U.S. Department of EnergyOffice of Scientific and Technical Information
Substrate-explicit Modeling Tutorial
Abstract
This tutorial Narrative demonstrates how to apply thermodynamic theory, also known as lambda theory, to convert molecular formulas of compounds (derived from FTICR-MS peaks using Formulatiry and R codes) 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. It will address under what conditions respiration rates are driven by thermodynamics, and how respiration rates respond to the variations in parameters and input variables and how to interpret the results.
- Authors:
-
;
- University of Nebraska-Lincoln
- Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
- Publication Date:
- Research Org.:
- Pacific Northwest National Laboratory (PNNL), Richland, WA (United States) University of Nebraska-Lincoln, Lincoln, NE (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- Subject:
- 96 KNOWLEDGE MANAGEMENT AND PRESERVATION; 54 ENVIRONMENTAL SCIENCES
- Keywords:
- FTICR-MS, batch reactors, continuous stirred tank reactors (CSTR)
- OSTI Identifier:
- 1755438
- DOI:
- https://doi.org/10.25982/65526.69/1755438
Citation Formats
Song, Hyun-Seob, and Lee, Joon-Yong. Substrate-explicit Modeling Tutorial. United States: N. p., 2020.
Web. doi:10.25982/65526.69/1755438.
Song, Hyun-Seob, & Lee, Joon-Yong. Substrate-explicit Modeling Tutorial. United States. doi:https://doi.org/10.25982/65526.69/1755438
Song, Hyun-Seob, and Lee, Joon-Yong. 2020.
"Substrate-explicit Modeling Tutorial". United States. doi:https://doi.org/10.25982/65526.69/1755438. https://www.osti.gov/servlets/purl/1755438. Pub date:Wed Sep 30 00:00:00 EDT 2020
@article{osti_1755438,
title = {Substrate-explicit Modeling Tutorial},
author = {Song, Hyun-Seob and Lee, Joon-Yong},
abstractNote = {This tutorial Narrative demonstrates how to apply thermodynamic theory, also known as lambda theory, to convert molecular formulas of compounds (derived from FTICR-MS peaks using Formulatiry and R codes) 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. It will address under what conditions respiration rates are driven by thermodynamics, and how respiration rates respond to the variations in parameters and input variables and how to interpret the results.},
doi = {10.25982/65526.69/1755438},
journal = {},
number = ,
volume = ,
place = {United States},
year = {Wed Sep 30 00:00:00 EDT 2020},
month = {Wed Sep 30 00:00:00 EDT 2020}
}
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Works referenced in this record:
KBase: The United States Department of Energy Systems Biology Knowledgebase
journal, July 2018
- Arkin, Adam P.; Cottingham, Robert W.; Henry, Christopher S.
- Nature Biotechnology, Vol. 36, Issue 7