The study, led by Jesse Bash of the US Environmental Protection Agency, now at the Norwegian Meteorological Institute, together with colleagues from the EPA, Environment and Climate Change Canada, and partner institutions, scrutinized the Surface Tiled Aerosol and Gaseous Exchange option, known as STAGE, in version 5.3.2 of the Community Multiscale Air Quality model, or CMAQ. STAGE is a unified framework that estimates both dry deposition, the uptake of gases by surfaces, and bidirectional exchange, the two-way traffic of gases between the atmosphere and soils or vegetation. What makes STAGE distinctive is that it applies the same resistance model to every modeled gas, whether that gas only deposits, like nitric acid, or can flow in both directions, like ammonia. That consistency matters, because in earlier versions of CMAQ, ammonia bidirectional exchange and the deposition of all other species were handled by two separate, parallel resistance schemes with different structural assumptions.

The mathematical heart of STAGE is a resistance analog borrowed from electrical circuit theory, following the widely used parameterizations of Nemitz and colleagues from 2001 and Massad and colleagues from 2010. The flux of a trace gas is driven by the difference between the ambient concentration and a compensation point concentration at the surface, divided by the aerodynamic resistance. For ammonia, the compensation point is built from a two-layer canopy and soil model: gases diffuse through leaf boundary layers, stomata, cuticles, and in-canopy air, with each pathway assigned its own resistance. The model even solves for the leaf-level compensation point using a system of equations analogous to Kirchhoff’s current law, balancing exchange between the atmosphere, stomata, cuticular surfaces, and the ground. When the compensation points are set to zero, the framework collapses gracefully into a conventional dry deposition velocity, which is precisely what allows one model to serve both unidirectional and bidirectional species.

Several technical refinements were introduced to make this framework work at regional scale. Deposition to wet leaf surfaces, previously treated as instantaneous diffusion into canopy water, now uses a mass transfer formulation adapted from CMAQ’s aqueous chemistry module, accounting for gaseous diffusivity and bulk accommodation into roughly spherical droplets sitting on hydrophobic leaves. The depth of surface moisture is derived from relative humidity using Brunauer-Emmett-Teller adsorption theory calibrated against leaf wetness observations, and droplet radius follows from that water depth and the leaf area index. In-canopy aerodynamic resistance is computed by integrating eddy diffusivity through the canopy using a momentum attenuation approach. Soil processes were also updated: the diffusive length for soil gas exchange was increased to two centimeters to match the measurements underlying the model, and soil ammonium availability is now estimated with a nonlinear sorption curve rather than a fixed solution fraction.

To test whether all this machinery reflects reality, the team turned the regional model into a field-scale box model written in the R statistical language, using identical resistance parameterizations, and ran it against micrometeorological flux measurements from two North Carolina sites. The first was a managed, unfertilized 15-hectare grass field at Duke Forest, where fluxes of ammonia, nitric acid, and sulfur dioxide were measured with a MARGA instrument during the second half of 2012. The second was a 200-hectare fertilized corn field near Lillington, where ammonia gradients were measured with a continuous-flow wet denuder system in 2007. When the box model was fed observed soil and vegetation ammonia emission potentials, the compensation points that quantify how much ammonia the soil and plant tissues are ready to release, the modeled fluxes of all three gases agreed well with observations, with mean biases within or near the reported measurement uncertainty.

The trouble emerged when the model was run with the default tabular values built into CMAQ. At the Duke Forest grassland, the defaults for soil and vegetation emission potentials, a soil gamma of 20 and an apoplast gamma of 247, produced a simulated mean net deposition of minus 1.3 nanograms per square meter per hour, while the towers actually recorded a mean evasive flux of 8.4 nanograms per square meter per hour in the opposite direction. In plain terms, the model said the grassland was absorbing ammonia when it was actually emitting it. Sensitivity experiments showed the modeled flux was most sensitive to the vegetation emission potential, and that perturbing resistances alone could not reverse the sign of the error. The measured compensation points at the site simply exceeded the tabular assumptions, which were drawn from parameterizations based on annual nitrogen deposition fields for non-agricultural land.

The corn field told a more encouraging but nuanced story. Using median measured soil ammonium, soil pH, and an apoplast emission potential of 153.5 reported in earlier work, the model captured the observed fluxes with a normalized mean bias of minus 23.4 percent, rising to 40.5 percent with the default parameterizations. The site also displayed a persistent mid-morning emission peak that the model could not fully explain. Dew on the leaves carried a high emission potential, but there was not enough ammonium in the dew, and the dew dried too early, to account for emissions that continued between eight and eleven in the morning on a dry canopy. The authors speculate that wetting and drying of ammonium-rich exposed soil between the rows, a process the soil moisture probes missed, may drive the morning pulse, contrasting with earlier dew-evaporation explanations at a Colorado grassland.

The decisive test came at continental scale. The team compared an annual 2016 CMAQ simulation against ammonia retrievals from the Cross-Track Infrared Sounder, a satellite instrument capable of detecting ammonia down to roughly half a part per billion under typical conditions. The model captured the broad magnitude and spatial patterns of satellite-observed ammonia, but the biases were revealing. CMAQ overestimated concentrations by 0.5 to 0.9 parts per billion on average in intensely agricultural regions such as California, the Upper Midwest, and eastern North Carolina, while underestimating observations across the Great Plains and other vegetated areas, with a broad shortfall of roughly one to two parts per billion over non-agricultural land. That pattern mirrors the grassland box model result almost exactly, pointing to a common cause: default emission potentials for natural vegetation and soils that sit at the low end of what field measurements show.

The implications extend beyond model diagnostics. The team estimates that of the 10.3 megatonnes of nitrogen applied as fertilizer to row crops in the 2016 simulation, about 0.5 megatonnes, an emission factor of 4.8 percent, was re-emitted as ammonia, a figure consistent with published ranges. Deposition peaked near 30 kilograms of nitrogen per hectare downwind of agricultural sources in eastern North Carolina, within measured values but higher than some earlier net deposition estimates for the region. The authors conclude that raising the grassland vegetation emission potential by about 30 percent and the soil surface emission potential roughly fivefold would better match both the Duke Forest observations and the satellite data, changes that remain well within the natural variability reported across measurement studies. Because non-agricultural land covers roughly three quarters of the terrestrial surface in the model domain, the path forward is clear: more micrometeorological flux measurements and soil and vegetation chemistry across different land uses, soil types, and growth stages. The multi-resolution evaluation strategy, spanning flux towers, monitoring networks, and satellites, offers the modeling community a template for building the next generation of air-surface exchange models on firmer empirical ground.

Subject of Research: Evaluation of bidirectional ammonia, nitric acid, and sulfur dioxide air-surface exchange in the CMAQ model's STAGE deposition option against field, network, and satellite observations

Article Title: Evaluation of HNO3, SO2, and NH3 in the Surface Tiled Aerosol and Gaseous Exchange (STAGE) option in the Community Multiscale Air Quality Model version 5.3.2 against field-scale, in situ and satellite observations

Article References: Bash, J. O., Walker, J. T., Wu, Z., Rumsey, I. C., Murphy, B., Hogrefe, C., Fahey, K. M., Pye, H. O. T., Jones, M. R., Appel, K. W., Shephard, M. W., Alnsour, N. I., & Cady-Periera, K. E. (2026). Evaluation of HNO 3 , SO 2 , and NH 3 in the Surface Tiled Aerosol and Gaseous Exchange (STAGE) option in the Community Multiscale Air Quality Model version 5.3.2 against field-scale, in situ and satellite observations. Geoscientific Model Development, 19(19), 9377-9393. https://doi.org/10.5194/gmd-19-9377-2026

Image Credits: AI Generated

DOI: 10.5194/gmd-19-9377-2026

Keywords: ammonia, air quality modeling, CMAQ, STAGE, dry deposition, bidirectional exchange, satellite observations, CrIS, grassland flux, emission potential, nitrogen deposition, particulate matter