begin name
arnold4
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
Gamma = 3.74116898182615
J = 0.0307678189755062
Kc = 27.2372124161502
Ko = 16.5788431231261
Nt = 0.5
Rd = 0.0307674936008629
Rp = 3.2
TPU = 0.0307585098788555
Vcmax = 0.0307602623029146
gm = 0.0307740792044142
CO2 = 24.5
O2 = 21.0
RuBP = 2.0
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
phi := (0.21*gm*Kc*O2)/(Ko*(CO2*gm + Rd - vc))
vc := (-Abs[-Vp + (-Abs[Vc - Vj] + Abs[Vc + Vj])/2] + Abs[Vp + (-Abs[Vc - Vj] + Abs[Vc + Vj])/2])/2
Vc := (Vcmax*(CO2 + (-CO2 - Kc*(1 + O2/Ko) - (-Rd + Vcmax)/gm + Sqrt[(4*((CO2 + Kc*(1 + O2/Ko))*Rd + (-CO2 + Gamma)*Vcmax))/gm + (CO2 + Kc*(1 + O2/Ko) + (-Rd + Vcmax)/gm)^2])/2))/(CO2 + Kc*(1 + O2/Ko) + (-CO2 - Kc*(1 + O2/Ko) - (-Rd + Vcmax)/gm + Sqrt[(4*((CO2 + Kc*(1 + O2/Ko))*Rd + (-CO2 + Gamma)*Vcmax))/gm + (CO2 + Kc*(1 + O2/Ko) + (-Rd + Vcmax)/gm)^2])/2)
Vp := (3*TPU*(CO2 - (-Rd + 3*TPU)/gm))/(CO2 - Gamma - (-Rd + 3*TPU)/gm)
NADP := Nt - NADPH[t]
Vj := (J*(CO2 + (-CO2 - 2*Gamma - (J - 4*Rd)/(4*gm) + Sqrt[(CO2 + 2*Gamma + (J - 4*Rd)/(4*gm))^2 + (4*(((-CO2 + Gamma)*J)/4 + (CO2 + 2*Gamma)*Rd))/gm])/2))/(4*(CO2 + 2*Gamma + (-CO2 - 2*Gamma - (J - 4*Rd)/(4*gm) + Sqrt[(CO2 + 2*Gamma + (J - 4*Rd)/(4*gm))^2 + (4*(((-CO2 + Gamma)*J)/4 + (CO2 + 2*Gamma)*Rd))/gm])/2))
end assignment rules

begin function definitions
oxygenation[phi_,Vc_,Vj_,Vp_] := (phi*(Vp + (Vc + Vj - Abs[Vc - Vj])/2 - Abs[-Vp + (Vc + Vj - Abs[Vc - Vj])/2]))/2
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
end function definitions

begin events
end events

begin process annotations
end process annotations

begin species annotations
end species annotations

begin units
end units