def stateLifetimes2(spec, concs, r, labelAddition = '', constants={'q':10e-3, 'O2':0.1*air_sat_O2_conc}, **kwargs):
lineSpec = {'lw':2}
lineSpec.update(kwargs)
#figure()
#constants={'q':10e-3, 'O2':0.1*air_sat_O2_conc}
I = Stimulus(0, [], [])
t = linspace(1, 1e5, 1000)
tXs = []
tRs = []
nConc = constants[spec]
rates = []
initConc = 1e-3
s = System(r,constants={}, ties={'S1':('0', 'S0')},stimulae={'I':I})#
s.GenerateGradAndJacCode()
s.initialConditions['S0'] = 1e-3 #conc of fluorophores on an antibody ~ 100M
#s.initialConditions['X'] = initConc
#s.initialConditions['R'] = initConc
s.initialConditions['q'] = constants['q']
s.initialConditions['O2'] = constants['O2']
for i in range(len(concs)):
s.initialConditions[spec] = concs[i]
rates.append(s.GradFcn(0, s.initialConditions.view('f8')).view(s.dtype))
rates = hstack(rates)
loglog(concs, 1e-6/(-rates['X']/initConc), c = 'b', label='X' + labelAddition, **lineSpec)
loglog(concs, 1e-6/(-rates['R']/initConc), c = 'g', label='R' + labelAddition, **lineSpec)
plot([nConc, nConc], ylim(), 'k--')
ylabel('Dark state lifetime [s]')
xlabel('[%s]' % spec)
legend()
def dyeConc2(concs):
constants={'q':5e-3, 'O2':0.1*air_sat_O2_conc}
#constants = {}
#constants={'q':0, 'O2':0}
s = System(r,constants=constants, ties={'S1':('I', 'S0')},stimulae={'I':I})#
s.GenerateGradAndJacCode()
rates = []
for c in concs:
s.initialConditions['S0'] = c
res = s.solve([1e3])
rates.append(s.GradFcn(0, res.view('f8')).view(s.dtype))
rates = hstack(rates)
figure()
#plot(concs, rates['S0']/concs)
plot(concs, rates['T1']/concs)