#arnold5

FIX: CO2 O2 RuBP starch

#reactions
NADPH_prod:
 $pool = {1.0}NADPH
  chloroplast * NADPH_production(J, NADP, Nt)
PGA_cons:
 {1.0}PGA = {1.0}RuBP
  chloroplast * PGA_consumption(PGA, Rp, NADPH, Nt, Vcmax)
PGA_prod_Vc:
 {1.0}RuBP + {1.0}CO2 + {2.0}NADPH = {2.0}PGA
  chloroplast * carboxylation(Vc, Vj, Vp)
PGA_prod_Vo:
 {1.0}RuBP + {1.0}O2 + {2.0}NADPH = {1.5}PGA
  chloroplast * oxygenation(phi, Vc, Vj, Vp)


#parameters
Jmax = 142.047003854271
Kc = 26.7125313821435
Ko = 187891.032274486
Nt = 0.5
Q = 1000.0
Rp = 3.2
TPU = 0.259027750094988
Vcmax = 1.91141270310584
a = 0.0434
alpha = 0.24
CO2 = 24.5
O2 = 21000.0
RuBP = 2.0
starch = 0.5
chloroplast = 1.0


#initial values
NADPH = 0.21
PGA = 2.4


#assignment rules
!F Vj = J / 4.0 * CO2 / (CO2 + 2.0 * Gamma)
!F J = Cst * alpha * 0.9 * Q / sqrt(1.0 + pow(alpha * 0.9 * Q / Jmax, 2.0)) / (65.0 * 0.5)
!F NADP = Nt - NADPH
!F Vp = 3.0 * TPU / (1.0 - Gamma / CO2)
!F Vc = Vcmax * CO2 / ((1.0 + O2 / Ko) * (CO2 + Kc))
!F phi = 0.21 * (O2 / Ko) / (CO2 / Kc)
!F Cst = exp(-0.0398 * starch * a)
!F Gamma = O2 / (2.0 * exp(-7.458 + 37830.0 / (8.3143 * 298.15)))