jagropp/aom.bioiso.model

Files for a manuscript titled "Sulfate-dependent reversibility of intracellular reactions explains the opposing isotope effects in the anaerobic oxidation of methane", currently under review.

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.