The TRACERS_SPECIAL_Shindell selection of tracers, in conjuction with the option SHINDELL_STRAT_CHEM is described in Shindell et al., 2012 as follows:
The chemical mechanism is fully embedded within modelE, so that chemical constituents are treated consistently with the physics of other parts of the model such as surface fluxes of fundamental physical quantities (e.g. heat) and with transport of momentum and other constituents such as water vapor. Tropospheric chemistry includes basic NOx-HOx-Ox-CO-CH4 chemistry as well as PANs and the hydrocarbons isoprene, alkyl nitrates, aldehydes, alkenes, and paraffins. The lumped hydrocarbon family scheme was derived from the Carbon Bond Mechanism-4 (CBM-4) [Gery et al., 1989] and from the more extensive Regional Atmospheric Chemistry Model (RACM) [Stockwell et al., 1997], following [Houweling et al., 1998]. To represent stratospheric chemistry, the model includes chlorine- and bromine-containing compounds, and CFC and N2O source gases (as well as an 'age-of-air' passive tracer). Aerosol species and chemistry are also included, and chemistry and aerosols are fully integrated, so that these components interact with each other and with the physics of the climate model. The model contains 51 species for gas-phase chemistry interacting via 156 reactions. We use a chemical time step of 1/2 hour, including the calculation of photolysis rates using the Fast-J2 scheme [H. Bian and Prather, 2002]. We include transport and phase transformations of soluble species within convective plumes, scavenging within and below updrafts, rainout within both convective and large-scale clouds, washout below precipitating regions, evaporation of falling precipitation, and both detrainment and evaporation from convective plumes. A full description is given in Shindell et al. [2006] and references therein.
The only substantial chemistry changes since [D T Shindell et al., 2006] are as follows: acetone chemistry has been added to the model [Houweling et al., 1998], we have incorporated a newly identified reaction channel of OH + NO2 to form HNO3 whose branching ratio is pressure and temperature dependent [Butkovskaya et al., 2007], polar stratospheric cloud (PSC) formation in the stratosphere is now dependent upon water vapor, temperature and HNO3 [Hanson and Mauersberger, 1988], the heterogeneous hydrolysis of N2O5 on sulfate now follows [Kane et al., 2001] and [Hallquist et al., 2003], and the model now includes terpene emissions and oxidation by OH, O3 and NO3 [Tsigaridis et al., 2005].
Another development is that now light attenuation by modeled aerosol tracers affects the photolysis rates of gases, following Bian et al. [2003]. Modeled aerosol optical depths are passed to the photolysis code at every timestep, while the tabulated optical properties required for different aerosol types (extinction efficiency, single scattering albedo, scattering phase function expansion terms) are prescribed according to prior calculations to be consistent with what is used in the model's radiation code.
Shindell, D.T., O. Pechony, A. Voulgarakis, G. Faluvegi, L. Nazarenko, J.-F. Lamarque, K. Bowman, G. Milly, B. Kovari, R. Ruedy, and G. Schmidt, 2012: Interactive ozone and methane chemistry in GISS-E2 historical and future climate simulations. Atmos. Chem. Phys., submitted, doi:10.5194/acpd-12-23513-2012.
Bian, H., and M. Prather (2002), Fast-J2: Accurate simulations of photolysis in global climate models, J. Atmos. Chem., 41, 281-296.
Bian, H., M. Prather, and T. Takemura (2003), Tropospheric aerosol impacts on trace gas budgets through photolysis, Journal of Geophysical Research-Atmospheres, 108(D8), doi:10.1029/2002JD002743|10.1029/2002JD002743.
Butkovskaya, N., A. Kukui, and G. Le Bras (2007), HNO3 Forming Channel of the HO2 + NO Reaction as a Function of Pressure and Temperature in the Ranges of 72-600 Torr and 223-323 K J. Phys. Chem. A, 111, 9047-9053.
Gery, M. W., G. Z. Whitten, J. P. Killus, and M. C. Dodge (1989), A photochemical kinetics mechanism for urban and regional scale computer modeling, J. Geophys. Res., 94, 925-956.
Hallquist, M., D. J. Stewart, S. K. Stephenson, and R. A. Cox (2003), Hydrolysis of N2O5 on sub-micron sulfate aerosols, Phys. Chem. Chem. Phys., 5, 3453-3463.
Hanson, D., and K. Mauersberger (1988), Laboratory studies of the nitric acid tridydrate: Implications for the south polar stratosphere, Geophys. Res. Lett., 15, 855-858.
Houweling, S., F. Dentener, and J. Lelieveld (1998), The impact of non-methane hydrocarbon compounds on tropospheric photochemistry, J. Geophys. Res., 103, 10673-10696.
Kane, S. M., F. Caloz, and M.-T. Leu (2001), Heterogeneous Uptake of Gaseous N2O5 by (NH4)2SO4, NH4HSO4, and H2SO4 Aerosols, J. Phys. Chem. A, 105, 6465-6470.
Shindell, D. T., G. Faluvegi, N. Unger, E. Aguilar, G. A. Schmidt, D. Koch, S. E. Bauer, and R. L. Miller (2006), Simulations of preindustrial, present-day, and 2100 conditions in the NASA GISS composition and climate model G-PUCCINI, Atmos. Chem. Phys., 6, 4427-4459.
Stockwell, W. R., F. Kirchner, M. Kuhn, and S. Seefeld (1997), A new mechanism for regional atmospheric chemistry modeling, 102, 25847-25879.
Tsigaridis, K., J. Lathiere, M. Kanakidou, and D. Hauglustaine (2005), Naturally driven variability in the global secondary organic aerosol over a decade, Atmospheric Chemistry and Physics, 5, 1891-1904.