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.

Thylakoid membrane

"Is a subcellular oganelle of photosynthetic eukaryotes where photosynthetic light-reactions and dark-reactions occur. Chloroplasts are semiautonomous arganelles comprising an envelope formed of two membranes, an aqueous matrix known as stroma, and an extensive system of internal membranes known as thylakoids. All of the light-harvesting and energy-transducing functions are located in the thylakoids." [PMID:15187262]
chloroplast
"A membranous cellular structure that bears the photosynthetic complexes in plants, algae, and cyanobacteria. In cyanobacteria thylakoids are of various shapes and are attached to, or continuous with, the plasma membrane. In eukaryotes they are flattened, membrane-bounded disk-like structures located in the chloroplasts; in the chloroplasts of higher plants the thylakoids are differentiated into stacked membrane regions (grana thylakoids) and non-stacked membranes (stroma thylakoids). The internal aqueous space of the thylakoids is called lumen." [GOC:ds, GOC:mtg_sensu, ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology", PMID:15187262, PMID:16307126]
thylakoid
"In the oxygenic photosynthesis, the thylakoid membrane is the site of primary photosynthetic processes, the light-reactions. Photochemical utilization of light leads to the production of ATP and reduced nicotinamide adenine dinucleotide phosphate (NADPH), both required for photosynthetic carbon assimilation and other biochemical reactions." [GOC:jl, PMID:16307126]
thylakoid membrane
The light reactions of photosynthesis, which take place in photosystems II and I. Light energy is harvested and used to power the transfer of electrons among a series of electron donors and acceptors. The final electron acceptor is NADP+, which is reduced to NADPH. NADPH generated from light reactions is used in sugar synthesis in dark reactions. Light reactions also generate a proton motive force across the thylakoid membrane, and the proton gradient is used to synthesize ATP.
GO:0019684
Model states corresponding to the currently selected level:
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Simulation type: reaction
"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-/N
Product: S1, P680/Qa-/N
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-/N
Product: S3, P680/Qa-/N
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: k1*S2 * P680+/Qa-/N
Product: S0, P680/Qa-/N
Kinetic rate constant Value
k1 1000
"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*P680/Qa-/Qb * PQH
Product: P680/Qa-/Qb, PQH
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-/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
"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-/N
Product: S2, P680/Qa/N
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 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
”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
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
"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
”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
“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 P700 and Fb with rate constant kL1 leading to formation of P700+ and Fb-. Value of kL1 is determined by amount of excitations coming to reaction centre of photosystem I and concentration of chlorophylls in a sample.”


Function: Mass Action (irreversible)
Reaction rate: kL1*P700/Fb
Product: P700+/Fb-
Kinetic rate constant Value
“Reduced Pc (Pc) donates electron to oxidized P700 (P700+). This reaction is considered reversible with forward and backward rate constants kfR and kbR, respectively.”


Function: Mass Action (reversible)
Reaction rate: kfR*Pc * P700+/Fb-kbR*Pc+ * P700/Fb
Product: Pc+, P700/Fb
Kinetic rate constant Value
“Reduced state of the last iron-sulfur cluster in photosystem I (Fb-) donates its electron to oxidized Fd. This reaction is considered reversible with forward and backward rate constants kfX and kbX, respectively.”


Function: Mass Action (reversible)
Reaction rate: kfX*Fd * P700/Fb--kbX*P700/Fb * Fd-
Product: P700/Fb, Fd-
Kinetic rate constant Value
“Reduced Pc (Pc) donates electron to oxidized P700 (P700+). This reaction is considered reversible with forward and backward rate constants kfR and kbR, respectively.”


Function: Mass Action (reversible)
Reaction rate: kfR*Pc * P700+/Fb--kbR*Pc+ * P700/Fb-
Product: Pc+, P700/Fb-
Kinetic rate constant Value
“Reduced state of the last iron-sulfur cluster in photosystem I (Fb-) donates its electron to oxidized Fd. This reaction is considered reversible with forward and backward rate constants kfX and kbX, respectively.”


Function: Mass Action (reversible)
Reaction rate: kfX*Fd * P700+/Fb--kbX*P700+/Fb * Fd-
Product: P700+/Fb, Fd-
Kinetic rate constant Value
“Reduced haem f (f-) of cytochrome b6/f donates its electron to oxidized Pc (Pc+). This reaction is considered reversible with forward and backward rate constants kfF and kbF, respectively.”


Function: Mass Action (reversible)
Reaction rate: kfF*bL/bH.c-/f- * Pc+-kbF*bL/bH.c-/f * Pc
Product: bL/bH.c-/f, Pc
Kinetic rate constant Value
“Reduced Fd (Fd-) donates its electron to to oxidized or singly reduced state of the pair of the high-potential form of haem b and of haem c ((bH.c) or (bH.c)-, respectively) of cytochrome b6/f with the same forward rate constants kfct. Both these reactions are considered reversible with the same backward rate constants kbct.”


Function: Mass Action (reversible)
Reaction rate: kfct*Fd- * bL/bH.c/f-kbct*Fd * bL/bH.c-/f
Product: Fd, bL/bH.c-/f
Kinetic rate constant Value
“Reduced Fd (Fd-) donates its electron to to oxidized or singly reduced state of the pair of the high-potential form of haem b and of haem c ((bH.c) or (bH.c)-, respectively) of cytochrome b6/f with the same forward rate constants kfct. Both these reactions are considered reversible with the same backward rate constants kbct.”


Function: Mass Action (reversible)
Reaction rate: kfct*Fd- * bL/bH.c-/f-kbct*Fd * bL/bH.c2-/f
Product: Fd, bL/bH.c2-/f
Kinetic rate constant Value
“When both haem f (f) and low-potential form of haem b (bL) of cytochrome b6/f are oxidized, they are reduced by reduced and protonated PQ molecule (PQH) from the pool: PQH is oxidized (its deprotonation is assumed implicitely) in lumenal side of cytochrome b6/f leading to transport of one electron to bL and one electron to f. This reaction is considered reversible with forward and backward rate constants kfLF and kbLF respectively.”


Function: Mass Action (reversible)
Reaction rate: "kfL,F"*PQH * bL/bH.c-/f-"kbL,F"*PQ * bL-/bH.c-/f-
Product: PQ, bL-/bH.c-/f-
Kinetic rate constant Value
“It occurs from reduced state of low-potential form of haem b (bL-) to oxidized or singly reduced state of the pair of the high-potential form of haem b and of haem c ((bH.c) or (bH.c)-, respectively) with the same forward rate constants kLHC. Both these reactions aree considered reversible with the same backward rate constants kHCL.”


Function: Mass Action (reversible)
Reaction rate: "kL(HC)"*bL-/bH.c/f-"k(HC)L"*bL/bH.c-/f
Product: bL/bH.c-/f
Kinetic rate constant Value
“Reduced Fd (Fd-) donates its electron to to oxidized or singly reduced state of the pair of the high-potential form of haem b and of haem c ((bH.c) or (bH.c)-, respectively) of cytochrome b6/f with the same forward rate constants kfct. Both these reactions are considered reversible with the same backward rate constants kbct.”


Function: Mass Action (reversible)
Reaction rate: kfct*Fd- * bL/bH.c/f--kbct*Fd * bL/bH.c-/f-
Product: Fd, bL/bH.c-/f-
Kinetic rate constant Value
“Reduced Fd (Fd-) donates its electron to to oxidized or singly reduced state of the pair of the high-potential form of haem b and of haem c ((bH.c) or (bH.c)-, respectively) of cytochrome b6/f with the same forward rate constants kfct. Both these reactions are considered reversible with the same backward rate constants kbct.”


Function: Mass Action (reversible)
Reaction rate: kfct*Fd- * bL/bH.c-/f--kbct*Fd * bL/bH.c2-/f-
Product: Fd, bL/bH.c2-/f-
Kinetic rate constant Value
“It occurs from reduced state of low-potential form of haem b (bL-) to oxidized or singly reduced state of the pair of the high-potential form of haem b and of haem c ((bH.c) or (bH.c)-, respectively) with the same forward rate constants kLHC. Both these reactions aree considered reversible with the same backward rate constants kHCL.”


Function: Mass Action (reversible)
Reaction rate: "kL(HC)"*bL-/bH.c/f--"k(HC)L"*bL/bH.c-/f-
Product: bL/bH.c-/f-
Kinetic rate constant Value
“Reduced haem f (f-) of cytochrome b6/f donates its electron to oxidized Pc (Pc+). This reaction is considered reversible with forward and backward rate constants kfF and kbF, respectively.”


Function: Mass Action (reversible)
Reaction rate: kfF*bL/bH.c/f- * Pc+-kbF*bL/bH.c/f * Pc
Product: bL/bH.c/f, Pc
Kinetic rate constant Value
“When the pair of the high-potential form of haem b and of haem c is doubly reduced ((bH.c)2-) it transports electron to oxidized PQ molecule form the pool (protonation is assumed implicitly). This reaction is considered reversible with forward and backward rate constants kfHC and kbHC, respectively.”


Function: Mass Action (reversible)
Reaction rate: "kf(HC)"*PQ * bL/bH.c2-/f-"kb(HC)"*bL/bH.c/f * PQH
Product: bL/bH.c/f, PQH
Kinetic rate constant Value
“When both haem f (f) and low-potential form of haem b (bL) of cytochrome b6/f are oxidized, they are reduced by reduced and protonated PQ molecule (PQH) from the pool: PQH is oxidized (its deprotonation is assumed implicitely) in lumenal side of cytochrome b6/f leading to transport of one electron to bL and one electron to f. This reaction is considered reversible with forward and backward rate constants kfLF and kbLF respectively.”


Function: Mass Action (reversible)
Reaction rate: "kfL,F"*PQH * bL/bH.c/f-"kbL,F"*PQ * bL-/bH.c/f-
Product: PQ, bL-/bH.c/f-
Kinetic rate constant Value
“When the pair of the high-potential form of haem b and of haem c is doubly reduced ((bH.c)2-) it transports electron to oxidized PQ molecule form the pool (protonation is assumed implicitly). This reaction is considered reversible with forward and backward rate constants kfHC and kbHC, respectively.”


Function: Mass Action (reversible)
Reaction rate: "kf(HC)"*PQ * bL/bH.c2-/f--"kb(HC)"*PQH * bL/bH.c/f-
Product: PQH, bL/bH.c/f-
Kinetic rate constant Value
“Reduced haem f (f-) of cytochrome b6/f donates its electron to oxidized Pc (Pc+). This reaction is considered reversible with forward and backward rate constants kfF and kbF, respectively.”


Function: Mass Action (reversible)
Reaction rate: kfF*bL/bH.c2-/f- * Pc+-kbF*bL/bH.c2-/f * Pc
Product: bL/bH.c2-/f, Pc
Kinetic rate constant Value
“When both haem f (f) and low-potential form of haem b (bL) of cytochrome b6/f are oxidized, they are reduced by reduced and protonated PQ molecule (PQH) from the pool: PQH is oxidized (its deprotonation is assumed implicitely) in lumenal side of cytochrome b6/f leading to transport of one electron to bL and one electron to f. This reaction is considered reversible with forward and backward rate constants kfLF and kbLF respectively.”


Function: Mass Action (reversible)
Reaction rate: "kfL,F"*PQH * bL/bH.c2-/f-"kbL,F"*PQ * bL-/bH.c2-/f-
Product: PQ, bL-/bH.c2-/f-
Kinetic rate constant Value
“It occurs from reduced state of low-potential form of haem b (bL-) to oxidized or singly reduced state of the pair of the high-potential form of haem b and of haem c ((bH.c) or (bH.c)-, respectively) with the same forward rate constants kLHC. Both these reactions aree considered reversible with the same backward rate constants kHCL.”


Function: Mass Action (reversible)
Reaction rate: "kL(HC)"*bL-/bH.c-/f-"k(HC)L"*bL/bH.c2-/f
Product: bL/bH.c2-/f
Kinetic rate constant Value
“It occurs from reduced state of low-potential form of haem b (bL-) to oxidized or singly reduced state of the pair of the high-potential form of haem b and of haem c ((bH.c) or (bH.c)-, respectively) with the same forward rate constants kLHC. Both these reactions aree considered reversible with the same backward rate constants kHCL.”


Function: Mass Action (reversible)
Reaction rate: "kL(HC)"*bL-/bH.c-/f--"k(HC)L"*bL/bH.c2-/f-
Product: bL/bH.c2-/f-
Kinetic rate constant Value
“Reduced haem f (f-) of cytochrome b6/f donates its electron to oxidized Pc (Pc+). This reaction is considered reversible with forward and backward rate constants kfF and kbF, respectively.”


Function: Mass Action (reversible)
Reaction rate: kfF*bL-/bH.c-/f- * Pc+-kbF*bL-/bH.c-/f * Pc
Product: bL-/bH.c-/f, Pc
Kinetic rate constant Value
“Reduced Fd (Fd-) donates its electron to to oxidized or singly reduced state of the pair of the high-potential form of haem b and of haem c ((bH.c) or (bH.c)-, respectively) of cytochrome b6/f with the same forward rate constants kfct. Both these reactions are considered reversible with the same backward rate constants kbct.”


Function: Mass Action (reversible)
Reaction rate: kfct*Fd- * bL-/bH.c/f-kbct*Fd * bL-/bH.c-/f
Product: Fd, bL-/bH.c-/f
Kinetic rate constant Value
“Reduced Fd (Fd-) donates its electron to to oxidized or singly reduced state of the pair of the high-potential form of haem b and of haem c ((bH.c) or (bH.c)-, respectively) of cytochrome b6/f with the same forward rate constants kfct. Both these reactions are considered reversible with the same backward rate constants kbct.”


Function: Mass Action (reversible)
Reaction rate: kfct*Fd- * bL-/bH.c-/f-kbct*Fd * bL-/bH.c2-/f
Product: Fd, bL-/bH.c2-/f
Kinetic rate constant Value
“Reduced Fd (Fd-) donates its electron to to oxidized or singly reduced state of the pair of the high-potential form of haem b and of haem c ((bH.c) or (bH.c)-, respectively) of cytochrome b6/f with the same forward rate constants kfct. Both these reactions are considered reversible with the same backward rate constants kbct.”


Function: Mass Action (reversible)
Reaction rate: kfct*Fd- * bL-/bH.c/f--kbct*Fd * bL-/bH.c-/f-
Product: Fd, bL-/bH.c-/f-
Kinetic rate constant Value
“Reduced Fd (Fd-) donates its electron to to oxidized or singly reduced state of the pair of the high-potential form of haem b and of haem c ((bH.c) or (bH.c)-, respectively) of cytochrome b6/f with the same forward rate constants kfct. Both these reactions are considered reversible with the same backward rate constants kbct.”


Function: Mass Action (reversible)
Reaction rate: kfct*Fd- * bL-/bH.c-/f--kbct*Fd * bL-/bH.c2-/f-
Product: Fd, bL-/bH.c2-/f-
Kinetic rate constant Value
“Reduced haem f (f-) of cytochrome b6/f donates its electron to oxidized Pc (Pc+). This reaction is considered reversible with forward and backward rate constants kfF and kbF, respectively.”


Function: Mass Action (reversible)
Reaction rate: kfF*bL-/bH.c/f- * Pc+-kbF*bL-/bH.c/f * Pc
Product: bL-/bH.c/f, Pc
Kinetic rate constant Value
“When the pair of the high-potential form of haem b and of haem c is doubly reduced ((bH.c)2-) it transports electron to oxidized PQ molecule form the pool (protonation is assumed implicitly). This reaction is considered reversible with forward and backward rate constants kfHC and kbHC, respectively.”


Function: Mass Action (reversible)
Reaction rate: "kf(HC)"*PQ * bL-/bH.c2-/f-"kb(HC)"*PQH * bL-/bH.c/f
Product: PQH, bL-/bH.c/f
Kinetic rate constant Value
“When the pair of the high-potential form of haem b and of haem c is doubly reduced ((bH.c)2-) it transports electron to oxidized PQ molecule form the pool (protonation is assumed implicitly). This reaction is considered reversible with forward and backward rate constants kfHC and kbHC, respectively.”


Function: Mass Action (reversible)
Reaction rate: "kf(HC)"*PQ * bL-/bH.c2-/f--"kb(HC)"*PQH * bL-/bH.c/f-
Product: PQH, bL-/bH.c/f-
Kinetic rate constant Value
“Reduced haem f (f-) of cytochrome b6/f donates its electron to oxidized Pc (Pc+). This reaction is considered reversible with forward and backward rate constants kfF and kbF, respectively.”


Function: Mass Action (reversible)
Reaction rate: kfF*bL-/bH.c2-/f- * Pc+-kbF*bL-/bH.c2-/f * Pc
Product: bL-/bH.c2-/f, Pc
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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