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

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.

本模型数据包关联发表于《土壤生物学与生物化学（Soil Biology and Biochemistry）》的研究论文《不同电子受体下有机质分解的热力学调控（Thermodynamic control on the decomposition of organic matter across different electron acceptors）》（Zheng等，2023；https://doi.org/10.1016/j.soilbio.2024.109364）。本研究构建了一套热力学建模框架，可灵活整合有机质（organic matter, OM）分子与电子受体，用以估算各类氧化还原反应的潜在自由能释放量，并基于微生物过渡态理论（Microbial Transition State Theory）进一步预测反应速率。本模型数据包包含热力学建模与后处理相关脚本。输入的傅里叶变换离子回旋共振（Fourier-transform ion cyclotron resonance, FTICR）数据来自一项既往实验研究（Boye等，2018），模型输出结果涵盖所有可能氧化还原反应相关的自由能预测值与化学计量系数。本数据包关联的项目GitHub仓库地址为MM_bioenergetic_modeling。本数据包包含四个文件夹：Input_FTICR、Model、Output及Output_processing，一份文件级元数据（file-level metadata, FLMD）格式的csv文件，以及一份数据字典（data dictionary, dd）格式的csv文件。请查阅Zheng_bioenergetic_modeling_flmd.csv文件，以获取本数据包内所有文件的清单及各文件的说明。Zheng_bioenergetic_modeling_dd.csv文件用于说明各csv文件的列标题。"Model"文件夹包含用于开展各电子受体能量平衡计算的脚本。"Output"文件夹包含存储了模型模拟所得化学计量信息的csv文件。而"Output_processing"文件夹包含用于反应速率计算及绘图生成的脚本。