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parametersPETC.py
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# File parametersPETC.py
# -*- coding: utf-8 -*-
"""
Copyright (C) 2014-2015 Anna Matuszyńska, Oliver Ebenhöh
This program 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, either version 3 of the License, or
(at your option) any later version.
This program 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
along with this program (license.txt). If not, see <http://www.gnu.org/licenses/>.
"""
from numpy import log, exp
class ParametersPETC:
defaultparameterset = {
# pool sizes
'PSIItot': 2.5, # [mmol/molChl] total concentration of PSII
'PSItot': 2.5,
'PQtot': 17.5, # [mmol/molChl]
'PCtot': 4., # Bohme1987, but other sources give different values - seems to depend greatly on organism and conditions
'Fdtot': 5., # Bohme1987
'Ctot': 2.5, #source unclear (Schoettler says 0.4...?, but plausible to assume that complexes (PSII,PSI,b6f) have approx. same abundance)
'NADPtot': 25., # estimate from ~ 0.8 mM, Heineke1991
'APtot': 60., # [mmol/molChl] Bionumbers ~2.55mM (=81mmol/molChl) (FIXME: Soma had 50)
# parameters associated with photosystem II
'kH': 0.,
'kH0': 5.e8, # base quenching' after calculation with Giovanni
'kF': 6.25e7, # fluorescence 16ns
'k1': 5.e9, # excitation of Pheo / charge separation 200ps
'k1rev': 1.e10,
'k2': 5.e9, # original 5e9 (charge separation limiting step ~ 200ps) - made this faster for higher Fs fluorescence
# parameters associated with photosystem I
'kStt7': 0.0035, # [s-1] fitted to the FM dynamics
'kPph1': 0.0013, # [s-1] fitted to the FM dynamics
'KM_ST': 0.2, # Switch point (half-activity of Stt7) for 20% PQ oxidised (80% reduced)
'n_ST': 2., # Hill coefficient of 4 -> 1/(2.5^4)~1/40 activity at PQox=PQred
'staticAntI': 0.2,
'staticAntII': 0.0,
# ATP and NADPH parameters
'kATPsynth': 20., # taken from MATLAB
'kATPcons': 10., # taken from MATLAB
'kATPimport': 0., # TODO possibility for ATP import at night - NOT YET IMPLEMENTED!
'ATPcyt': 0.5, # only relative levels are relevant (normalised to 1) to set equilibrium
'Pi_mol': 0.01,
'DeltaG0_ATP': 30.6, # 30.6kJ/mol / RT
'HPR': 14./3.,
'kNADPHimport': 0., # TODO possibility for NADPH import - NOT YET IMPLEMENTED!
'kNADPHcons': 15., # taken from MATLAB
'NADPHcyt': 0.5, # only relatice levels
# global conversion factor of PFD to excitation rate
'cPFD': 4., # [m^2/mmol PSII]
# pH and protons
'pHstroma': 7.8,
'kLeak': 0.010, # [1/s] leakage rate -- inconsistency with Kathrine
'bH': 100., # proton buffer: ratio total / free protons
# rate constants
'kPQred': 250., # [1/(s*(mmol/molChl))]
'kCytb6f': 2.5, # a rough estimate: transfer PQ->cytf should be ~10ms
'kPTOX': .01, # ~ 5 electrons / seconds. This gives a bit more (~20)
'kPCox': 2500., # a rough estimate: half life of PC->P700 should be ~0.2ms
'kFdred': 2.5e5, # a rough estimate: half life of PC->P700 should be ~2micro-s
'kcatFNR': 500., # Carrillo2003 (kcat~500 1/s)
'kcyc': 1.,
'O2ext': 8., # corresponds to 250 microM, corr. to 20%
'kNDH': .002, # re-introduce e- into PQ pool. Only positive for anaerobic (reducing) condition
'kNh': 0.05,
'kNr': 0.004,
'NPQsw': 5.8,
'nH': 5.,
'EFNR': 3., # Bohme1987
'KM_FNR_F': 1.56, # corresponds to 0.05 mM (Aliverti1990)
'KM_FNR_N': 0.22, # corresponds to 0.007 mM (Shin1971, Aliverti2004)
# standard redox potentials (at pH=0) in V
'E0_QA': -0.140,
'E0_PQ': 0.354,
'E0_cytf': 0.350,
'E0_PC': 0.380,
'E0_P700': 0.480,
'E0_FA': -0.550,
'E0_Fd': -0.430,
'E0_NADP': -0.113,
# physical constants
'F': 96.485, # Faraday constant
'R': 8.3e-3, # universal gas constant
'T': 298., # Temperature in K - for now assumed to be constant at 25 C
}
def __init__(self, pars = {}):
mypars = pars.copy()
for k in ParametersPETC.defaultparameterset.keys():
mypars.setdefault(k,ParametersPETC.defaultparameterset[k])
for k in mypars.keys():
setattr(self,k,mypars[k])
self.setCompositeParameters()
setattr(self,'KeqPQred',self.Keq_PQred())
setattr(self,'KeqCyc', self.Keq_cyc())
setattr(self,'KeqCytfPC', self.Keq_cytfPC())
setattr(self,'KeqFAFd', self.Keq_FAFd())
setattr(self,'KeqPCP700', self.Keq_PCP700())
setattr(self,'KeqNDH', self.Keq_NDH())
setattr(self,'KeqFNR', self.Keq_FNR())
def setCompositeParameters(self):
setattr(self, 'RT', self.R * self.T)
setattr(self, 'dG_pH', log(10)*self.RT)
setattr(self, 'Hstroma', 3.2e4*10**(-self.pHstroma)) # proton concentration in stroma
setattr(self, 'kProtonation', 4e-3 / self.Hstroma) # [1/s] converted from 4 * 10^-6 [1/ms] protonation of LHCs (L), depends on pH value in lumen
def Keq_PQred(self):
DG1 = -self.E0_QA * self.F
DG2 = -2 * self.E0_PQ * self.F
DG = -2 * DG1 + DG2 + 2 * self.pHstroma * self.dG_pH
K = exp(-DG/self.RT)
return K
def Keq_cyc(self):
DG1 = -self.E0_Fd * self.F
DG2 = -2 * self.E0_PQ * self.F
DG = -2 * DG1 + DG2 + 2 * self.dG_pH * self.pHstroma
K = exp(-DG/self.RT)
return K
def Keq_cytfPC(self):
DG1 = -self.E0_cytf * self.F
DG2 = -self.E0_PC * self.F
DG = -DG1 + DG2
K = exp(-DG/self.RT)
return K
def Keq_FAFd(self):
DG1 = -self.E0_FA * self.F
DG2 = -self.E0_Fd * self.F
DG = -DG1 + DG2
K = exp(-DG/self.RT)
return K
def Keq_PCP700(self):
DG1 = -self.E0_PC * self.F
DG2 = -self.E0_P700 * self.F
DG = -DG1 + DG2
K = exp(-DG/self.RT)
return K
def Keq_NDH(self):
DG1 = -2 * self.E0_NADP * self.F
DG2 = -2 * self.E0_PQ * self.F
DG = -DG1 + DG2 + self.dG_pH * self.pHstroma
K = exp(-DG/self.RT)
return K
def Keq_FNR(self):
DG1 = -self.E0_Fd * self.F
DG2 = -2 * self.E0_NADP * self.F
DG = -2 * DG1 + DG2 + self.dG_pH * self.pHstroma
K = exp(-DG/self.RT)
return K