References

ACP

Atmospheric Chemistry and Physics

ACP

1680-7324

Copernicus GmbH

Göttingen, Germany

10.5194/acp-10-279-2010

Simulating atmospheric composition over a South-East Asian tropical rainforest: performance of a chemistry box model

Pugh

T. A. M.

¹ MacKenzie

A. R.

¹ Hewitt

C. N.

¹ Langford

¹ Edwards

P. M.

² Furneaux

K. L.

² ⁹ Heard

D. E.

² Hopkins

J. R.

³ Jones

C. E.

⁴ Karunaharan

⁵ Lee

³ Mills

⁶ Misztal

⁷ ⁸ Moller

⁴ Monks

P. S.

⁵ Whalley

L. K.

Lancaster Environment Centre, Lancaster University, Lancaster, UK

School of Chemistry, University of Leeds, Leeds, UK

National Centre for Atmospheric Science, University of York, York, UK

Department of Chemistry, University of York, York, UK

Department of Chemistry, University of Leicester, Leicester, UK

School of Environmental Sciences, University of East Anglia, UK

Centre for Ecology and Hydrology Edinburgh, U.K.

School of Chemistry, The University of Edinburgh, U.K.

Sadly passed away on 28 July 2009

14 01 2010

10 1 279 298

This is an open-access article ditributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

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Atmospheric composition and chemistry above tropical rainforests is currently not well established, particularly for south-east Asia. In order to examine our understanding of chemical processes in this region, the performance of a box model of atmospheric boundary layer chemistry is tested against measurements made at the top of the rainforest canopy near Danum Valley, Malaysian Borneo. Multi-variate optimisation against ambient concentration measurements was used to estimate average canopy-scale emissions for isoprene, total monoterpenes and nitric oxide. The excellent agreement between estimated values and measured fluxes of isoprene and total monoterpenes provides confidence in the overall modelling strategy, and suggests that this method may be applied where measured fluxes are not available, assuming that the local chemistry and mixing are adequately understood. The largest contributors to the optimisation cost function at the point of best-fit are OH (29%), NO (22%) and total peroxy radicals (27%). Several factors affect the modelled VOC chemistry. In particular concentrations of methacrolein (MACR) and methyl-vinyl ketone (MVK) are substantially overestimated, and the hydroxyl radical (OH) concentration is substantially underestimated; as has been seen before in tropical rainforest studies. It is shown that inclusion of dry deposition of MACR and MVK and wet deposition of species with high Henry's Law values substantially improves the fit of these oxidised species, whilst also substantially decreasing the OH sink. Increasing OH production arbitrarily, through a simple OH recycling mechanism , adversely affects the model fit for volatile organic compounds (VOCs). Given the constraints on isoprene flux provided by measurements, a substantial decrease in the rate of reaction of VOCs with OH is the only remaining option to explain the measurement/model discrepancy for OH. A reduction in the isoprene+OH rate constant of 50%, in conjunction with increased deposition of intermediates and some modest OH recycling, is able to produce both isoprene and OH concentrations within error of those measured. Whilst we cannot rule out an important role for missing chemistry, particularly in areas of higher isoprene flux, this study demonstrates that the inadequacies apparent in box and global model studies of tropical VOC chemistry may be more strongly influenced by representation of detailed physical and micrometeorological effects than errors in the chemical scheme.

References 1

Andreae, M. and Merlet, P.: Emissions of trace gases and aerosols from biomass burning, Global Biogeochem. Cy., 15, 955–966, 2001.

Atkinson, R. and Arey, J.: Gas-phase tropospheric chemistry of biogenic volatile organic compounds: a review, Atmos. Environ., 37, S197–S219, 2003.

Butler, T. M., Taraborrelli, D., Brühl, C., Fischer, H., Harder, H., Martinez, M., Williams, J., Lawrence, M. G., and Lelieveld, J.: Improved simulation of isoprene oxidation chemistry with the ECHAM5/MESSy chemistry-climate model: lessons from the GABRIEL airborne field campaign, Atmos. Chem. Phys., 8, 4529–4546, 2008.

Carslaw, N., Creasey, D. J., Harrison, D., Heard, D. E., Hunter, M. C., Jacobs, P. J., Jenkin, M. E., Lee, J. D., Lewis, A. C., Pilling, M. J., Saunders, S. M., and Seakins, P. W.: OH and \chemHO_2 radical chemistry in a forested region of north-western Greece, Atmos. Environ., 35, 4725–4737, 2001.

Carter, W. P. L. and Atkinson, R.: Development and evaluation of a detailed meachanism for the atmospheric reactions of isoprene and NOx, Int. J. Chem. Kinet., 28, 497–530, 1996.

Chappell, N., Bidin, K., and Tych, W.: Modelling rainfall and canopy controls on net-precipitation beneath selectively-logged forest, Plant Ecol., 153, 215–229, 2001.

Chen, X., Hulbert, D., and Shepson, P. B.: Measurement of the origanic nitrate yield from OH reaction with isoprene, J. Geophys. Res., 95, 22319–22341, 1998.

Cleveland, C. C. and Yavitt, J. B.: Consumption of atmospheric isopene in soil, Geophys. Res. Lett., 24, 2379–2382, 1997.

Cook, P., Savage, N., Turquety, S., Carver, G., O'Connor, F., Heckel, A., Stewart, D., Whalley, L., Parker, A., Schlager, H., Avery, H. S M., Sachse, G., Brune, W., Richter, A., Burrows, J., Purvis, R., Lewis, A., Reeves, C., Monks, P., Levine, J., and Pyle., J.: Forest fire plumes over the North Atlantic: p-TOMCAT model simulations with aircraft and satellite measurements from the ITOP/ICARTT campaign, J. Geophys. Res., 112, D10S43, \doi10.1029/2006JD007563, 2007.

Dillon, T. J. and Crowley, J. N.: Direct detection of OH formation in the reactions of HO2 with CH3C(O)O2 and other substituted peroxy radicals, Atmos. Chem. Phys., 8, 4877–4889, 2008.

Donovan, R., Hope, E., Owen, S., Mackenzie, A., and Hewitt, C.: Development and Application of an Urban Tree Air Quality Score for Photochemical Pollution Episodes Using the Birmingham, United Kingdom, Area as a Case Study, Environ. Sci. Technol., 39, 6730–6738, 2005.

Edwards, P., Whalley, L. K., Heard, D. E., et al.: OH reactivity measurements in a South-East Asian tropical Rainforest, Atmos. Chem. Phys. Discuss., in preparation, 2010.

Eerdekens, G., Yassaa, N., Sinha, V., Aalto, P. P., Aufmhoff, H., Arnold, F., Fiedler, V., Kulmala, M., and Williams, J.: VOC measurements within a boreal forest during spring 2005: on the occurrence of elevated monoterpene concentrations during night time intense particle concentration events, Atmos. Chem. Phys., 9, 8331–8350, 2009.

Emmerson, K. M., MacKenzie, A. R., Owen, S. M., Evans, M. J., and Shallcross, D. E.: A Lagrangian model with simple primary and secondary aerosol scheme 1: comparison with UK PM$_10$ data, Atmos. Chem. Phys., 4, 2161–2170, 2004.

Emmerson, K. M., Carslaw, N., Carpenter, L. J., Heard, D. E., Lee, J. D., and Pilling, M. J.: Urban Atmospheric Chemistry during the PUMA Campaign, 1: Comparison of Modelled OH and \chemHO_2 Concentrations with Measurements, J. Atmos. Chem., 52(2), 143–164, 2005.

Emmerson, K. M., Carslaw, N., Carslaw, D. C., Lee, J. D., McFiggans, G., Bloss, W. J., Gravestock, T., Heard, D. E., Hopkins, J., Ingham, T., Pilling, M. J., Smith, S. C., Jacob, M., and Monks, P. S.: Free radical modelling studies during the UK TORCH Campaign in Summer 2003, Atmos. Chem. Phys., 7, 167–181, 2007.

Evans, M., Shallcross, D., Law, K., Wild, J., Simmonds, P., Spain, T., Berrisford, P., Methven, J., Lewis, A., McQuaid, J., Pilling, M., Bandy, B., Penkett, S., and Pyle, J.: Evaluation of a Lagrangian box model using field measurements from EASE (Eastern Atlantic Summer Experiment) 1996, Atmos. Environ., 34, 3843–3863, 2000.

Fisch, G., Tota, J., Machado, L. A. T., Silva Dias, M. A. F., da Lyra, R. F., Nobre, C. A., Dolman, A. J., and Gash, J. H. C.: The convective boundary layer over pasture and forest in Amazonia, Theor. Appl. Climatol., 78(1–3), 47–59, doi:10.1007/s00704-004-0043-x, 2004.

Farmer, D. K. and Cohen, R. C.: Observations of HNO3, $§igma$AN, $§igma$PN and NO2 fluxes: evidence for rapid HOx chemistry within a pine forest canopy, Atmos. Chem. Phys., 8, 3899–3917, 2008.

Fuentes, J., Lerdau, M., Atkinson, R., Baldocchi, D., Bottenheim, J., Ciccioli, P., Lamb, B., Geron, C., Gu, L., Guenther, A., Sharkey, T., and Stockwell, W.: Biogenic hydrocarbons in the atmospheric boundary layer: A review, B. Am. Meteor. Soc., 81, 1537–1575, 2000.

Fuentes, J. D., Wang, D., Bowling, D. R., Potosnak, M., Monson, R. K., Goliff, W. S., and Stockwell, W. R.: Biogenic Hydrocarbon Chemistry within and Above a Mixed Deciduous Forest, J. Atmos. Chem., 56, 165–185, 2007.

Ganzeveld, L. N., Lelieveld, J. Dentener, F. J., Krol, M. C., Bouwman, A. J., and Roelofs, G.-J.: Global soil-biogenic NOx emissions and the role of canopy processes, J. Geophys. Res., 107(D16), 4298, doi:10.1029/2001JD001289, 2002.

Ganzeveld, L., Eerdekens, G., Feig, G., Fischer, H., Harder, H., Königstedt, R., Kubistin, D., Martinez, M., Meixner, F. X., Scheeren, H. A., Sinha, V., Taraborrelli, D., Williams, J., Vilà-Guerau de Arellano, J., and Lelieveld, J.: Surface and boundary layer exchanges of volatile organic compounds, nitrogen oxides and ozone during the GABRIEL campaign, Atmos. Chem. Phys., 8, 6223–6243, 2008.

George, L. A., Hard, T. M., and O'Brien, R. J.: Measurement of free radicals OH and \chemHO_2 in Los Angeles smog, J. Geophys. Res., 104, 11643–11655, 1999.

Geyer, A. and Stutz, J.: The vertical structure of OH-\chemHO_2-\chemRO_2 chemistry in the nocturnal boundary layer: A one-dimensional model study, J. Geophys. Res., 109, D16301, \doi10.1029/2003JD004425, 2004.

Giacopelli, P., Ford, K., Espada, C. and Shepson, P. B.: Comparison of the measured and simulated isoprene nitrate distributions above a forest canopy, J. Geophys. Res., 110, D01304, doi:10.1029/2004JD005123, 2005.

Guenther, A., Hewitt, C., Erickson, D., Fall, R., Geron, C., Graedel, T., Harley, P., Klinger, L., Lerdau, M., McKay, W., Pierce, T., Scholes, B., Steinbrecher, R., Tallamraju, R., Taylor, J., and Zimmerman, P.: A global model of natural volatile organic compound emissions, J. Geophys. Res., 100, 8873–8892, 1995.

Guenther, A., Karl, T., Harley, P., Wiedinmyer, C., Palmer, P. I., and Geron, C.: Estimates of global terrestrial isoprene emissions using MEGAN (Model of Emissions of Gases and Aerosols from Nature), Atmos. Chem. Phys., 6, 3181–3210, 2006.

Hasson, A., Tyndall, G., and Orlando, J.: A product yield study of the reaction of \chemHO_2 radicals with ethyl peroxy (\chemC_2H_5O_2), acetyl peroxy (\chemCH_3C(O)O_2), and acetonyl peroxy (\chemCH_3C(O)CH_2O_2) radicals, J. Phys. Chem. A, 108, 5979–5989, \doi10.1021/jp048873t, 2004.

Hewitt, C. N., Lee, J. D., MacKenzie, A. R., Barkley, M. P., Carslaw, N., Carver, G. D., Chappell, N. A., Coe, H., Collier, C., Commane, R., Davies, F., Davison, B., DiCarlo, P., Di Marco, C. F., Dorsey, J. R., Edwards, P. M., Evans, M. J., Fowler, D., Furneaux, K. L., Gallagher, M., Guenther, A., Heard, D. E., Helfter, C., Hopkins, J., Ingham, T., Irwin, M., Jones, C., Karunaharan, A., Langford, B., Lewis, A. C., Lim, S. F., MacDonald, S. M., Mahajan, A. S., Malpass, S., McFiggans, G., Mills, G., Misztal, P., Moller, S., Monks, P. S., Nemitz, E., Nicolas-Perea, V., Oetjen, H., Oram, D. E., Palmer, P. I., Phillips, G. J., Pike, R., Plane, J. M. C., Pugh, T., Pyle, J. A., Reeves, C. E., Robinson, N. H., Stewart, D., Stone, D., Whalley, L. K., and Yin, X.: Overview: oxidant and particle photochemical processes above a south-east Asian tropical rainforest (the OP3 project): introduction, rationale, location characteristics and tools, Atmos. Chem. Phys., 10, 169–199, 2010.

Hewitt, C. N., MacKenzie, A. R., Di Carlo, P., Di Marco, C. F., Dorsey, J. R., Evans, M., Fowler, D., Gallagher, M. W., Hopkins, J. R., Jones, C. E., Langford, B., Lee, J. D., Lewis, A. C., Lim, S. F., McQuaid, J., Misztal, P., Moller, S. J., Monks, P. S., Nemitz, E., Oram, D. E., Owen, S. M., Phillips, G. J., Pugh, T. A. M., Pyle, J. A., Reeves, C. E., Ryder, J., Siong, J., Skiba, U., and Stewart, D. J.: Nitrogen management is essential to prevent tropical oil palm plantations from causing ground-level ozone pollution, P. Natl. Acad. Sci. USA, 106, 18447–18451, 2009.

Hofzumahaus, A., Rohrer, F., Lu, K., Bohn, B., Brauers, T., Chang, C.-C., Fuchs, H., Holland, F., Kita, K., Kondo, Y., Li, X., Lou, S., Shao, M., Zeng, L., Wahner, A., and Zhang, Y.: Amplified Trace Gas Removal in the Troposphere, Science, 324, 1702–1704, \doi10.1126/science.1164566, 2009.

Holzinger, R., Lee, A., Paw, K. T., and Goldstein, U. A. H.: Observations of oxidation products above a forest imply biogenic emissions of very reactive compounds, Atmos. Chem. Phys., 5, 67–75, 2005.

Horowitz, L W., Fiore, A M., Milly, G P., Cohen, R C., Perring, A., Wooldridge, P J., Hess, P G., Emmons, L K., and Lamarque, J.-F.: Observational constraints on the chemistry of isoprene nitrates over the eastern United States, J. Geophys. Res., 112, \doi10.1029/2006JD007747, 2007.

Horii, C. V., Munger, J. W., Wofsy, S. C., Zahniser, M., Nelson, D., and McManus, J. B.: Atmospheric reactive nitrogen concentration and flux budgets at a northeastern US forest site, Agric. For. Meteorol., 136, 159–-174, 2006.

IUPAC: Evaluated kinetic data, prefixhttp://www.iupac-kinetic.ch.cam.ac.uk/, last access: 19th March 2009, 2009.

Jenkin, M.: Chemical Mechanisms forming condensable material, Tech. Rep. AEA/RAMP/2001 0010/002, AEA, 1996.

Jenkin, M E., Hurley, M D., and Wallington, T J.: Investigation of the radical product channel of the \chemCH_3C(O)O_2+\chemHO_2 reaction in the gas phase, Phys. Chem. Chem. Phys., 9, 3149–3162, \doi10.1039/b702757e, 2007.

Kanaya, Y., Cao, R., Kato, S., Miyakawa, Y., Kajii, Y., Tanimoto, H., Yokouchi, Y., Mochida, M., Kawamura, K., and Akimoto, H.: Chemistry of OH and \chemHO_2 radicals observed at Rishiri Island, Japan, in September 2003: Missing daytime sink of \chemHO_2 and positive nighttime correlations with monoterpenes, J. Geophys. Res., 112, D11308, doi:10.1029/2006JD007987, 2007.

Karl, T., Potosnak, M., Guenther, A., Clark, D., Walker, J., Herrick, J., and Geron, C.: Exchange processes of volatile organic compounds above a tropical rain forest: Implications for modeling tropospheric chemistry above dense vegetation, J. Geophys. Res., 109, D18306, \doi10.1029/2004JD004738, 2004.

Karl, T., Guenther, A., Yokelson, R J., Greenberg, J., Potosnak, M., Blake, D R., and Artaxo, P.: The tropical forest and fire emissions experiment: Emission, chemistry, and transport of biogenic volatile organic compounds in the lower atmosphere over Amazonia, J. Geophys. Res., 112, D18302, \doi10.1029/2007JD008539, 2007.

Karl, T., Guenther, A., Turnipseed, A., Tyndall, G., Artaxo, P., and Martin, S.: Rapid formation of isoprene photo-oxidation products observed in Amazonia, Atmos. Chem. Phys., 9, 7753–7767, 2009.

Karl, T.: Interactive comment on "Simulating atmospheric composition over a South-East Asian tropical rainforest: Performance of a chemistry box model" by T. A. M. Pugh et al., Atmos. Chem. Phys. Discuss., 9, C6470–C6473, 2009.

Kleffmann, J.: Daytime Sources of Nitrous Acid (HONO) in the Atmospheric Boundary Layer, Chem. Phys. Chem., 8, 1137–1144, 2007.

Konrad, S., Schmitz, Th., Buers, H.-J., Houben, N., Mannschreck, K., Mihelcic, D., Müsgen, P., Pätz, H.-W., Holland, F., Hofzumahaus, A., Schäfer, H.-J., Schröder, S., and Volz-Thomas, A.: Hydrocarbon measurements at Pabstthum during the BERLIOZ campaign and modelling of free radicals, J. Geophys. Res., 108, 8251, doi:10.1029/2001JD000866, 2003.

Krejci, R., Ström, J., de Reus, M., Williams, J., Fischer, H., Andreae, M. O., and Hansson, H.-C.: Spatial and temporal distribution of atmospheric aerosols in the lowermost tropospher over the Amazonian tropical rainforest, Atmos. Chem. Phys., 5, 1527-1543, 2005.

Krol, M., Molemaker, M., and de~Arellano, J.: Effects of turbulence and heterogeneous emissions on photochemically active species in the convective boundary layer, J. Geophys. Res., 105, 6871–6884, 2000.

Kubistin, D., Harder, H., Martinez, M., Rudolf, M., Sander, R., Bozem, H., Eerdekens, G., Fischer, H., Gurk, C., Klüpfel, T., K�nigstedt, R., Parchatka, U., Schiller, C. L., Stickler, A., Taraborrelli, D., Williams, J., and Lelieveld, J.: Hydroxyl radicals in the tropical troposphere over the Suriname rainforest: comparison of measurements with the box model MECCA, Atmos. Chem. Phys. Discuss., 8, 15239–15289, 2008.

Kuhn, U., Rottenberger, S., Biesenthal, T., Wolf, A., Schebeske, G., Ciccioli, P., Brancaleoni, E., Frattoni, M., Tavares, T., and Kesselmeier, J.: Seasonal differences in isoprene and light-dependent monoterpene emission by Amazonian tree species, Glob. Change Biol., 10, 663–682, \doi10.1111/j.1529-8817.2003.00771.x, 2004.

Kuhn, U., Andreae, M. O., Ammann, C., Ara\'ujo, A. C., Brancaleoni, E., Ciccioli, P., Dindorf, T., Frattoni, M., Gatti, L. V., Ganzeveld, L., Kruijt, B., Lelieveld, J., Lloyd, J., Meixner, F. X., Nobre, A. D., Pöschl, U., Spirig, C., Stefani, P., Thielmann, A., Valentini, R., and Kesselmeier, J.: Isoprene and monoterpene fluxes from Central Amazonian rainforest inferred from tower-based and airborne measurements, and implications on the atmospheric chemistry and the local carbon budget, Atmos. Chem. Phys., 7, 2855–2879, 2007.

Langford, B., Davison, B., Nemitz, E., and Hewitt, C. N.: Mixing ratios and eddy covariance flux measurements of volatile organic compounds from an urban canopy (Manchester, UK), Atmos. Chem. Phys., 9, 1971–1987, 2009.

Langford, B., Misztal, P., Nemitz, E., Davison, B., Helfter, C., Lee, J., MacKenzie, A. R., and Hewitt, C. N.: Fluxes of volatile organic compounds from a south-east Asian tropical rainforest, Atmos. Chem. Phys. Discuss., in preparation, 2010.

Lelieveld, J., Butler, T M., Crowley, J N., Dillon, T J., Fischer, H., Ganzeveld, L., Harder, H., Lawrence, M G., Martinez, M., Taraborrelli, D., and Williams, J.: Atmospheric oxidation capacity sustained by a tropical forest, Nature, 452, 737–740, \doi10.1038/nature06870, 2008.

Martin, C. L., Fitzjarrald, D., Garstang, M., Oliveira, S. P., Greco, S., and Browell, E.: Structure and growth of the mixing layer over the Amazonian rain forest, J. Geophys. Res., 93, 1361–1375, 1988.

Martinez, M., Harder, H., Kubistin, D., Rudolf, M., Bozem, H., Eerdekens, G., Fischer, H., Gurk, C., Klüpfel, T., Königstedt, R., Parchatka, U., Schiller, C. L., Stickler, A., Williams, J., and Lelieveld, J.: Hydroxyl radicals in the tropical troposphere over the Suriname rainforest: airborne measurements, Atmos. Chem. Phys. Discuss., 8, 15491–15536, 2008.

Misztal, P. K., Nemitz, E., Langford, B., Coyle, M., Ryder, J., DiMarco, C., Phillips, G., Oram, D., Owen, S., and Cape, J. N.: First direct ecosystem fluxes of VOCs from oil palms in SE Asia, Atmos. Chem. Phys. Discuss., in preparation, 2010.

Murphy, J. G., Day, D. A., Cleary, P. A., Wooldridge, P. J., Millet, D. B., Goldstein, A. H., and Cohen, R. C.: The weekend effect within and downwind of Sacramento – Part 1: Observations of ozone, nitrogen oxides, and VOC reactivity, Atmos. Chem. Phys., 7, 5327–5339, 2007.

Müller, J.-F., Stavrakou, T., Wallens, S., De Smedt, I., Van Roozendael, M., Potosnak, M. J., Rinne, J., Munger, B., Goldstein, A., and Guenther, A. B.: Global isoprene emissions estimated using MEGAN, ECMWF analyses and a detailed canopy environment model, Atmos. Chem. Phys., 8, 1329–1341, 2008.

Ohara, T., Akimoto, H., Kurokawa, J., Horii, N., Yamaji, K., Yan, X., and Hayasaka, T.: An Asian emission inventory of anthropogenic emission sources for the period 1980�2020, Atmos. Chem. Phys., 7, 4419–4444, 2007.

Paulot, F., Crounse, J. D., Kjaergaard, H. G., Kroll, J. H., Seinfeld, J. H., and Wennberg, P. O.: Isoprene photooxidation: new insights into the production of acids and organic nitrates, Atmos. Chem. Phys., 9, 1479–1501, 2009.

Pearson, G. and et al.: Remote sensing of the tropical rain forest boundary layer using pulsed Doppler lidar, Atmos. Chem. Phys. Discuss., in preparation, 2010.

Peeters, J., Nguyen, T L., and Vereecken, L.: HOx radical regeneration in the oxidation of isoprene, Phys. Chem. Chem. Phys., 11, 5935–5939, \doi10.1039/b908511d, 2009.

Pegoraro, E., Rey, A., Abrell, L., Vanharen, J. and Lin, G.: Drought effect on isoprene production and consumption in Biosphere 2 tropical rainforest, Glob. Change Biol., 12, 456–469, doi:10.1111/j.1365-2486.2006.01112.x, 2006.

Pike, R. C., Lee, J. D., Young, P. J., Moller, S., Carver, G. D., Yang, X., Misztal, P., Langford, B., Stewart, D., Reeves, C. E., Hewitt, C. N., and Pyle, J. A.: Can a global model chemical mechanism reproduce NO, NO2, and O3 measurements above a tropical rainforest?, Atmos. Chem. Phys. Discuss., 9, 27611–27648, 2009.

Pinho, P., Pio, C., and Jenkin, M.: Evaluation of isoprene degradation in the detailed tropospheric chemical mechanism, MCM v3, using environmental chamber data, Atmos. Environ., 39, 1303–1322, \doi10.1016/j.atmosenv.2004.11.014, 2005.

Poisson, N., Kanakidou, M., and Crutzen, P.: Impact of non-methane hydrocarbons on tropospheric chemistry and the oxidizing power of the global troposphere: 3-dimensional modelling results, J. Atmos. Chem., 36, 157–230, 2000.

Pugh, T. and et al.: Nocturnal profiles of NOx and \chemO_3 over a South-East Asian rainforest, in preparation, 2010.

Real, E., Law, K. S., Schlager, H., Roiger, A., Huntrieser, H., Methven, J., Cain, M., Holloway, J., Neuman, J. A., Ryerson, T., Flocke, F., de Gouw, J., Atlas, E., Donnelly, S., and Parrish, D.: Lagrangian analysis of low altitude anthropogenic plume processing across the North Atlantic, Atmos. Chem. Phys., 8, 7737–7754, 2008.

Ren, X., Brune, W.H., Oliger, A., Metcalf, A.R., Simpas, J.B., Shirley, T., Schwab, J.J., Bai, C., Roychowdhury, U., Li, Y., Cai, C., Demerjian, K.L., He, Y., Zhou, X., Gao, H., and Hou, J.: OH, \chemHO_2, and OH reactivity during the PMTACS-NY Whiteface Mountain 2002 campaign: Observations and model comparison, J. Geophys. Res., 111, D10S03, doi:10.1029/2005JD006126, 2006.

Ren, X., Olson, J. R., Crawford, J. H., Brune, W. H., Mao, J., Long, R. B., Chen, Z., Avery, M. A., Sachse, G. W., Barrick, J. D., Diskin, G. S., Huey, L. G., Fried, A., Cohen, R. C., Heikes, B., Wennberg, P. O., Singh, H. B., Blake, D. R. and Shetter, R. E.: HOx chemistry during INTEX-A 2004: Observation, model calculation, and comparison with previous studies, J. Geophys. Res., 113, D05310, doi:10.1029/2007JD009166, 2008.

Rosen, R. S., Wood, E. C., Wooldridge, P. J., Thornton, J. A., Day, D. A., Kuster, W., Williams, E. J., Jobson, B. T., and Cohen, R. C.: Observations of total alkyl nitrates during Texax Air Quality Study 2000: Implications of \chemO_3 and alkyl nitrate photochemistry, J. Geophys. Res., 109, D07303, doi:10.1029/2003JD004227, 2004.

Sander, R.: Compilation of Henry's Law Constants for Inorganic and Organic Species of Potential Importance in Environmental Chemistry (Version 3), online available at: prefixhttp://www.henrys-law.org, 2009.

Saunders, S. M., Jenkin, M. E., Derwent, R. G., and Pilling, M. J.: Protocol for the development of the Master Chemical Mechanism, MCM v3 (Part A): tropospheric degradation of non-aromatic volatile organic compounds, Atmos. Chem. Phys., 3, 161–180, 2003.

Schmitt, C., Belokurov, A., Besancon, C., Boisrobert, L., Burgess, N. D., Campbell, A., Coad, L., Fish, L., Gliddon, D., Humphries, K., Kapos, V., Loucks, C., Lysenko, I., Miles, L., Mills, C., Minnemeyer, S., Pistorius, T., Ravilious, C., and Winkel, G.: Global Ecological Forest Classification and Forest Protected Area Gap Analysis: Analyses and Recommendations in view of the 10% target for forest protection under the Convention on Biological Diversity (CBD), Freiburg University Press, Freiburg, Germany, 2008.

Shepson, P. B., Mackay, E., and Muthuramu, K.: Henry's law constants and removal processes for several atmospheric β-hydroxy alkyl nitrates, Enivron. Sci. Technol., 30, 3618–3623, 1996.

Sprengnether, M., Demerjian, K. L., Donahue, N. M., and Anderson, J. G.: Product analysis of the OH oxidation of isoprene and 1,3-butadiene in the presence of NO, J. Geophys. Res., 107, 4269, doi:10.1029/2001JD000716, 2002.

Stockwell, W., Kirchner, F., Kuhn, M., and Seefeld, S.: A new mechanism for regional atmospheric chemistry modeling, J. Geophys. Res., 102, 25847–25879, 1997.

Strong, J., Whyatt, J. D., Hewitt, C. N. and Derwent, R. G.: Development and application of a Lagrangian model to determine the origins of ozone episodes in the UK, Atmos. Environ., doi:10.1016/j.atmosenv.2009.11.019, in press, 2009.

Tan, D., Faloona, I., Simpas, J., Brune, W., Olson, J., Crawford, J., Avery, M., Sachse, G., Vay, S., Sandholm, S., Guan, H., Vaughn, T., Mastromarino, J., Heikes, B., Snow, J., Podolske, J., and Singh, H.: OH and \chemHO_2 in the tropical Pacific: Results from PEM-Tropics B, J. Geophys. Res., 106, 32667–32681, 2001.

Tangki, H. and Chappell, A.: Biomass variation across selectively logged forest within a 225-km2 region of Borneo and its prediction by Landsat TM, Forest Ecol. Manag., 256, 1960–1970, 2008.

Taraborrelli, D., Lawrence, M. G., Butler, T. M., Sander, R., and Lelieveld, J.: Mainz Isoprene Mechanism 2 (MIM2): an isoprene oxidation mechanism for regional and global atmospheric modelling, Atmos. Chem. Phys., 9, 2751–2777, 2009.

Thornton, J. A., Wooldridge, P. J., Cohen, R. C., Martinez, M., Harder, H., Brune, W. H., Williams, E. J., Roberts, J. M., Fehsenfeld, F. C., Hall, S. R., Shetter, R. E., Wert, B. P., and Fried, A.: Ozone production rates as a function of NOx abundances and HOx production rates in the Nashville urban plume, J. Geophys. Res., 107(D12), 4146, doi:10.1029/2001JD000932, 2002.

Treves, K., Shragina, L., and Rudich, Y.: Henry's Law Constants of some β-, γ-, and δ-Hydroxy Alkyl Nitrates of Atmospheric Interest, Environ. Sci. Technol., 34, 1197–1203, 2000.

Tucker, A. C., Brewer, W. A., Banta, R. M., Senff, C. J., Sandberg, S. P., Law, D. C., Weickmann, A. M. and Hardesty, R. M.: Doppler Lidar Estimation of Mixing Height Using Turbulence, Shear, and Aerosol Profiles, J. Atmos. Ocean Tech., 26, 673–688, 2009.

Turnipseed, A. A., Huey, L. G., Nemitz, E., Stickel, R., Higgs, J., Tanner, D. J., Slusher, D. L., Sparks, J. P., Flocke, F., and Guenther, A.: Eddy covariance fluxes of peroxyacetyl nitrates (PANs) and NOy to a coniferous forest, J. Geophys. Res., 111, D09304, doi:10.1029/2005JD006631, 2006.

van Dijk, S. and Duyzer, J.: Nitric oxide emissions from forest soils, J. Geophys. Res., 104, 15955–15961, 1999.

Vinuesa, J.-F. and Vilà-Guerau de Arellano, J.: Introducing effective reaction rates to account for the inefficient mixing of the convective boundary layer, Atmos. Environ., 39, 445–461, 2005.

Walsh, R. P. D.: Climate, The Tropical Rain Forest, edited by: Richards, P. W., Cambridge University Press, Cambridge, 159–205, 352 pp., 1996.

Whalley, L. K., Furneaux, K. L., Edwards, P. E., Heard, D. E.: The chemistry of OH and \chemHO_2 in a tropical rainforest, Atmos. Chem. Phys. Discuss., in preparation, 2010a.

Whalley, L. K., Furneaux, K. L., Edwards, P. E., and Heard, D. E.: Resolving the missing OH source in forested regions, Geophys. Res. Lett., in preparation, 2010b.

Wild, O., Law, K., McKenna, D., Bandy, B., Penkett, S., and Pyle, J.: Photochemical trajectory modeling studies of the North Atlantic region during August 1993, J. Geophys. Res., 101, 29269–29288, 1996.

WMO: Scientific assessment of ozone depletion: 1995 Global Ozone Research and Monitoring Project, Geneva, Switzerland, 1995.

Yienger, J. and Levy, H.: Empirical model of global soil biogenic NOx emissions, J. Geophys. Res., 100, 11447–11464, 1995.

Zhang, L., Moran, M., Maker, P., Brook, J., and Gong, S.: Modelling gaseous dry deposition in AURAMS: a unified regional air-quality modelling system, Atmos. Environ., 36, 537–560, 2002.