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microbial growth and C,N and P mass conservation

T.C. Onstott

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Dear Tom,


I would like to grow biomass using the microbe reaction and monitor depletion of critical carbon substrate, N (i.e. NH3(a) and P (HPO4--) to determine when an environment becomes substrate limited as opposed to energy limited. I am not sure how to do this.

I created a mineral phase bioacetate(s) with the formula C36O40H102N9P1 and comprised of 4 species, Acetic_acid(aq), NH3(aq), HPO4-- and H+. this work fine. I then have a microbe reaction that uses Acetic_acid(aq) and calculates biomass. What I then tried to do is to create a custom rate law for C36O40H102N9P1 where the rate is equal to (biomass-biomass0)/Deltat. I thought that the custom rate laws could import these values like they do in the ratelaw_custom4.bas example, but no luck. I just get a can't evaluate the rate error message. Before I beat my head against a wall, I thought I would check in to see if you can offer some advice. If my code reads as follows:


kinetic microbe-24 rxn = "Acetate + H2O -> Methane(aq) + HCO3-" rate_law = ratelaw_example5.bas rate_con = 9e-10

kinetic microbe-24 biomass = 2e-14

kinetic microbe-24 growth_yield = 1

kinetic microbe-24 ATP_energy = -6

kinetic microbe-24 ATP_number = 1

kinetic microbe-24 Decay_con = 1e-11

kinetic microbe-24 power(Acetate) = 1

kinetic microbe-24 powerD(Acetate) = 1

kinetic microbe-24 order1 = 1

kinetic microbe-24 order2 = 1

kinetic microbe-24 KD = 8.6e-4


react 0.1 grams of "bioacetate(s)"

kinetic "bioacetate(s)" rate_law = ratelaw_bioacetate2.bas rate_con = 3.18e-8 surface = 1



do I need to explicitly state something like


kinetic "bioacetate(s)" biomass0 = ???

kinetic "bioacetate(s)" biomass = ???


in order for this ratelaw to be evaluated? Ideally I want to use the same biomass given by microbe-24.


Thanks, tco

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Hi T.C.:


The problem is that both reactants, the microbial population and your bioacetate mineral, have their own biomass and biomass0 variable. The only way to have one reactant set the value of the 2 variables for the other would be to write a C++ function, and link it into a DLL.


I hope that helps,


Tom Meuzelaar

RockWare, Inc.

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