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Abstract. Ground-level ozone (O3) is a major air pollutant that adversely affects human health and ecosystem productivity. Removal of troposphericO3 by plant stomatal uptake can in turn cause damage to plant tissues with ramifications for ecosystem and crop health. In manyatmospheric and land surface models, the functionality of stomata opening is represented by a bulk stomatal conductance, which is oftensemi-empirically parameterized and highly fitted to historical observations. A lack of mechanistic linkage to ecophysiological processes such asphotosynthesis may render models inadequate to represent plant-mediated responses of atmospheric chemistry to long-term changes in CO2,climate, and short-lived air pollutant concentrations. A new ecophysiology module was thus developed to mechanistically simulate land−atmosphereexchange of important gas species in GEOS-Chem, a chemical transport model widely used in atmospheric chemistry studies. The implementation not onlyallows for dry deposition to be coupled with plant ecophysiology but also enables plant and crop productivity and functions to respond dynamically toatmospheric chemical changes. We conduct simulations to evaluate the effects of the ecophysiology module on simulated dry deposition velocity andconcentration of surface O3 against an observation-derived dataset known as SynFlux. Our estimated stomatal conductance and dry depositionvelocity of O3 are close to SynFlux with root-mean-squared errors (RMSEs) below 0.3 cm s−1 across different plant functionaltypes (PFTs), despite an overall positive bias in surface O3 concentration (by up to 16 ppbv). Representing ecophysiology wasfound to reduce the simulated biases in deposition fluxes from the prior model but worsen the positive biases in simulated O3concentrations. The increase in positive concentration biases is mostly attributable to the ecophysiology-based stomatal conductance being generallysmaller (and closer to SynFlux values) than that estimated by the prior semi-empirical formulation, calling for further improvements in non-stomataldepositional and non-depositional processes relevant for O3 simulations. The estimated global O3 deposition flux is864 Tg O3 yr−1 with GEOS-Chem, and the new module decreases this estimate by 92 Tg O3 yr−1. Estimated global grossprimary production (GPP) without O3 damage is 119 Pg C yr−1. O3-induced reduction in GPP is 4.2 Pg C yr−1(3.5 %). An elevated CO2 scenario (580 ppm) yields higher global GPP (+16.8 %) and lower global O3depositional sink (−3.3 %). Global isoprene emission simulated with a photosynthesis-based scheme is 317.9 Tg C yr−1, which is31.2 Tg C yr−1 (−8.9 %) less than that calculated using the MEGAN(Model of Emissions of Gases and Aerosols from Nature) emission algorithm. This new model development dynamicallyrepresents the two-way interactions between vegetation and air pollutants and thus provides a unique capability in evaluating vegetation-mediatedprocesses and feedbacks that can shape atmospheric chemistry and air quality, as well as pollutant impacts on vegetation health, especially for anytimescales shorter than the multidecadal timescale. 

Abstract. Dry deposition is a key process for surface ozone(O3) removal. Stomatal uptake is a major component of O3 drydeposition, which is parameterized differently in current land surfacemodels and chemical transport models. We developed and used a standaloneterrestrial biosphere model, driven by a unified set of prescribedmeteorology, to evaluate two widely used dry deposition modeling frameworks,Wesely (1989) and Zhang et al. (2003), with different configurations ofstomatal resistance: (1) the default multiplicative method in the Weselyscheme (W89) and Zhang et al. (2003) scheme (Z03), (2) the traditionalphotosynthesis-based Farquhar–Ball–Berry (FBB) stomatal algorithm, and (3) theMedlyn stomatal algorithm (MED) based on optimization theory. We found thatusing the FBB stomatal approach that captures ecophysiological responses toenvironmental factors, especially to water stress, can generally improve thesimulated dry deposition velocities compared with multiplicative schemes.The MED stomatal approach produces higher stomatal conductance than FBB andis likely to overestimate dry deposition velocities for major vegetationtypes, but its performance is greatly improved when spatially varying slopeparameters based on annual mean precipitation are used. Large discrepancieswere also found in stomatal responses to rising CO2 levels from 390to 550 ppm: the multiplicative stomatal method with an empirical CO2response function produces reduction (−35 %) in global stomatalconductance on average much larger than that with the photosynthesis-basedstomatal method (−14 %–19 %). Our results show the potential biases inO3 sink caused by errors in model structure especially in the Weselydry deposition scheme and the importance of using photosynthesis-basedrepresentation of stomatal resistance in dry deposition schemes under achanging climate and rising CO2 concentration. 

The NOAA/NASA Fire Influence on Regional to Global Environments and Air Quality (FIREX‐AQ) experiment was a multi‐agency, inter‐disciplinary research effort to: (a) obtain detailed measurements of trace gas and aerosol emissions from wildfires and prescribed fires using aircraft, satellites and ground‐based instruments, (b) make extensive suborbital remote sensing measurements of fire dynamics, (c) assess local, regional, and global modeling of fires, and (d) strengthen connections to observables on the ground such as fuels and fuel consumption and satellite products such as burned area and fire radiative power. From Boise, ID western wildfires were studied with the NASA DC‐8 and two NOAA Twin Otter aircraft. The high‐altitude NASA ER‐2 was deployed from Palmdale, CA to observe some of these fires in conjunction with satellite overpasses and the other aircraft. Further research was conducted on three mobile laboratories and ground sites, and 17 different modeling forecast and analyses products for fire, fuels and air quality and climate implications. From Salina, KS the DC‐8 investigated 87 smaller fires in the Southeast with remote and in‐situ data collection. Sampling by all platforms was designed to measure emissions of trace gases and aerosols with multiple transects to capture the chemical transformation of these emissions and perform remote sensing observations of fire and smoke plumes under day and night conditions. The emissions were linked to fuels consumed and fire radiative power using orbital and suborbital remote sensing observations collected during overflights of the fires and smoke plumes and ground sampling of fuels.

 

Abstract. The formation of inorganic nitrate is the main sink for nitrogenoxides (NOx = NO + NO2). Due to the importance of NOx forthe formation of tropospheric oxidants such as the hydroxyl radical (OH) andozone, understanding the mechanisms and rates of nitrate formation isparamount for our ability to predict the atmospheric lifetimes of mostreduced trace gases in the atmosphere. The oxygen isotopic composition ofnitrate (Δ17O(nitrate)) is determined by the relativeimportance of NOx sinks and thus can provide an observationalconstraint for NOx chemistry. Until recently, the ability to utilizeΔ17O(nitrate) observations for this purpose was hindered by ourlack of knowledge about the oxygen isotopic composition of ozone (Δ17O(O3)). Recent and spatially widespread observations of Δ17O(O3) motivate an updated comparison of modeled andobserved Δ17O(nitrate) and a reassessment of modeled nitrateformation pathways. Model updates based on recent laboratory studies ofheterogeneous reactions render dinitrogen pentoxide (N2O5)hydrolysis as important as NO2 + OH (both 41 %) for globalinorganic nitrate production near the surface (below 1 km altitude). Allother nitrate production mechanisms individually represent less than 6 %of global nitrate production near the surface but can be dominant locally.Updated reaction rates for aerosol uptake of NO2 result in significantreduction of nitrate and nitrous acid (HONO) formed through this pathway inthe model and render NO2 hydrolysis a negligible pathway for nitrateformation globally. Although photolysis of aerosol nitrate may haveimplications for NOx, HONO, and oxidant abundances, it does notsignificantly impact the relative importance of nitrate formation pathways.Modeled Δ17O(nitrate) (28.6±4.5 ‰)compares well with the average of a global compilation of observations (27.6±5.0 ‰) when assuming Δ17O(O3) = 26 ‰, giving confidence in the model'srepresentation of the relative importance of ozone versus HOx (= OH + HO2 + RO2) in NOx cycling and nitrate formation on theglobal scale. 

Abstract. We present an updated mechanism for tropospheric halogen (Cl + Br + I) chemistry in the GEOS-Chem global atmospheric chemical transportmodel and apply it to investigate halogen radical cycling and implications for tropospheric oxidants. Improved representation of HOBr heterogeneouschemistry and its pH dependence in our simulation leads to less efficient recycling and mobilization of bromine radicals and enables the model toinclude mechanistic sea salt aerosol debromination without generating excessive BrO. The resulting global mean tropospheric BrO mixingratio is 0.19 ppt (parts per trillion), lower than previous versions of GEOS-Chem. Model BrO shows variable consistency and biases in comparison tosurface and aircraft observations in marine air, which are often near or below the detection limit. The model underestimates the daytimemeasurements of Cl2 and BrCl from the ATom aircraft campaign over the Pacific and Atlantic, which if correct would imply a very largemissing primary source of chlorine radicals. Model IO is highest in the marine boundary layer and uniform in the free troposphere, with a globalmean tropospheric mixing ratio of 0.08 ppt, and shows consistency with surface and aircraft observations. The modeled global meantropospheric concentration of Cl atoms is 630 cm−3, contributing 0.8 % of the global oxidation of methane, 14 % of ethane,8 % of propane, and 7 % of higher alkanes. Halogen chemistry decreases the global tropospheric burden of ozone by 11 %,NOx by 6 %, and OH by 4 %. Most of the ozone decrease is driven by iodine-catalyzed loss. The resulting GEOS-Chem ozonesimulation is unbiased in the Southern Hemisphere but too low in the Northern Hemisphere. 

Abstract. We present in this technical note the research protocol for phase 4 of theAir Quality Model Evaluation International Initiative (AQMEII4). Thisresearch initiative is divided into two activities, collectively having threegoals: (i) to define the current state of the science with respect torepresentations of wet and especially dry deposition in regional models,(ii) to quantify the extent to which different dry depositionparameterizations influence retrospective air pollutant concentration andflux predictions, and (iii) to identify, through the use of a common set ofdetailed diagnostics, sensitivity simulations, model evaluation, andreduction of input uncertainty, the specific causes for the current range ofthese predictions. Activity 1 is dedicated to the diagnostic evaluation ofwet and dry deposition processes in regional air quality models (describedin this paper), and Activity 2 to the evaluation of dry deposition pointmodels against ozone flux measurements at multiple towers with multiyearobservations (to be described in future submissions as part of the specialissue on AQMEII4). The scope of this paper is to present the scientificprotocols for Activity 1, as well as to summarize the technical informationassociated with the different dry deposition approaches used by theparticipating research groups of AQMEII4. In addition to describing allcommon aspects and data used for this multi-model evaluation activity, mostimportantly, we present the strategy devised to allow a common process-levelcomparison of dry deposition obtained from models using sometimes verydifferent dry deposition schemes. The strategy is based on adding detaileddiagnostics to the algorithms used in the dry deposition modules of existingregional air quality models, in particular archiving diagnostics specific to land use–land cover(LULC) and creating standardized LULC categories tofacilitate cross-comparison of LULC-specific dry deposition parameters andprocesses, as well as archiving effective conductance and effective flux asmeans for comparing the relative influence of different pathways towards thenet or total dry deposition. This new approach, along with an analysis ofprecipitation and wet deposition fields, will provide an unprecedentedprocess-oriented comparison of deposition in regional air quality models.Examples of how specific dry deposition schemes used in participating modelshave been reduced to the common set of comparable diagnostics defined forAQMEII4 are also presented. 

Oceans emit large quantities of dimethyl sulfide (DMS) to the marine atmosphere. The oxidation of DMS leads to the formation and growth of cloud condensation nuclei (CCN) with consequent effects on Earth’s radiation balance and climate. The quantitative assessment of the impact of DMS emissions on CCN concentrations necessitates a detailed description of the oxidation of DMS in the presence of existing aerosol particles and clouds. In the unpolluted marine atmosphere, DMS is efficiently oxidized to hydroperoxymethyl thioformate (HPMTF), a stable intermediate in the chemical trajectory toward sulfur dioxide (SO 2 ) and ultimately sulfate aerosol. Using direct airborne flux measurements, we demonstrate that the irreversible loss of HPMTF to clouds in the marine boundary layer determines the HPMTF lifetime ( τ HPMTF < 2 h) and terminates DMS oxidation to SO 2 . When accounting for HPMTF cloud loss in a global chemical transport model, we show that SO 2 production from DMS is reduced by 35% globally and near-surface (0 to 3 km) SO 2 concentrations over the ocean are lowered by 24%. This large, previously unconsidered loss process for volatile sulfur accelerates the timescale for the conversion of DMS to sulfate while limiting new particle formation in the marine atmosphere and changing the dynamics of aerosol growth. This loss process potentially reduces the spatial scale over which DMS emissions contribute to aerosol production and growth and weakens the link between DMS emission and marine CCN production with subsequent implications for cloud formation, radiative forcing, and climate. 

The oxidation of carbonyl sulfide (OCS) is the primary, continuous source of stratospheric sulfate aerosol particles, which can scatter shortwave radiation and catalyze heterogeneous reactions in the stratosphere. While it has been estimated that the oxidation of dimethyl sulfide (DMS), emitted from the surface ocean accounts for 8%–20% of the global OCS source, there is no existing DMS oxidation mechanism relevant to the marine atmosphere that is consistent with an OCS source of this magnitude. We describe new laboratory measurements and theoretical analyses of DMS oxidation that provide a mechanistic description for OCS production from hydroperoxymethyl thioformate, a ubiquitous, soluble DMS oxidation product. We incorporate this chemical mechanism into a global chemical transport model, showing that OCS production from DMS is a factor of 3 smaller than current estimates, displays a maximum in the tropics consistent with field observations and is sensitive to multiphase cloud chemistry.