The modeling of the atmospheric boundary layer during convective conditions has long been a major source of uncertainty in the numerical modeling of meteorological conditions and air quality. Much of the difficulty stems from the large range of turbulent scales that are effective in the convective boundary layer (CBL). Both small-scale turbulence that is subgrid in most mesoscale grid models and large-scale turbulence extending to the depth of the CBL are important for the vertical transport of atmospheric properties and chemical species. Eddy diffusion schemes assume that all of the turbulence is subgrid and therefore cannot realistically simulate convective conditions. Simple nonlocal closure PBL models, such as the Blackadar convective model that has been a mainstay PBL option in the fifth-generation Pennsylvania State University–National Center for Atmospheric Research Mesoscale Model (MM5) for many years and the original asymmetric convective model (ACM), also an option in MM5, represent large-scale transport driven by convective plumes but neglect small-scale, subgrid turbulent mixing. A new version of the ACM (ACM2) has been developed that includes the nonlocal scheme of the original ACM combined with an eddy diffusion scheme. Thus, the ACM2 is able to represent both the supergrid- and subgrid-scale components of turbulent transport in the convective boundary layer. Testing the ACM2 in one-dimensional form and comparing it with large-eddy simulations and field data from the 1999 Cooperative Atmosphere–Surface Exchange Study demonstrates that the new scheme accurately simulates PBL heights, profiles of fluxes and mean quantities, and surface-level values. The ACM2 performs equally well for both meteorological parameters (e.g., potential temperature, moisture variables, and winds) and trace chemical concentrations, which is an advantage over eddy diffusion models that include a nonlocal term in the form of a gradient adjustment.

A new combined local and nonlocal closure atmospheric boundary layer model called the Asymmetric Convective Model, version 2, (ACM2) was described and tested in one-dimensional form and was compared with large-eddy simulations and field data in Part I. Herein, the incorporation of the ACM2 into the fifth-generation Pennsylvania State University–NCAR Mesoscale Model (MM5) is described. Model simulations using the MM5 with the ACM2 are made for the summer of 2004 and evaluated through comparison with surface meteorological measurements, rawinsonde profile measurements, and observed planetary boundary layer (PBL) heights derived from radar wind profilers. Overall model performance is as good as or better than similar MM5 evaluation studies. The MM5 simulations with the ACM2 compare particularly well to PBL heights derived from radar wind profilers during the afternoon hours. The ACM2 is designed to simulate the vertical mixing of any modeled quantity realistically for both meteorological models and air quality models. The next step, to be described in a subsequent article, is to incorporate the ACM2 into the Community Multiscale Air Quality (CMAQ) model for testing and evaluation.

For many gasses and aerosols, dry deposition is an important sink of atmospheric mass. Dry deposition fluxes are also important sources of pollutants to terrestrial and aquatic ecosystems. The surface fluxes of some gases, such as ammonia, mercury, and certain volatile organic compounds, can be upward into the air as well as downward to the surface and therefore should be modeled as bi-directional fluxes. Model parameterizations of dry deposition in air quality models have been represented by simple electrical resistance analogs for almost 30 years. Uncertainties in surface flux modeling in global to mesoscale models are being slowly reduced as more field measurements provide constraints on parameterizations. However, at the same time, more chemical species are being added to surface flux models as air quality models are expanded to include more complex chemistry and are being applied to a wider array of environmental issues. Since surface flux measurements of many of these chemicals are still lacking, resistances are usually parameterized using simple scaling by water or lipid solubility and reactivity. Advances in recent years have included bi-directional flux algorithms that require a shift from pre-computation of deposition velocities to fully integrated surface flux calculations within air quality models. Improved modeling of the stomatal component of chemical surface fluxes has resulted from improved evapotranspiration modeling in land surface models and closer integration between meteorology and air quality models. Satellite-derived land use characterization and vegetation products and indices are improving model representation of spatial and temporal variations in surface flux processes. This review describes the current state of chemical dry deposition modeling, recent progress in bi-directional flux modeling, synergistic model development research with field measurements, and coupling with meteorological land surface models.

The Pleim–Xiu land surface model (PX LSM) has been improved by the addition of a second indirect data assimilation scheme. The first, which was described previously, is a technique in which soil moisture is nudged according to the biases in 2-m air temperature and relative humidity between the model- and observation-based analyses. The new technique involves nudging the deep soil temperature in the soil temperature force–restore (FR) model according to model bias in 2-m air temperature only during nighttime. While the FR technique is computationally efficient and very accurate for the special conditions for which it was derived, it is very dependent on the deep soil temperature that drives the restoration term of the surface soil temperature equation. Thus, adjustment of the deep soil temperature to optimize the 2-m air temperature during the night, when surface forcing is minimal, provides significant advantages over other methods of deep soil moisture initialization. Simulations of the Weather Research and Forecasting Model (WRF) using the PX LSM with and without the new deep soil temperature nudging scheme demonstrate substantial benefits of the new scheme for reducing error and bias of the 2-m air temperature. The effects of the new nudging scheme are most pronounced in the winter (January 2006) during which the model’s cold bias is greatly reduced. Air temperature error and bias are also reduced in a summer simulation (August 2006) with the greatest benefits in less vegetated and more arid regions. Thus, the deep temperature nudging scheme complements the soil moisture nudging scheme because it is most effective for conditions in which the soil moisture scheme is least effective, that is, when evapotranspiration is not important (winter and arid climates).

A new windblown dust emission treatment was incorporated in the Community Multiscale Air Quality (CMAQ) modeling system. This new model treatment has been built upon previously developed physics‐based parameterization schemes from the literature. A distinct and novel feature of this scheme, however, is the incorporation of a newly developed dynamic relation for the surface roughness length relevant to small‐scale dust generation processes. Through this implementation, the effect of nonerodible elements on the local flow acceleration, drag partitioning, and surface coverage protection is modeled in a physically based and consistent manner. Careful attention is paid in integrating the new windblown dust treatment in the CMAQ model to ensure that the required input parameters are correctly configured. To test the performance of the new dust module in CMAQ, the entire year 2011 is simulated for the continental United States, with particular emphasis on the southwestern United States (SWUS) where windblown dust concentrations are relatively large. Overall, the model shows good performance with the daily mean bias of soil concentrations fluctuating in the range of ±1 µg m⁻³ for the entire year. Springtime soil concentrations are in quite good agreement (normalized mean bias of 8.3%) with observations, while moderate to high underestimation of soil concentration is seen in the summertime. The latter is attributed to the issue of representing the convective dust storms in summertime. Evaluations against observations for seven elevated dust events in the SWUS indicate that the new windblown dust treatment is capable of capturing spatial and temporal characteristics of dust outbreaks.

Ammonia surface flux is bidirectional; that is, net flux can be either upward or downward. In fertilized agricultural croplands and grasslands there is usually more emission than deposition especially in midday during warmer seasons. In North America, most of the ammonia emissions are from agriculture with a significant fraction of that coming from fertilizer. A new bidirectional ammonia flux modeling system has been developed in the Community Multiscale Air Quality (CMAQ) model, which has close linkages with the Environmental Policy Integrated Climate (EPIC) agricultural ecosystem model. Daily inputs from EPIC are used to calculate soil ammonia concentrations that are combined with air concentrations in CMAQ to calculate bidirectional surface flux. The model is evaluated against surface measurements of NH₃ concentrations, NH₄⁺ and SO₄²⁻ aerosol concentrations, NH₄⁺ wet deposition measurements, and satellite retrievals of NH₃ concentrations. The evaluation shows significant improvement over the base model without bidirectional ammonia flux. Comparisons to monthly average satellite retrievals show similar spatial distribution with the highest ammonia concentrations in the Central Valley of California (CA), the Snake River valley in Idaho, and the western High Plains. In most areas the model underestimates, but in the Central Valley of CA, it generally overestimates ammonia concentration. Case study analyses indicate that modeled high fluxes of ammonia in CA are often caused by anomalous high soil ammonia loading from EPIC for particular crop types. While further improvements to parameterizations in EPIC and CMAQ are recommended, this system is a significant advance over previous ammonia bidirectional surface flux models.