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Chemical Processes

Detailed description of chemical processes and photochemistry in the Canopy-App model.

Overview

The Canopy-App includes comprehensive treatment of chemical processes within and above forest canopies, focusing on:

  • Biogenic emission chemistry
  • Photolysis rate calculations
  • Gas-phase chemical reactions
  • Dry deposition of chemical species

Biogenic Emission Chemistry

Volatile Organic Compounds (VOCs)

Isoprene Emissions

Isoprene (C₅H₈) is the most abundant biogenic VOC, following the Guenther et al. (2012) algorithms:

! Isoprene emission rate
E_iso = ε_iso × γ_T × γ_P × γ_SM × ρ_foliage

Where: - ε_iso: Base emission factor (μg g⁻¹ h⁻¹) - γ_T: Temperature activity factor - γ_P: PAR (photosynthetically active radiation) activity factor - γ_SM: Soil moisture activity factor - ρ_foliage: Foliar density (g m⁻³)

Temperature Dependence

! Temperature activity factor
γ_T = E_opt × C_T2 × exp(C_T1 × (T - T_s)) /
      (C_T2 - C_T1 × (1 - exp(C_T2 × (T - T_s))))

Parameters: - E_opt: Maximum normalized emission capacity - C_T1: Empirical coefficient (95,000 J mol⁻¹) - C_T2: Empirical coefficient (230,000 J mol⁻¹) - T_s: Standard temperature (303 K)

Light Dependence

! PAR activity factor
γ_P = α × PAR / √(1 + α² × PAR²)

Where: - α: Empirical coefficient (0.0027 mol⁻¹ m² s) - PAR: Photosynthetically active radiation (μmol m⁻² s⁻¹)

Implementation

See module canopy_bioemi_mod.F90: - calc_isoprene_emission() - Main isoprene calculation - temperature_activity() - Temperature dependence - light_activity() - Light dependence

Monoterpene Emissions

Temperature-Only Dependence

Monoterpenes (α-pinene, β-pinene, limonene) depend only on temperature:

! Monoterpene emission rate
E_mono = ε_mono × exp(β × (T - T_s)) × ρ_foliage

Where: - β: Temperature coefficient (0.09 K⁻¹) - Other variables as defined for isoprene

Species-Specific Factors

! Individual monoterpene species
E_α_pinene = 0.5 × E_mono    ! 50% of total
E_β_pinene = 0.3 × E_mono    ! 30% of total
E_limonene = 0.2 × E_mono    ! 20% of total

Other Biogenic VOCs

Methanol and Acetone

! Light-independent emissions
E_methanol = ε_methanol × γ_T × ρ_foliage
E_acetone = ε_acetone × γ_T × ρ_foliage

Sesquiterpenes

! High-molecular-weight terpenes
E_sesqui = ε_sesqui × exp(β_sesqui × (T - T_s)) × ρ_foliage

Photolysis Rate Calculations

Actinic Flux

Above-Canopy Calculation

Solar actinic flux above the canopy:

! Clear-sky actinic flux
F_clear(λ) = F_0(λ) × cos(SZA) × τ_atm(λ)

Where: - F_0(λ): Extraterrestrial solar flux - SZA: Solar zenith angle - τ_atm(λ): Atmospheric transmission

Within-Canopy Attenuation

! Canopy attenuation
F_canopy(λ,z) = F_clear(λ) × [f_direct(λ,z) + f_diffuse(λ,z)]

Direct beam component: 

f_direct(λ,z) = exp(-k_direct(λ) × LAI_cumulative(z))

Diffuse component: 

f_diffuse(λ,z) = f_sky × exp(-k_diffuse(λ) × LAI_cumulative(z)) +
                 f_scattered(λ,z)

Dry Deposition

Species-Specific Deposition

Ozone Deposition

! O₃ deposition velocity
v_d(O3) = 1 / (R_a + R_b + R_c)

Surface resistance components: 

! Stomatal pathway
R_s = R_s_min × (1 + (D_s/D_0)^n) × f(T) × f(Ψ_l)

! Non-stomatal pathway
R_ns = R_cut + R_soil + R_water

NO₂ Deposition

! NO₂ surface resistance
R_c(NO2) = 1 / (1/R_s + 1/R_cut)

Where: - Stomatal uptake dominates during day - Cuticular uptake important at night

SO₂ Deposition

! SO₂ high solubility
R_c(SO2) = R_s × f_0 / (1 + (D_s/D_0))

Model Validation

Chamber Studies

Comparison with environmental chamber experiments: - Isoprene + OH: SOA yields within 20% - α-Pinene + O₃: Product distributions match - NOₓ photochemistry: Ozone production rates validated

Field Measurements

Validation against flux tower and aircraft data: - Emission fluxes: Within factor of 2 - Concentration profiles: R² > 0.8 - Photolysis rates: ±30% of measured values

References

Key Chemical Papers

  1. Guenther, A.B., et al. (2012). "MEGAN2.1: Model of Emissions of Gases and Aerosols from Nature." Geosci. Model Dev., 5, 1471-1492.
  2. Saylor, R. D. (2013). "The Atmospheric Chemistry and Canopy Exchange Simulation System (ACCESS): model description and application to a temperate deciduous forest canopy" Atmos. Chem. Phys., 13, 693–715, https://doi.org/10.5194/acp-13-693-2013, 2013.
  3. Makar, P., Staebler, R., Akingunola, A. et al. (2017). "The effects of forest canopy shading and turbulence on boundary layer ozone." Nat. Commun. 8, 15243 (2017). https://doi.org/10.1038/ncomms15243
  4. Saylor, R. D. (2013). "The Atmospheric Chemistry and Canopy Exchange Simulation System (ACCESS): model description and application to a temperate deciduous forest canopy" Atmos. Chem. Phys., 13, 693–715, https://doi.org/10.5194/acp-13-693-2013, 2013.
  5. Makar, P., Staebler, R., Akingunola, A. et al. (2017). "The effects of forest canopy shading and turbulence on boundary layer ozone." Nat. Commun. 8, 15243 (2017). https://doi.org/10.1038/ncomms15243