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BF_Ini.m
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Copyright Xin-Guang Zhu, Yu Wang, Donald R. ORT and Stephen P. LONG
%CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, CAS, Shanghai,200031
%China Institute of Genomic Biology and Department of Plant Biology, Shanghai Institutes for Biological Sciences, CAS, Shanghai,200031
%University of Illinois at Urbana Champaign
%Global Change and Photosynthesis Research Unit, USDA/ARS, 1406 Institute of Genomic Biology, Urbana, IL 61801, USA.
% This file is part of e-photosynthesis.
% e-photosynthesis is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation;
% e-photosynthesis is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
% You should have received a copy of the GNU General Public License (GPL)
% along with this program. If not, see <http://www.gnu.org/licenses/>.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function BF_con = BF_Ini(begin)
global BFRatio;
K1 = 10^6*BFRatio(1) ; % The rate constant for formation of ISP.QH2 complex; Vmax is used here.
K2 = 500*BFRatio(2) ; % The rate constant for ISP.QH2-->QH(semi) + ISPH(red)
K3 = 5 * 10^7*BFRatio(3) ; % The rate constant for QH. + cytbL --> Q + cytbL- + H+;
K4 = 5 * 10^7*BFRatio(4) ; % The rate constant for cytbL- + cytbH --> cytbL + cytbH-
K5 = 5 * 10^7*BFRatio(5) ; % The rate constant for CytbH- + Q --> cytbH + Q-
K6 = 5 * 10^7*BFRatio(6) ; % The rate constant for CytbH- + Q- --> cytbH + Q2-
K7 = 10^4*BFRatio(7) ; % The rate constant for Q binding to Qi site
K8 = 1000*BFRatio(8) ; % The rate constant for ISPH + CytC1 --> ISPH(ox) + CytC1+
K9 = 8.3 * 10^6*BFRatio(9) ; % The rate constant for the electron transport from cytc1 to cytc2
K10 = 8 * 10 ^ 8*BFRatio(10) ; % The rate constant for the electron transport from cytc2 to P700
Vmax11 = 6 *BFRatio(11); % The maximum rate of ATP synthesis; unit: mmol l-1 s-1; default 1.47;
Kqi = 10^ 3*BFRatio(12) ; % The rate constant for the uptake of 2 protons from stroma; Unit: s-1; the calculation is done based on a simplified assumption of first order kinetics for these reaction. The half time for the uptake of two protons is assumed, following Crofts "http://pop.life.uiuc.edu/~a-crofts/ahab/qcycle1.html"--The modified Q cycle, as <150 microsecond. 150 microsecond is used as an estimate of the halftime for this electron transfer.
PMODTEM = 1;
PK = 3.6 * 10^(-8) * PMODTEM*BFRatio(13); % The permeability constant for K, cm s-1
PMg = 3.6 * 10^(-8) * PMODTEM*BFRatio(14); % The permeability constant for Mg, cm s-1
PCl = 1.8 * 10^(-8) * PMODTEM*BFRatio(15); % The permeability constant for Cl, cm s-1
Kau = 10^10*BFRatio(16) ; % The rate constant for exciton transfer from perpheral antenna to core antenna, see FI, unit: s-1
Kua = 10^10 *BFRatio(17); % The rate constant for exciton transfer from core antenna to peripheral antenna, SEE FI, unit: s-1
Kf = 6.3 * 10 ^6 *BFRatio(18); % The rate constant for fluorescence emission, see the note in FI, unit: s-1
Kd = 2 * 10^8*BFRatio(19) ; % The rate constant for heat dissipation; see the note for FI, unit: s-1
K15 = 10^10*BFRatio(20) ; % The rate constant for the primary charge sepration in PSI, assuming the half time 30ps, unit: s-1
K16 = 10^5*BFRatio(21); % The rate constant for the electron transfer from electron acceptor A- to Fd, unit: s-1; following reference of Setif PQ and Bottin H, 1995, Biochemistry.
Em_ISP = 0.31*BFRatio(22) ; % The midpoint potential fo ISP; unit: V
Em_CytC1 = 0.27*BFRatio(23) ; % The midpoint potential for cytc1; unit: V
Em_CytbL = -0.09*BFRatio(24) ; % The midpoint potential for cytbL; unit: V
Em_CytbH = 0.05*BFRatio(25) ; % The midpoint potential for cytbH; UNIT: V
Em_CytC2 = 0.35*BFRatio(26) ; % The midpoint potential for cytc2, unit: V
% ISPHr + cytc1 --> ISPHox + cytc1-
DeltaEm = Em_CytC1 - Em_ISP ;
DeltaG = DeltaEm *(-9.649) * 10^4 ;
RT = 8.314 * 298;
KE8 = exp(-DeltaG/RT) ;
% cytc1- + cytc2 --> cytc1 + cytc2-
DeltaEm = Em_CytC2 - Em_CytC1 ;
DeltaG = DeltaEm *(-9.649) * 10^4 ;
RT = 8.314 * 298;
KE9 = exp(-DeltaG/RT) ;
MemCap = 0.6 * 10^(-6)*BFRatio(27) ; % The membrane capacity, microFarady/cm2.
RVA = 8*10^(-10)*BFRatio(28) ; % THe ratio of the lumen volume to thylakoid membrane; unit: L/cm2. The data from Cruz 2001.
KBs = 1.1*10^(-8)*BFRatio(29) ; % The buffer equilibrium constant
KBl = 5.1 * 10^(-6)*BFRatio(30) ; % The buffer equilibrium constant
KM1ATP = 0.12*BFRatio(31);
KM1ADP = 0.014*BFRatio(32); % Originally
KM1PI = 0.3*BFRatio(33); % Originally
KM2NADP = 0.05*BFRatio(34); % From Fridlyand and Scheibe 1999
KM2NADPH= 0.035*BFRatio(35); % From Fridlyand and Scheibe 1999
V2M = 27.8*BFRatio(36); % Calcualted based on 6.4 mmol (mg chl)-1h-1; Unit: mmol/l/s;
KE2 = 495*BFRatio(37); % From Fridlyand paper , 1999, BBA, 1413, 1, 31-42
% The rate constant used in the model
global BF_RC;
BF_RC= zeros(5,1);
% Assign values to the array for rate constant
BF_RC ( 1 ) = K1 ; % The rate constant for formation of ISP.QH2 complex; unit: per second
BF_RC ( 2 ) = K2 ; % The rate constant for ISP.QH2-->QH(semi) + ISPH(red) ; unit: per second
BF_RC ( 3 ) = K3 ; % The rate constant for QH. + cytbL --> Q + cytbL- + H+ Unit: s-1
BF_RC ( 4 ) = K4 ; % The rate constant for cytbL- + cytbH --> cytbL + cytbH- Unit: s-1
BF_RC ( 5 ) = K5 ; % The rate constant for CytbH- + Q --> cytbH + Q- Unit: s-1
BF_RC ( 6 ) = K6 ; % The rate constant for CytbH- + Q- --> cytbH + Q2- Unit: s-1
BF_RC ( 7 ) = K7 ; % The rate constant for Q binding to Qi site; which assumed half time as 200 us, following Croft's website Unit: s-1
BF_RC ( 8 ) = K8 ; % The rate constant for ISPH + CytC1 --> ISPH(ox) + CytC1+ Unit: s-1
BF_RC ( 9 ) = K9 ; % The rate constant for the electron transport from cytc1 to cytc2 Unit: s-1
BF_RC ( 10 ) = K10 ; % The rate constant for the electron transport from cytc2 to P700 Unit: s-1
BF_RC ( 11 ) = Vmax11 ; % The maximum rate of ATP synthesis Unit: mmol l-1 s-1; The unit for the reactions occurrs in stroma is mmol l-1 s-1
BF_RC ( 12 ) = Kqi ; % The rate constant for uptake of two protons from the stroma to Q2- s-1
BF_RC ( 13 ) = PK ; % The permeability constant for K Unit: cm s-1
BF_RC ( 14 ) = PMg ; % The permeability constant for Mg Unit: cm s-1
BF_RC ( 15 ) = PCl ; % The permeability constant for Cl Unit: cm s-1
BF_RC ( 16 ) = Kau ; % The rate constant for exciton transfer from perpheral antenna to core antenna, see FI Unit: s-1
BF_RC ( 17 ) = Kua ; % The rate constant for exciton transfer from core antenna to peripheral antenna, SEE FI Unit: s-1
BF_RC ( 18 ) = Kf ; % The rate constant for fluorescence emission, see the note in FI Unit: s-1
BF_RC ( 19 ) = Kd ; % The rate constant for heat dissipation; see the note for FI Unit: s-1
BF_RC ( 20 ) = KE8 ; % ISPHr + cytc1 --> ISPHox + cytc1- Unit: s-1
BF_RC ( 21 ) = KE9 ; % cytc1- + cytc2 --> cytc1 + cytc2- Unit: s-1
BF_RC ( 22 ) = K15 ; % The rate constant for primary charge separation in PSI Unit: s-1
BF_RC ( 23 ) = K16 ; % The rate constant for electron tranfer from electron acceptor of PSI to Fd Unit: s-1
BF_RC ( 24 ) = MemCap ; % The membrane capacity
BF_RC ( 25 ) = RVA ; % The ratio of lumen volume to thylakoid membrane area
BF_RC ( 26 ) = KBs ; % The buffer equilibrium constant in stroma
BF_RC ( 27 ) = KBl ; % The buffer equilibrium constant in lumen
BF_RC ( 28 ) = KM1ATP ; % The michaelis menton constant for ATP for ATP synthesis
BF_RC ( 29 ) = KM1ADP ; % The michaelis menton constant for ATP for ADP synthesis
BF_RC ( 30 ) = KM1PI ; % The michaelis menton constant for ATP for PI synthesis
BF_RC ( 31 ) = KM2NADP ; % The michaelis menten constant for NADP Unit: mmol l-1 s-1; The unit for the reactions occurrs in stroma is mmol l-1 s-1
BF_RC ( 32 ) = KM2NADPH ; % The michaelis menten constant for NADPH Unit: mmol l-1 s-1; The unit for the reactions occurrs in stroma is mmol l-1 s-1
BF_RC ( 33 ) = V2M ; % The maximum rate of NADPH formation Unit: mmol l-1 s-1; The unit for the reactions occurrs in stroma is mmol l-1 s-1
BF_RC ( 34 ) = KE2 ; % Equilibrium constatn
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Initialization of the initial concentration of the different component %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Initialize the leaves for a dark adapted leaves;
% Unit micro mol per m2 or mmol l-2 stroma volume
% The initialization of the model with concentration of each substrate in dark-adapted leaves
% The total concentration of PSII is assumed to be 1 micromole per meter square
ISPHr = 0 ; % The reduced ion sulfer protein (ISPH); unit: micromole per m2
cytc1 = 1 ; % The oxidized state of cytc1; unit: micromole per meter square
ISPo = 1 ; % The oxidized ion sulfer protein (ISP); unit: micromole per meter square
ISPoQH2 = 0 ; % The complex of oxidized ion sulfer protein and reduced quinone; unit: micromole per meter square
QHsemi = 0 ; % Semiquinone; micromole per meter square
cytbL = 1 ; % The oxidized cytbL; micromole per meter square
Qi = 0 ; % The binding quinone on the quinone site; micromole per meter square
Q = 1 ; % Quinone; micromole per meter square
cytbH =1 ; % The oxidized form of cytbH; micromole per meter square
Qn = 0 ; % Q- ; unit: micromole per meter square
Qr = 0 ; % The reduced quinone Q2- ; micromole per meter square
QH2 = 5 ; % The reduced quinone PQH2; micromole per meter square
cytc2 = 1 ; % oxidized cytc2; micromole per meter square
P700 = 0.5 ; % The reduced state of P700, including both P700 and excited P700; micromole per meter square
ADP = 0.82 ; % ADP in stroma, from the earlier photorespiration model; mmol l-1
Pi = 0.9 ; % Phosphate in stroma, from the photorespiration model; mmol l-1
ATP = 0.68 ; % ATP in stroma, from the photorespiration model; mmol l-1
Ks = 10 ; % K ions in stroma, mM, from the literature; mmol l-1; 90 might be an default;
Mgs = 5;%2.5 ; % Mg ions in stroma, mM, from the literature of the ion estimate
Cls = 1 ; % Cl ions in stroma, mM, from the literature of the ion estimate
Aip = 0 ; % The number of photons in peripheral antenna; micromole per meter square
U = 0 ; % The number of photons in core antenna; micromole per meter square
An = 0 ; % The reduced electron acceptor in PSI; micromole per meter square
Fdn = 0.3 ; % The reduced ferrodoxin; micromole per meter square leaf area
BFHs = 19.0001; %50.0001 ; % The protonated buffer species and free proton together in stroma; mmol l-1; The value follows Laisk and Walker, 1989. But they did not give reference about the source of this number.; default 25
BFHl = 19.0001; % The protonated buffer species and free proton together in lumen; mmol l-1; The value follows Laisk and Walker, 1989. But they did not give reference about the source of this number. ; default 5
PHs = 7 ; % PH of stroma
PHl = 7 ; % PH of lumen
NADPH = 0.21; % The NADPH concentration in stroma at dark
% Assign the value to a array
% BF_ini.m
% This is the initialization step for the module of the Q cycle, and ATP synthesis steps
global BF_con;
BF_con ( 1 ) = ISPHr ; % The reduced ion sulfer protein (ISPH)
BF_con ( 2 ) = cytc1 ; % The oxidized state of cytc1
BF_con ( 3 ) = ISPo ; % The oxidized ion sulfer protein (ISP)
BF_con ( 4 ) = ISPoQH2 ; % The complex of oxidized ion sulfer protein and reduced quinone
BF_con ( 5 ) = QHsemi ; % Semiquinone
BF_con ( 6 ) = cytbL ; % The oxidized cytbL
BF_con ( 7 ) = Qi ; % The binding Quinone
BF_con ( 8 ) = Q ; % Quinone
BF_con ( 9 ) = cytbH ; % The oxidized form of cytbH
BF_con ( 10 ) = Qn ; % Q-
BF_con ( 11 ) = Qr ; % Q2-
BF_con ( 12 ) = QH2 ; % QH2
BF_con ( 13 ) = cytc2 ; % oxidized cytc2
BF_con ( 14 ) = P700 ; % The reduced state of P700, including both P700 and excited P700
BF_con ( 15 ) = ADP ; % ADP in stroma
BF_con ( 16 ) = Pi ; % Phosphate in stroma
BF_con ( 17 ) = ATP ; % ATP in stroma
BF_con ( 18 ) = Ks ; % K ions in stroma
BF_con ( 19 ) = Mgs ; % Mg ions in stroma
BF_con ( 20 ) = Cls ; % Cl ions in stroma
BF_con ( 21 ) = Aip ; % The number of photons in peripheral antenna
BF_con ( 22 ) = U ; % The number of photons in core antenna
BF_con ( 23 ) = An ; % The reduced electron acceptor in PSI
BF_con ( 24 ) = Fdn ; % The reduced ferrodoxin
BF_con ( 25 ) = BFHs ; % The total concentration of proton and protonated buffer species in stroma, put in unit: mmol l-1
BF_con ( 26 ) = BFHl ; % The total concentration of proton and protonated buffer species in lumen, unit: mmol l-1
BF_con ( 27 ) = PHs ; % The PH value of the stroma
BF_con ( 28 ) = PHl ; % The PH value of the lumen
BF_con ( 29 ) = NADPH ; % The NADPH concentration in stroma, Unit: mmol l-1;
% Assigning the pool variables
% The sizes of different pools in the model
Tcyt = 1*BFRatio(38) ; % Unit: micromole m-2 The total concentration of cytochrome. It is assumed that the concentration of cytbL, cytbH, and cytc1 is equal as Tcyt.
Tcytc2 = 1*BFRatio(39) ; % Unit: micromole m-2 The total concentration of cytc2, as Tcyt , the unit is micromole per meter square leaf area
TK = 20*BFRatio(40) ; % Unit: mmol l-1 The total concentration of potassium, 180 mM, in the bigining assuming the concentration of ions in stroma and lumen are same
TMg = 10*BFRatio(41) ; % Unit: mmol l-1 The total concentraiton of Mg2+, 18 mM, in the beginning assuming the concentration of the ions in the stroma and lumen are same
TCl = 2*BFRatio(42);%1 ; % Unit: mmol l-1 The total concentraiton of Cl-, 1 mM, assuming equal concentrations of ion concentrations in stroma and lumen in the beginning.
TFd = 1*BFRatio(43) ; % Unit: micromole m-2 The total concentration of Ferrodoxin, this assumed that only 1 Fd is associated with one PSI unit.
TA = 1*BFRatio(44) ; % Unit: micromole m-2 The total concentration of electron acceptor of PSI
TQ = 8*BFRatio(45) ; % Unit: micromole m-2 The total concentration of quinone at all different states
BFTs = 38*BFRatio(46) ; % Unit: mmol l-1 The total concentration of buffer in stroma;
BFTl = 38*BFRatio(47) ; % Unit: mmol l-1 The total concentration of buffer in lumen
P700T = 1*BFRatio(48) ; % % The total number of P700 unit: micromole m-2 leaf area
NADPHT = 1*BFRatio(49); % The total concentration of NADPH in stroma; 1 is an guessed value;
% Assign the pools to the global pool variables
global BF_Pool;
BF_Pool = zeros(5,1);
BF_Pool ( 1 ) = Tcyt; % The total amount of cytbH or cytbL; Unit: micromole m-2 leaf area
BF_Pool ( 2 ) = Tcytc2; % The total amount of cytc; Unit: micromole m-2 leaf area
BF_Pool ( 3 ) = TK ; % The total concentration of K in both stroma and lumen. Unit: mmol l-1. In this model, it was assumed that the total concentration of K, and Mg and Cl as well, is constant.
BF_Pool ( 4 ) = TMg ; % The total concentration of Mg in both stroma and lumen. Unit: mmol l-1. In this model, it was assumed that the total concentration of Mg, and K and Cl as well, is constant.
BF_Pool ( 5 ) = TCl ; % The total concentration of Cl in both stroma and lumen. Unit: mmol l-1. In this model, it was assumed that the total concentration of Cl in both stroma and lumen is constant.
BF_Pool ( 6 ) = TFd ; % The total concentration of Ferrodoxin
BF_Pool ( 7 ) = TA ; % The total concentration of the primary electron acceptor of PSI; Unit: micromole m-2 leaf area
BF_Pool ( 8 ) = TQ ; % The total concentration of plastoquinone in thylakoid membrane. ; Unit: micromole m-2 leaf area
BF_Pool ( 9 ) = BFTs ; % The total concentration of buffer in stroma; unit: mmol per liter
BF_Pool ( 10 ) = BFTl ; % The total concentration of buffer in lumen; unit: mmol per liter
BF_Pool ( 11 ) = P700T ; % The total number of P700; unit: micromole m-2 leaf area
BF_Pool ( 12 ) = NADPHT ; % The total concentration of NADPH in stroma; 1 is an guessed value;
global HPR ;
HPR = 4.66;
global BF2RROEA_Fdn;
global BF2RROEA_FdT;
BF2RROEA_Fdn = Fdn;
BF2RROEA_FdT = TFd;