TUTORIALS

1. Yeast growth comparison under glucose and hexane substrates
2. Respiratory quotient from gaseous inlet-outlet exchange values
3. Biomass molecular composition and biomass molecular weight with dry weights and ash fraction
4. Time to achieve given titer under exponential biomass growth (doubling)

1. Yeast growth comparison under glucose and hexane substrates

from bioreactor_model import calc
yeast = calc.CellComposition(values={'C':1,'H':1.66,'N':0.194,'O':0.269,'ash_fraction':8}, molecular_formula=True)
ysol_hex=calc.BiomassEquation(yeast.biomass_composition,substrate='hexane')
ysol_glu=calc.BiomassEquation(yeast.biomass_composition,substrate='glucose')
ysol_hex.solve_biomass_equation(biomass_yield_gram=1.4, biomass_molar_weight=yeast.biomass_molar_weight) # yield by gram
ysol_glu.solve_biomass_equation(biomass_yield_mol=0.4)  # molar yield
yeast_hexane_sol = ysol_hex.biomass_equation_solution
yeast_glucose_sol = ysol_glu.biomass_equation_solution
print('Respiratory quotient with glucose substrate: ',yeast_glucose_sol['rq'])
print('Respiratory quotient with hexane substrate: ',yeast_hexane_sol['rq'])

Out:
Respiratory quotient with glucose substrate: 1.01
Respiratory quotient under hexane substrate: 0.187

Respiratory growth of yeast in glucose substrate is close to 1. Respiratory growth of yeast in hexane substrate is much less than 1. This is because glucose needs less dioxygen (O2) for respiration because it contains oxygen (C6H12O6). Respiratory quotient is defined as the ratio between moles of carbon dioxide produced per mole of dioxygen (O2). Since hexane (C6H14) lacks oxygen (O), yeast requires more dioxygen (O2) for respiration when using hexane as substrate, hence respiratory quotient is lower in that case.

2. Respiratory quotient from gaseous inlet-outlet exchange values

from bioreactor_model import calc
expt = calc.CellComposition(values={'C':47,'H':4.15,'N':10,'O':31,'ash_fraction':7.85}, dry_weights=True)
biomass = expt.biomass_composition
be = calc.BiomassEquation(biomass)
be.set_gas_io_values(inlet_N2=79,inlet_O2=21,outlet_CO2=10,outlet_N2=83,outlet_O2=7)
print(be.rq_from_gas_io())

Out:
0.664

3. Biomass molecular composition and biomass molecular weight with dry weights and ash fraction

from bioreactor_model import calc
expt = calc.CellComposition(values={'C':47,'H':4.15,'N':10,'O':31,'ash_fraction':7.85}, dry_weights=True)
print(expt.biomass_molar_weight)
print(expt.biomass_composition['formula'])

Out:
25.545
C(H-1.052)(N-0.182)(O-0.495)

4. Time to achieve given titer under exponential biomass growth (doubling)

Given a batch bioprocess for recombinant protein production with specific production rate (q_p)=4x10^-6 g product / 10⁶ cells . h, reactor seeded with 5x10⁵ cells/ml, and cells doubling every 15 hours, time to achieve product titer of 5 g/l (under balanced growth conditions) is:

from bioreactor-model import bioreactor
print(bioreactor.time_to_titer(titer=5,qp=0.000000000004,cell_seed_volume=500000,doubling_time=15,seed_unit='cell/ml')['value'])

Out:
103