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Matuszyńska 2016 PhD model
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Model Details
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Generated Python Code
import numpy as np
def model(
time: float,
variables: list[float],
):
atp, pq_ox, pc_ox, fd_ox, protons_lumen, lhc, psbs_de, vx = variables
pH = 7.9
PPFD = 100
nadph = 0.6
O2_lumen = 8
bH = 100
F = 96.485
E_0_PC = 0.38
E_0_P700 = 0.48
E_0_FA = -0.55
E_0_Fd = -0.43
E_0_NADP = -0.113
NADP_ = 0.8
R = 0.0083
T = 298
A_P = 2.55
Carotenoids_tot = 1
Fd_ = 5
PC_tot = 4
PSBS_tot = 1
LHC_tot = 1
gamma0 = 0.1
gamma1 = 0.25
gamma2 = 0.6
gamma3 = 0.15
kZSat = 0.12
E_0_QA = -0.14
E_0_PQ = 0.354
PQ_tot = 17.5
staticAntII = 0.1
staticAntI = 0.37
kf_atp_synthase = 20
HPR = 4.666666666666667
Pi_mol = 0.01
DeltaG0_ATP = 30.6
kcat_b6f = 2.5
kh_lhc_protonation = 3
kf_lhc_protonation = 0.0096
ksat_lhc_protonation = 5.8
kf_lhc_deprotonation = 0.0096
kf_cyclic_electron_flow = 1
kf_violaxanthin_deepoxidase = 0.0024
kh_violaxanthin_deepoxidase = 5
ksat_violaxanthin_deepoxidase = 5.8
kf_zeaxanthin_epoxidase = 0.00024
E0_fnr = 3
kcat_fnr = 500
km_fnr_fd_red = 1.56
km_fnr_nadp = 0.22
kf_ndh = 0.002
PSII_total = 2.5
PSI_total = 2.5
kH0 = 500000000
kPQred = 250
kPCox = 2500
kFdred = 250000
k2 = 5000000000
kH = 5000000000
kF = 625000000
convf = 0.032
kf_proton_leak = 10
kPTOX = 0.01
kStt7 = 0.0035
km_lhc_state_transition_12 = 0.2
n_ST = 2
kPph1 = 0.0013
kf_ex_atp = 10
k_H = 5000000000
k_F = 625000000
k_P = 5000000000
nadp = NADP_ + - nadph
RT = R * T
adp = A_P + - atp
dG_pH = 2.302585092994046 * R * T
pH_lumen = - (np.log(0.00025 * protons_lumen)) / (np.log(10))
zx = Carotenoids_tot + - vx
fd_red = Fd_ + - fd_ox
pc_red = PC_tot + - pc_ox
psbs_pr = PSBS_tot + - psbs_de
lhc_prot = LHC_tot + - lhc
Q = gamma0 * psbs_de * vx + gamma1 * psbs_pr * vx + (gamma2 * psbs_pr * zx) / (kZSat + zx) + (gamma3 * psbs_de * zx) / (kZSat + zx)
keq_pq_red = np.exp((2 * E_0_PQ * F + - 2 * E_0_QA * F + - 2 * dG_pH * pH) / (RT))
pq_red = PQ_tot + - pq_ox
PSII_cross_section = staticAntII + lhc * (1 + - staticAntI + - staticAntII)
keq_atp_synthase = Pi_mol * np.exp((- DeltaG0_ATP + HPR * dG_pH * (pH + - pH_lumen)) / (RT))
keq_b6f = np.exp((2 * E_0_PC * F + 2 * dG_pH * pH_lumen + - 2 * E_0_PQ * F + - 2 * dG_pH * (pH + - pH_lumen)) / (RT))
keq_fnr = np.exp((- dG_pH * pH + 2 * E_0_NADP * F + - 2 * E_0_Fd * F) / (RT))
vmax_fnr = E0_fnr * kcat_fnr
keq_PCP700 = np.exp((E_0_P700 * F + - E_0_PC * F) / (RT))
keq_ferredoxin_reductase = np.exp((E_0_Fd * F + - E_0_FA * F) / (RT))
A1 = (PSI_total) / (1 + (1 + (fd_red) / (fd_ox * keq_ferredoxin_reductase)) * ((pc_ox) / (keq_PCP700 * pc_red) + (PPFD * (1 + - PSII_cross_section)) / (kPCox * pc_red)) + (PPFD * (1 + - PSII_cross_section)) / (fd_ox * kFdred))
B0 = (PSII_total * kPQred * keq_pq_red * pq_ox * ((kF) ** (2) + (kH0) ** (2) + k2 * kF + k2 * kH0 + (Q) ** (2) * (kH) ** (2) + 2 * kF * kH0 + Q * k2 * kH + 2 * Q * kF * kH + 2 * Q * kH * kH0)) / (kPQred * pq_red * (kF) ** (2) + kPQred * pq_red * (kH0) ** (2) + k2 * kF * kPQred * pq_red + k2 * kH0 * kPQred * pq_red + k2 * keq_pq_red * (PPFD) ** (2) * (PSII_cross_section) ** (2) + kPQred * keq_pq_red * pq_ox * (kF) ** (2) + kPQred * keq_pq_red * pq_ox * (kH0) ** (2) + kPQred * pq_red * (Q) ** (2) * (kH) ** (2) + 2 * kF * kH0 * kPQred * pq_red + PPFD * PSII_cross_section * k2 * kF * keq_pq_red + PPFD * PSII_cross_section * k2 * kH0 * keq_pq_red + PPFD * PSII_cross_section * k2 * kPQred * pq_red + PPFD * PSII_cross_section * kF * kPQred * pq_red + PPFD * PSII_cross_section * kH0 * kPQred * pq_red + Q * k2 * kH * kPQred * pq_red + k2 * kF * kPQred * keq_pq_red * pq_ox + k2 * kH0 * kPQred * keq_pq_red * pq_ox + kPQred * keq_pq_red * pq_ox * (Q) ** (2) * (kH) ** (2) + 2 * Q * kF * kH * kPQred * pq_red + 2 * Q * kH * kH0 * kPQred * pq_red + 2 * kF * kH0 * kPQred * keq_pq_red * pq_ox + PPFD * PSII_cross_section * Q * k2 * kH * keq_pq_red + PPFD * PSII_cross_section * Q * kH * kPQred * pq_red + PPFD * PSII_cross_section * kF * kPQred * keq_pq_red * pq_ox + PPFD * PSII_cross_section * kH0 * kPQred * keq_pq_red * pq_ox + Q * k2 * kH * kPQred * keq_pq_red * pq_ox + 2 * Q * kF * kH * kPQred * keq_pq_red * pq_ox + 2 * Q * kH * kH0 * kPQred * keq_pq_red * pq_ox + PPFD * PSII_cross_section * Q * kH * kPQred * keq_pq_red * pq_ox)
B1 = (PPFD * PSII_cross_section * PSII_total * kPQred * keq_pq_red * pq_ox * (kF + kH0 + Q * kH)) / (kPQred * pq_red * (kF) ** (2) + kPQred * pq_red * (kH0) ** (2) + k2 * kF * kPQred * pq_red + k2 * kH0 * kPQred * pq_red + k2 * keq_pq_red * (PPFD) ** (2) * (PSII_cross_section) ** (2) + kPQred * keq_pq_red * pq_ox * (kF) ** (2) + kPQred * keq_pq_red * pq_ox * (kH0) ** (2) + kPQred * pq_red * (Q) ** (2) * (kH) ** (2) + 2 * kF * kH0 * kPQred * pq_red + PPFD * PSII_cross_section * k2 * kF * keq_pq_red + PPFD * PSII_cross_section * k2 * kH0 * keq_pq_red + PPFD * PSII_cross_section * k2 * kPQred * pq_red + PPFD * PSII_cross_section * kF * kPQred * pq_red + PPFD * PSII_cross_section * kH0 * kPQred * pq_red + Q * k2 * kH * kPQred * pq_red + k2 * kF * kPQred * keq_pq_red * pq_ox + k2 * kH0 * kPQred * keq_pq_red * pq_ox + kPQred * keq_pq_red * pq_ox * (Q) ** (2) * (kH) ** (2) + 2 * Q * kF * kH * kPQred * pq_red + 2 * Q * kH * kH0 * kPQred * pq_red + 2 * kF * kH0 * kPQred * keq_pq_red * pq_ox + PPFD * PSII_cross_section * Q * k2 * kH * keq_pq_red + PPFD * PSII_cross_section * Q * kH * kPQred * pq_red + PPFD * PSII_cross_section * kF * kPQred * keq_pq_red * pq_ox + PPFD * PSII_cross_section * kH0 * kPQred * keq_pq_red * pq_ox + Q * k2 * kH * kPQred * keq_pq_red * pq_ox + 2 * Q * kF * kH * kPQred * keq_pq_red * pq_ox + 2 * Q * kH * kH0 * kPQred * keq_pq_red * pq_ox + PPFD * PSII_cross_section * Q * kH * kPQred * keq_pq_red * pq_ox)
B2 = (PSII_total * (kPQred * pq_red * (kF) ** (2) + kPQred * pq_red * (kH0) ** (2) + k2 * kF * kPQred * pq_red + k2 * kH0 * kPQred * pq_red + kPQred * pq_red * (Q) ** (2) * (kH) ** (2) + 2 * kF * kH0 * kPQred * pq_red + PPFD * PSII_cross_section * k2 * kF * keq_pq_red + PPFD * PSII_cross_section * k2 * kH0 * keq_pq_red + Q * k2 * kH * kPQred * pq_red + 2 * Q * kF * kH * kPQred * pq_red + 2 * Q * kH * kH0 * kPQred * pq_red + PPFD * PSII_cross_section * Q * k2 * kH * keq_pq_red)) / (kPQred * pq_red * (kF) ** (2) + kPQred * pq_red * (kH0) ** (2) + k2 * kF * kPQred * pq_red + k2 * kH0 * kPQred * pq_red + k2 * keq_pq_red * (PPFD) ** (2) * (PSII_cross_section) ** (2) + kPQred * keq_pq_red * pq_ox * (kF) ** (2) + kPQred * keq_pq_red * pq_ox * (kH0) ** (2) + kPQred * pq_red * (Q) ** (2) * (kH) ** (2) + 2 * kF * kH0 * kPQred * pq_red + PPFD * PSII_cross_section * k2 * kF * keq_pq_red + PPFD * PSII_cross_section * k2 * kH0 * keq_pq_red + PPFD * PSII_cross_section * k2 * kPQred * pq_red + PPFD * PSII_cross_section * kF * kPQred * pq_red + PPFD * PSII_cross_section * kH0 * kPQred * pq_red + Q * k2 * kH * kPQred * pq_red + k2 * kF * kPQred * keq_pq_red * pq_ox + k2 * kH0 * kPQred * keq_pq_red * pq_ox + kPQred * keq_pq_red * pq_ox * (Q) ** (2) * (kH) ** (2) + 2 * Q * kF * kH * kPQred * pq_red + 2 * Q * kH * kH0 * kPQred * pq_red + 2 * kF * kH0 * kPQred * keq_pq_red * pq_ox + PPFD * PSII_cross_section * Q * k2 * kH * keq_pq_red + PPFD * PSII_cross_section * Q * kH * kPQred * pq_red + PPFD * PSII_cross_section * kF * kPQred * keq_pq_red * pq_ox + PPFD * PSII_cross_section * kH0 * kPQred * keq_pq_red * pq_ox + Q * k2 * kH * kPQred * keq_pq_red * pq_ox + 2 * Q * kF * kH * kPQred * keq_pq_red * pq_ox + 2 * Q * kH * kH0 * kPQred * keq_pq_red * pq_ox + PPFD * PSII_cross_section * Q * kH * kPQred * keq_pq_red * pq_ox)
B3 = (PPFD * PSII_cross_section * PSII_total * (k2 * kPQred * pq_red + kF * kPQred * pq_red + kH0 * kPQred * pq_red + PPFD * PSII_cross_section * k2 * keq_pq_red + Q * kH * kPQred * pq_red)) / (kPQred * pq_red * (kF) ** (2) + kPQred * pq_red * (kH0) ** (2) + k2 * kF * kPQred * pq_red + k2 * kH0 * kPQred * pq_red + k2 * keq_pq_red * (PPFD) ** (2) * (PSII_cross_section) ** (2) + kPQred * keq_pq_red * pq_ox * (kF) ** (2) + kPQred * keq_pq_red * pq_ox * (kH0) ** (2) + kPQred * pq_red * (Q) ** (2) * (kH) ** (2) + 2 * kF * kH0 * kPQred * pq_red + PPFD * PSII_cross_section * k2 * kF * keq_pq_red + PPFD * PSII_cross_section * k2 * kH0 * keq_pq_red + PPFD * PSII_cross_section * k2 * kPQred * pq_red + PPFD * PSII_cross_section * kF * kPQred * pq_red + PPFD * PSII_cross_section * kH0 * kPQred * pq_red + Q * k2 * kH * kPQred * pq_red + k2 * kF * kPQred * keq_pq_red * pq_ox + k2 * kH0 * kPQred * keq_pq_red * pq_ox + kPQred * keq_pq_red * pq_ox * (Q) ** (2) * (kH) ** (2) + 2 * Q * kF * kH * kPQred * pq_red + 2 * Q * kH * kH0 * kPQred * pq_red + 2 * kF * kH0 * kPQred * keq_pq_red * pq_ox + PPFD * PSII_cross_section * Q * k2 * kH * keq_pq_red + PPFD * PSII_cross_section * Q * kH * kPQred * pq_red + PPFD * PSII_cross_section * kF * kPQred * keq_pq_red * pq_ox + PPFD * PSII_cross_section * kH0 * kPQred * keq_pq_red * pq_ox + Q * k2 * kH * kPQred * keq_pq_red * pq_ox + 2 * Q * kF * kH * kPQred * keq_pq_red * pq_ox + 2 * Q * kH * kH0 * kPQred * keq_pq_red * pq_ox + PPFD * PSII_cross_section * Q * kH * kPQred * keq_pq_red * pq_ox)
Fluo = (B0 * k_F) / (k_F + k_P + Q * k_H) + (B2 * k_F) / (k_F + Q * k_H)
atp_synthase = kf_atp_synthase * (adp + - (atp) / (keq_atp_synthase))
b6f = max(- kcat_b6f, kcat_b6f * (pq_red * (pc_ox) ** (2) + - (pq_ox * (pc_red) ** (2)) / (keq_b6f)))
lhc_protonation = (kf_lhc_protonation * psbs_de * (protons_lumen) ** (kh_lhc_protonation)) / ((protons_lumen) ** (kh_lhc_protonation) + (4000 * (10) ** (- ksat_lhc_protonation)) ** (kh_lhc_protonation))
lhc_deprotonation = kf_lhc_deprotonation * psbs_pr
cyclic_electron_flow = kf_cyclic_electron_flow * pq_ox * (fd_red) ** (2)
violaxanthin_deepoxidase = (kf_violaxanthin_deepoxidase * vx * (protons_lumen) ** (kh_violaxanthin_deepoxidase)) / ((protons_lumen) ** (kh_violaxanthin_deepoxidase) + (4000 * (10) ** (- ksat_violaxanthin_deepoxidase)) ** (kh_violaxanthin_deepoxidase))
zeaxanthin_epoxidase = kf_zeaxanthin_epoxidase * zx
fnr = (vmax_fnr * ((nadp * ((fd_red) / (km_fnr_fd_red)) ** (2)) / (km_fnr_nadp) + - (nadph * ((fd_ox) / (km_fnr_fd_red)) ** (2)) / (keq_fnr * km_fnr_nadp))) / (-1 + (1 + (nadp) / (km_fnr_nadp)) * (1 + ((fd_red) / (km_fnr_fd_red)) ** (2) + (fd_red) / (km_fnr_fd_red)) + (1 + (nadph) / (km_fnr_nadp)) * (1 + ((fd_ox) / (km_fnr_fd_red)) ** (2) + (fd_ox) / (km_fnr_fd_red)))
ndh = kf_ndh * pq_ox
PSII = 0.5 * B1 * k2
PSI = A1 * PPFD * (1 + - PSII_cross_section)
proton_leak = kf_proton_leak * (protons_lumen + - 4000 * (10) ** (- pH))
PTOX = O2_lumen * kPTOX * pq_red
lhc_state_transition_12 = (1 * kStt7 * lhc) / (1 + ((pq_ox) / (PQ_tot * km_lhc_state_transition_12)) ** (n_ST))
lhc_state_transition_21 = kPph1 * lhc_prot
ex_atp = atp * kf_ex_atp
datpdt = +atp_synthase-ex_atp
dpq_oxdt = +b6f-cyclic_electron_flow-ndh-PSII+PTOX
dpc_oxdt = -2*b6f+PSI
dfd_oxdt = +2*cyclic_electron_flow+2*fnr-PSI
dprotons_lumendt = +(- (HPR) / (bH))*atp_synthase+((4) / (bH))*b6f+((2) / (bH))*PSII+(- (1) / (bH))*proton_leak
dlhcdt = -lhc_state_transition_12+lhc_state_transition_21
dpsbs_dedt = -lhc_protonation+lhc_deprotonation
dvxdt = -violaxanthin_deepoxidase+zeaxanthin_epoxidase
return [datpdt, dpq_oxdt, dpc_oxdt, dfd_oxdt, dprotons_lumendt, dlhcdt, dpsbs_dedt, dvxdt]
def all_derived(
time: float,
variables: list[float],
):
atp, pq_ox, pc_ox, fd_ox, protons_lumen, lhc, psbs_de, vx = variables
pH = 7.9
PPFD = 100
nadph = 0.6
O2_lumen = 8
bH = 100
F = 96.485
E_0_PC = 0.38
E_0_P700 = 0.48
E_0_FA = -0.55
E_0_Fd = -0.43
E_0_NADP = -0.113
NADP_ = 0.8
R = 0.0083
T = 298
A_P = 2.55
Carotenoids_tot = 1
Fd_ = 5
PC_tot = 4
PSBS_tot = 1
LHC_tot = 1
gamma0 = 0.1
gamma1 = 0.25
gamma2 = 0.6
gamma3 = 0.15
kZSat = 0.12
E_0_QA = -0.14
E_0_PQ = 0.354
PQ_tot = 17.5
staticAntII = 0.1
staticAntI = 0.37
kf_atp_synthase = 20
HPR = 4.666666666666667
Pi_mol = 0.01
DeltaG0_ATP = 30.6
kcat_b6f = 2.5
kh_lhc_protonation = 3
kf_lhc_protonation = 0.0096
ksat_lhc_protonation = 5.8
kf_lhc_deprotonation = 0.0096
kf_cyclic_electron_flow = 1
kf_violaxanthin_deepoxidase = 0.0024
kh_violaxanthin_deepoxidase = 5
ksat_violaxanthin_deepoxidase = 5.8
kf_zeaxanthin_epoxidase = 0.00024
E0_fnr = 3
kcat_fnr = 500
km_fnr_fd_red = 1.56
km_fnr_nadp = 0.22
kf_ndh = 0.002
PSII_total = 2.5
PSI_total = 2.5
kH0 = 500000000
kPQred = 250
kPCox = 2500
kFdred = 250000
k2 = 5000000000
kH = 5000000000
kF = 625000000
convf = 0.032
kf_proton_leak = 10
kPTOX = 0.01
kStt7 = 0.0035
km_lhc_state_transition_12 = 0.2
n_ST = 2
kPph1 = 0.0013
kf_ex_atp = 10
k_H = 5000000000
k_F = 625000000
k_P = 5000000000
nadp = NADP_ + - nadph
RT = R * T
adp = A_P + - atp
dG_pH = 2.302585092994046 * R * T
pH_lumen = - (np.log(0.00025 * protons_lumen)) / (np.log(10))
zx = Carotenoids_tot + - vx
fd_red = Fd_ + - fd_ox
pc_red = PC_tot + - pc_ox
psbs_pr = PSBS_tot + - psbs_de
lhc_prot = LHC_tot + - lhc
Q = gamma0 * psbs_de * vx + gamma1 * psbs_pr * vx + (gamma2 * psbs_pr * zx) / (kZSat + zx) + (gamma3 * psbs_de * zx) / (kZSat + zx)
keq_pq_red = np.exp((2 * E_0_PQ * F + - 2 * E_0_QA * F + - 2 * dG_pH * pH) / (RT))
pq_red = PQ_tot + - pq_ox
PSII_cross_section = staticAntII + lhc * (1 + - staticAntI + - staticAntII)
keq_atp_synthase = Pi_mol * np.exp((- DeltaG0_ATP + HPR * dG_pH * (pH + - pH_lumen)) / (RT))
keq_b6f = np.exp((2 * E_0_PC * F + 2 * dG_pH * pH_lumen + - 2 * E_0_PQ * F + - 2 * dG_pH * (pH + - pH_lumen)) / (RT))
keq_fnr = np.exp((- dG_pH * pH + 2 * E_0_NADP * F + - 2 * E_0_Fd * F) / (RT))
vmax_fnr = E0_fnr * kcat_fnr
keq_PCP700 = np.exp((E_0_P700 * F + - E_0_PC * F) / (RT))
keq_ferredoxin_reductase = np.exp((E_0_Fd * F + - E_0_FA * F) / (RT))
A1 = (PSI_total) / (1 + (1 + (fd_red) / (fd_ox * keq_ferredoxin_reductase)) * ((pc_ox) / (keq_PCP700 * pc_red) + (PPFD * (1 + - PSII_cross_section)) / (kPCox * pc_red)) + (PPFD * (1 + - PSII_cross_section)) / (fd_ox * kFdred))
B0 = (PSII_total * kPQred * keq_pq_red * pq_ox * ((kF) ** (2) + (kH0) ** (2) + k2 * kF + k2 * kH0 + (Q) ** (2) * (kH) ** (2) + 2 * kF * kH0 + Q * k2 * kH + 2 * Q * kF * kH + 2 * Q * kH * kH0)) / (kPQred * pq_red * (kF) ** (2) + kPQred * pq_red * (kH0) ** (2) + k2 * kF * kPQred * pq_red + k2 * kH0 * kPQred * pq_red + k2 * keq_pq_red * (PPFD) ** (2) * (PSII_cross_section) ** (2) + kPQred * keq_pq_red * pq_ox * (kF) ** (2) + kPQred * keq_pq_red * pq_ox * (kH0) ** (2) + kPQred * pq_red * (Q) ** (2) * (kH) ** (2) + 2 * kF * kH0 * kPQred * pq_red + PPFD * PSII_cross_section * k2 * kF * keq_pq_red + PPFD * PSII_cross_section * k2 * kH0 * keq_pq_red + PPFD * PSII_cross_section * k2 * kPQred * pq_red + PPFD * PSII_cross_section * kF * kPQred * pq_red + PPFD * PSII_cross_section * kH0 * kPQred * pq_red + Q * k2 * kH * kPQred * pq_red + k2 * kF * kPQred * keq_pq_red * pq_ox + k2 * kH0 * kPQred * keq_pq_red * pq_ox + kPQred * keq_pq_red * pq_ox * (Q) ** (2) * (kH) ** (2) + 2 * Q * kF * kH * kPQred * pq_red + 2 * Q * kH * kH0 * kPQred * pq_red + 2 * kF * kH0 * kPQred * keq_pq_red * pq_ox + PPFD * PSII_cross_section * Q * k2 * kH * keq_pq_red + PPFD * PSII_cross_section * Q * kH * kPQred * pq_red + PPFD * PSII_cross_section * kF * kPQred * keq_pq_red * pq_ox + PPFD * PSII_cross_section * kH0 * kPQred * keq_pq_red * pq_ox + Q * k2 * kH * kPQred * keq_pq_red * pq_ox + 2 * Q * kF * kH * kPQred * keq_pq_red * pq_ox + 2 * Q * kH * kH0 * kPQred * keq_pq_red * pq_ox + PPFD * PSII_cross_section * Q * kH * kPQred * keq_pq_red * pq_ox)
B1 = (PPFD * PSII_cross_section * PSII_total * kPQred * keq_pq_red * pq_ox * (kF + kH0 + Q * kH)) / (kPQred * pq_red * (kF) ** (2) + kPQred * pq_red * (kH0) ** (2) + k2 * kF * kPQred * pq_red + k2 * kH0 * kPQred * pq_red + k2 * keq_pq_red * (PPFD) ** (2) * (PSII_cross_section) ** (2) + kPQred * keq_pq_red * pq_ox * (kF) ** (2) + kPQred * keq_pq_red * pq_ox * (kH0) ** (2) + kPQred * pq_red * (Q) ** (2) * (kH) ** (2) + 2 * kF * kH0 * kPQred * pq_red + PPFD * PSII_cross_section * k2 * kF * keq_pq_red + PPFD * PSII_cross_section * k2 * kH0 * keq_pq_red + PPFD * PSII_cross_section * k2 * kPQred * pq_red + PPFD * PSII_cross_section * kF * kPQred * pq_red + PPFD * PSII_cross_section * kH0 * kPQred * pq_red + Q * k2 * kH * kPQred * pq_red + k2 * kF * kPQred * keq_pq_red * pq_ox + k2 * kH0 * kPQred * keq_pq_red * pq_ox + kPQred * keq_pq_red * pq_ox * (Q) ** (2) * (kH) ** (2) + 2 * Q * kF * kH * kPQred * pq_red + 2 * Q * kH * kH0 * kPQred * pq_red + 2 * kF * kH0 * kPQred * keq_pq_red * pq_ox + PPFD * PSII_cross_section * Q * k2 * kH * keq_pq_red + PPFD * PSII_cross_section * Q * kH * kPQred * pq_red + PPFD * PSII_cross_section * kF * kPQred * keq_pq_red * pq_ox + PPFD * PSII_cross_section * kH0 * kPQred * keq_pq_red * pq_ox + Q * k2 * kH * kPQred * keq_pq_red * pq_ox + 2 * Q * kF * kH * kPQred * keq_pq_red * pq_ox + 2 * Q * kH * kH0 * kPQred * keq_pq_red * pq_ox + PPFD * PSII_cross_section * Q * kH * kPQred * keq_pq_red * pq_ox)
B2 = (PSII_total * (kPQred * pq_red * (kF) ** (2) + kPQred * pq_red * (kH0) ** (2) + k2 * kF * kPQred * pq_red + k2 * kH0 * kPQred * pq_red + kPQred * pq_red * (Q) ** (2) * (kH) ** (2) + 2 * kF * kH0 * kPQred * pq_red + PPFD * PSII_cross_section * k2 * kF * keq_pq_red + PPFD * PSII_cross_section * k2 * kH0 * keq_pq_red + Q * k2 * kH * kPQred * pq_red + 2 * Q * kF * kH * kPQred * pq_red + 2 * Q * kH * kH0 * kPQred * pq_red + PPFD * PSII_cross_section * Q * k2 * kH * keq_pq_red)) / (kPQred * pq_red * (kF) ** (2) + kPQred * pq_red * (kH0) ** (2) + k2 * kF * kPQred * pq_red + k2 * kH0 * kPQred * pq_red + k2 * keq_pq_red * (PPFD) ** (2) * (PSII_cross_section) ** (2) + kPQred * keq_pq_red * pq_ox * (kF) ** (2) + kPQred * keq_pq_red * pq_ox * (kH0) ** (2) + kPQred * pq_red * (Q) ** (2) * (kH) ** (2) + 2 * kF * kH0 * kPQred * pq_red + PPFD * PSII_cross_section * k2 * kF * keq_pq_red + PPFD * PSII_cross_section * k2 * kH0 * keq_pq_red + PPFD * PSII_cross_section * k2 * kPQred * pq_red + PPFD * PSII_cross_section * kF * kPQred * pq_red + PPFD * PSII_cross_section * kH0 * kPQred * pq_red + Q * k2 * kH * kPQred * pq_red + k2 * kF * kPQred * keq_pq_red * pq_ox + k2 * kH0 * kPQred * keq_pq_red * pq_ox + kPQred * keq_pq_red * pq_ox * (Q) ** (2) * (kH) ** (2) + 2 * Q * kF * kH * kPQred * pq_red + 2 * Q * kH * kH0 * kPQred * pq_red + 2 * kF * kH0 * kPQred * keq_pq_red * pq_ox + PPFD * PSII_cross_section * Q * k2 * kH * keq_pq_red + PPFD * PSII_cross_section * Q * kH * kPQred * pq_red + PPFD * PSII_cross_section * kF * kPQred * keq_pq_red * pq_ox + PPFD * PSII_cross_section * kH0 * kPQred * keq_pq_red * pq_ox + Q * k2 * kH * kPQred * keq_pq_red * pq_ox + 2 * Q * kF * kH * kPQred * keq_pq_red * pq_ox + 2 * Q * kH * kH0 * kPQred * keq_pq_red * pq_ox + PPFD * PSII_cross_section * Q * kH * kPQred * keq_pq_red * pq_ox)
B3 = (PPFD * PSII_cross_section * PSII_total * (k2 * kPQred * pq_red + kF * kPQred * pq_red + kH0 * kPQred * pq_red + PPFD * PSII_cross_section * k2 * keq_pq_red + Q * kH * kPQred * pq_red)) / (kPQred * pq_red * (kF) ** (2) + kPQred * pq_red * (kH0) ** (2) + k2 * kF * kPQred * pq_red + k2 * kH0 * kPQred * pq_red + k2 * keq_pq_red * (PPFD) ** (2) * (PSII_cross_section) ** (2) + kPQred * keq_pq_red * pq_ox * (kF) ** (2) + kPQred * keq_pq_red * pq_ox * (kH0) ** (2) + kPQred * pq_red * (Q) ** (2) * (kH) ** (2) + 2 * kF * kH0 * kPQred * pq_red + PPFD * PSII_cross_section * k2 * kF * keq_pq_red + PPFD * PSII_cross_section * k2 * kH0 * keq_pq_red + PPFD * PSII_cross_section * k2 * kPQred * pq_red + PPFD * PSII_cross_section * kF * kPQred * pq_red + PPFD * PSII_cross_section * kH0 * kPQred * pq_red + Q * k2 * kH * kPQred * pq_red + k2 * kF * kPQred * keq_pq_red * pq_ox + k2 * kH0 * kPQred * keq_pq_red * pq_ox + kPQred * keq_pq_red * pq_ox * (Q) ** (2) * (kH) ** (2) + 2 * Q * kF * kH * kPQred * pq_red + 2 * Q * kH * kH0 * kPQred * pq_red + 2 * kF * kH0 * kPQred * keq_pq_red * pq_ox + PPFD * PSII_cross_section * Q * k2 * kH * keq_pq_red + PPFD * PSII_cross_section * Q * kH * kPQred * pq_red + PPFD * PSII_cross_section * kF * kPQred * keq_pq_red * pq_ox + PPFD * PSII_cross_section * kH0 * kPQred * keq_pq_red * pq_ox + Q * k2 * kH * kPQred * keq_pq_red * pq_ox + 2 * Q * kF * kH * kPQred * keq_pq_red * pq_ox + 2 * Q * kH * kH0 * kPQred * keq_pq_red * pq_ox + PPFD * PSII_cross_section * Q * kH * kPQred * keq_pq_red * pq_ox)
Fluo = (B0 * k_F) / (k_F + k_P + Q * k_H) + (B2 * k_F) / (k_F + Q * k_H)
atp_synthase = kf_atp_synthase * (adp + - (atp) / (keq_atp_synthase))
b6f = max(- kcat_b6f, kcat_b6f * (pq_red * (pc_ox) ** (2) + - (pq_ox * (pc_red) ** (2)) / (keq_b6f)))
lhc_protonation = (kf_lhc_protonation * psbs_de * (protons_lumen) ** (kh_lhc_protonation)) / ((protons_lumen) ** (kh_lhc_protonation) + (4000 * (10) ** (- ksat_lhc_protonation)) ** (kh_lhc_protonation))
lhc_deprotonation = kf_lhc_deprotonation * psbs_pr
cyclic_electron_flow = kf_cyclic_electron_flow * pq_ox * (fd_red) ** (2)
violaxanthin_deepoxidase = (kf_violaxanthin_deepoxidase * vx * (protons_lumen) ** (kh_violaxanthin_deepoxidase)) / ((protons_lumen) ** (kh_violaxanthin_deepoxidase) + (4000 * (10) ** (- ksat_violaxanthin_deepoxidase)) ** (kh_violaxanthin_deepoxidase))
zeaxanthin_epoxidase = kf_zeaxanthin_epoxidase * zx
fnr = (vmax_fnr * ((nadp * ((fd_red) / (km_fnr_fd_red)) ** (2)) / (km_fnr_nadp) + - (nadph * ((fd_ox) / (km_fnr_fd_red)) ** (2)) / (keq_fnr * km_fnr_nadp))) / (-1 + (1 + (nadp) / (km_fnr_nadp)) * (1 + ((fd_red) / (km_fnr_fd_red)) ** (2) + (fd_red) / (km_fnr_fd_red)) + (1 + (nadph) / (km_fnr_nadp)) * (1 + ((fd_ox) / (km_fnr_fd_red)) ** (2) + (fd_ox) / (km_fnr_fd_red)))
ndh = kf_ndh * pq_ox
PSII = 0.5 * B1 * k2
PSI = A1 * PPFD * (1 + - PSII_cross_section)
proton_leak = kf_proton_leak * (protons_lumen + - 4000 * (10) ** (- pH))
PTOX = O2_lumen * kPTOX * pq_red
lhc_state_transition_12 = (1 * kStt7 * lhc) / (1 + ((pq_ox) / (PQ_tot * km_lhc_state_transition_12)) ** (n_ST))
lhc_state_transition_21 = kPph1 * lhc_prot
ex_atp = atp * kf_ex_atp
return [nadp, RT, adp, dG_pH, pH_lumen, zx, fd_red, pc_red, psbs_pr, lhc_prot, Q, keq_pq_red, pq_red, PSII_cross_section, keq_atp_synthase, keq_b6f, keq_fnr, vmax_fnr, keq_PCP700, keq_ferredoxin_reductase, A1, B0, B1, B2, B3, Fluo, atp_synthase, b6f, lhc_protonation, lhc_deprotonation, cyclic_electron_flow, violaxanthin_deepoxidase, zeaxanthin_epoxidase, fnr, ndh, PSII, PSI, proton_leak, PTOX, lhc_state_transition_12, lhc_state_transition_21, ex_atp]
derived = all_derived
y0 = {"atp": 1.6999999999999997, "pq_ox": 4.706348349506148, "pc_ox": 3.9414515288091567, "fd_ox": 3.7761613271207324, "protons_lumen": 7.737821100836988, "lhc": 0.5105293511676007, "psbs_de": 0.5000000001374878, "vx": 0.09090909090907397}
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Generated LaTeX Code
\begin{align*}
\frac{d atp}{dt} &= kf\_atp\_synthase \cdot (adp - \frac{atp}{keq\_atp\_synthase}) \\
& - atp \cdot kf\_ex\_atp\\
\frac{d pq\_ox}{dt} &= \max(- kcat\_b6f, kcat\_b6f \cdot (pq\_red \cdot {pc\_ox}^{2} - \frac{pq\_ox \cdot {pc\_red}^{2}}{keq\_b6f})) \\
& - kf\_cyclic\_electron\_flow \cdot pq\_ox \cdot {fd\_red}^{2} \\
& - kf\_ndh \cdot pq\_ox - 0.5 \cdot ps2states \cdot k2 \\
& + O2\_lumen \cdot kPTOX \cdot pq\_red\\
\frac{d pc\_ox}{dt} &= - 2 \cdot \max(- kcat\_b6f, kcat\_b6f \cdot (pq\_red \cdot {pc\_ox}^{2} - \frac{pq\_ox \cdot {pc\_red}^{2}}{keq\_b6f})) \\
& + A1 \cdot PPFD \cdot (1 - PSII\_cross\_section)\\
\frac{d fd\_ox}{dt} &= 2 \cdot kf\_cyclic\_electron\_flow \cdot pq\_ox \cdot {fd\_red}^{2} \\
& + 2 \cdot \frac{vmax\_fnr \cdot (\frac{nadp \cdot {\frac{fd\_red}{km\_fnr\_fd\_red}}^{2}}{km\_fnr\_nadp} - \frac{nadph \cdot {\frac{fd\_ox}{km\_fnr\_fd\_red}}^{2}}{keq\_fnr \cdot km\_fnr\_nadp})}{-1 + (1 + \frac{nadp}{km\_fnr\_nadp}) \cdot (1 + {\frac{fd\_red}{km\_fnr\_fd\_red}}^{2} + \frac{fd\_red}{km\_fnr\_fd\_red}) + (1 + \frac{nadph}{km\_fnr\_nadp}) \cdot (1 + {\frac{fd\_ox}{km\_fnr\_fd\_red}}^{2} + \frac{fd\_ox}{km\_fnr\_fd\_red})} \\
& - A1 \cdot PPFD \cdot (1 - PSII\_cross\_section)\\
\frac{d protons\_lumen}{dt} &= - \frac{HPR}{bH} \cdot kf\_atp\_synthase \cdot (adp - \frac{atp}{keq\_atp\_synthase}) \\
& + \frac{4}{bH} \cdot \max(- kcat\_b6f, kcat\_b6f \cdot (pq\_red \cdot {pc\_ox}^{2} - \frac{pq\_ox \cdot {pc\_red}^{2}}{keq\_b6f})) \\
& + \frac{2}{bH} \cdot 0.5 \cdot ps2states \cdot k2 \\
& - \frac{1}{bH} \cdot kf\_proton\_leak \cdot (protons\_lumen - 4000 \cdot {10}^{- pH})\\
\frac{d lhc}{dt} &= - \frac{1 \cdot kStt7 \cdot lhc}{1 + {\frac{pq\_ox}{PQ\_tot \cdot km\_lhc\_state\_transition\_12}}^{n\_ST}} \\
& + kPph1 \cdot lhc\_prot\\
\frac{d psbs\_de}{dt} &= - \frac{kf\_lhc\_protonation \cdot psbs\_de \cdot {protons\_lumen}^{kh\_lhc\_protonation}}{{protons\_lumen}^{kh\_lhc\_protonation} + {4000 \cdot {10}^{- ksat\_lhc\_protonation}}^{kh\_lhc\_protonation}} \\
& + kf\_lhc\_deprotonation \cdot psbs\_pr\\
\frac{d vx}{dt} &= - \frac{kf\_violaxanthin\_deepoxidase \cdot vx \cdot {protons\_lumen}^{kh\_violaxanthin\_deepoxidase}}{{protons\_lumen}^{kh\_violaxanthin\_deepoxidase} + {4000 \cdot {10}^{- ksat\_violaxanthin\_deepoxidase}}^{kh\_violaxanthin\_deepoxidase}} \\
& + kf\_zeaxanthin\_epoxidase \cdot zx
\end{align*}Edit analysis
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