Thermodynamic modeling based on the lambda theory

Release notes

• Click the Code icon (in green) to download the latest version designed for general purpose.
• Code for the Frontiers paper: A repository for the publication entitled Representing Organic Matter Thermodynamics in Biogeochemical Reactions via Substrate-Explicit Modeling (https://doi.org/10.3389/fmicb.2020.531756). In this paper, we proposed a new concept of biogeochemical modeling (termed substrate-explicit modeling) that enables parameterizing organic matter (OM)-specific oxidative degradation pathways and reaction rates based on the thermodynamic properties of OM pools.

Links

• Substrate-explicit Modeling Tutorial (KBase narrative): It demonstates how to apply a thermodynamic theory (known as λ theory) to convert molecular formulas of compounds (derived from FTICR-MS peaks using Formularity) into stoichiometric and kinetic forms of biogeochemical reactions and how to use the resulting kinetic equations to simulate dynamic conversion of compounds in batch and continuous stirred tank reactors.
• KBase app to build stoichiometric reaction models from chemical formulas (KBase link, GitHub)
• KBase app to perform λ analysis (KBase link, GitHub)
• KBase app to simulate biogeochemical models in a batch reactor (KBase link, GitHub)
• KBase app to simulate biogeochemical models in a continuous stirred tank reactor (CSTR) (KBase link, GitHub)

System requirements

R > 3.5.0

Run the demo dataset

################## User input ##################
outfile <- "demo_input_out.txt"
fticr_data <- read_csv("demo_input.csv")
################################################

Citation

Song H-S, Stegen JC, Graham EB, Lee J-Y, Garayburu-Caruso VA, Nelson WC, Chen X, Moulton JD and Scheibe TD (2020) Representing Organic Matter Thermodynamics in Biogeochemical Reactions via Substrate-Explicit Modeling. Front. Microbiol. 11:531756. doi: 10.3389/fmicb.2020.531756

Contacts

Hyun-Seob Song ([email protected]); Joon-Yong Lee ([email protected])