Projects

Navigation
To browse the projects in the ontology view use either the graphical scheme below or the navigation panel on the left. The root level is displayed after clicking on the Projects button in the main menu bar at the top of the screen. For switching to model view, click on the project name in the navigation tree.

The central feature of the ontology view is the graphical scheme representing the projection of the project to respective biological structures. The graphical scheme is active, the individual model parts implemented in the project are emphasized yellow when moving the mouse over them. After clicking on any implemented part, the scheme is zoomed in. The description panel at the bottom contains all the detailed information relevant for the currently focused project level.

Annotations Tab
All the annotation terms relevant for the currently focused level of the project are displayed on the Annotation Tab below the scheme. Individual annotation data can be unfolded by clicking on the requested annotation item header.

Components Tab
The Components Tab displays all the model species (state variables) relevant for the currently focused project level. Annotation data for particular components are accessible after clicking on the requested component header.

Reactions Tab
Reactions Tab contains information regarding the modeled reactions. After clicking on the particular reaction header, the reacting components and relevant kinetic parameters are displayed.

Parameters Tab
All quantitative parameters are managed under Parameters Tab. Constants are separated from algebraically evaluated parameters.

Simulation Tab
Simulation and SBML export are available by clicking on appropriate buttons at the bottom of the tab. All relevant settings of parameters and initial conditions is listed in respective folders. Folder Options contains parameters of the simulation algorithm.

'Qb'

“Oxidized state of the secondary quinone electron acceptor in photosystem II. It is plastoquinone molecule from the plastoquinone pool which is loosely bound to the Qb-pocket at D1 protein of photosystem II. It accepts electrons from reduced primary quinone electron acceptor in photosystem II, Qa, and unlike Qa, Qb is two-electron acceptor.”

Qb
“Reduced state of Qb which is firmly bound to the Qb-pocket of photosystem II.”
Qb-
“Doubly reduced state of Qb. When subsequently doubly protonated (assumed implicitly) by protons from stroma, it becomes loosely bound to the Qb-pocket of photosystem II and it unbinds from the pocket to the thylakoid membrane becoming plastoquinol molecule from the plastoquionone pool.”

Qb2-
Model states corresponding to the currently selected level:
Initial value: 0
Simulation type: reaction
Initial value: 0
Simulation type: reaction
Initial value: 0
Simulation type: reaction
Initial value: 1
Simulation type: reaction
Initial value: 0
Simulation type: reaction
Initial value: 0
Simulation type: reaction
Initial value: 0
Simulation type: reaction
Initial value: 0
Simulation type: reaction
Initial value: 0
Simulation type: reaction
Initial value: 0
Simulation type: reaction
Initial value: 0
Simulation type: reaction
Initial value: 0
Simulation type: reaction
”It occurs in the model between P680 and Qa with rate constant kL2 leading to formation of P680+ and Qa-. Value of kL2 is determined by amount of excitations coming to reaction centre of photosystem II and concentration of chlorophylls in a sample.”


Function: Mass Action (irreversible)
Reaction rate: kL2*P680/Qa/Qb
Product: P680+/Qa-/Qb
Kinetic rate constant Value
"It leads to formation of Si+1-state and P680 with rate constants k01, k12, k23 and k30 for the S0-S1, S1-S2, S2-S3 and S3-S0 transition, respectively." []

Function: Mass Action (irreversible)
Reaction rate: k01*S0 * P680+/Qa-/Qb
Product: S1, P680/Qa-/Qb
Kinetic rate constant Value
"It leads to formation of Si+1-state and P680 with rate constants k01, k12, k23 and k30 for the S0-S1, S1-S2, S2-S3 and S3-S0 transition, respectively." []

Function: Mass Action (irreversible)
Reaction rate: k12*S1 * P680+/Qa-/Qb
Product: S2, P680/Qa-/Qb
Kinetic rate constant Value
"It leads to formation of Si+1-state and P680 with rate constants k01, k12, k23 and k30 for the S0-S1, S1-S2, S2-S3 and S3-S0 transition, respectively." []

Function: Mass Action (irreversible)
Reaction rate: k23*S2 * P680+/Qa-/Qb
Product: S3, P680/Qa-/Qb
Kinetic rate constant Value
"It leads to formation of Si+1-state and P680 with rate constants k01, k12, k23 and k30 for the S0-S1, S1-S2, S2-S3 and S3-S0 transition, respectively." []

Function: Mass Action (irreversible)
Reaction rate: k30*S3 * P680+/Qa-/Qb
Product: S0, P680/Qa-/Qb
Kinetic rate constant Value
"When Qa is reduced, it donates its electron to oxidized Qb. This reaction occurs with forward rate constant kAB1 and the reaction is considered reversible with backward rate constant kBA1." []

Function: Mass Action (reversible)
Reaction rate: kAB1*P680+/Qa-/Qb-kBA1*P680+/Qa/Qb-
Product: P680+/Qa/Qb-
Kinetic rate constant Value
“When Qb is doubly reduced and protonated (protonation is assumed implicitly), it exchanges with oxidized PQ molecule from the pool leading to presence of oxidized Qb in photosystem II and doubly reduced and protonated PQ molecule (PQH) in the pool. The exchange is is reversible second order reaction with forward and backward rate constants kfB and kbB, respectively.”


Function: Mass Action (reversible)
Reaction rate: kfB*PQ * P680+/Qa-/Qb2--kbB*PQH * P680+/Qa-/Qb
Product: PQH, P680+/Qa-/Qb
Kinetic rate constant Value
"It leads to formation of Si+1-state and P680 with rate constants k01, k12, k23 and k30 for the S0-S1, S1-S2, S2-S3 and S3-S0 transition, respectively." []

Function: Mass Action (irreversible)
Reaction rate: k01*S0 * P680+/Qa/Qb
Product: S1, P680/Qa/Qb
Kinetic rate constant Value
"It leads to formation of Si+1-state and P680 with rate constants k01, k12, k23 and k30 for the S0-S1, S1-S2, S2-S3 and S3-S0 transition, respectively." []

Function: Mass Action (irreversible)
Reaction rate: k12*S1 * P680+/Qa/Qb
Product: S2, P680/Qa/Qb
Kinetic rate constant Value
"It leads to formation of Si+1-state and P680 with rate constants k01, k12, k23 and k30 for the S0-S1, S1-S2, S2-S3 and S3-S0 transition, respectively." []

Function: Mass Action (irreversible)
Reaction rate: k23*S2 * P680+/Qa/Qb
Product: S3, P680/Qa/Qb
Kinetic rate constant Value
"It leads to formation of Si+1-state and P680 with rate constants k01, k12, k23 and k30 for the S0-S1, S1-S2, S2-S3 and S3-S0 transition, respectively." []

Function: Mass Action (irreversible)
Reaction rate: k30*S3 * P680+/Qa/Qb
Product: S0, P680/Qa/Qb
Kinetic rate constant Value
“When Qb is doubly reduced and protonated (protonation is assumed implicitly), it exchanges with oxidized PQ molecule from the pool leading to presence of oxidized Qb in photosystem II and doubly reduced and protonated PQ molecule (PQH) in the pool. The exchange is is reversible second order reaction with forward and backward rate constants kfB and kbB, respectively.”


Function: Mass Action (reversible)
Reaction rate: kfB*PQ * P680+/Qa/Qb2--kbB*PQH * P680+/Qa/Qb
Product: PQH, P680+/Qa/Qb
Kinetic rate constant Value
"When Qa is reduced, it donates its electron to oxidized Qb. This reaction occurs with forward rate constant kAB1 and the reaction is considered reversible with backward rate constant kBA1." []

Function: Mass Action (reversible)
Reaction rate: kAB1*P680/Qa-/Qb-kBA1*P680/Qa/Qb-
Product: P680/Qa/Qb-
Kinetic rate constant Value
“When Qb is doubly reduced and protonated (protonation is assumed implicitly), it exchanges with oxidized PQ molecule from the pool leading to presence of oxidized Qb in photosystem II and doubly reduced and protonated PQ molecule (PQH) in the pool. The exchange is is reversible second order reaction with forward and backward rate constants kfB and kbB, respectively.”


Function: Mass Action (reversible)
Reaction rate: kfB*PQ * P680/Qa-/Qb2--kbB*P680/Qa-/Qb * PQH
Product: P680/Qa-/Qb, PQH
Kinetic rate constant Value
“When Qb is doubly reduced and protonated (protonation is assumed implicitly), it exchanges with oxidized PQ molecule from the pool leading to presence of oxidized Qb in photosystem II and doubly reduced and protonated PQ molecule (PQH) in the pool. The exchange is is reversible second order reaction with forward and backward rate constants kfB and kbB, respectively.”


Function: Mass Action (reversible)
Reaction rate: kfB*PQ * P680/Qa/Qb2--kbB*PQH * P680/Qa/Qb
Product: PQH, P680/Qa/Qb
Kinetic rate constant Value
”It occurs in the model between P680 and Qa with rate constant kL2 leading to formation of P680+ and Qa-. Value of kL2 is determined by amount of excitations coming to reaction centre of photosystem II and concentration of chlorophylls in a sample.”


Function: Mass Action (irreversible)
Reaction rate: kL2*P680/Qa/Qb-
Product: P680+/Qa-/Qb-
Kinetic rate constant Value
"It leads to formation of Si+1-state and P680 with rate constants k01, k12, k23 and k30 for the S0-S1, S1-S2, S2-S3 and S3-S0 transition, respectively." []

Function: Mass Action (irreversible)
Reaction rate: k01*S0 * P680+/Qa-/Qb-
Product: S1, P680/Qa-/Qb-
Kinetic rate constant Value
"It leads to formation of Si+1-state and P680 with rate constants k01, k12, k23 and k30 for the S0-S1, S1-S2, S2-S3 and S3-S0 transition, respectively." []

Function: Mass Action (irreversible)
Reaction rate: k12*S1 * P680+/Qa-/Qb-
Product: S2, P680/Qa-/Qb-
Kinetic rate constant Value
"It leads to formation of Si+1-state and P680 with rate constants k01, k12, k23 and k30 for the S0-S1, S1-S2, S2-S3 and S3-S0 transition, respectively." []

Function: Mass Action (irreversible)
Reaction rate: k23*S2 * P680+/Qa-/Qb-
Product: S3, P680/Qa-/Qb-
Kinetic rate constant Value
"It leads to formation of Si+1-state and P680 with rate constants k01, k12, k23 and k30 for the S0-S1, S1-S2, S2-S3 and S3-S0 transition, respectively." []

Function: Mass Action (irreversible)
Reaction rate: k30*S3 * P680+/Qa-/Qb-
Product: S0, P680/Qa-/Qb-
Kinetic rate constant Value
”When Qa is reduced, it donates its electron to singly reduced Qb. This reaction occurs with forward rate constant kAB2 and the reaction is considered reversible with backward rate constant kBA2.”


Function: Mass Action (reversible)
Reaction rate: kAB2*P680+/Qa-/Qb--kBA2*P680+/Qa/Qb2-
Product: P680+/Qa/Qb2-
Kinetic rate constant Value
"It leads to formation of Si+1-state and P680 with rate constants k01, k12, k23 and k30 for the S0-S1, S1-S2, S2-S3 and S3-S0 transition, respectively." []

Function: Mass Action (irreversible)
Reaction rate: k01*S0 * P680+/Qa/Qb-
Product: S1, P680/Qa/Qb-
Kinetic rate constant Value
"It leads to formation of Si+1-state and P680 with rate constants k01, k12, k23 and k30 for the S0-S1, S1-S2, S2-S3 and S3-S0 transition, respectively." []

Function: Mass Action (irreversible)
Reaction rate: k12*S1 * P680+/Qa/Qb-
Product: S2, P680/Qa/Qb-
Kinetic rate constant Value
"It leads to formation of Si+1-state and P680 with rate constants k01, k12, k23 and k30 for the S0-S1, S1-S2, S2-S3 and S3-S0 transition, respectively." []

Function: Mass Action (irreversible)
Reaction rate: k23*S2 * P680+/Qa/Qb-
Product: S3, P680/Qa/Qb-
Kinetic rate constant Value
"It leads to formation of Si+1-state and P680 with rate constants k01, k12, k23 and k30 for the S0-S1, S1-S2, S2-S3 and S3-S0 transition, respectively." []

Function: Mass Action (irreversible)
Reaction rate: k30*S3 * P680+/Qa/Qb-
Product: S0, P680/Qa/Qb-
Kinetic rate constant Value
”When Qa is reduced, it donates its electron to singly reduced Qb. This reaction occurs with forward rate constant kAB2 and the reaction is considered reversible with backward rate constant kBA2.”


Function: Mass Action (reversible)
Reaction rate: kAB2*P680/Qa-/Qb--kBA2*P680/Qa/Qb2-
Product: P680/Qa/Qb2-
Kinetic rate constant Value
”It occurs in the model between P680 and Qa with rate constant kL2 leading to formation of P680+ and Qa-. Value of kL2 is determined by amount of excitations coming to reaction centre of photosystem II and concentration of chlorophylls in a sample.”


Function: Mass Action (irreversible)
Reaction rate: kL2*P680/Qa/Qb2-
Product: P680+/Qa-/Qb2-
Kinetic rate constant Value
"It leads to formation of Si+1-state and P680 with rate constants k01, k12, k23 and k30 for the S0-S1, S1-S2, S2-S3 and S3-S0 transition, respectively." []

Function: Mass Action (irreversible)
Reaction rate: k01*S0 * P680+/Qa-/Qb2-
Product: S1, P680/Qa-/Qb2-
Kinetic rate constant Value
"It leads to formation of Si+1-state and P680 with rate constants k01, k12, k23 and k30 for the S0-S1, S1-S2, S2-S3 and S3-S0 transition, respectively." []

Function: Mass Action (irreversible)
Reaction rate: k12*S1 * P680+/Qa-/Qb2-
Product: S2, P680/Qa-/Qb2-
Kinetic rate constant Value
"It leads to formation of Si+1-state and P680 with rate constants k01, k12, k23 and k30 for the S0-S1, S1-S2, S2-S3 and S3-S0 transition, respectively." []

Function: Mass Action (irreversible)
Reaction rate: k23*S2 * P680+/Qa-/Qb2-
Product: S3, P680/Qa-/Qb2-
Kinetic rate constant Value
"It leads to formation of Si+1-state and P680 with rate constants k01, k12, k23 and k30 for the S0-S1, S1-S2, S2-S3 and S3-S0 transition, respectively." []

Function: Mass Action (irreversible)
Reaction rate: k30*S3 * P680+/Qa-/Qb2-
Product: S0, P680/Qa-/Qb2-
Kinetic rate constant Value
Function: Mass Action (irreversible)
Reaction rate: k01*S0 * P680+/Qa/Qb2-
Product: S1, P680/Qa/Qb2-
Kinetic rate constant Value
"It leads to formation of Si+1-state and P680 with rate constants k01, k12, k23 and k30 for the S0-S1, S1-S2, S2-S3 and S3-S0 transition, respectively." []

Function: Mass Action (irreversible)
Reaction rate: k12*S1 * P680+/Qa/Qb2-
Product: S2, P680/Qa/Qb2-
Kinetic rate constant Value
"It leads to formation of Si+1-state and P680 with rate constants k01, k12, k23 and k30 for the S0-S1, S1-S2, S2-S3 and S3-S0 transition, respectively." []

Function: Mass Action (irreversible)
Reaction rate: k23*S2 * P680+/Qa/Qb2-
Product: S3, P680/Qa/Qb2-
Kinetic rate constant Value
"It leads to formation of Si+1-state and P680 with rate constants k01, k12, k23 and k30 for the S0-S1, S1-S2, S2-S3 and S3-S0 transition, respectively." []

Function: Mass Action (irreversible)
Reaction rate: k30*S3 * P680+/Qa/Qb2-
Product: S0, P680/Qa/Qb2-
Kinetic rate constant Value

Constant quantities

Initial value: 7
Simulation type: fixed
Initial value: 20000
Simulation type: fixed
Initial value: 10000
Simulation type: fixed
Initial value: 3330
Simulation type: fixed
Initial value: 1000
Simulation type: fixed
Initial value: 0.01
Simulation type: fixed
Initial value: 3500
Simulation type: fixed
Initial value: 1750
Simulation type: fixed
Initial value: 10
Simulation type: fixed
Initial value: 175
Simulation type: fixed
Initial value: 35
Simulation type: fixed
Initial value: 250
Simulation type: fixed
Initial value: 100
Simulation type: fixed
Initial value: 10
Simulation type: fixed
Initial value: 5
Simulation type: fixed
Initial value: 10
Simulation type: fixed
Initial value: 10
Simulation type: fixed
Initial value: 10
Simulation type: fixed
Initial value: 100
Simulation type: fixed
Initial value: 250
Simulation type: fixed
Initial value: 100
Simulation type: fixed
Initial value: 100
Simulation type: fixed
Initial value: 5
Simulation type: fixed
Initial value: 100
Simulation type: fixed
Initial value: 220
Simulation type: fixed
Initial value: 100
Simulation type: fixed
Initial value: 100
Simulation type: fixed
Initial value: 2300
Simulation type: fixed
Initial value: 200
Simulation type: fixed
Initial value: 4000
Simulation type: fixed

Assigned quantities

Initial expression: ((1-0.55)*("P680+/Qa-/Qb"+"P680+/Qa-/Qb-"+"P680+/Qa-/Qb2-"+"P680/Qa-/Qb2-"+"P680/Qa-/Qb"+"P680/Qa-/Qb-")/(1-0.55*("P680+/Qa-/Qb"+"P680+/Qa-/Qb-"+"P680+/Qa-/Qb2-"+"P680/Qa-/Qb2-"+"P680/Qa-/Qb"+"P680/Qa-/Qb-")))/(1+((1/45+(("P680+/Qa-/Qb"+"P680+/Qa-/Qb-"+"P680+/Qa-/Qb2-"+"P680/Qa-/Qb2-"+"P680/Qa-/Qb"+"P680/Qa-/Qb-")*4/63))*"PQ"))
Simulation type: assignment
Initial expression: (1-0.55)*("P680+/Qa-/Qb"+"P680+/Qa-/Qb-"+"P680+/Qa-/Qb2-"+"P680/Qa-/Qb2-"+"P680/Qa-/Qb"+"P680/Qa-/Qb-")/(1-0.55*("P680+/Qa-/Qb"+"P680+/Qa-/Qb-"+"P680+/Qa-/Qb2-"+"P680/Qa-/Qb2-"+"P680/Qa-/Qb"+"P680/Qa-/Qb-"))
Simulation type: assignment
Initial expression: 10^(-(2.16*10^(-7)*1590*"Pc+" + 2.16*10^(-7)*10300*("P700+/Fb"+"P700+/Fb-")))
Simulation type: assignment
Name Value
bL-/bH.c-/f 0
bL-/bH.c-/f- 0
bL-/bH.c/f 0
bL-/bH.c/f- 0
bL-/bH.c2-/f 0
bL-/bH.c2-/f- 0
bL/bH.c-/f 0
bL/bH.c-/f- 0
bL/bH.c/f 1
bL/bH.c/f- 0
bL/bH.c2-/f 0
bL/bH.c2-/f- 0
Fd 3
Fd- 0
FNRa 0
FNRa- 0
FNRa2- 0
FNRi 3
P680+/Qa-/N 0
P680+/Qa-/Qb 0
P680+/Qa-/Qb- 0
P680+/Qa-/Qb2- 0
P680+/Qa/Qb 0
P680+/Qa/Qb- 0
P680+/Qa/Qb2- 0
P680/Qa-/N 0
P680/Qa-/Qb 0
P680/Qa-/Qb- 0
P680/Qa-/Qb2- 0
P680/Qa/N 0
P680/Qa/Qb 1
P680/Qa/Qb- 0
P680/Qa/Qb2- 0
P700+/Fb 0
P700+/Fb- 0
P700/Fb 1
P700/Fb- 0
Pc 3
Pc+ 0
PQ 2.5
PQH 2.5
S0 0.25
S1 0.75
S2 0
S3 0

Constant quantities

Name Value
k(HC)L 7
k01 20000
k12 10000
k23 3330
k30 1000
ka 0.01
kAB1 3500
kAB2 1750
kb(HC) 10
kBA1 175
kBA2 35
kbB 250
kbct 100
kbF 10
kbFd 5
kbL,F 10
kbR 10
kbX 10
kf(HC) 100
kfB 250
kfct 100
kfF 100
kfFd 5
kfL,F 100
kFNR 220
kfR 100
kfX 100
kL(HC) 2300
kL1 200
kL2 4000

Assigned quantities

Name Value
Fq(t)
Funq(t)
I820
Name Value
Simulation end 1
Use log time scale 1
Multiplication of time scale 1
Simulation start 0.000001
Number of steps 200
Simulation tolerance 0.01
Label x-axis time [s]

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