Conceptual Models > Design of conceptual models
Methanogenic bacteria and Methane formation
stfmtu:
Dear all,
I am trying to generate biomass that should be linked with methane formation, but the biomass doesn't appear in the plot. When I attempt to change the number of days from 10 to 100, it seems that after the 10th day, I only get constant values for all the plotted data. Could someone explain what I am doing wrong?
As my model was partially adapted from this forum, I would also like to ask why, in the kinetics of methane formation, only hydrogen is mentioned and there's no mention of other elements such as oxygen, water, or methane itself.
SOLUTION_MASTER_SPECIES
Biomass Biomass 0 Biomass 1
SOLUTION_SPECIES
Biomass = Biomass
-gamma 3
log_k 0
RATES
Methane_formation
-start
10 if (m < 0) then goto 70
20 rate = 2.3e-09*(TOT("C(4)")/1e-3 + TOT("C(4)"))
30 moles = rate * TIME
40 if (moles > m) then moles = m
50 SAVE moles
60 put(rate,1)
70 END
-end
Biomass
-start
1 Y = parm(1)
2 d = parm(2)
10 rate_M = get(1)
20 B = kin("Biomass")
30 rate = -Y*rate_M - d*B
40 dB = rate * time
50 save -dB
-end
End
SOLUTION 1
temp 37
pH 7 charge
pe 4
redox pe
units ppm
density 1
-water 1 # kg
END
GAS_PHASE 1
-fixed_pressure
-pressure 100
-volume 1
-temperature 37
CH4(g) 0
CO2(g) 40
Hdg(g) 160 #In Phreeqc Database is Hdg
END
INCREMENTAL_REACTIONS true
KINETICS 1
Methane_formation
-formula H2 1 Hdg -1
-m0 1
-tol 1e-08
Biomass
-formula H 0.0
-m 1.36e-4
-parms 0.89 5.78E-7
-steps 864000 in 100 steps # seconds; 100 Tage
-step_divide 1
-runge_kutta 3
-bad_step_max 500
END
USE solution 1
USE kinetics 1
USE gas_phase 1
USER_GRAPH 1
-headings time TDIC CH4(aq) Hdg(aq) Biomass CO2(g) Hdg(g) CH4(g)
-axis_titles "Days" "Mole concentration" "Pressure gas phase [atm]"
-axis_scale y_axis 1e-6 2 auto auto log
-initial_solutions false
-connect_simulations true
-plot_concentration_vs x
-start
10 GRAPH_X TOTAL_TIME / 86400
30 GRAPH_Y TOT("C(4)"), TOT("C(-4)"), TOT("Hdg"), TOT("Biomass")
40 GRAPH_SY GAS("CO2(g)"), GAS("Hdg(g)"), GAS("CH4(g)")
-end
-active true
Thank you!
dlparkhurst:
The -formula for biomass is H 0, which is fine. There will be no change in the solution composition from this reaction. However, it implies that the moles of kinetic reactant Biomass is the quantity representing the biomass. As such, a positive value for the SAVE quantity will decrease the biomass, and a negative value for the SAVE quantity will
--- Code: ---increase
--- End code ---
biomass. Therefore the growth rate should be negative and the death rate should be positive. Sorry, maybe it should be the other way, but that is the way it is; it makes more sense if the reaction were dissolving a mineral, where concentrations in solution increase with positive rates.
By converting Hdg to H2, you are adding reductant to the solution. Electron acceptors will be used in the sequence determined by thermodynamics. This is generally the way you expect redox reactions to proceed. In simple terms, O2 will be consumed then NO3- then SO4-2, and finally C(4) will be reduced. If you don't have any other electron acceptors, then you will only see methanogenesis.
--- Code: ---RATES
Methane_formation
-start
10 if (m < 0) then goto 70
20 rate = 2.3e-09*(TOT("C(4)")/1e-3 + TOT("C(4)"))
30 moles = rate * TIME
40 if (moles > m) then moles = m
50 SAVE moles
60 put(rate,1)
70 END
-end
Biomass
-start
1 Y = parm(1)
2 d = parm(2)
10 rate_M = get(1)
20 B = kin("Biomass")
30 rate = -Y*rate_M + d*B # negative rate increases M (biomass)
# positive rate (d*B) decreases M (biomass)
40 dB = rate * time
50 save dB
-end
End
SOLUTION 1
temp 37
pH 7 charge
pe 4
redox pe
units ppm
density 1
-water 1 # kg
END
GAS_PHASE 1
-fixed_pressure
-pressure 100
-volume 1
-temperature 37
CH4(g) 0
CO2(g) 40
Hdg(g) 160 #In Phreeqc Database is Hdg
END
INCREMENTAL_REACTIONS true
KINETICS 1
Methane_formation
-formula H2 1 Hdg -1
-m0 1
-tol 1e-08
Biomass
-formula H 0.0
-m 1.36e-4
-parms 0.89 5.78E-7
-steps 864000 in 100 steps # seconds; 100 Tage
-step_divide 1
-runge_kutta 3
-bad_step_max 500
END
USE solution 1
USE kinetics 1
USE gas_phase 1
USER_GRAPH 1
-headings time TDIC CH4(aq) Hdg(aq) Biomass CO2(g) Hdg(g) CH4(g)
-axis_titles "Days" "Mole concentration" "Pressure gas phase [atm]"
-axis_scale y_axis 1e-6 2 auto auto log
-initial_solutions false
-connect_simulations true
-plot_concentration_vs x
-start
10 GRAPH_X TOTAL_TIME / 86400
30 GRAPH_Y TOT("C(4)"), TOT("C(-4)"), TOT("Hdg"), KIN("Biomass")
40 GRAPH_SY GAS("CO2(g)"), GAS("Hdg(g)"), GAS("CH4(g)")
-end
-active true
--- End code ---
stfmtu:
The following code is based on the recommendations given. Would you be so kind as to take a look at why the HDG has a negative value and results in an error?
RATES
Methane_formation
-start
10 if (m < 0) then goto 70
20 rate = 1.643e-5*TOT("C(4)")/(1.094e-7 + TOT("C(4)"))
30 moles = rate * TIME
40 if (moles > m) then moles = m
50 SAVE moles
60 put(rate,1)
70 END
-end
Biomass
-start
1 Y = parm(1)
2 d = parm(2)
10 rate_M = get(1)
20 B = kin("Biomass")
30 rate = -Y*rate_M + d*B # negative rate increases M (biomass)
# positive rate (d*B) decreases M (biomass)
40 dB = rate * time
50 save dB
-end
End
SOLUTION 1
temp 45 #optimal 45degC, max 122degC, min 10degC
pH 7.7 charge #optimal 7.7, max 10.2, min 4.1
pe 4
redox pe
units ppm
density 1
-water 1 # kg
END
GAS_PHASE 1
-fixed_pressure
-pressure 100
-volume 1
-temperature 45 #optimal 45degC, max 122degC, min 10degC
CH4(g) 0
CO2(g) 40
Hdg(g) 160 #In Phreeqc Database is Hdg
END
INCREMENTAL_REACTIONS true
KINETICS 1
Methane_formation
-formula H2 1 Hdg -1
-m0 6.118 #all available moles of Hdg --> see phr.out file in the beginning when reaction starts
-tol 1e-08
Biomass
-formula CH1.8O0.5N0.2 0.0
-m 1.36e-4
-parms 0.03 8.565e-7 # Methanogeic bacteria: Y=0.03, d=8.565e-07
#-steps 8640000 in 100 steps # seconds; 100 Tage
#-steps 86400000 in 100 steps # seconds; 1000 Tage
#-steps 1728000 in 100 steps # seconds; 20 Tage
-steps 34560000 in 100 steps # seconds; 400 Tage
-step_divide 1
-runge_kutta 3
-bad_step_max 500
END
USE solution 1
USE kinetics 1
USE gas_phase 1
USER_GRAPH 1
-chart_title "Gaseous components during methanogenesis"
-headings CO2(g) CH4(g) Hdg(g)
-axis_titles "Days" "Pressure gas phase [atm]"
-axis_scale y_axis auto auto #log
-axis_scale x_axis 0 400
-initial_solutions false
-connect_simulations true
-plot_concentration_vs x
-start
10 PLOT_XY TOTAL_TIME/86400, GAS("CO2(g)"), color=Black,symbol=Square,symbol_size=0,y_axis=1,line_width=3
20 PLOT_XY TOTAL_TIME/86400, GAS("CH4(g)"),color=Orange,symbol=Triangle,symbol_size=0,y_axis=1,line_width=3
30 PLOT_XY TOTAL_TIME/86400, GAS("Hdg(g)"), color=Blue,symbol=Diamond,symbol_size=0,y_axis=1,line_width=3
-end
-active true
USER_GRAPH 2
-chart_title "Aqueous species during methanogenesis"
-headings CO2(aq) CH4(aq) Hdg(aq) Biomass(aq)
-axis_titles "Days" "Mole concentration of aqu. species" "Moles of Biomass in aqu. phase"
-axis_scale y_axis auto auto #log
-axis_scale sy_axis auto auto #log
-axis_scale x_axis 0 400
-initial_solutions false
-connect_simulations true
-plot_concentration_vs x
-start
10 PLOT_XY TOTAL_TIME/86400, TOT("C(4)"), color=Black,symbol=Square,symbol_size=0,y_axis=1,line_width=3
20 PLOT_XY TOTAL_TIME/86400, TOT("C(-4)"),color=Orange,symbol=Triangle,symbol_size=0,y_axis=1,line_width=3
30 PLOT_XY TOTAL_TIME/86400, TOT("Hdg"), color=Blue,symbol=Diamond,symbol_size=0,y_axis=1,line_width=3
40 PLOT_XY TOTAL_TIME/86400, KIN("Biomass"), color=Green,symbol=Circle,symbol_size=6,y_axis=2,line_width=1
-end
-active true
USER_GRAPH 3
-chart_title "Total Moles in the System"
-headings CO2 CH4 Hdg
-axis_titles "Days" "Moles" "Moles"
-axis_scale y_axis auto auto #log
-axis_scale sy_axis auto auto #log
-axis_scale x_axis 0 400
-initial_solutions false
-connect_simulations true
-plot_concentration_vs x
-start
10 PLOT_XY TOTAL_TIME/86400, TOTMOLE("C(4)")+GAS("CO2(g)"), color=Black,symbol=Square,symbol_size=0,y_axis=1,line_width=3
20 PLOT_XY TOTAL_TIME/86400, TOT("C(-4)")+GAS("CH4(g)"),color=Orange,symbol=Triangle,symbol_size=0,y_axis=2,line_width=3
30 PLOT_XY TOTAL_TIME/86400, TOT("Hdg")+GAS("Hdg(g)"), color=Blue,symbol=Diamond,symbol_size=0,y_axis=1,line_width=3
-end
-active true
dlparkhurst:
The sign of moles in SAVE moles in the methane_formation rate is positive. The coefficient of Hdg in KINETICS is negative. The combination is trying to remove Hdg from solution, but there is no Hdg to be removed. The rate calculation cannot procede because no matter what time step is used, it will make a negative concentration of Hdg.
stfmtu:
Hello,
I have tried changing the sign of moles or the one for Hdg, but neither way works. I have also tried modifying the KINETICS formula to: H2 -4 CO2 -1 CH4 1 H2O 2, but still no results. My code should consume the available hydrogen and produce methane and a biomass that will decay the moment hydrogen or carbon dioxide is not available.
Any help on identifying my mistakes would be greatly appreciated.
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