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.

'PhD1'

"Is the primary electron acceptor of photosystem II (PS II). When the primary charge separation in PSII occurs, the ChlD1+PhD1- state is formed and the electron of reduced Pheo is then transported to the primary quinone electron acceptor in PSII, QA."
Chemical formula: C56H76N4O6" [source: local, PMID:19805064 ]

Pheophytin
Model states corresponding to the currently selected level:
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

"Excitation delocalized into all antenna chlorophylls, ac, is radiatively lost via fluorescence emission."



Function: Mass Action (irreversible)
Reaction rate: kF*P680 / Qa / PhD1 / ac* / ChlD1
Product: P680 / Qa / PhD1 / ac / ChlD1
Kinetic rate constant Value

"Excitation delocalized into all antenna chlorophylls, ac, is non-radiatively lost via heat dissipation."



Function: Mass Action (irreversible)
Reaction rate: k1*P680 / Qa / PhD1 / ac* / ChlD1
Product: P680 / Qa / PhD1 / ac / ChlD1
Kinetic rate constant Value
k1 200000
"Excited state of the primary electron donor in photosystem II, ChlD1, is radiatively lost via fluorescence emission."


Function: Mass Action (irreversible)
Reaction rate: kF*P680 / Qa / PhD1 / ac / ChlD1*
Product: P680 / Qa / PhD1 / ac / ChlD1
Kinetic rate constant Value
"Excited state of the primary electron donor in photosystem II, ChlD1, is non-radiatively lost via heat dissipation."


Function: Mass Action (irreversible)
Reaction rate: k1*P680 / Qa / PhD1 / ac / ChlD1*
Product: P680 / Qa / PhD1 / ac / ChlD1
Kinetic rate constant Value
k1 200000
"The primary charge separation in photosystem II between the primary electron donor, ChlD1, and the primary electron acceptor, pheophytin PhD1, is a reversible process accompanied by the charge recombination between the electron donor and electron acceptor leading to formation of the excited state of the primary electron donor in photosystem II."


Function: Mass Action (irreversible)
Reaction rate: k1*P680 / Qa / PhD1- / ac / ChlD1+
Product: P680 / Qa / PhD1 / ac / ChlD1*
Kinetic rate constant Value
k1 500000000000
"Excitation delocalized into all antenna chlorophylls, ac, is reversibly transferred to the primary electron donor in photosystem II, ChlD1."


Function: Mass Action (reversible)
Reaction rate: k1*P680 / Qa / PhD1 / ac* / ChlD1-k2*P680 / Qa / PhD1 / ac / ChlD1*
Product: P680 / Qa / PhD1 / ac / ChlD1*
Kinetic rate constant Value
k1 19200000000
k2 25000000000

"After excitation of the primary electron donor in photosystem II, ChlD1, the primary charge separation between the primary electron donor and the primary electron acceptor, pheophytin PhD1, in photosystem II occurs."



Function: Mass Action (irreversible)
Reaction rate: k1*P680 / Qa / PhD1 / ac / ChlD1*
Product: P680 / Qa / PhD1- / ac / ChlD1+
Kinetic rate constant Value
k1 500000000000

"The charge stabilization in photosystem II occurs by means of reduction of the primary quinone electron acceptor in photosystem II, Qa, by the reduced primary electron acceptor in photosystem II, pheophytin PhD1."



Function: Mass Action (irreversible)
Reaction rate: k1*P680+ / Qa / PhD1- / ac / ChlD1
Product: P680+ / Qa- / PhD1 / ac / ChlD1
Kinetic rate constant Value
k1 4800000000
"The charge stabilization in photosystem II by means of reduction of the primary quinone electron acceptor in photosystem II, Qa, by the reduced primary electron acceptor in photosystem II, pheophytin PhD1, is a reversible process accompanied by reverse electron flow from the reduced primary quinone electron acceptor back to the oxidized primary electron acceptor."


Function: Mass Action (irreversible)
Reaction rate: k1*P680+ / Qa- / PhD1 / ac / ChlD1
Product: P680+ / Qa / PhD1- / ac / ChlD1
Kinetic rate constant Value
k1 2400000000

"The oxidized primary electron donor in photosystem II, ChlD1, is reduced by electron donated by the secondary electron donor in photosystem II, P680, which was originally thought to be the primary electron donor in photosystem II."



Function: Mass Action (irreversible)
Reaction rate: k1*P680 / Qa / PhD1- / ac / ChlD1+
Product: P680+ / Qa / PhD1- / ac / ChlD1
Kinetic rate constant Value
k1 250000000000

"The reduction of oxidized primary electron donor in photosystem II, ChlD1, by the secondary electron donor in photosystem II, P680, is a reversible process accompanied by reverse electron flow from the reduced primary electron donor back to the oxidized secondary electron donor."



Function: Mass Action (irreversible)
Reaction rate: k1*P680+ / Qa / PhD1- / ac / ChlD1
Product: P680 / Qa / PhD1- / ac / ChlD1+
Kinetic rate constant Value
k1 67000000000

Constant quantities

Initial value: 67000000
Simulation type: fixed

Assigned quantities

Initial expression: "kF" * ( "P680 / Qa / PhD1 / ac* / ChlD1" + "P680 / Qa / PhD1 / ac / ChlD1*" )
Simulation type: assignment
Name Value
P680 / Qa / PhD1 / ac / ChlD1 0
P680 / Qa / PhD1 / ac / ChlD1* 0
P680 / Qa / PhD1 / ac* / ChlD1 1
P680 / Qa / PhD1- / ac / ChlD1+ 0
P680+ / Qa / PhD1- / ac / ChlD1 0
P680+ / Qa- / PhD1 / ac / ChlD1 0

Constant quantities

Name Value
kF 67000000

Assigned quantities

Name Value
F(t)
Name Value
Simulation end 0.002
Use log time scale 1
Multiplication of time scale 10
Simulation start 0.0000000000001
Number of steps 100
Label x-axis time [s]
Label y-axis rel. units

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