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Rate Law for Microbial Metabolism


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I just started using GWB React to simulate microbial metabolism and growth. The general form of GWB's Built-in Rate Law is shown below.  I am wondering how it is written in GWB.  For example, for the reaction Slide17.png, its dual Monod equation is Slide19.png. The plot shows no microbial growth after running when I write down the equation for 'Kinetic microbe 1' in 'rate law' box of 'Reactants' pane  as 

(rate_con * activity("CH3COO-")/(activity("CH3COO-")+KD) * activity("SO4--")/(activity("SO4--")+KA) * ( 1 - (Q/K)^(order1) * exp(-(order1)*ATP_number*ATP_energy/R/TK))^(order2) * growth_yield - decay_con)*biomass

Does anyone know what is wrong with this expression?


rate law 1.png

rate law 2.png

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The rate law for microbial metabolism isn't quite correct in the way you have entered it. In the user guide, if you are using the dual monod model, you would include both the electron donor and acceptor terms in your equations, however, you wouldn't include the terms for growth yield and decay rate in the same rate equation.

To update the biomass in a custom rate law, you would need to call a special function setgwbvar at every time step. If not, the biomass specified will not update from what is entered in the Reactants pane. I believe a custom rate law script or a compiled rate law script will allow you to use setgwbvar to update biomass at the end of every step of the calculation, but not with the equation option. You can see an example of this in section 5.2 of the GWB Reaction Modeling guide. Note that if you use the built in option for your rate law, GWB will automatically update the biomass calculation according to the growth yield and decay rate specified at each step.

I think there are a few other small issues in terms of the equation you entered:

The equation shown in the user guide also accounts for water mass (n_w), you would also need to do that if you are trying to replicate the default rate law by entering your own custom version.

R, is the variable commonly used as the gas constant, but it is not a default value built in. You should enter the actual value of the gas constant. You can find all the parameters accepted in setting up a custom rate law in Tables 5.1. The complete list of helper functions are available in Table 5.2.

In the second picture, the rate is figured in terms of molalities of the species "m_Ac" and "m_SO4" but in the equation you entered, the species are accounted for in terms of activity.

Hope this helps,
Jia Wang
Aqueous Solutions LLC

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