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[OLD] Modeling with microbes


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From: Brian Gibney

Subject: Modeling with microbes

I am a microbiologist with limited geochemistry modeling experience. I would like to model sorption of arsenic during the reduction of insoluble iron hydroxides by microbes under anaerobic conditions, but I have stumbled at the following hurdles:

1) REACT does not allow me to model without O2 in the system

2) I can't seem to enter the right equation for reduction of FeOOH in the "kinetic redox" box under the REACTANTS tab

3) I don't know all parameters to enter into the "kinetic redox" box under the REACTANTS tab--only the rate constant of FeOOH reduction. Will it function with only that rate constant?

4) I have data for "biomass," "growth yield" and "decay constant" values within the the "kinetic microbe" box under the REACTANTS tab, but don't know values for reaction, rate constant, pKa, etc.


From: Craig Bethke

Subject: Re: Modeling with microbes

(1) If you must add O2(aq) to complete the chemical system, you probably haven't decoupled all of the necessary redox reactions.

(2) You will, of course, need a complete set of kinetic parameters to trace a kinetic model. But it's not clear to me that you need to define two kinetic reactions, one for FeOOH reduction and another for microbial activity. Since the reduction is driven by the microbes, it seems to me that a single kinetic reaction would do.

(3) You should ask yourself if you need a kinetic model at all. Could your purposes be served by tracing a parametric model in terms of the amount of FeOOH reduced, without specifically accounting for time? If so, simply write a balanced chemical reaction for FeOOH reduction, titrate in the reactions products (Fe++, etc.) while you remove (titrate out) the reactants (FeOOH, etc.).

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