Modeling

GECKO-A

GECKO-A is the Generator of Explicit Chemistry and Kinetics of Organics in the Atmosphere. It is used to self generate fully explicit gas-phase oxidation schemes of organic compounds under general tropospheric conditions. It is based on laboratory kinetic and mechanistic data extended by use of structure-activity relationships. The generated mechanism is used inside a 0D box model, and has typically been applied to study chemistry in urban and rural plumes, or simulate chamber experiments.

The development of GECKO-A is a collaborative effort between scientists at NCAR/ACOM and LISA/CNRS France. The GECKO-A generator is still a research code and can only be obtained for collaborative projects. However, number of pre-generated mechanisms (see list below) can be made available for use with the box model.

Research highlights

Aerosol mass by carbon numberModeling of SOA formation in the Mexico City outflow during MILAGRO-2006: The mechanisms by which secondary organic aerosols (SOA) form in the atmosphere are a topic of much current research. Parameterizations used in air quality and climate have difficulty reproducing observed quantities of ambient aerosol, at least in part because of their inability to account for the diversity of chemical species involved in SOA formation. Read more.

Water droplets on a leaf, by Siddharth Patil at Wikimedia CommonsDry deposition of organic vapors as a major sink of SOA: Removal of secondary organic aerosols (SOA) from the atmosphere has been studied far less than its equal, production. In current regional and global chemistry models rainout is the dominant loss of SOA. Here we show the importance of a less direct pathway, in which large scale evaporation of SOA particles occurs as a re-adjustment to gas-particle partitioning when semi-volatile organic gases are lost by dry deposition to the Earth’s surface. Read more.

 

Available data

1) Henry’s Law Constants (Water solubilities)

We provide here Henry’s Law constants (H in M/atm) used in Hodzic et al., 2014: Volatility Dependence of Henry's Law Constants Of Condensable Organics: Application to Estimate Depositional Loss of Secondary Organic Aerosols, Geophys. Res. Lett., 41, 13, 4795-4804, doi: 10.1002/2014GL060649, 2014. The provided H values refer to the effective Henry's law constant, which includes the hydration process. Values of H for organic compounds are estimated at 298 K using the group contribution method for Henry's law estimate [Raventos-Duran et al. 2010] based on data for 488 organic compounds (393 aliphatic and 95 aromatic) with a wide range of functional groups. A multiple linear regression based on functional groups and the number of carbon and hydrogen atoms is applied to derive H for species that were not measured.

H (M/atm) and vapor pressures (atm) are given for oxidation products of isoprene0.1/10ppb, terpene0.1/10-pinene, β-pinene, limonene), toluene0.1/10, xylene0.1/10, hexadecane0.1/10 at 0.1ppb and 10ppb NOx.

H (M/atm) used in the MOZART mechanism

Additional data can be obtained upon request. Other H databases can be found at http://www.henrys-law.org/.

2) Selected Presentations

 

Contact NCAR scientists for specific collaborations

Sasha Madronich –  original creator of the code
Julia Lee-Taylor – code developement and user support
Alma Hodzic – field campaign studies, parameterization development for 3D models.
Geoff Tyndall – expert on organic chemistry behind the generator
John Orlando - expert on organic chemistry behind the generator

 

Publications

  • Lee-Taylor, J., Hodzic, A., Madronich, S., Aumont, B., Camredon, M., and Valorso, R.: Multiday production of condensing organic aerosol mass in urban and forest outflow, Atmos. Chem. Phys., 15, 595-615, doi:10.5194/acpd-15-595-2015, 2015.

  • Hodzic A., Aumont B., Knote C., et al., Volatility Dependence of Henry's Law Constants Of Condensable Organics: Application to Estimate Depositional Loss of Secondary Organic Aerosols, Geophys. Res. Lett., 41, 13, 4795-4804, doi: 10.1002/2014GL060649, 2014.

  • Aumont B., Camredon M., Mouchel-Vallon C., La S., Ouzebidour F., Valorso R., Lee-Taylor J. and Madronich S., Modeling the influence of alkane molecular structure on secondary organic aerosol formation, Faraday Discuss., 165, 105-122, 2013.

  • Hodzic A., Madronich S., Aumont B., Lee-Taylor J., Karl T., Camredon M. and Mouchel-Vallon C., Limited influence of dry deposition of semi-volatile organic vapors on secondary organic aerosol formation in the urban plume, Geophys. Res. Lett., vol. 40, 3302–3307, doi:10.1002/grl.50611, 2013.

  • Mouchel-Vallon, C., Bräuer, P., Marie Camredon, M., Valorso, R., Madronich, S., Herrmann, H., Bernard Aumont, Explicit modeling of volatile organic compounds partitioning in the atmospheric aqueous phase, Atmos. Chem. Phys., 13, 1023-1037, doi:10.5194/acp-13-1023-2013, 2013.

  • Lee-Taylor J., S. Madronich, B. Aumont, M. Camredon, A. Hodzic, G. S. Tyndall, E. Apel, and R. A. Zaveri, Explicit modeling of organic chemistry and secondary organic aerosol partitioning for Mexico City and its outflow plume, Atmos. Chem. Phys., 11, 13219-13241, 2011.

  • Aumont B., Szopa S. and Madronich S., Modelling the evolution of organic carbon during its gas-phase tropospheric oxidation: development of an explicit model based on a self generating approach, Atmospheric Chemistry Physics, 5, 2497-2517, 2005.

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