Boundary-Layer Meteorol (2008) 128:1–32 DOI 10.1007/s10546-008-9273-2 ORIGINAL PAPER Investigating a Hierarchy of Eulerian Closure Models for Scalar Transfer Inside Forested Canopies Jehn-Yih Juang · Gabriel G. Katul · Mario B. Siqueira · Paul C. Stoy · Heather R. McCarthy Received: 21 February 2007 / Accepted: 27 March 2008 / Published online: 25 April 2008 © Springer Science+Business Media B.V. 2008 Abstract Modelling the transfer of heat, water vapour, and CO 2 between the biosphere and the atmosphere is made difficult by the complex two-way interaction between leaves and their immediate microclimate. When simulating scalar sources and sinks inside canopies on seasonal, inter-annual, or forest development time scales, the so-called well-mixed assump- tion (WMA) of mean concentration (i.e. vertically constant inside the canopy but dynamically evolving in time) is often employed. The WMA eliminates the need to model how vegeta- tion alters its immediate microclimate, which necessitates formulations that utilize turbulent transport theories. Here, two inter-related questions pertinent to the WMA for modelling scalar sources, sinks, and fluxes at seasonal to inter-annual time scales are explored: (1) if the WMA is to be replaced so as to resolve this two-way interaction, how detailed must the turbulent transport model be? And (2) what are the added predictive skills gained by resolving the two-way interaction vis-à-vis other uncertainties such as seasonal variations in physiological parameters. These two questions are addressed by simulating multi-year mean J.-Y. Juang · G. G. Katul · M. B. Siqueira · P. C. Stoy · H. R. McCarthy Nicholas School of the Environment and Earth Sciences, Duke University, Durham, NC, USA J.-Y. Juang (B ) Department of Geography, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan e-mail: jjuang@ntu.edu.tw G. G. Katul Department of Civil and Environmental Engineering, Duke University, Durham, NC, USA Present Address: M. B. Siqueira Departamento de Engenharia Mecânica, Universidade de Brasília, Brasilia, Brazil Present Address: P. C. Stoy School of GeoSciences, Department of Atmospheric and Environmental Science, University of Edinburgh, Edinburgh, UK Present Address: H. R. McCarthy Department of Earth System Science, University of California at Irvine, Irvine, CA, USA 123