Model associated with: "Thermodynamic control on the decomposition of organic matter across different electron acceptors"
- Pacific Northwest National Laboratory; Pacific Northwest National Laboratory
- Pacific Northwest National Laboratory
- SLAC National Accelerator Laboratory
- University of Nebraska-Lincoln
This model data package is associated with the publication “Thermodynamic control on the decomposition of organic matter across different electron acceptors” submitted to Soil Biology and Biochemistry (Zheng et al., 2023; https://doi.org/10.1016/j.soilbio.2024.109364).In this research, a thermodynamic modeling framework is built to flexibly incorporate both organic matter (OM) molecules and electron acceptors for estimating potential free energy release from various redox reactions and to further predict reaction rates based on Microbial Transition State Theory. The model package includes scripts for thermodynamic modeling and postprocessing. Input Fourier-transform ion cyclotron resonance (FTICR) data are from a previous experimental study (Boye et al., 2018), and model outputs are free energy predictions and stoichiometric coefficients associated with all possible redox reactions.This data package is associated with the project GitHub repository found at MM_bioenergetic_modeling.This data package contains four folders (Input_FTICR, Model, Output, and Output_processing), a file-level metadata (FLMD) csv, and a data dictionary (dd) csv. Please see Zheng_bioenergetic_modeling_flmd.csv for a list of all files contained in this data package and descriptions for each. The Zheng_bioenergetic_modeling_dd.csv file describes the csv column headers. The “Model” folder contains scripts to run energy balance calculations for each electron acceptor. The “Output” folder contains csv files with stoichiometric information from model simulations. And the "Output_processing" folder contains scripts for reaction rate calculations and to generate plots.
- Research Organization:
- Environmental System Science Data Infrastructure for a Virtual Ecosystem
- Sponsoring Organization:
- U.S. DOE > Office of Science > Biological and Environmental Research (BER)
- OSTI ID:
- 2335801
- Country of Publication:
- United States
- Language:
- English
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ESS-DIVE CSV File Formatting Guidelines Reporting Format
ESS-DIVE File Level Metadata Reporting Format
ESS-DIVE Model Data Archiving Guidelines
Electron acceptors
FTI
FTICR
Fourier-transform ion cyclotron resonance
H
Hydrogen
N
Nitrogen
O
OM
Organic Matter
Oxygen
P
Phosphorous
S
Sulfur
Thermodynamic theory