remain practically affordable. Yet transported oil plumes evolve to large scales extending to tens or even hundreds of kilometers. In this study, the Extended Nonperiodic Domain LES for Scalar transport (ENDLESS) is proposed as a multi-scale approach to tackle this challenge while being computationally affordable. The basic idea is to simulate the shear turbulence and Langmuir circulations on a small horizontal domain with periodic boundary conditions while the resulting transport velocity field is replicated periodically following adaptively the large-scale plume as it evolves spatially towards much larger scales. This approach also permits the superposition of larger-scale quasi two-dimensional flow motions on the oil advection, allowing for coupling with regional circulation models. A validation case and two sample applications to oil plume evolution in the OML are presented in order to demonstrate key features and computational speedup associated with the ENDLESS method.

From April 2014 to January 2015, ozone (O3) dynamics were investigated as part of GoAmazon 2014/5 project in the central Amazon rainforest of Brazil. Just above the forest canopy, maximum hourly O3 mixing ratios averaged 20 ppbv (parts per billion on a volume basis) during the June–September dry months and 15 ppbv during the wet months. Ozone levels occasionally exceeded 75 ppbv in response to influences from biomass burning and regional air pollution. Individual convective storms transported O3-rich air parcels from the mid-troposphere to the surface and abruptly enhanced the regional atmospheric boundary layer by as much as 25 ppbv. In contrast to the individual storms, days with multiple convective systems produced successive, cumulative ground-level O3 increases. The magnitude of O3 enhancements depended on the vertical distribution of O3 within storm downdrafts and origin of downdrafts in the troposphere. Ozone mixing ratios remained enhanced for > 2 h following the passage of storms, which enhanced chemical processing of rainforest-emitted isoprene and monoterpenes. Reactions of isoprene and monoterpenes with O3 are modeled to generate maximum hydroxyl radical formation rates of 6 × 106 radicals cm−3s−1. Therefore, one key conclusion of the present study is that downdrafts of convective storms are estimated to transport enough O3 to the surface to initiate a series of reactions that reduce the lifetimes of rainforest-emitted hydrocarbons.

In this study, large eddy simulation (LES) is adopted to evaluate the aerodynamic and deposition effects of street trees on fine particulate matter (PM2.5) concentration within street canyons. The Extended Nonperiodic Domain LES for Scalar Transport (ENDLESS) is used to allow exploration of vegetation effects at a neighborhood scale (up to 100 canyons) while maintaining a reasonable resolution required to resolve flow patterns within each canyon. We investigate three emission scenarios: (i) only local traffic emissions within the canyon (the first canyon in the urban environment); (ii) only background pollution originating from the upwind canyons; and (iii) a combination of scenarios (i) and (ii). Numerical results show that the presence of trees has different effects on the PM2.5 level within canyons in different emission scenarios and at different spatial scales. At the street scale with only local traffic emissions, aerodynamic effect of trees results in an increase in the concentration near leeward walls and a decrease in the concentration near windward walls, which overwhelms the deposition effect. On the other hand, trees have a negligible impact on the transport of background pollution into the canyon or its distribution within the canyons. The deposition has beneficial effects that only manifest in a considerable way at the neighborhood scale. Finally, the effect of trees on a simple operational urban pollution model (OUPM) is investigated. After modifications for aerodynamic and deposition effect of trees, the predictions of the OUPM show good agreement with LES results.

Plant disease epidemics caused by pathogenic spores are common threat to agricultural crops. Pathogenic spores are often produced and released inside plant canopies but are transported out of the canopy region by turbulent motions and advected longitudinally over long distances so as to infect other fields. Hence, the fraction of spores that “escape” the canopy sets the effective source strength that determines how fast and far plant diseases can spread. To explore the governing variables of this escape and spatial spread of spores, extensive spore release and recapture experiments were conducted in a maize field and interpreted using a coupled Eulerian–Lagrangian stochastic model (LSM). Spores were released from point sources located at three prototypical depths inside the canopy. Concentration measurements were obtained inside and above the canopy with a 3-dimensional grid of spore collectors. The experimental measurements of mean spore concentration were then used to evaluate an LSM for spore dispersion. The drift and dispersion terms of the LSM were predicted employing a conventional second-order closure model of turbulence within plant canopies thereby allowing this combined Eulerian–Lagrangian formulation to be applied to a broad set of agricultural crops. The dispersion model includes spore deposition on and rebound from canopy elements. The combination of experimental and numerical simulations was then used to quantify the fraction of spores that escape the canopy. Effects of release height and friction velocity on the escape fraction of spores were explored with the LSM.

An analytical model for dispersion of biological particles such as spores and pollens released from finite area sources into the atmospheric boundary layer is proposed. The model is applicable to rectangular fields aligned with the mean wind and accounts for effects of turbulent dispersion in the vertical and crosswind direction, as well as depletion of airborne material due to dry deposition. Predictions for the mean particle concentration above the area source and ground deposition downwind from it are derived and validated against detailed numerical simulations of pollen dispersal using large eddy simulation. Effects of particle settling velocity and area source size and geometry on dispersal patterns are investigated. Results show that along the centerline above the source, effects of crosswind dispersion are negligible (except for very narrow area sources). Ground deposition fluxes downwind from the source are strongly affected by crosswind dispersion. Similarly to area sources infinitely long in the crosswind direction, deposition fluxes far from rectangular sources display a power-law decay with distance. The power-law exponent is larger than the one for infinitely wide fields and depends on the relative importance of gravitational settling and turbulent dispersion in the vertical and crosswind directions, but does not depend on source geometry. However, the distance from the source at which the power-law decay is first observed does depend on source geometry.

Settlingvelocityofmaize(ZeamaysL.)pollenplaysanimportantroleinitsdispersaland,therefore,cross-pollination. Estimated probability density functions (PDFs) of settling velocity based on experimentalmeasurements show strong variation between early morning and noon. The variation is correlated tothe time-integrated vapor pressure deficit (VPDT) and reflects the drying of pollen grains. A model forthe decrease in germination rate of pollen grains exposed to atmospheric conditions suggests that thedecrease in settling velocity is accompanied by a decrease in pollen viability. A simple dispersion modelis used to illustrate the possible consequences of changes in settling velocity and germination rate forpollen dispersal and cross-pollination of maize. Results suggest that current models of pollen dispersalthat do not account for these changes overestimate cross-pollination rates.© 2011 Elsevier B.V. All rights reserved. 1. IntroductionQuantifying and predicting gene flow and rates of cross-pollination in maize (Zea mays L.) have been the focus of muchresearch in the past few decades. This information is important inthe development of strategies for gene flow management, whichare required to ensure maximum kernel set and high levels ofgeneticpurityinhybridseedproduction(Aylor,2003;FonsecaandWestgate, 2005) and to minimize risks associated with the spreadof genetically modified traits (Wolfenbarger and Phifer, 2000). Acomplete model of cross-pollination has to account for pollen pro-duction and release at the source, pollen entrainment into theturbulent atmosphere, pollen dispersion and deposition, pollenviability, competition with local pollen at the receptor plant, andfertilization (e.g., see Aylor et al., 2003). The entrainment, disper-sion and deposition processes are governed by the characteristicsof atmospheric turbulence and physical properties of pollen grainssuch as shape, size, density and surface characteristics (Chameckietal.,2007).Pollenpropertiesdeterminetheinertiaofpollengrainsand, therefore, their response to turbulent motion. Typically, dis-persion models neglect pollen inertia using its settling velocity instillfluidtorepresenttheeffectsofthepollenpropertiesondisper-sion (Jarosz et al., 2004; Dupont et al., 2006; Chamecki et al., 2009;Viner and Arritt, 2010). In this simplified modeling approach, the

Diurnal cycles of pollen dispersal are an important aspect of gene flow between wind-pollinated plants. Previous attempts to correlate these cycles with variation in meteorological factors have had little success. In Ambrosia artemisiifolia (common ragweed) and other species which produce aeroallergenic pollen, these cycles also present a major burden to public health. In a large field dominated by A. artemisiifolia, we collected measurements of low-atmosphere pollen concentration and pollen release from individual A. artemisiifolia flowers. We then constructed a relatively simple model that relates early morning variations in relative humidity to the probability distribution of anther dehiscence initiation timing and incorporates quantitative data on the progression of diurnal pollen release from individual male flowers. The model successfully predicts normalized pollen concentration above the field. We suggest that the extension of a tiny floral organ unique to this genus and some closely related taxa explains a ubiquitous, but previously overlooked, large-scale feature in patterns of A. artemisiifolia pollen dispersal. Our study shows that pollen release at the flower scale is a physiological characteristic that is intrinsically bimodal, but highly asynchronous anther rupture caused by variations in relative humidity sometimes obscures this effect and determines the overall pattern of pollen release at the scale of the entire field. We suggest that future attempts to predict diurnal pollen dispersal cycles should consider direct observations of species-specific floral development and morphology.

This paper presents a framework to simulate pollen dispersal by the wind based on the large eddy simulation (LES) technique. Important phenomena such as the pollen emission by the plants and the ground deposition are parameterized by the lower boundary condition. The numerical model is validated against previously published experiments of point source releases of glass beads and pollen grains in the atmospheric boundary layer. The numerical model is used together with experimental data of pollen emission and downwind deposition from a natural field obtained near Washington, DC, in the summer of 2006. The combined analysis of experimental and numerical data allows to elucidate the emission/transport/deposition process in considerable detail. In particular, the relative fractions of pollen deposited inside the source field and airborne at the edge of the field can be quantified. The use of LES allows quantification of important intermittent deposition events far from the source field.

Field experiments were performed to study the diurnal cycle of corn pollen emission and its relation to local meteorological conditions, including temperature, relative humidity, solar radiation, mean wind speed, and turbulence quantities. Pollen concentrations were measured from canopy height to twice this level using four Rotorod samplers located on a pole in the middle of the corn field. The measured pollen concentration at canopy height was used as a surrogate for the pollen source strength while the concentrations above canopy represented the pollen transported upwards from canopy height. At twice the canopy height, the pollen concentration decreased considerably to about 30% of the canopy height values. During the mornings, pollen was emitted in large quantities while during the afternoons, airborne pollen concentrations decreased and no significant atmospheric pollen was measured from about 2 h prior to sunset until sunrise the next morning. The actual time that airborne pollen was first recorded differed from day-to-day and depended on the time required for the anthers to dry and open, as well as there being sufficiently strong winds to entrain the pollen away from the plants. On four consecutive mornings diurnal atmospheric pollen concentration distributions were bi-modal in time. The first pollen concentration peak happened shortly before the direct irradiance peak on the anthers suggesting that direct solar irradiation might be important for drying the anthers. The subsequent dip in pollen concentration seemed to be linked to a lull in mean and turbulent wind conditions. Analysis of the vertical velocity fluctuations, sw, showed that the fraction of pollen transported upwards from canopy height increased with increasing sw. In addition, Quadrant– Hole analysis applied to the turbulence data sets of 2 days suggested that low values of ejection duration fractions were associated with low values of pollen concentration, while high values were associated with high concentration values. The diurnal pattern of ejection duration fractions was similar to the pattern of the fraction of pollen that reached twice the canopy height, indicating