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Some problems in modeling kinetic reduction of Goethite using React


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Hey, I am working to model  kinetic reduction of Goethite  using kinetic-Microbial reduction in React. And I met some trouble. The questions as follows.

  1. I don't know the difference among power, powerA and powerD.
  2. I don't know how to solve the error: Fe++ is not in the crruent chemical system.
  3. I find I don't wanna simulation microbial growth, so whether I have to choose kinetic-Microbial reduction in React? I can't determine the value of ATP or ATP number.
  4. To add lactate in React, I choose Thermo+Lactate.tdat instead of Thermo.tdat. However, lactate can't be found unless setting up a new file. I felt so puzzled.
  5. I have try to open thermo-microbes.tdat loaded from the website of GWB, but in vain. It shows a error that It is not a valid thermo dataset.

Looking forward to your early reply, thank you!

Best wishes! 

Wen. 

monitor2.rea

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Hello Wen,

1. The power, powerA, and powerD are the power terms for numerator and denominator terms in the generalized rate law for calculating microbial metabolic rate. You can find the equation and terms explained in section 4.7.1. Metabolic rate in the GWB Reaction Modeling User Guide. 

2. The redox pair for Fe+++/Fe++ is decoupled so you have to add in both Fe++ and Fe+++ to your system in the Basis pane.  

3. You might want to look at the different types of kinetic models that the GWB has to offer to determine which one is suitable for your needs. Please refer to section 4.6 Kinetics of redox reactions and section 4.7 Microbial metabolism and growth in the GWB Reaction Modeling User Guide. In the sections described above, the equation for each type of microbial reaction is described in detail. 
 
4. I am not really sure what you mean here. If you open a saved React input file and go to File -> Open -> thermo file -> thermo+Lactate.tdat, React loads the new thermo dataset. If there are any conflicts within the existing setup, React will display a pop up showing the conflicts and ask if you would like to proceed. Note that Lactate is a redox species in thermo+Lactate.tdat. If you want to constrain it separately in the Basis pane, you would need to decouple the redox reaction first and then you are able to find it under "add" in the Basis pane. For more information on redox disequilibrium, refer to section 7.3 in the GWB Reaction Modeling User Guide.
 
5. The datasets available on the GWB academy are in the latest format (currently apr20), used in GWB 2021 (or version 15.0.1). If you are using an older version of the GWB, TEdit is not going to be able to open and edit the dataset. You can still open the dataset in a text editor, such as Notepad, to view the reactions. Alternatively, you can obtain a free GWB Community license, which includes the latest version of TEdit and will allow you to open the dataset.
 
Hope this helps,
Jia Wang
Aqueous Solutions LLC
 
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Hello Jia, 

Thank you for your rapid reply! I find the software GWB has no "Save" function instead of "Save as".  I have to overwrite it in order to update the file.  When I open a saved React input file after choosing Thermo+lactate tdat.  in preferences,I still do not find Lactate\HCO3-. So I guess whether there is a relationship between them.

Best whishes,

Wen.

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Hello Wen,

Thanks for the clarification. If you change the thermo dataset in the Preferences window, The GWB will then use whatever dataset set when launching a new instance of React (or any other GWB apps other than the plotting apps). Changing the dataset in Preferences, does not change the dataset loaded for your current input file. To change the dataset loaded for your current file, you have to go to File -> Open -> Thermo Data... and then select the file you want. To see the current thermo file loaded for the simulation, you can go to File --> View --> and select the file with the extension .tdat. 

Hope this helps,
Jia

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Hello Jia,

Thanks for the accurate answer. Now Imeet a  Error: Redox reaction microbe-1 does not mass balance (error = 105.067300), which confuses me. I don't know if it concerns ion banlance. It seems that the ionic charge of the solution is conserved. I try to search "mass balance" in the community or GWB User Guide,  there is something  unrelated.

Hope for your helps. 

Best wishes,

Wen.

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Hello Wen,

You're welcome. The error indicates that the kinetic reaction specified in the Reactants pane is not balanced. I took a quick look in monitor2.rea and that does seem to be the case. In general, it is good practice to double-check your input file when issues like this arise.

Best regards,
Jia

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Hey Jia,

sorry to interrupt you again . I check the file in the basis and rectant pane for much time. I add the value of CH3COO-、powerD and so on. But the error is still same as before. It seems not matter with ion style.  I wonder if the answer is about ion concentration.

I have learned the reason, it may be the input of biomass.

Best wishes,

Wen

 

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