Large eddy simulation for investigating coupled forest canopy and turbulence influences on atmospheric chemistry

Exchanges of reactive gases between forests and the atmosphere influence tropospheric chemistry, climate, and ecosystems. Chemistry inside canopies can alter these exchanges yet understanding of the chemistry and processes influencing the chemistry is incomplete. Previous work prioritizes complex chemical mechanisms over micrometeorology in the multilayer models of forests used to understand in-canopy chemistry and its impacts. Instead, here we use a new simplified chemical mechanism and resolve turbulence in a multilayer canopy model. Specifically, we describe a new version of the National Center for Atmospheric Research large eddy simulation (LES) coupled to both a multilayer canopy model and a chemical mechanism. The mechanism has 41 reactions and 19 gases for ozone, NOx (=NO + NO2), HOx (=OH + HO2), and isoprene chemistry. We evaluate the mechanism against two more complex mechanisms using box modeling. We configure the LES for a temperate deciduous forest and summer midday weak-wind buoyancy-forced conditions. The multilayer canopy model necessitates estimates of reactant sources and sinks at each canopy level, and thus we describe multilayer parameterizations for dry deposition and biogenic emissions. For the first time with an LES coupled to both a multilayer canopy and chemistry, we demonstrate variability in chemical reactions due to turbulence-induced segregation of reactants inside and just above the canopy. For the cases examined here, in-canopy segregation alters reaction rates that only consider well-mixed conditions by up to -48% to +23%. For many reactions, segregation is stronger when soil NO emissions reflect the upper bound of observed values for temperate forests.