Model repository

Models

Miyoshi et al. 2007

Plyusnina et al. (in prep.)

Hertel et al. 2013

Jablonsky et al. 2014

Grimaud et al. 2014

E-cyano team 2017, clock & C-N metabolism

Müller et al. 2019

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Plyusnina et al. (in prep.)

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

model: Plyusnina et al. (2016)

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:

general

Initial expression: 1
Simulation type: fixed
Details

Initial expression: 1.5
Simulation type: reaction
Details

ATP

Initial expression: 0.3
Simulation type: reaction
Details

NADH

Initial expression: 0.4
Simulation type: reaction
Details

NADPH

Initial expression: 0.3
Simulation type: reaction
Details

PQH2

Initial expression: 0.57
Simulation type: reaction
Details

Initial expression: 0.4
Simulation type: reaction
Details

Initial expression: 0.5
Simulation type: reaction
Details

Equation: -> pc
Function: Product generation (irreversible)
Reaction rate: V_pc/pc

Kinetic rate constant	Value
V_pc	"Vcyt2"-("Vy2"+"Vy2i")-"Vcox1"

Equation: -> fd
Function: Product generation (irreversible)
Reaction rate: V_fd/fd

Kinetic rate constant	Value
V_fd	"Vf1"-("Vy2"+"Vy2i")+"Vcyc"

Equation: -> PQH2
Function: Product generation (irreversible)
Reaction rate: V_PQH2/PQH2

Kinetic rate constant	Value
V_PQH2	"Vx2"+"Vx2i"-"Vcyt1"+"Vnd2"+"Vnh2"+"Vsdh2"-"Vcyd1"

Equation: -> NADPH
Function: Product generation (irreversible)
Reaction rate: V_NADPH/NADPH

Kinetic rate constant	Value
V_NADPH	"Vf2"-"Vnd1"+"Vnadp_gl"-"knadp_gl"*"NADPH"

Equation: -> NADH
Function: Product generation (irreversible)
Reaction rate: V_NADH/NADH

Kinetic rate constant	Value
V_NADH	-"Vnh1"+"Vnad_gl"-"knad_gl"*"NAD"

Equation: -> ATP
Function: Product generation (irreversible)
Reaction rate: V_ATP/ATP

Kinetic rate constant	Value
V_ATP	-"Va1"+"Vatp_gl"-"katp_gl"*"ATP"

Equation: -> Ho
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"

Equation: -> Hi
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

kcox_1

Initial expression: 0.01
Simulation type: fixed

kcox2

Initial expression: 0.1
Simulation type: fixed

kcox1

Initial expression: 0.2
Simulation type: fixed

katp_gl

Initial expression: 0.001
Simulation type: fixed

ka_2

Initial expression: 0.01
Simulation type: fixed

ka_1

Initial expression: 0.01
Simulation type: fixed

ka2

Initial expression: 0.1
Simulation type: fixed

ka1

Initial expression: 0.1
Simulation type: fixed

k_cyc

Initial expression: 0.001
Simulation type: fixed

kHo

Initial expression: 0.01
Simulation type: fixed

ftot

Initial expression: 1
Simulation type: fixed

fdtot

Initial expression: 1
Simulation type: fixed

cyttot

Initial expression: 1
Simulation type: fixed

cydtot

Initial expression: 1
Simulation type: fixed

coxtot

Initial expression: 1
Simulation type: fixed

atot

Initial expression: 1
Simulation type: fixed

Vnadp_gl

Initial expression: 0.01
Simulation type: fixed

Vnad_gl

Initial expression: 0.01
Simulation type: fixed

Initial expression: 0
Simulation type: fixed

Vatp_gl

Initial expression: 0.01
Simulation type: fixed

VHo

Initial expression: 0.05
Simulation type: fixed

VHi

Initial expression: 0.05
Simulation type: fixed

Suc

Initial expression: 4.5
Simulation type: fixed

Initial expression: 1
Simulation type: fixed

PS2

Initial expression: 1
Simulation type: fixed

PS1

Initial expression: 1
Simulation type: fixed

PQtot

Initial expression: 1
Simulation type: fixed

PBS

Initial expression: 0.3
Simulation type: fixed

Initial expression: 1
Simulation type: fixed

NADtot

Initial expression: 1
Simulation type: fixed

NADPtot

Initial expression: 1
Simulation type: fixed

Initial expression: 0.5
Simulation type: fixed

light

Initial expression: 1
Simulation type: fixed

Fum

Initial expression: 0.4
Simulation type: fixed

Initial expression: 1
Simulation type: fixed

ATPtot

Initial expression: 1
Simulation type: fixed

kcox_2

Initial expression: 0.01
Simulation type: fixed

kcyc

Initial expression: 0.01
Simulation type: fixed

kcyd

Initial expression: 0.01
Simulation type: fixed

kcyd1

Initial expression: 0.1
Dynamic expression:
Simulation type: fixed

kcyd2

Initial expression: 0.2
Simulation type: fixed

kcyd_1

Initial expression: 0.1
Simulation type: fixed

kcyd_2

Initial expression: 0.1
Simulation type: fixed

kcyt1

Initial expression: 0.1
Simulation type: fixed

kcyt2

Initial expression: 0.1
Simulation type: fixed

kcyt_1

Initial expression: 0.01
Simulation type: fixed

kcyt_2

Initial expression: 0.01
Simulation type: fixed

kf1

Initial expression: 0.1
Simulation type: fixed

kf2

Initial expression: 0.22
Simulation type: fixed

kf_1

Initial expression: 0.01
Simulation type: fixed

kf_2

Initial expression: 0.01
Simulation type: fixed

knad_gl

Initial expression: 0.001
Simulation type: fixed

knadp_gl

Initial expression: 0.001
Simulation type: fixed

knd1

Initial expression: 0.2
Simulation type: fixed

knd2

Initial expression: 0.2
Simulation type: fixed

knd_1

Initial expression: 0.1
Simulation type: fixed

knd_2

Initial expression: 0.1
Simulation type: fixed

knh1

Initial expression: 0.1
Simulation type: fixed

knh2

Initial expression: 0.1
Simulation type: fixed

knh_1

Initial expression: 0.1
Simulation type: fixed

knh_2

Initial expression: 0.1
Simulation type: fixed

ksdh1

Initial expression: 0.1
Simulation type: fixed

ksdh2

Initial expression: 0.1
Simulation type: fixed

kx1

Initial expression: 4
Simulation type: fixed

kx1i

Initial expression: 2
Simulation type: fixed

kx2

Initial expression: 0.3
Simulation type: fixed

kx_1

Initial expression: 1
Simulation type: fixed

kx_2

Initial expression: 1
Simulation type: fixed

kx_tr

Initial expression: 0.1
Simulation type: fixed

kxtr

Initial expression: 0.01
Simulation type: fixed

ky1

Initial expression: 1.5
Simulation type: fixed

ky1i

Initial expression: 2.5
Simulation type: fixed

ky2

Initial expression: 0.1
Simulation type: fixed

ky_1

Initial expression: 1
Simulation type: fixed

ky_2

Initial expression: 0.5
Simulation type: fixed

ky_tr

Initial expression: 0.01
Simulation type: fixed

kytr

Initial expression: 0.1
Simulation type: fixed

ndtot

Initial expression: 1
Simulation type: fixed

nhtot

Initial expression: 1
Simulation type: fixed

pctot

Initial expression: 1
Simulation type: fixed

sdhtot

Initial expression: 1
Simulation type: fixed

Initial expression: 0
Simulation type: fixed

xtot

Initial expression: 1
Simulation type: fixed

ytot

Initial expression: 1
Simulation type: fixed

H2O

Initial expression: 1
Simulation type: fixed

ksdh_1

Initial expression: 0.1
Simulation type: fixed

ksdh_2

Initial expression: 0.1
Simulation type: fixed

kHi

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

ADP

Initial expression: ATPtot - ATP
Simulation type: assignment

cox0

Initial expression: (coxtot*(qcox_1+qcox2))/(qcox1+qcox_1+qcox2+qcox_2)
Simulation type: assignment

cox1

Initial expression: (coxtot*(qcox1+qcox_2))/(qcox1+qcox_1+qcox2+qcox_2)
Simulation type: assignment

cyd0

Initial expression: (cydtot*(qcyd_1+qcyd2))/(qcyd1+qcyd_1+qcyd2+qcyd_2)
Simulation type: assignment

cyd1

Initial expression: (cydtot*(qcyd1+qcyd_2))/(qcyd1+qcyd_1+qcyd2+qcyd_2)
Simulation type: assignment

cyt0

Initial expression: (cyttot*(qcyt_1+q_cyc+qcyt2))/(qcyt1+qcyc+qcyt_1+q_cyc+qcyt2+qcyt_2)
Simulation type: assignment

cyt1

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

fd_r

Initial expression: fdtot-fd
Simulation type: assignment

Fun

Initial expression: 1+(Vm*PQH2*PQH2)/(Km+PQH2*PQH2)
Simulation type: assignment

NAD

Initial expression: NADtot-NADH
Simulation type: assignment

NADP

Initial expression: NADPtot-NADPH
Simulation type: assignment

nd0

Initial expression: (ndtot*(qnd_1+qnd2))/(qnd1+qnd_1+qnd2+qnd_2)
Simulation type: assignment

nd1

Initial expression: (ndtot*(qnd1+qnd_2))/(qnd1+qnd_1+qnd2+qnd_2)
Simulation type: assignment

nh0

Initial expression: (nhtot*(qnh_1+qnh2))/(qnh1+qnh_1+qnh2+qnh_2)
Simulation type: assignment

nh1

Initial expression: (nhtot*(qnh1+qnh_2))/(qnh1+qnh_1+qnh2+qnh_2)
Simulation type: assignment

pc_ox

Initial expression: pctot-pc
Simulation type: assignment

Initial expression: PQtot-PQH2
Simulation type: assignment

q_cyc

Initial expression: k_cyc*fd*Hi
Simulation type: assignment

qa1

Initial expression: ka1*ATP
Simulation type: assignment

qa2

Initial expression: ka2*Hi*Hi*Hi
Simulation type: assignment

qa_1

Initial expression: ka_1*ADP
Simulation type: assignment

qa_2

Initial expression: ka_2*Ho*Ho*Ho
Simulation type: assignment

qcox1

Initial expression: kcox1*pc*Ho*Ho
Simulation type: assignment

qcox2

Initial expression: kcox2
Simulation type: assignment

qcox_1

Initial expression: kcox_1*pc_ox
Simulation type: assignment

qcox_2

Initial expression: kcox_2*Hi*O2^(1/4)
Simulation type: assignment

qcyc

Initial expression: kcyc*fd_r*Ho
Simulation type: assignment

qcyd1

Initial expression: kcyd1*PQH2
Simulation type: assignment

qcyd2

Initial expression: kcyd2*O2^(1/2)
Simulation type: assignment

qcyd_1

Initial expression: kcyd_1*PQ
Simulation type: assignment

qcyd_2

Initial expression: kcyd_2
Simulation type: assignment

qcyt1

Initial expression: kcyt1*PQH2*pc_ox
Simulation type: assignment

qcyt2

Initial expression: kcyt2
Simulation type: assignment

qcyt_1

Initial expression: kcyt_1
Simulation type: assignment

qcyt_2

Initial expression: kcyt_2*PQ*pc*Hi*Hi
Simulation type: assignment

qf1

Initial expression: kf1*fd_r*fd_r
Simulation type: assignment

qf2

Initial expression: kf2*NADP*Ho
Simulation type: assignment

qf_1

Initial expression: kf_1*fd*fd
Simulation type: assignment

qf_2

Initial expression: kf_2*NADPH
Simulation type: assignment

qnd1

Initial expression: knd1*NADPH*Ho*Ho
Simulation type: assignment

qnd2

Initial expression: knd2*PQ
Simulation type: assignment

qnd_1

Initial expression: knd_1*NADP
Simulation type: assignment

qnd_2

Initial expression: knd_2*PQH2*Hi
Simulation type: assignment

qnh1

Initial expression: knh1*NADH*Ho
Simulation type: assignment

qnh2

Initial expression: knh2*PQ
Simulation type: assignment

qnh_1

Initial expression: knh_1*NAD
Simulation type: assignment

qnh_2

Initial expression: knh_2*PQH2
Simulation type: assignment

qsdh1

Initial expression: ksdh1*Suc
Simulation type: assignment

qsdh2

Initial expression: ksdh2*PQ
Simulation type: assignment

qsdh_1

Initial expression: ksdh_1*Fum
Simulation type: assignment

qsdh_2

Initial expression: ksdh_2*PQH2
Simulation type: assignment

qx1

Initial expression: kx1*light
Simulation type: assignment

qx1i

Initial expression: kx1i*light
Simulation type: assignment

qx2

Initial expression: kx2*PQ*Ho*Ho
Simulation type: assignment

qx2i

Initial expression: qx2
Simulation type: assignment

qx_1

Initial expression: kx_1
Simulation type: assignment

qx_1i

Initial expression: qx_1
Simulation type: assignment

qx_2

Initial expression: kx_2*PQH2*Hi*Hi*O2^(1/2)
Simulation type: assignment

qx_2i

Initial expression: qx_2
Simulation type: assignment

qx_tr

Initial expression: kx_tr*Fun
Simulation type: assignment

qxtr

Initial expression: kxtr*PBS
Simulation type: assignment

qy1

Initial expression: ky1*light
Simulation type: assignment

qy1i

Initial expression: ky1i*light
Simulation type: assignment

qy2

Initial expression: ky2*pc*fd
Simulation type: assignment

qy2i

Initial expression: qy2
Simulation type: assignment

qy_1

Initial expression: ky_1
Simulation type: assignment

qy_1i

Initial expression: qy_1
Simulation type: assignment

qy_2

Initial expression: ky_2*fd_r*pc_ox
Simulation type: assignment

qy_2i

Initial expression: qy_2
Simulation type: assignment

qy_tr

Initial expression: ky_tr
Simulation type: assignment

qytr

Initial expression: kytr*PBS
Simulation type: assignment

Rx1

Initial expression: (qx_1i+qx2i)*qxtr+(qx_1+qx2)*qx_tr+(qx1i+qx_1i+qx2i+qx_2i)*(qx_1+qx2)
Simulation type: assignment

Rx2

Initial expression: (qx1i+qx_2i)*qxtr+(qx1+qx_2)*qx_tr+(qx1i+qx_1i+qx2i+qx_2i)*(qx1+qx_2)
Simulation type: assignment

Rx3

Initial expression: (qx_1i+qx2i)*qxtr+(qx_1+qx2)*qx_tr+(qx1+qx_1+qx2+qx_2)*(qx_1i+qx2i)
Simulation type: assignment

Rx4

Initial expression: (qx1i+qx_2i)*qxtr+(qx1+qx_2)*qx_tr+(qx1+qx_1+qx2+qx_2)*(qx1i+qx_2i)
Simulation type: assignment

Rx5

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

Ry1

Initial expression: (qy_1i+qy2i)*qytr+(qy_1+qy2)*qy_tr+(qy1i+qy_1i+qy2i+qy_2i)*(qy_1+qy2)
Simulation type: assignment

Ry2

Initial expression: (qy1i+qy_2i)*qytr+(qy1+qy_2)*qy_tr+(qy1i+qy_1i+qy2i+qy_2i)*(qy1+qy_2)
Simulation type: assignment

Ry3

Initial expression: (qy_1i+qy2i)*qytr+(qy_1+qy2)*qy_tr+(qy1+qy_1+qy2+qy_2)*(qy_1i+qy2i)
Simulation type: assignment

Ry4

Initial expression: (qy1i+qy_2i)*qytr+(qy1+qy_2)*qy_tr+(qy1+qy_1+qy2+qy_2)*(qy1i+qy_2i)
Simulation type: assignment

Ry5

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

sdh0

Initial expression: (sdhtot*(qsdh_1+qsdh2))/(qsdh1+qsdh_1+qsdh2+qsdh_2)
Simulation type: assignment

sdh1

Initial expression: (sdhtot*(qsdh1+qsdh_2))/(qsdh1+qsdh_1+qsdh2+qsdh_2)
Simulation type: assignment

V_a1

Initial expression: Va1-Va2
Simulation type: assignment

V_ATP

Initial expression: -Va1+Vatp_gl-katp_gl*ATP
Simulation type: assignment

V_cox1

Initial expression: Vcox1-Vcox2
Simulation type: assignment

V_cyd1

Initial expression: Vcyd1-Vcyd2
Simulation type: assignment

V_cyt1

Initial expression: Vcyt1+Vcyc-Vcyt2
Simulation type: assignment

V_f1

Initial expression: Vf1-Vf2
Simulation type: assignment

V_fd

Initial expression: Vf1-(Vy2+Vy2i)+Vcyc
Simulation type: assignment

V_hi

Initial expression: Vx2+Vx2i+Vcyt1+Vcyc+Vnd2+Vcox2-Va2+VHi-kHi*Hi
Simulation type: assignment

V_Ho

Initial expression: -(Vx2+Vx2i)-Vcyc-Vf2-Vnd1-Vnh1-Vcox1+Va2+VHo-kHo*Ho
Simulation type: assignment

V_NADH

Initial expression: -Vnh1+Vnad_gl-knad_gl*NAD
Simulation type: assignment

V_NADPH

Initial expression: Vf2-Vnd1+Vnadp_gl-knadp_gl*NADPH
Simulation type: assignment

V_nd1

Initial expression: Vnd1-Vnd2
Simulation type: assignment

V_nh1

Initial expression: Vnh1-Vnh2
Simulation type: assignment

V_pc

Initial expression: Vcyt2-(Vy2+Vy2i)-Vcox1
Simulation type: assignment

V_PQH2

Initial expression: Vx2+Vx2i-Vcyt1+Vnd2+Vnh2+Vsdh2-Vcyd1
Simulation type: assignment

V_sdh1

Initial expression: Vsdh1-Vsdh2
Simulation type: assignment

Va1

Initial expression: qa1*a0-qa_1*a1
Simulation type: assignment

Va2

Initial expression: qa2*a1-qa_2*a0
Simulation type: assignment

Vcox1

Initial expression: (qcox1*cox0-qcox_1*cox1)*CX
Simulation type: assignment

Vcox2

Initial expression: (qcox2*cox1-qcox_2*cox0)*CX
Simulation type: assignment

Vcyc

Initial expression: qcyc*cyt0-q_cyc*cyt1
Simulation type: assignment

Vcyd1

Initial expression: (qcyd1*cyd0-qcyd_1*cyd1)*CD
Simulation type: assignment

Vcyd2

Initial expression: (qcyd2*cyd1-qcyd_2*cyd0)*CD
Simulation type: assignment

Vcyt1

Initial expression: qcyt1*cyt0-qcyt_1*cyt1
Simulation type: assignment

Vcyt2

Initial expression: qcyt2*cyt1-qcyt_2*cyt0
Simulation type: assignment

Vf1

Initial expression: qf1*f0-qf_1*f1
Simulation type: assignment

Vf2

Initial expression: qf2*f1-qf_2*f0
Simulation type: assignment

Vnd1

Initial expression: (qnd1*nd0-qnd_1*nd1)*ND
Simulation type: assignment

Vnd2

Initial expression: (qnd2*nd1-qnd_2*nd0)*ND
Simulation type: assignment

Vnh1

Initial expression: (qnh1*nh0-qnh_1*nh1)*NH
Simulation type: assignment

Vnh2

Initial expression: (qnh2*nh1-qnh_2*nh0)*NH
Simulation type: assignment

Vsdh1

Initial expression: (qsdh1*sdh0-qsdh_1*sdh1)*SD
Simulation type: assignment

Vsdh2

Initial expression: (qsdh2*sdh1-qsdh_2*sdh0)*SD
Simulation type: assignment

Vx0tr

Initial expression: qxtr*x0a-qx_tr*x0i
Simulation type: assignment

Vx1

Initial expression: (qx1*x0a-qx_1*x1)*PS2
Simulation type: assignment

Vx1i

Initial expression: (qx1*x0i-qx_1*x1i)*PS2
Simulation type: assignment

Vx1tr

Initial expression: qxtr*x1-qx_tr*x1i
Simulation type: assignment

Vx2

Initial expression: (qx2*x1-qx_2*x0a)*PS2
Simulation type: assignment

Vx2i

Initial expression: (qx2*x1i-qx_2*x0i)*PS2
Simulation type: assignment

Vy0tr

Initial expression: qytr*y0-qy_tr*y0i
Simulation type: assignment

Vy1

Initial expression: (qy1*y0-qy_1*y1)*PS1
Simulation type: assignment

Vy1i

Initial expression: (qy1*y0i-qy_1*y1i)*PS1
Simulation type: assignment

Vy1tr

Initial expression: qytr*y1-qy_tr*y1i
Simulation type: assignment

Vy2

Initial expression: (qy2*y1-qy_2*y0)*PS1
Simulation type: assignment

Vy2i

Initial expression: (qy2*y1i-qy_2*y0i)*PS1
Simulation type: assignment

x0a

Initial expression: (((qx_tr)/(qx_tr+qxtr))*xtot*Rx1)/(Rx5)
Simulation type: assignment

x0i

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

x1i

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

y0i

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

y1i

Initial expression: (((qytr)/(qy_tr+qytr))*ytot*Ry4)/(Ry5)
Simulation type: assignment

Initial conditions

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

Parameters

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+(VmPQH2PQH2)/(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_cycfdHi
qa1	ka1*ATP
qa2	ka2HiHi*Hi
qa_1	ka_1*ADP
qa_2	ka_2HoHo*Ho
qcox1	kcox1pcHo*Ho
qcox2	kcox2
qcox_1	kcox_1*pc_ox
qcox_2	kcox_2HiO2^(1/4)
qcyc	kcycfd_rHo
qcyd1	kcyd1*PQH2
qcyd2	kcyd2*O2^(1/2)
qcyd_1	kcyd_1*PQ
qcyd_2	kcyd_2
qcyt1	kcyt1PQH2pc_ox
qcyt2	kcyt2
qcyt_1	kcyt_1
qcyt_2	kcyt_2PQpcHiHi
qf1	kf1fd_rfd_r
qf2	kf2NADPHo
qf_1	kf_1fdfd
qf_2	kf_2*NADPH
qnd1	knd1NADPHHo*Ho
qnd2	knd2*PQ
qnd_1	knd_1*NADP
qnd_2	knd_2PQH2Hi
qnh1	knh1NADHHo
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	kx2PQHo*Ho
qx2i	qx2
qx_1	kx_1
qx_1i	qx_1
qx_2	kx_2PQH2HiHiO2^(1/2)
qx_2i	qx_2
qx_tr	kx_tr*Fun
qxtr	kxtr*PBS
qy1	ky1*light
qy1i	ky1i*light
qy2	ky2pcfd
qy2i	qy2
qy_1	ky_1
qy_1i	qy_1
qy_2	ky_2fd_rpc_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	qa1a0-qa_1a1
Va2	qa2a1-qa_2a0
Vcox1	(qcox1cox0-qcox_1cox1)*CX
Vcox2	(qcox2cox1-qcox_2cox0)*CX
Vcyc	qcyccyt0-q_cyccyt1
Vcyd1	(qcyd1cyd0-qcyd_1cyd1)*CD
Vcyd2	(qcyd2cyd1-qcyd_2cyd0)*CD
Vcyt1	qcyt1cyt0-qcyt_1cyt1
Vcyt2	qcyt2cyt1-qcyt_2cyt0
Vf1	qf1f0-qf_1f1
Vf2	qf2f1-qf_2f0
Vnd1	(qnd1nd0-qnd_1nd1)*ND
Vnd2	(qnd2nd1-qnd_2nd0)*ND
Vnh1	(qnh1nh0-qnh_1nh1)*NH
Vnh2	(qnh2nh1-qnh_2nh0)*NH
Vsdh1	(qsdh1sdh0-qsdh_1sdh1)*SD
Vsdh2	(qsdh2sdh1-qsdh_2sdh0)*SD
Vx0tr	qxtrx0a-qx_trx0i
Vx1	(qx1x0a-qx_1x1)*PS2
Vx1i	(qx1x0i-qx_1x1i)*PS2
Vx1tr	qxtrx1-qx_trx1i
Vx2	(qx2x1-qx_2x0a)*PS2
Vx2i	(qx2x1i-qx_2x0i)*PS2
Vy0tr	qytry0-qy_try0i
Vy1	(qy1y0-qy_1y1)*PS1
Vy1i	(qy1y0i-qy_1y1i)*PS1
Vy1tr	qytry1-qy_try1i
Vy2	(qy2y1-qy_2y0)*PS1
Vy2i	(qy2y1i-qy_2y0i)*PS1
x0a	(((qx_tr)/(qx_tr+qxtr))xtotRx1)/(Rx5)
x0i	(((qxtr)/(qx_tr+qxtr))xtotRx3)/(Rx5)
x1	(((qx_tr)/(qx_tr+qxtr))xtotRx2)/(Rx5)
x1i	(((qxtr)/(qx_tr+qxtr))xtotRx4)/(Rx5)
y0	(((qy_tr)/(qy_tr+qytr))ytotRy1)/(Ry5)
y0i	(((qytr)/(qy_tr+qytr))ytotRy3)/(Ry5)
y1	(((qy_tr)/(qy_tr+qytr))ytotRy2)/(Ry5)
y1i	(((qytr)/(qy_tr+qytr))ytotRy4)/(Ry5)

Options

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

Simulate Export sbml

Conservation analysis

Conservation

Modes analysis

Modes

Matrix analysis

Matrix

Please use the following reference to cite this web site:
M. Trojak, D. Safranek, J. Hrabec, J. Salagovic, F. Romanovska, J. Cerveny: E-Cyanobacterium.org: A Web-Based Platform for Systems Biology of Cyanobacteria. In: Computational Methods in Systems Biology, CMSB 2016, Vol. 9859 of LNCS, pp. 316-322. Springer, 2016. DOI

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