Conceptual Models > Database selection and modification

Modify database for adding kinetics to a solution species reactions

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ahmadreza_shojaee:
Dear PHREEQC users

Hi
I would like to add the kinetics of methanogenesis reaction to my model. According to the manual and examples (9 and 15), we should modify and re-define the database in order to consider the kinetics of aqueous species.

The methanogenesis reaction consists of two reactions: the anabolic reaction and catabolic reaction.

--- Code: ---#Anabolic reaction
HCO3- + 2.1H2 + 0.2NH4+ + 0.8H+ = CH1.8O0.5N0.2 + 2.5H2O
#Catabolic reaction:
0.25HCO3- + H2 + 0.25H+ = 0.25CH4 + 0.75H2O
--- End code ---

The full metabolism reaction is the summation of the above reactions.

--- Code: ---#Full reaction
1.25HCO3- + 3.1H2 + 1.05H+ +0.2NH4+ = CH1.8O0.5N0.2 + 0.25CH4 + 3.25H2O
--- End code ---

If I want to add the kinetics of this reaction to my code, what changes should I make in the new database?

Regards

dlparkhurst:
Assuming organic decomposition is the driver for methanogenesis, the simplest approach is to write a rate expression for how fast organic matter decomposes. The expression could be as simple as first-order decomposition (example below), or more complicated expressions depending on available electron acceptors with inhibitor and Michelis-Menton factors.

I think you are looking at the Version 2 manual. Example 7 in the Version 3 manual gives an example of organic decomposition with formation of a gas bubble.

I don't know your system, but you have written your chemical equations with H2. If some source of H2 is the driver for methanogenesis, you can replace the organic matter (CH2O) with H2. Your rate equation would then describe the consumption of H2. Here is an example script that uses a constant rate of H2 consumption.


--- Code: ---RATES
Organic_decomposition
20 rate = 1e-2/86400  # mol/sec
30 moles = rate* TIME
40 SAVE moles
50 END
END
SOLUTION 1
EQUILIBRIUM_PHASES
Calcite 0
Dolomite 0
CO2(g) -1.0
SAVE solution 1
END
INCREMENTAL_REACTIONS true
KINETICS
Organic_decomposition
-M 1 moles
-formula H2 1
-step 864000 in 100 steps
END
USE solution 1
USE kinetics 1
USER_GRAPH 1
    -headings               time TDIC CH4(aq) P(CH4(g)) P(H2(g))
    -axis_titles            "Days" "Molality" "P(CH4(g)), atm"
    -axis_scale y_axis      1e-4 2 auto auto log
    -initial_solutions      false
    -connect_simulations    true
    -plot_concentration_vs  x
  -start
10 GRAPH_X TOTAL_TIME / 86400
20 IF (TOT("C(4)") >= 1e-10) THEN tdic = TOT("C(4)") ELSE tdic = 1e-10
30 GRAPH_Y tdic, TOT("C(-4)")
40 GRAPH_SY SI("CH4(g)"), SI("H2(g)")
  -end
    -active                 true

--- End code ---

ahmadreza_shojaee:
Thank you David For your response.
My system contains two phases;  a water phase and a gas phase as follow:

--- Code: ---SOLUTION 1
-pressure 200
-temp 90
-density 1
pH 7 charge
units ppm
K 1152
        Na 47520
        Mg 771
        Ca 5840
        Cl 86500
        C 586.7
        S(6) 61.5
-water 1
Gas_Phase 1
-pressure 200
-temp 90
        -fixed_volume
H2(g)  160
CO2(g) 40
CH4(g) 0
END

--- End code ---

The methanogenesis reactions depends on some scenarios: I) dissolution of H2 and CO2 in the water phase in equilibrium state in each time step, II) the kinetic rate of H2 and CO2 consumption and biomass formation, III) Mass transfer of CH4 to the gas phase. Step I and III are in equilibrium state; however, in step II the kinetics should be considered. For the kinetics model, I am going to use dual Monod equation.

I need a model to consider the kinetics of the above system in order to calculating the amount of biomass, hydrogen/CO2 consumption, and methane as a function of time.

dlparkhurst:
Here is one possibility for your calculation. It uses the inert gas Hdg as the initial gas phase hydrogen, which will partition with the aqueous phase. The kinetic reaction is to transform inert dissolved Hdg to reactive H2 at a rate determined by the RATES definition. I have used an arbitrary constant reaction for the rate at which H2 is introduced; equilibrium will immediately consume the H2 with the most thermodynamically favorable electron acceptor. The rate is sufficiently high to show the consumption of Hdg and TDIC and the production of CH4(aq) and CH4(g).

The gas has a fixed volume, and the overall pressure decreases over the course of the reaction.


--- Code: ---RATES
Organic_decomposition
20 rate = 1e-1/86400  # mol/sec
30 moles = rate* TIME
40 SAVE moles
50 END
END
SOLUTION 1
-pressure 200
-temp 90
-density 1
pH 7 charge
units ppm
K 1152
        Na 47520
        Mg 771
        Ca 5840
        Cl 86500
        C 586.7
        S(6) 61.5
-water 1
END
Gas_Phase 1
-pressure 200
-temp 90
      -fixed_volume
Hdg(g)  160
CO2(g) 40
CH4(g) 0
END
INCREMENTAL_REACTIONS true
KINETICS
Organic_decomposition
-M 1 moles
-formula H2 1 Hdg -1
-step 864000 in 100 steps
END
USE solution 1
USE kinetics 1
USE gas_phase 1
USER_GRAPH 1
    -headings               time TDIC CH4(aq) Hdg(aq) CO2(g) Hdg(g) CH4(g)
    -axis_titles            "Days" "Molality" "P(CH4(g)), atm"
    -axis_scale y_axis      1e-4 2 auto auto log
    -initial_solutions      false
    -connect_simulations    true
    -plot_concentration_vs  x
  -start
10 GRAPH_X TOTAL_TIME / 86400
20 IF (TOT("C(4)") >= 1e-10) THEN tdic = TOT("C(4)") ELSE tdic = 1e-10
30 GRAPH_Y tdic, TOT("C(-4)"), TOT("Hdg")
40 GRAPH_SY GAS("CO2(g)"), GAS("Hdg(g)"), GAS("CH4(g)")
  -end
    -active                 true

--- End code ---

ahmadreza_shojaee:
It seems it is a nice idea to use inert Hdg.
I have some doubts about this method.
For example, does the output pH represent the correct pH value? If we want to add more reactions, can we still use this method? Acetogenesis is another reaction which could happen in this situation. I think this reaction is not in the database.
Another thing that I observed is that the in this method, first the reactions with higher K value happens. Is it true? By converting Hdg to H2, reactions with higher equilibrium constant compete to use H2 in the water phase.

Another question about calculating the amount of biomass. If I want to calculate the amount of biomass after each time step, I should define a new master specie in a database?

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