AOM.bioiso.model

Source code to calculate carbon and hydrogen isotope evolution in anaerobic oxidation of methane (AOM), depending on availbility of sulfate. This code is part of a paper published in Science Advances with the title "Sulfate-dependent reversibility of intracellular reactions explains the opposing isotope effects in the anaerobic oxidation of methane" (Wegener G., Gropp J., Taubner H., Halevy I. and Elvert M.) [Link to paper]. In this manuscript, we describe the evolution of carbon and hydrogen isotopic composition of methane and the reversibility of the metabolic pathway as a function of sulfate concentrations.

Using the repository

This repository contains two versions of the model:

1. A two-box model based on the model presented in Yoshinaga et al., 2014 (Nat. Geo. Sci., doi.org/10.1038/ngeo2069). This model includes methane and DIC.
2. A four-box model that is presented in the manuscript, which includes the metabolites methane, DIC, CH₃-H₄MPT, CHO-MFR and HS-CoB.

There are two main functions to run the models:

Two-box model

Run the function run_AOM_model_twobox().

Four-box model

Consists of three functions, which are initiallized by running the function run_AOM_model(), which will use the best fit model parameters to generate a figure for the change of isptope compositions of methane and DIC with time. In the function run_bioiso_model the user can manually change the initial model conditions (concentrations, kinetic fractionation factors from the literature, equilibrium fractionation factors). The function AOM_ODEs_solver is the ODE solver for the model.

Additional information

Please contact me for questions/help with using this code at ja[dot]gropp[at]gmail[dot]com.