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All quantitative parameters are managed under Parameters Tab. Constants are separated from assigned quantities.

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Plyusnina et al. 2017 (in prep)

A mathematical model of electron transport on thylakoid membrane of cyanobacteria.

The specific feature of electron transport on thylakoid membrane of cyanobacteria is a combination of photosynthetic and respiratory pathways in one reaction space.
The linear photosynthetic transport includes reactions for photosystem II (PSII), plastoquinone (PQ), cytochrome b6f (Cyt b6f), plastocyanin (PC), photosystem I (PSI), ferredoxin (Fd), and ferredoxin NADP oxidoreductase (FNR). We consider also the possibility of cyclic electron transport (CET) around PSI including the donation of electrons by Fd to Cyt b6f.

To describe state transitions we considered the complexes of phycobilisomes (PBS) that interact with PSII and PSI. Taking into account PBS also allowed us to describe non-photochemical quenching (NPQ).
The respiration pathway includes NAD(P)H dehydrogenase complexes (NDH1 and NDH2), succinate dehydrogenase (SDH), the aa3-type terminal oxidase or cytoсhrom с oxidase (Cox) and the PQ oxidase (Cyt bd).
We added proton ATP-ase for complete description of pH changes in luminal and cytoplasmic spaces.
The photosynthetic and the respiration pathways are connected through plastoquinone pool (PQ). 
To couple electron transfer in thylakoid membrane with metabolic reactions of central metabolism we considered influx and outflux of NAD(P)H and ATP in cytoplasm in simple form.
 For every complex we consider redox reactions as transitions between two states - more oxidized (with index “o”) and more reduced (with index “r”). Although such consideration is rather rough, nevertheless it allows to represent electron pathways in the most simple form and to reflect the main features and stoichiometry of redox reactions. 
For PSII and PSI initially we considered the transitions between four states, taking into account interaction with PBS.


model: Plyusnina et al. (2016)
Contains:
Initial expression: 1
Simulation type: fixed
Details
Initial expression: 1.5
Simulation type: reaction
Details
Initial expression: 1.5
Simulation type: reaction
Details
Initial expression: 0.3
Simulation type: reaction
Details
Initial expression: 0.4
Simulation type: reaction
Details
Initial expression: 0.3
Simulation type: reaction
Details
Initial expression: 0.57
Simulation type: reaction
Details
Initial expression: 0.4
Simulation type: reaction
Details
Initial expression: 0.5
Simulation type: reaction
Details
Function: Product generation (irreversible)
Reaction rate: V_pc/pc
Kinetic rate constant Value
V_pc "Vcyt2"-("Vy2"+"Vy2i")-"Vcox1"
Function: Product generation (irreversible)
Reaction rate: V_fd/fd
Kinetic rate constant Value
V_fd "Vf1"-("Vy2"+"Vy2i")+"Vcyc"
Function: Product generation (irreversible)
Reaction rate: V_PQH2/PQH2
Kinetic rate constant Value
V_PQH2 "Vx2"+"Vx2i"-"Vcyt1"+"Vnd2"+"Vnh2"+"Vsdh2"-"Vcyd1"
Function: Product generation (irreversible)
Reaction rate: V_NADPH/NADPH
Kinetic rate constant Value
V_NADPH "Vf2"-"Vnd1"+"Vnadp_gl"-"knadp_gl"*"NADPH"
Function: Product generation (irreversible)
Reaction rate: V_NADH/NADH
Kinetic rate constant Value
V_NADH -"Vnh1"+"Vnad_gl"-"knad_gl"*"NAD"
Function: Product generation (irreversible)
Reaction rate: V_ATP/ATP
Kinetic rate constant Value
V_ATP -"Va1"+"Vatp_gl"-"katp_gl"*"ATP"
Function: Product generation (irreversible)
Reaction rate: V_Ho/Ho
Kinetic rate constant Value
V_Ho -("Vx2"+"Vx2i")-"Vcyc"-"Vf2"-"Vnd1"-"Vnh1"-"Vcox1"+"Va2"+"VHo"-"kHo"*"Ho"
Function: Product generation (irreversible)
Reaction rate: V_hi/Hi
Kinetic rate constant Value
V_hi "Vx2"+"Vx2i"+"Vcyt1"+"Vcyc"+"Vnd2"+"Vcox2"-"Va2"+"VHi"-"kHi"*"Hi"

Constant quantities

Initial expression: 0.01
Simulation type: fixed
Initial expression: 0.1
Simulation type: fixed
Initial expression: 0.2
Simulation type: fixed
Initial expression: 0.001
Simulation type: fixed
Initial expression: 0.01
Simulation type: fixed
Initial expression: 0.01
Simulation type: fixed
Initial expression: 0.1
Simulation type: fixed
Initial expression: 0.1
Simulation type: fixed
Initial expression: 0.001
Simulation type: fixed
Initial expression: 0.01
Simulation type: fixed
Initial expression: 1
Simulation type: fixed
Initial expression: 1
Simulation type: fixed
Initial expression: 1
Simulation type: fixed
Initial expression: 1
Simulation type: fixed
Initial expression: 1
Simulation type: fixed
Initial expression: 1
Simulation type: fixed
Initial expression: 0.01
Simulation type: fixed
Initial expression: 0.01
Simulation type: fixed
Initial expression: 0
Simulation type: fixed
Initial expression: 0.01
Simulation type: fixed
Initial expression: 0.05
Simulation type: fixed
Initial expression: 0.05
Simulation type: fixed
Initial expression: 4.5
Simulation type: fixed
Initial expression: 1
Simulation type: fixed
Initial expression: 1
Simulation type: fixed
Initial expression: 1
Simulation type: fixed
Initial expression: 1
Simulation type: fixed
Initial expression: 0.3
Simulation type: fixed
Initial expression: 1
Simulation type: fixed
Initial expression: 1
Simulation type: fixed
Initial expression: 1
Simulation type: fixed
Initial expression: 1
Simulation type: fixed
Initial expression: 1
Simulation type: fixed
Initial expression: 0.5
Simulation type: fixed
Initial expression: 1
Simulation type: fixed
Initial expression: 0.4
Simulation type: fixed
Initial expression: 1
Simulation type: fixed
Initial expression: 1
Simulation type: fixed
Initial expression: 1
Simulation type: fixed
Initial expression: 0.01
Simulation type: fixed
Initial expression: 0.01
Simulation type: fixed
Initial expression: 0.01
Simulation type: fixed
Initial expression: 0.1
Dynamic expression:
Simulation type: fixed
Initial expression: 0.2
Simulation type: fixed
Initial expression: 0.1
Simulation type: fixed
Initial expression: 0.1
Simulation type: fixed
Initial expression: 0.1
Simulation type: fixed
Initial expression: 0.1
Simulation type: fixed
Initial expression: 0.01
Simulation type: fixed
Initial expression: 0.01
Simulation type: fixed
Initial expression: 0.1
Simulation type: fixed
Initial expression: 0.22
Simulation type: fixed
Initial expression: 0.01
Simulation type: fixed
Initial expression: 0.01
Simulation type: fixed
Initial expression: 0.001
Simulation type: fixed
Initial expression: 0.001
Simulation type: fixed
Initial expression: 0.2
Simulation type: fixed
Initial expression: 0.2
Simulation type: fixed
Initial expression: 0.1
Simulation type: fixed
Initial expression: 0.1
Simulation type: fixed
Initial expression: 0.1
Simulation type: fixed
Initial expression: 0.1
Simulation type: fixed
Initial expression: 0.1
Simulation type: fixed
Initial expression: 0.1
Simulation type: fixed
Initial expression: 0.1
Simulation type: fixed
Initial expression: 0.1
Simulation type: fixed
Initial expression: 4
Simulation type: fixed
Initial expression: 2
Simulation type: fixed
Initial expression: 0.3
Simulation type: fixed
Initial expression: 1
Simulation type: fixed
Initial expression: 1
Simulation type: fixed
Initial expression: 0.1
Simulation type: fixed
Initial expression: 0.01
Simulation type: fixed
Initial expression: 1.5
Simulation type: fixed
Initial expression: 2.5
Simulation type: fixed
Initial expression: 0.1
Simulation type: fixed
Initial expression: 1
Simulation type: fixed
Initial expression: 0.5
Simulation type: fixed
Initial expression: 0.01
Simulation type: fixed
Initial expression: 0.1
Simulation type: fixed
Initial expression: 1
Simulation type: fixed
Initial expression: 1
Simulation type: fixed
Initial expression: 1
Simulation type: fixed
Initial expression: 1
Simulation type: fixed
Initial expression: 0
Simulation type: fixed
Initial expression: 1
Simulation type: fixed
Initial expression: 1
Simulation type: fixed
Initial expression: 1
Simulation type: fixed
Initial expression: 0.1
Simulation type: fixed
Initial expression: 0.1
Simulation type: fixed
Initial expression: 0.01
Simulation type: fixed

Assigned quantities

Initial expression: (atot*(qa_1+qa2))/(qa1+qa_1+qa2+qa_2)
Simulation type: assignment
Initial expression: (atot*(qa1+qa_2))/(qa1+qa_1+qa2+qa_2)
Simulation type: assignment
Initial expression: ATPtot - ATP
Simulation type: assignment
Initial expression: (coxtot*(qcox_1+qcox2))/(qcox1+qcox_1+qcox2+qcox_2)
Simulation type: assignment
Initial expression: (coxtot*(qcox1+qcox_2))/(qcox1+qcox_1+qcox2+qcox_2)
Simulation type: assignment
Initial expression: (cydtot*(qcyd_1+qcyd2))/(qcyd1+qcyd_1+qcyd2+qcyd_2)
Simulation type: assignment
Initial expression: (cydtot*(qcyd1+qcyd_2))/(qcyd1+qcyd_1+qcyd2+qcyd_2)
Simulation type: assignment
Initial expression: (cyttot*(qcyt_1+q_cyc+qcyt2))/(qcyt1+qcyc+qcyt_1+q_cyc+qcyt2+qcyt_2)
Simulation type: assignment
Initial expression: (cyttot*(qcyt1+q_cyc+qcyt_2))/(qcyt1+qcyc+qcyt_1+q_cyc+qcyt2+qcyt_2)
Simulation type: assignment
Initial expression: (ftot*(qf_1+qf2))/(qf1+qf_1+qf2+qf_2)
Simulation type: assignment
Initial expression: (ftot*(qf1+qf_2))/(qf1+qf_1+qf2+qf_2)
Simulation type: assignment
Initial expression: fdtot-fd
Simulation type: assignment
Initial expression: 1+(Vm*PQH2*PQH2)/(Km+PQH2*PQH2)
Simulation type: assignment
Initial expression: NADtot-NADH
Simulation type: assignment
Initial expression: NADPtot-NADPH
Simulation type: assignment
Initial expression: (ndtot*(qnd_1+qnd2))/(qnd1+qnd_1+qnd2+qnd_2)
Simulation type: assignment
Initial expression: (ndtot*(qnd1+qnd_2))/(qnd1+qnd_1+qnd2+qnd_2)
Simulation type: assignment
Initial expression: (nhtot*(qnh_1+qnh2))/(qnh1+qnh_1+qnh2+qnh_2)
Simulation type: assignment
Initial expression: (nhtot*(qnh1+qnh_2))/(qnh1+qnh_1+qnh2+qnh_2)
Simulation type: assignment
Initial expression: pctot-pc
Simulation type: assignment
Initial expression: PQtot-PQH2
Simulation type: assignment
Initial expression: k_cyc*fd*Hi
Simulation type: assignment
Initial expression: ka1*ATP
Simulation type: assignment
Initial expression: ka2*Hi*Hi*Hi
Simulation type: assignment
Initial expression: ka_1*ADP
Simulation type: assignment
Initial expression: ka_2*Ho*Ho*Ho
Simulation type: assignment
Initial expression: kcox1*pc*Ho*Ho
Simulation type: assignment
Initial expression: kcox2
Simulation type: assignment
Initial expression: kcox_1*pc_ox
Simulation type: assignment
Initial expression: kcox_2*Hi*O2^(1/4)
Simulation type: assignment
Initial expression: kcyc*fd_r*Ho
Simulation type: assignment
Initial expression: kcyd1*PQH2
Simulation type: assignment
Initial expression: kcyd2*O2^(1/2)
Simulation type: assignment
Initial expression: kcyd_1*PQ
Simulation type: assignment
Initial expression: kcyd_2
Simulation type: assignment
Initial expression: kcyt1*PQH2*pc_ox
Simulation type: assignment
Initial expression: kcyt2
Simulation type: assignment
Initial expression: kcyt_1
Simulation type: assignment
Initial expression: kcyt_2*PQ*pc*Hi*Hi
Simulation type: assignment
Initial expression: kf1*fd_r*fd_r
Simulation type: assignment
Initial expression: kf2*NADP*Ho
Simulation type: assignment
Initial expression: kf_1*fd*fd
Simulation type: assignment
Initial expression: kf_2*NADPH
Simulation type: assignment
Initial expression: knd1*NADPH*Ho*Ho
Simulation type: assignment
Initial expression: knd2*PQ
Simulation type: assignment
Initial expression: knd_1*NADP
Simulation type: assignment
Initial expression: knd_2*PQH2*Hi
Simulation type: assignment
Initial expression: knh1*NADH*Ho
Simulation type: assignment
Initial expression: knh2*PQ
Simulation type: assignment
Initial expression: knh_1*NAD
Simulation type: assignment
Initial expression: knh_2*PQH2
Simulation type: assignment
Initial expression: ksdh1*Suc
Simulation type: assignment
Initial expression: ksdh2*PQ
Simulation type: assignment
Initial expression: ksdh_1*Fum
Simulation type: assignment
Initial expression: ksdh_2*PQH2
Simulation type: assignment
Initial expression: kx1*light
Simulation type: assignment
Initial expression: kx1i*light
Simulation type: assignment
Initial expression: kx2*PQ*Ho*Ho
Simulation type: assignment
Initial expression: qx2
Simulation type: assignment
Initial expression: kx_1
Simulation type: assignment
Initial expression: qx_1
Simulation type: assignment
Initial expression: kx_2*PQH2*Hi*Hi*O2^(1/2)
Simulation type: assignment
Initial expression: qx_2
Simulation type: assignment
Initial expression: kx_tr*Fun
Simulation type: assignment
Initial expression: kxtr*PBS
Simulation type: assignment
Initial expression: ky1*light
Simulation type: assignment
Initial expression: ky1i*light
Simulation type: assignment
Initial expression: ky2*pc*fd
Simulation type: assignment
Initial expression: qy2
Simulation type: assignment
Initial expression: ky_1
Simulation type: assignment
Initial expression: qy_1
Simulation type: assignment
Initial expression: ky_2*fd_r*pc_ox
Simulation type: assignment
Initial expression: qy_2
Simulation type: assignment
Initial expression: ky_tr
Simulation type: assignment
Initial expression: kytr*PBS
Simulation type: assignment
Initial expression: (qx_1i+qx2i)*qxtr+(qx_1+qx2)*qx_tr+(qx1i+qx_1i+qx2i+qx_2i)*(qx_1+qx2)
Simulation type: assignment
Initial expression: (qx1i+qx_2i)*qxtr+(qx1+qx_2)*qx_tr+(qx1i+qx_1i+qx2i+qx_2i)*(qx1+qx_2)
Simulation type: assignment
Initial expression: (qx_1i+qx2i)*qxtr+(qx_1+qx2)*qx_tr+(qx1+qx_1+qx2+qx_2)*(qx_1i+qx2i)
Simulation type: assignment
Initial expression: (qx1i+qx_2i)*qxtr+(qx1+qx_2)*qx_tr+(qx1+qx_1+qx2+qx_2)*(qx1i+qx_2i)
Simulation type: assignment
Initial expression: (qx1i+qx_1i+qx2i+qx_2i)*qxtr+(qx1+qx_1+qx2+qx_2)*qx_tr+(qx1i+qx_1i+qx2i+qx_2i)*(qx1+qx_1+qx2+qx_2)
Simulation type: assignment
Initial expression: (qy_1i+qy2i)*qytr+(qy_1+qy2)*qy_tr+(qy1i+qy_1i+qy2i+qy_2i)*(qy_1+qy2)
Simulation type: assignment
Initial expression: (qy1i+qy_2i)*qytr+(qy1+qy_2)*qy_tr+(qy1i+qy_1i+qy2i+qy_2i)*(qy1+qy_2)
Simulation type: assignment
Initial expression: (qy_1i+qy2i)*qytr+(qy_1+qy2)*qy_tr+(qy1+qy_1+qy2+qy_2)*(qy_1i+qy2i)
Simulation type: assignment
Initial expression: (qy1i+qy_2i)*qytr+(qy1+qy_2)*qy_tr+(qy1+qy_1+qy2+qy_2)*(qy1i+qy_2i)
Simulation type: assignment
Initial expression: (qy1i+qy_1i+qy2i+qy_2i)*qytr+(qy1+qy_1+qy2+qy_2)*qy_tr+(qy1i+qy_1i+qy2i+qy_2i)*(qy1+qy_1+qy2+qy_2)
Simulation type: assignment
Initial expression: (sdhtot*(qsdh_1+qsdh2))/(qsdh1+qsdh_1+qsdh2+qsdh_2)
Simulation type: assignment
Initial expression: (sdhtot*(qsdh1+qsdh_2))/(qsdh1+qsdh_1+qsdh2+qsdh_2)
Simulation type: assignment
Initial expression: Va1-Va2
Simulation type: assignment
Initial expression: -Va1+Vatp_gl-katp_gl*ATP
Simulation type: assignment
Initial expression: Vcox1-Vcox2
Simulation type: assignment
Initial expression: Vcyd1-Vcyd2
Simulation type: assignment
Initial expression: Vcyt1+Vcyc-Vcyt2
Simulation type: assignment
Initial expression: Vf1-Vf2
Simulation type: assignment
Initial expression: Vf1-(Vy2+Vy2i)+Vcyc
Simulation type: assignment
Initial expression: Vx2+Vx2i+Vcyt1+Vcyc+Vnd2+Vcox2-Va2+VHi-kHi*Hi
Simulation type: assignment
Initial expression: -(Vx2+Vx2i)-Vcyc-Vf2-Vnd1-Vnh1-Vcox1+Va2+VHo-kHo*Ho
Simulation type: assignment
Initial expression: -Vnh1+Vnad_gl-knad_gl*NAD
Simulation type: assignment
Initial expression: Vf2-Vnd1+Vnadp_gl-knadp_gl*NADPH
Simulation type: assignment
Initial expression: Vnd1-Vnd2
Simulation type: assignment
Initial expression: Vnh1-Vnh2
Simulation type: assignment
Initial expression: Vcyt2-(Vy2+Vy2i)-Vcox1
Simulation type: assignment
Initial expression: Vx2+Vx2i-Vcyt1+Vnd2+Vnh2+Vsdh2-Vcyd1
Simulation type: assignment
Initial expression: Vsdh1-Vsdh2
Simulation type: assignment
Initial expression: qa1*a0-qa_1*a1
Simulation type: assignment
Initial expression: qa2*a1-qa_2*a0
Simulation type: assignment
Initial expression: (qcox1*cox0-qcox_1*cox1)*CX
Simulation type: assignment
Initial expression: (qcox2*cox1-qcox_2*cox0)*CX
Simulation type: assignment
Initial expression: qcyc*cyt0-q_cyc*cyt1
Simulation type: assignment
Initial expression: (qcyd1*cyd0-qcyd_1*cyd1)*CD
Simulation type: assignment
Initial expression: (qcyd2*cyd1-qcyd_2*cyd0)*CD
Simulation type: assignment
Initial expression: qcyt1*cyt0-qcyt_1*cyt1
Simulation type: assignment
Initial expression: qcyt2*cyt1-qcyt_2*cyt0
Simulation type: assignment
Initial expression: qf1*f0-qf_1*f1
Simulation type: assignment
Initial expression: qf2*f1-qf_2*f0
Simulation type: assignment
Initial expression: (qnd1*nd0-qnd_1*nd1)*ND
Simulation type: assignment
Initial expression: (qnd2*nd1-qnd_2*nd0)*ND
Simulation type: assignment
Initial expression: (qnh1*nh0-qnh_1*nh1)*NH
Simulation type: assignment
Initial expression: (qnh2*nh1-qnh_2*nh0)*NH
Simulation type: assignment
Initial expression: (qsdh1*sdh0-qsdh_1*sdh1)*SD
Simulation type: assignment
Initial expression: (qsdh2*sdh1-qsdh_2*sdh0)*SD
Simulation type: assignment
Initial expression: qxtr*x0a-qx_tr*x0i
Simulation type: assignment
Initial expression: (qx1*x0a-qx_1*x1)*PS2
Simulation type: assignment
Initial expression: (qx1*x0i-qx_1*x1i)*PS2
Simulation type: assignment
Initial expression: qxtr*x1-qx_tr*x1i
Simulation type: assignment
Initial expression: (qx2*x1-qx_2*x0a)*PS2
Simulation type: assignment
Initial expression: (qx2*x1i-qx_2*x0i)*PS2
Simulation type: assignment
Initial expression: qytr*y0-qy_tr*y0i
Simulation type: assignment
Initial expression: (qy1*y0-qy_1*y1)*PS1
Simulation type: assignment
Initial expression: (qy1*y0i-qy_1*y1i)*PS1
Simulation type: assignment
Initial expression: qytr*y1-qy_tr*y1i
Simulation type: assignment
Initial expression: (qy2*y1-qy_2*y0)*PS1
Simulation type: assignment
Initial expression: (qy2*y1i-qy_2*y0i)*PS1
Simulation type: assignment
Initial expression: (((qx_tr)/(qx_tr+qxtr))*xtot*Rx1)/(Rx5)
Simulation type: assignment
Initial expression: (((qxtr)/(qx_tr+qxtr))*xtot*Rx3)/(Rx5)
Simulation type: assignment
Initial expression: (((qx_tr)/(qx_tr+qxtr))*xtot*Rx2)/(Rx5)
Simulation type: assignment
Initial expression: (((qxtr)/(qx_tr+qxtr))*xtot*Rx4)/(Rx5)
Simulation type: assignment
Initial expression: (((qy_tr)/(qy_tr+qytr))*ytot*Ry1)/(Ry5)
Simulation type: assignment
Initial expression: (((qytr)/(qy_tr+qytr))*ytot*Ry3)/(Ry5)
Simulation type: assignment
Initial expression: (((qy_tr)/(qy_tr+qytr))*ytot*Ry2)/(Ry5)
Simulation type: assignment
Initial expression: (((qytr)/(qy_tr+qytr))*ytot*Ry4)/(Ry5)
Simulation type: assignment
Name Value
general 1
Hi 1.5
Ho 1.5
ATP 0.3
NADH 0.4
NADPH 0.3
PQH2 0.57
fd 0.4
pc 0.5

Constant quantities

Name Value
kcox_1 0.01
kcox2 0.1
kcox1 0.2
katp_gl 0.001
ka_2 0.01
ka_1 0.01
ka2 0.1
ka1 0.1
k_cyc 0.001
kHo 0.01
ftot 1
fdtot 1
cyttot 1
cydtot 1
coxtot 1
atot 1
Vnadp_gl 0.01
Vnad_gl 0.01
Vm 0
Vatp_gl 0.01
VHo 0.05
VHi 0.05
Suc 4.5
SD 1
PS2 1
PS1 1
PQtot 1
PBS 0.3
O2 1
NH 1
ND 1
NADtot 1
NADPtot 1
Km 0.5
light 1
Fum 0.4
CX 1
CD 1
ATPtot 1
kcox_2 0.01
kcyc 0.01
kcyd 0.01
kcyd1 0.1
kcyd2 0.2
kcyd_1 0.1
kcyd_2 0.1
kcyt1 0.1
kcyt2 0.1
kcyt_1 0.01
kcyt_2 0.01
kf1 0.1
kf2 0.22
kf_1 0.01
kf_2 0.01
knad_gl 0.001
knadp_gl 0.001
knd1 0.2
knd2 0.2
knd_1 0.1
knd_2 0.1
knh1 0.1
knh2 0.1
knh_1 0.1
knh_2 0.1
ksdh1 0.1
ksdh2 0.1
kx1 4
kx1i 2
kx2 0.3
kx_1 1
kx_2 1
kx_tr 0.1
kxtr 0.01
ky1 1.5
ky1i 2.5
ky2 0.1
ky_1 1
ky_2 0.5
ky_tr 0.01
kytr 0.1
ndtot 1
nhtot 1
pctot 1
sdhtot 1
t 0
xtot 1
ytot 1
H2O 1
ksdh_1 0.1
ksdh_2 0.1
kHi 0.01

Assigned quantities

Name Value
a0 (atot*(qa_1+qa2))/(qa1+qa_1+qa2+qa_2)
a1 (atot*(qa1+qa_2))/(qa1+qa_1+qa2+qa_2)
ADP ATPtot - ATP
cox0 (coxtot*(qcox_1+qcox2))/(qcox1+qcox_1+qcox2+qcox_2)
cox1 (coxtot*(qcox1+qcox_2))/(qcox1+qcox_1+qcox2+qcox_2)
cyd0 (cydtot*(qcyd_1+qcyd2))/(qcyd1+qcyd_1+qcyd2+qcyd_2)
cyd1 (cydtot*(qcyd1+qcyd_2))/(qcyd1+qcyd_1+qcyd2+qcyd_2)
cyt0 (cyttot*(qcyt_1+q_cyc+qcyt2))/(qcyt1+qcyc+qcyt_1+q_cyc+qcyt2+qcyt_2)
cyt1 (cyttot*(qcyt1+q_cyc+qcyt_2))/(qcyt1+qcyc+qcyt_1+q_cyc+qcyt2+qcyt_2)
f0 (ftot*(qf_1+qf2))/(qf1+qf_1+qf2+qf_2)
f1 (ftot*(qf1+qf_2))/(qf1+qf_1+qf2+qf_2)
fd_r fdtot-fd
Fun 1+(Vm*PQH2*PQH2)/(Km+PQH2*PQH2)
NAD NADtot-NADH
NADP NADPtot-NADPH
nd0 (ndtot*(qnd_1+qnd2))/(qnd1+qnd_1+qnd2+qnd_2)
nd1 (ndtot*(qnd1+qnd_2))/(qnd1+qnd_1+qnd2+qnd_2)
nh0 (nhtot*(qnh_1+qnh2))/(qnh1+qnh_1+qnh2+qnh_2)
nh1 (nhtot*(qnh1+qnh_2))/(qnh1+qnh_1+qnh2+qnh_2)
pc_ox pctot-pc
PQ PQtot-PQH2
q_cyc k_cyc*fd*Hi
qa1 ka1*ATP
qa2 ka2*Hi*Hi*Hi
qa_1 ka_1*ADP
qa_2 ka_2*Ho*Ho*Ho
qcox1 kcox1*pc*Ho*Ho
qcox2 kcox2
qcox_1 kcox_1*pc_ox
qcox_2 kcox_2*Hi*O2^(1/4)
qcyc kcyc*fd_r*Ho
qcyd1 kcyd1*PQH2
qcyd2 kcyd2*O2^(1/2)
qcyd_1 kcyd_1*PQ
qcyd_2 kcyd_2
qcyt1 kcyt1*PQH2*pc_ox
qcyt2 kcyt2
qcyt_1 kcyt_1
qcyt_2 kcyt_2*PQ*pc*Hi*Hi
qf1 kf1*fd_r*fd_r
qf2 kf2*NADP*Ho
qf_1 kf_1*fd*fd
qf_2 kf_2*NADPH
qnd1 knd1*NADPH*Ho*Ho
qnd2 knd2*PQ
qnd_1 knd_1*NADP
qnd_2 knd_2*PQH2*Hi
qnh1 knh1*NADH*Ho
qnh2 knh2*PQ
qnh_1 knh_1*NAD
qnh_2 knh_2*PQH2
qsdh1 ksdh1*Suc
qsdh2 ksdh2*PQ
qsdh_1 ksdh_1*Fum
qsdh_2 ksdh_2*PQH2
qx1 kx1*light
qx1i kx1i*light
qx2 kx2*PQ*Ho*Ho
qx2i qx2
qx_1 kx_1
qx_1i qx_1
qx_2 kx_2*PQH2*Hi*Hi*O2^(1/2)
qx_2i qx_2
qx_tr kx_tr*Fun
qxtr kxtr*PBS
qy1 ky1*light
qy1i ky1i*light
qy2 ky2*pc*fd
qy2i qy2
qy_1 ky_1
qy_1i qy_1
qy_2 ky_2*fd_r*pc_ox
qy_2i qy_2
qy_tr ky_tr
qytr kytr*PBS
Rx1 (qx_1i+qx2i)*qxtr+(qx_1+qx2)*qx_tr+(qx1i+qx_1i+qx2i+qx_2i)*(qx_1+qx2)
Rx2 (qx1i+qx_2i)*qxtr+(qx1+qx_2)*qx_tr+(qx1i+qx_1i+qx2i+qx_2i)*(qx1+qx_2)
Rx3 (qx_1i+qx2i)*qxtr+(qx_1+qx2)*qx_tr+(qx1+qx_1+qx2+qx_2)*(qx_1i+qx2i)
Rx4 (qx1i+qx_2i)*qxtr+(qx1+qx_2)*qx_tr+(qx1+qx_1+qx2+qx_2)*(qx1i+qx_2i)
Rx5 (qx1i+qx_1i+qx2i+qx_2i)*qxtr+(qx1+qx_1+qx2+qx_2)*qx_tr+(qx1i+qx_1i+qx2i+qx_2i)*(qx1+qx_1+qx2+qx_2)
Ry1 (qy_1i+qy2i)*qytr+(qy_1+qy2)*qy_tr+(qy1i+qy_1i+qy2i+qy_2i)*(qy_1+qy2)
Ry2 (qy1i+qy_2i)*qytr+(qy1+qy_2)*qy_tr+(qy1i+qy_1i+qy2i+qy_2i)*(qy1+qy_2)
Ry3 (qy_1i+qy2i)*qytr+(qy_1+qy2)*qy_tr+(qy1+qy_1+qy2+qy_2)*(qy_1i+qy2i)
Ry4 (qy1i+qy_2i)*qytr+(qy1+qy_2)*qy_tr+(qy1+qy_1+qy2+qy_2)*(qy1i+qy_2i)
Ry5 (qy1i+qy_1i+qy2i+qy_2i)*qytr+(qy1+qy_1+qy2+qy_2)*qy_tr+(qy1i+qy_1i+qy2i+qy_2i)*(qy1+qy_1+qy2+qy_2)
sdh0 (sdhtot*(qsdh_1+qsdh2))/(qsdh1+qsdh_1+qsdh2+qsdh_2)
sdh1 (sdhtot*(qsdh1+qsdh_2))/(qsdh1+qsdh_1+qsdh2+qsdh_2)
V_a1 Va1-Va2
V_ATP -Va1+Vatp_gl-katp_gl*ATP
V_cox1 Vcox1-Vcox2
V_cyd1 Vcyd1-Vcyd2
V_cyt1 Vcyt1+Vcyc-Vcyt2
V_f1 Vf1-Vf2
V_fd Vf1-(Vy2+Vy2i)+Vcyc
V_hi Vx2+Vx2i+Vcyt1+Vcyc+Vnd2+Vcox2-Va2+VHi-kHi*Hi
V_Ho -(Vx2+Vx2i)-Vcyc-Vf2-Vnd1-Vnh1-Vcox1+Va2+VHo-kHo*Ho
V_NADH -Vnh1+Vnad_gl-knad_gl*NAD
V_NADPH Vf2-Vnd1+Vnadp_gl-knadp_gl*NADPH
V_nd1 Vnd1-Vnd2
V_nh1 Vnh1-Vnh2
V_pc Vcyt2-(Vy2+Vy2i)-Vcox1
V_PQH2 Vx2+Vx2i-Vcyt1+Vnd2+Vnh2+Vsdh2-Vcyd1
V_sdh1 Vsdh1-Vsdh2
Va1 qa1*a0-qa_1*a1
Va2 qa2*a1-qa_2*a0
Vcox1 (qcox1*cox0-qcox_1*cox1)*CX
Vcox2 (qcox2*cox1-qcox_2*cox0)*CX
Vcyc qcyc*cyt0-q_cyc*cyt1
Vcyd1 (qcyd1*cyd0-qcyd_1*cyd1)*CD
Vcyd2 (qcyd2*cyd1-qcyd_2*cyd0)*CD
Vcyt1 qcyt1*cyt0-qcyt_1*cyt1
Vcyt2 qcyt2*cyt1-qcyt_2*cyt0
Vf1 qf1*f0-qf_1*f1
Vf2 qf2*f1-qf_2*f0
Vnd1 (qnd1*nd0-qnd_1*nd1)*ND
Vnd2 (qnd2*nd1-qnd_2*nd0)*ND
Vnh1 (qnh1*nh0-qnh_1*nh1)*NH
Vnh2 (qnh2*nh1-qnh_2*nh0)*NH
Vsdh1 (qsdh1*sdh0-qsdh_1*sdh1)*SD
Vsdh2 (qsdh2*sdh1-qsdh_2*sdh0)*SD
Vx0tr qxtr*x0a-qx_tr*x0i
Vx1 (qx1*x0a-qx_1*x1)*PS2
Vx1i (qx1*x0i-qx_1*x1i)*PS2
Vx1tr qxtr*x1-qx_tr*x1i
Vx2 (qx2*x1-qx_2*x0a)*PS2
Vx2i (qx2*x1i-qx_2*x0i)*PS2
Vy0tr qytr*y0-qy_tr*y0i
Vy1 (qy1*y0-qy_1*y1)*PS1
Vy1i (qy1*y0i-qy_1*y1i)*PS1
Vy1tr qytr*y1-qy_tr*y1i
Vy2 (qy2*y1-qy_2*y0)*PS1
Vy2i (qy2*y1i-qy_2*y0i)*PS1
x0a (((qx_tr)/(qx_tr+qxtr))*xtot*Rx1)/(Rx5)
x0i (((qxtr)/(qx_tr+qxtr))*xtot*Rx3)/(Rx5)
x1 (((qx_tr)/(qx_tr+qxtr))*xtot*Rx2)/(Rx5)
x1i (((qxtr)/(qx_tr+qxtr))*xtot*Rx4)/(Rx5)
y0 (((qy_tr)/(qy_tr+qytr))*ytot*Ry1)/(Ry5)
y0i (((qytr)/(qy_tr+qytr))*ytot*Ry3)/(Ry5)
y1 (((qy_tr)/(qy_tr+qytr))*ytot*Ry2)/(Ry5)
y1i (((qytr)/(qy_tr+qytr))*ytot*Ry4)/(Ry5)
Name Value
Label x-axis time [s]  
Number of steps 100  
Simulation end time 500  
Simulation start time 0.000000001  
Label y-axis rel. units  
Use log time scale 0  
mult_y 1  

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Conservation analysis

Conservation

Modes analysis

Modes

Matrix analysis

Matrix