begin name
arnold5
end name

begin reactions
NADPHprod {1.0}$EXTERNAL = {1.0}NADPH
PGAcons {1.0}PGA = {1.0}$RuBP
PGAprodVc {1.0}$RuBP + {1.0}$CO2 + {2.0}NADPH = {2.0}PGA
PGAprodVo {1.0}$RuBP + {1.0}$O2 + {2.0}NADPH = {1.5}PGA
end reactions

begin rate equations
NADPHprod = chloroplast*NADPHproduction[J, NADP, Nt]
PGAcons = chloroplast*PGAconsumption[PGA[t], Rp, NADPH[t], Nt, Vcmax]
PGAprodVc = chloroplast*carboxylation[Vc, Vj, Vp]
PGAprodVo = chloroplast*oxygenation[phi, Vc, Vj, Vp]
end rate equations

begin 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
end parameters

begin initial conditions
NADPH[0] = NADPHi
PGA[0] = PGAi
end initial conditions

begin initial values
NADPHi = 0.21
PGAi = 2.4
end initial values

begin assignment rules
Vj := (CO2*J)/(4*(CO2 + 2*Gamma))
J := (0.027692307692307693*alpha*Cst*Q)/Sqrt[1 + (0.81*alpha^2*Q^2)/Jmax^2]
NADP := Nt - NADPH[t]
Vp := (3*TPU)/(1 - Gamma/CO2)
Vc := (CO2*Vcmax)/((CO2 + Kc)*(1 + O2/Ko))
phi := (0.21*Kc*O2)/(CO2*Ko)
Cst := E^(-0.0398*a*starch)
Gamma := 0.00020430517273754983*O2
end assignment rules

begin function definitions
PGAconsumption[S1_,Rp_,R_,Nt_,Vc_] := (R*S1*Vc)/(Nt*Rp)
NADPHproduction[j_,S1_,Nt_] := (j*S1)/(2*Nt)
carboxylation[Vc_,Vj_,Vp_] := (Vp + (Vc + Vj - Abs[Vc - Vj])/2 - Abs[-Vp + (Vc + Vj - Abs[Vc - Vj])/2])/2
oxygenation[phi_,Vc_,Vj_,Vp_] := (phi*(Vp + (Vc + Vj - Abs[Vc - Vj])/2 - Abs[-Vp + (Vc + Vj - Abs[Vc - Vj])/2]))/2
end function definitions

begin events
end events

begin process annotations
end process annotations

begin species annotations
end species annotations

begin units
end units