Lizard by genma Created2016-03-14 Description: lagartixa verde - green gecko. Generator of Explicit Chemistry and Kinetics of Organics in the Atmosphere (GECKO-A) is a hyper-explicit mechanism for the atmospheric oxidation of organic compounds. GECKO-A uses mechanistic and kinetic data from laboratory measurements where available, and applies various Structure-Activity Relations (SARs) when laboratory data are not available, to estimate rate coefficients and their temperature & pressure dependencies, possible multiple reaction pathways and products, and other molecular properties such as saturation vapor pressure, solubility (Henry’s Law coefficients), and UV-visible chromophores that lead to absorption and photolysis. Typical mechanisms generated by GECKO-A have ~105 distinct explicit molecules partaking in ~10 6 thermal and photolytic reactions.

The generated mechanism is typically used inside a 0D box model, and has been applied to study chemistry in urban and rural plumes, or simulate chamber experiments. The GECKO-A box model comes with a solver capable of handling the large number of species and reactions.

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, a number of pre-generated mechanisms (see list below) can be made available for use with the box model.

GECKO-A Library for Selected Hydrocarbon Precursors

The GECKO-A Output Library provides the main gas and particle phase products from individual precursor hydrocarbons, under different conditions ranging from pristine remote to polluted urban. Results include distributions of functional groups, vapor pressures, solubility coefficients, yields of secondary organic aerosols (SOA) and van Krevelen diagrams of the oxidation pathways.

Research Highlights

Photolysis of Organic Aerosols (2015). Image by ACOM / NCAR / UCAR.

Photolysis of Organic Aerosols (2015)
A multitude of recent atmospheric observations show that organic aerosols are ubiquitous and often more abundant than other particles such as sulfate, nitrate, soot, and dust.  These large amounts of organic particles contribute to the health impacts of air pollution, to regional visibility reductions, to both cooling and warming tendencies of radiative forcing, and to modified cloud properties and precipitation patterns.

Multiday production of SOA in urban and forest outflow. Image by ACOM / NCAR / UCAR.

Multiday production of SOA in urban and forest outflow (2015)
Secondary organic aerosol (SOA) production in urban and biogenic outflow was investigated using the explicit gas-phase chemical mechanism generator GECKO-A [Lee-Taylor et al., 2015]. Urban outflow simulations show several-fold increases in SOA mass continuing for multiple days, whereas forest outflow simulations showed only modest SOA mass increases, and no long-term growth.

Water droplets on a leaf, by Siddharth Patil.

Gas-Phase Dry Deposition as a Major Removal Mechanism for Secondary Organic Aerosols (SOA) (2014)
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.

Modeling of SOA formation using an explicit gas-phase chemical mechanism. Image by ACOM / NCAR / UCAR.

Modeling of SOA formation using an explicit gas-phase chemical mechanism (2011)
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.



Sasha Madronich –  NCAR GECKO-A Lead
Julia Lee-Taylor
– Code development and user support
Camille Mouchel-Vallon – Code development and applications
Alma Hodzic Roux
– Formation and deposition of organics
Geoff Tyndall
– Laboratory kinetics and mechanisms
John Orlando
– Structure-Activity Relationships


GECKO-A Publications 

Lannuque, V., Camredon, M., Couvidat, F., Hodzic, A., Valorso, R., Madronich, S., Bessagnet, B., and Aumont, B.: Exploration of the influence of environmental conditions on secondary organic aerosol formation and organic species properties using explicit simulations: development of the VBS-GECKO parameterization, Atmos. Chem. Phys., 18, 13411–13428,, 2018.

La, Y. S., M. Camredon, P. J. Ziemann, R. Valorso, A. Matsunaga, V. Lannuque, J. Lee-Taylor, A. Hodzic, S. Madronich, and B. Aumont, Impact of chamber wall loss of gaseous organic compounds on secondary organic aerosol formation: explicit modeling of SOA formation from alkane and alkene oxidation, Atmos. Chem. Phys., 16, 1417-1431, 2016.

Madronich, S., A. Conley, J. Lee-Taylor, L. Kleinman, A. Hodzic and B. Aumont, Non-linear partitioning and organic volatility distributions in urban environments, Royal Soc. Chem. Faraday Discuss., 189, 515-528, doi:10.1039/C5FD00209E, 2016.!divAbs...

McVay, R. C., X. Zhang, B. Aumont, R. Valorso, M. Camredon, Y. S. La, P. O. Wennberg, and J. H. Seinfeld, Atmos. Chem. Phys., 16, 2785-2802, doi:10.5194/acp-16-2785-2016, 2016.

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., S. Madronich, P. S. Kasibhatla, G. Tyndall, B. Aumont, J. L. Jimenez, J. Lee-Taylor, and J. Orlando, Organic photolysis reactions in tropospheric aerosols: effect on secondary organic aerosol formation and lifetime, Atmos. Chem. Phys., 15, 9253-9269, 2015.

Denjean, C., Formenti, P., Picquet-Varrault, B., Camredon, M., Pangui, E., Zapf, P., Katrib, Y., Giorio, C., Tapparo, A., Temime-Roussel, B., Monod, A., Aumont, B., and Doussin, J. F.: Aging of secondary organic aerosol generated from the ozonolysis of alpha-pinene: effects of ozone, light and temperature, Atmos. Chem. Phys., 15, 883-897, doi:10.5194/acp-15-883-2015, 2015.

Hodzic A., B. Aumont, C. Knote, J. Lee-Taylor, S. Madronich, and G. Tyndall, Volatility dependence of Henry’s law constants of condensable organics: Application to estimate depositional loss of secondary organic aerosols, Geophys. Res. Lett., 41, 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, Royal Soc. Chem. Faraday Discuss., 165, 105-122, 2013. doi:10.1039/C3FD00029J, 2013.!divAbs...

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.,40, 3302–3307, doi:10.1002/grl.50611, 2013.

Waxman, E. M., K. Dzepina, B. Ervens, J. Lee-Taylor, B. Aumont, J. L. Jimenez, S. Madronich, and R. Volkamer, Secondary organic aerosol formation from S/IVOC and glyoxal: Relevance of O/C as a tracer for aqueous multiphase chemistry, Geophys. Res. Lett., 40, 1-5, doi:10.1002/GRL.50203, 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.

Aumont, B., R. Valorso, C. Mouchel-Vallon, M. Camredon, J. Lee-Taylor, and S. Madronich, Modeling SOA formation from the oxidation of intermediate volatility n-alkanes, Atmos. Chem. Phys., 12, 7577-7589, 2012.

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.

Valorso, R., B. Aumont, M. Camredon, T. Raventos-Duran, C. Mouchel-Vallon, N. L. Ng, J. H. Seinfeld, J. Lee-Taylor, and S. Madronich, Explicit modelling of SOA formation from α-pinene photooxidation: sensitivity to vapour pressure estimation, Atmos. Chem. Phys., 11, 6895-6910, 2011.

Raventos-Duran, T., M. Camredon, R. Valorso, C. Mouchel-Vallon and B. Aumont. Development and assessment of structure activity relationships to estimate the effective Henry's law coefficient of organics of atmospheric interest, Atmos. Chem. Phys., 10, 7643-7654, 2010.

Dufour, G., Wittrock, F., Camredon, M., Beekmann, M., Richter, A., Aumont, B., and Burrows, J. P.: SCIAMACHY formaldehyde observations: constraint for isoprene emission estimates over Europe? Atmos. Chem. Phys., 9, 1647-1664, doi:10.5194/acp-9-1647-2009, 2009.

Camredon, M., B. Aumont, J. Lee-Taylor, and S. Madronich, The SOA/VOC/NOx system: an explicit model of secondary organic aerosol formation, Atmos. Chem. Phys., 7, 5599-5610, 2007.

Szopa, S., B Aumont, and S. Madronich Assessment of the reduction methods used to develop chemical schemes: building of a new chemical scheme for VOC oxidation suited to three-dimensional multiscale HOx-NOx-VOC chemistry simulations, Atmos. Chem. Phys., 5, 2519-2538, 2005.

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, Atmos. Chem. Phys., 5, 2497-2517, 2005.


U.S. Funding:

National Center for Atmospheric Research (NCAR)
U.S. National Science Foundation
U.S. Department of Energy, Atmospheric System Research program

National Center for Atmospheric ResearchNational Science FoundationU.S. Department of Energy



Laboratoire Inter-Universitaire des Systèmes Atmosphériques (LISA)
Led by Prof. Bernard Aumont

Laboratoire Inter-Universitaire des Systèmes Atmosphériques (LISA)

The chemical gecko, by Camille Mouchel-Vallon (ACOM / NCAR / UCAR).




ACOM | Atmospheric Chemistry Observations & Modeling