This is a kinetic model of the dimeric photosystem II (PSII). The model has partially based on the earlier model used for simulation of the flash-induced period-four damped oscillation of oxygen evolution and chlorophyll fluorescence (Jablonsky J and Lazar D (2008) Biophys J, 94: 2725-2736 pubmedID: 18178650 ). For short description of reactions and initial concentrations, see the notes in the model file. For explanation of the value of the rate constants, see: Lazar D (2003) J. theor. Biol. 220:469-503 pubmedID: 12623282 ; Jablonsky J and Lazar D, 2008 Biophys J, 94: 2725-2736 pubmedID: 18178650 and Jablonsky, Susila and Lazar, 2008, DOI: 10.1093/bioinformatics/btn530 pubmedID: 18845578 ). In this model the hypothetic cooperation in the water splitting is considered as the cross-backward-oxidation of the P680 (in the PSII which is already in the S2-state) by [YZoxS1] (in the PSII in which the S1-S2 transition is not finished). The cooperation (between compartment1 = 1st PSII and compartment2 = 2nd PSII) is the best explanation of the second turnover of PSII induced by short flashes which is available now. We concluded that the double turnover of the PSII induced by short flashes is caused either by the cooperation in the water splitting or our knowledge of the main pathway of the electron transport through the PSII is incomplete and besides D1-Y161, other cofactor which enables oxidation of the special chlorophyll pair (P680), e.g., L-Y34, must be considered. The oxygen signal in the model is defined as a maximum of the sum of concentrations of the model forms in the iS3Yp-state (handled in MATLAB). This version of model cannot be used for simulation of the chlorophyll fluorescence because for simplicity the reactions behind the loss of excited state are not considered. The meaning of the particular letters in the model is as follows: P – P680 (special chlorophyll pair), H – pheophytin, A – QA (the first quinone electron acceptor), B – QB (the second quinone electron acceptor), PQ – oxidized plastoquinone molecules in the PQ pool, PQH – reduced and protonated PQ molecules in the PQ pool, Y/Yp – reduced/oxidized state of tyrosine 161-D1, YD/YDox – reduced/oxidized state of tyrosine 160-D2, Sn (n = 0, 1, 2, 3) – the S-states of oxygen evolving complex (OEC), iSn (n = 0, 1, 2, 3) – the intermediate S-states of OEC. All reactions describing electron transport through PSII entered into the model are assumed to be first order reactions with respect to one reactant and are defined as mass action reactions. Cooperation between photosystem II within dimer in the water splitting is described by the second order kinetics. This approach shows that the second order kinetics used for description of oxidation of the tyrosine D1-Y161 in the multi-units PSII model can be in this case justified. two compartments => two photosystems II connected by cooperation in the water splitting initial conditions: S1=100%, YDox=89% PHABm = 0.25 PHAB = 0.75 list of reactions (compartments 1 and 2): R1-R144 ... excitation R145- R180... charge separation_open R181- R216... charge separation_closed R217-R324 ... charge stabilisation R325-R360 ... recombination PpHm (P680+pheophytin-) R361-R396... recombination PpAm (P680+QA-) R397-R399 ... recombination S2Am (S2-state of OEC and QA-) R400-R471 ... electron transfer from QA to QB R472-R543 ... electron transfer from QA to QB- R544-R687 ... exchange of double reduced QB by free plastoquinone molecule from the PQ pool R688 ... Ox/red PQ and PQH R689-R700 ... reduction of Pp by Yz in S0 R701-R712 ... reduction of Pp by Yz in S1 R713-R724 ... reduction of Pp by Yz in S2 R725-R736 ... reduction of Pp by Yz in S3 R737-R784 ... formation of the intermediated S-states iS0,1,2, 3 R785-R832 ... electron donation from OEC to YZox during the S0->S1, S1->S2, S2->S3, S3->S0 transitions (Kok cycle) R833-R850 ... YD oxidation by S3/S2 state of OEC; YDox reduction by S0 state of OEC R1701-R1750 ... cooperation between 1st and 2nd PSII This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2011 The BioModels.net Team. To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information. In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not.. To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.