Model associated with: "Thermodynamic control on the decomposition of organic matter across different electron acceptors"

Zheng, Jianqiu; Scheibe, Timothy D.; Boye, Kristin; Song, Hyun-Seob

doi:10.15485/2335801

Title: Model associated with: "Thermodynamic control on the decomposition of organic matter across different electron acceptors"

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Abstract

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 modelmore »« less

Authors:

;

Pacific Northwest National Laboratory; Pacific Northwest National Laboratory
Pacific Northwest National Laboratory
SLAC National Accelerator Laboratory
University of Nebraska-Lincoln

Publication Date:: Mon Mar 11 04:00:00 UTC 2024

Research Org.:: Environmental System Science Data Infrastructure for a Virtual Ecosystem

Sponsoring Org.:: U.S. DOE > Office of Science > Biological and Environmental Research (BER)

Subject:: 54 ENVIRONMENTAL SCIENCES; Biogeochemistry; C; CUE; Carbon; Carbon Use Efficiency; EARTH SCIENCE > TERRESTRIAL HYDROSPHERE > WATER QUALITY/WATER CHEMISTRY > NUTRIENTS > NITROGEN; EARTH SCIENCE > TERRESTRIAL HYDROSPHERE > WATER QUALITY/WATER CHEMISTRY > NUTRIENTS > NITROGEN COMPOUNDS; EARTH SCIENCE > TERRESTRIAL HYDROSPHERE > WATER QUALITY/WATER CHEMISTRY > NUTRIENTS > PHOSPHOROUS; EARTH SCIENCE > TERRESTRIAL HYDROSPHERE > WATER QUALITY/WATER CHEMISTRY > WATER CHARACTERISTICS > NITROGEN COMPOUNDS; 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

OSTI Identifier:: 2335801

DOI:: https://doi.org/10.15485/2335801

Citation Formats


                    Zheng, Jianqiu, Scheibe, Timothy D., Boye, Kristin, and Song, Hyun-Seob. Model associated with: "Thermodynamic control on the decomposition of organic matter across different electron acceptors".  United States: N. p., 2024. 
        Web.  doi:10.15485/2335801.

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                    Zheng, Jianqiu, Scheibe, Timothy D., Boye, Kristin, & Song, Hyun-Seob. Model associated with: "Thermodynamic control on the decomposition of organic matter across different electron acceptors".  United States.  doi:https://doi.org/10.15485/2335801

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                    Zheng, Jianqiu, Scheibe, Timothy D., Boye, Kristin, and Song, Hyun-Seob. 2024.  
"Model associated with: "Thermodynamic control on the decomposition of organic matter across different electron acceptors"".  United States.  doi:https://doi.org/10.15485/2335801.  https://www.osti.gov/servlets/purl/2335801. Pub date:Mon Mar 11 04:00:00 UTC 2024

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@article{osti_2335801,

  title        = {Model associated with: "Thermodynamic control on the decomposition of organic matter across different electron acceptors"},

  author       = {Zheng, Jianqiu and Scheibe, Timothy D. and Boye, Kristin and Song, Hyun-Seob},

  abstractNote = {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.},

  doi          = {10.15485/2335801},

  journal      = {},

  number       = ,

  volume       = ,

  place        = {United States},

  year         = {Mon Mar 11 04:00:00 UTC 2024},

  month        = {Mon Mar 11 04:00:00 UTC 2024}

}

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DOI: https://doi.org/10.15485/2335801

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