Biodegradation of acetate (adding complexity to the model)

[maria15143]

Hello,

Thanks again for your answers to my previous doubts. Right now, I've come with a model that simulates the biodegradation of acetate with NO3 as both the electron acceptor and the nitrate source. However, I think I'm missing something because the model results such as pH, concentration of CO2 does not match even close the experimental results. I understand that may happen because the kinetic parameters are an aproximation and the biomass formula is also estimated. The thing is, I'm trying to define biodegradation following the reaction:

1.11CH3COO- + 0.86H+ + 0.86NO3- = 0.11CO2 + 1.12HCO3- + 0.2 C5H7O2N + 0.33N2 + 0.84H2O

I don't know how my current code is considering the H+ consumption, CO2 production.... Should I define it in the biomass formula? Should I create another Kintetics block? I want to add more complexity to my model to make it more accurate. Also, I've defined acetate as it is defined in the database minteq, but I don't know if this is creating problems... I apologize for the doubts and thank you for your time!

## Acetate defining (from database minteq)
SOLUTION_MASTER_SPECIES
Acetate  Acetate-       1.0     Acetate         59.05

SOLUTION_SPECIES
Acetate- = Acetate-
   log_k 0
H+ + Acetate- = H(Acetate)
   log_k   4.757
   delta_h   0.41   kJ
   -gamma   0   0
Fe+2 + Acetate- = Fe(Acetate)+
   log_k   1.4
   delta_h   0   kJ
   -gamma   0   0
Fe+3 + Acetate- = Fe(Acetate)+2
   log_k   4.0234
   delta_h   0   kJ
   -gamma   0   0
Fe+3 + 2Acetate- = Fe(Acetate)2+
   log_k   7.5723
   delta_h   0   kJ
   -gamma   0   0
Fe+3 + 3Acetate- = Fe(Acetate)3
   log_k   9.5867
   delta_h   0   kJ
   -gamma   0   0
Mn+2 + Acetate- = Mn(Acetate)+
   log_k   1.4
   delta_h   0   kJ
   -gamma   0   0
Mg+2 + Acetate- = Mg(Acetate)+
   log_k   1.27
   delta_h   0   kJ
   -gamma   0   0
Ca+2 + Acetate- = Ca(Acetate)+
   log_k   1.18
   delta_h   4   kJ
   -gamma   0   0
Na+ + Acetate- = Na(Acetate)
   log_k   -0.18
   delta_h   12   kJ
   -gamma   0   0
K+ + Acetate- = K(Acetate)
   log_k   -0.1955
   delta_h   4.184   kJ
   -gamma   0   0

############################################
SOLUTION 1
   temp    23
   pH   7.8
   units mmol/kgw
   Ca   1.42389
   Mg   1.26036
   K   0.2147
   Na   6.05401
   C(4)   0.8
   Cl   5.16867
   P    0.0147
   S(6)   0.0704
   N(5)   1.48363   
   Acetate   4.26829

INCREMENTAL_REACTIONS   true

RATES
S_degradation
-start
   1 q_max = parm(1)
   2 ks = parm(2)
   3 ka = parm(3)
   10 S = tot("Acetate")
   20 N = tot("N(5)")
   30 B = kin("Biomass")
   40 rate = - q_max*S/(S+ks)*N/(N+ka)*B
   50 dS = rate * time
   60 save dS
   70 put(rate,1)
-end

Biomass
-start
   1 Y = parm(1)
   2 d = parm(2) #mortalitat
   10 rate_S = get(1)
   20 B = kin("Biomass")
   30 rate = -Y*2*rate_S - d*B
   40 dB = rate * time
   50 save -dB
-end

Nitrate
-start
   10 rate_S = get(1)
   20 rate = parm(1)*rate_S
   30 dN = rate * time
   40 save -dN
-end

Consum_protons
-start
   10 rate_S = get(1)
   20 rate = parm(1)*rate_S
   30 dH = rate * time
   40 save -dH
-end

Calcite
-start
   10 si_mineral = SI("Calcite")
   20 if si_mineral < 0 then goto 50
   30 saturation_state = 1-((10^si_mineral))
   40 rate_cc = parm(1)* saturation_state
    50 molescalcite =  rate_cc* time
   60 put(molescalcite, 5)
   70 put (rate_cc, 6)
   80 save molescalcite
-end


KINETICS
S_degradation
   -formula Acetate 1 CH3COO -1
   -parms 1.04E-4 1.85E-2 1E-4      #qmax[mol acetat/mol C cell/s]   Ks_ED[mol/kgw]   Ks_EA[mol/kgw]
   -steps    0    200*17280   #40 days

Biomass
   -formula C5H7O2N 0.2
   -m0 1e-5
   -parms 0.89 5.78E-7      #Yield[mol C cell / mol acetate]         decay[s-1]

Calcite
   -m   0.4
   -parms 1.04E-10   # kobs, effective rate constant (mol/kgw/s)


USER_GRAPH 1
   -headings Temps Biomassa Acetate Nitrate SICalcite pH Balanç_C
   -axis_titles "time [d]" "concentració [mmol/kgw]" "pH"
   -chart_title "Biodegradation of acetate"
   -plot_concentration_vs  t
-start
10 GRAPH_X TOTAL_TIME/86400
20 GRAPH_Y    kin("Biomass")*1000
30 GRAPH_Y   tot("Acetate")*1000
40 GRAPH_Y   tot("N(5)")*1000
50 GRAPH_Y   SI("Calcite")
60 GRAPH_SY   -LA("H+")
70 total_carbon = tot("C(4)")+tot("C(-4)")+tot("Acetate")*2+kin("Biomass")+1.42389E-03-tot("Ca")
80 GRAPH_Y   total_carbon
-end


USER_GRAPH 2   
   -headings Temps CO2(aq) HCO3-(aq) pH
   -axis_titles "time [d]" "concentració [mmol/kgw]"
   -chart_title "pCO2(aq), HCO3-(aq)"
   -plot_concentration_vs  t
-start
10 GRAPH_X TOTAL_TIME/86400
20 GRAPH_Y   mol("CO2")*1000
30 GRAPH_Y   mol("HCO3-")*1000
40 GRAPH_SY   -LA("H+")
-end

[dlparkhurst]

I think you have the basic reactions defined correctly. However, you use up most of the NO3- and SO4-2 in about 8 days. After that, your are modeling methanogenesis because of the biomass decay.

You probably should use Amm.dat so that nitrogen reduction stops at N2(aq); phreeqc.dat and other databases would reduce N to ammonia.

Otherwise, you may need to adjust your relative rates. I think you may be generating too much biomass; you generate more biomass than you had initial acetate, which results in extensive methanogenesis.

[maria15143]

Thank you for your fast answer. I'll try using the Amm.dat database instead. I think that it results in more biomass than acetate because I'm defining biomass as C, while acetate contains two C. If I multiply acetate concentration * 2 it results in more logic results. On the other hand, do you know the possible reasons for pH to be so high when biomass is growing? (values of 10-11)

Thank you again for taking your time.   

[dlparkhurst]

Here is a balanced reaction that indicates why the pH increases. The last equality is most representative until the pH is over 10. I'll leave it to you to include the effect of the formation of C5H7O2N.

Code: [Select]

CH3COO- + 1.6NO3- = 0.8N2 + 2HCO3- + 0.6OH- + 0.2H2O = 0.8N2 + 1.4HCO3- + 0.6CO3-2 + 0.8H2O

If the calcite rate is faster (or at equilibrium), the pH will be maintained at a lower value.

Code: [Select]

SOLUTION 1
   temp    23
   pH   7.8
   units mmol/kgw
   Ca   1.42389
   Mg   1.26036
   K   0.2147
   Na   6.05401
   C(4)   0.8
   Cl   5.16867
   P    0.0147
   S(6)   0.0704
   N(5)   1.48363   
   Acetate   4.26829
END
USE solution 1
REACTION
Acetate -1
CH3COO  +1
.1 mmol
EQUILIBRIUM_PHASES
Calcite 0 0
END