Modeling and measuring biogeochemical reactions: System consistency, data needs, and rate formulations

Gour Tsyh Yeh, William D. Burgos, John M. Zachara

Research output: Contribution to journalArticle

21 Citations (Scopus)

Abstract

This paper intends to lay-out a foundation of protocols for planning and analyzing biogeochemical experiments. It presents critical theoretical issues that must be considered for proper application of reaction-based biogeochemical models. The selection of chemical components is not unique and a decomposition of the reaction matrix should be used for formal selection. The decomposition reduces the set of ordinary differential equations governing the production-consumption of chemical species into three subsets of equations: mass action; kinetic-variable; and mass conservation. The consistency of mass conservation equations must be assessed with experimental data before kinetic modeling is initiated. Assumptions regarding equilibrium reactions should also be assessed. For a system with M chemical species involved in N reactions with NI linearly-independent reactions and NE linearly-independent equilibrium reactions, the minimum number of chemical species concentration vs. time curves that must be measured to evaluate the kinetic suite of reactions using a reaction-based model will be (NI-NE). However, for a partial assessment of system consistency, at least one more species must be measured [i.e. (NI-NE+1)]. For a complete assessment of system consistency, (NI-NE+NC) additional species would have to be measured, where NC is the number of chemical components. Reaction rates for kinetic reactions that are linearly independent of other kinetic reactions can be determined based on only one profile of a kinetic-variable concentration vs. time for each kinetic reaction. Reaction rates for parallel kinetic reactions that are linearly dependent on each other cannot be uniquely segregated when they result in production of the same species, however, they must be included for simulation purposes. Kinetic reactions that are linearly dependent only on equilibrium reactions are redundant and do not have to be modeled. The bioreduction of ferric oxide is used as an example to functionally demonstrate these points, and shows that Henri-Michaelis-Benton-Monod kinetics should be applied with care to coupled abiotic and biotic systems.

Original languageEnglish (US)
Pages (from-to)219-237
Number of pages19
JournalAdvances in Environmental Research
Volume5
Issue number3
DOIs
StatePublished - Aug 1 2001

Fingerprint

Reaction kinetics
reaction kinetics
Kinetics
kinetics
modeling
Reaction rates
Conservation
reaction rate
Decomposition
decomposition
Ordinary differential equations
rate
measuring
need
Planning
chemical
oxide
Oxides
matrix
Experiments

All Science Journal Classification (ASJC) codes

  • Environmental Science(all)

Cite this

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title = "Modeling and measuring biogeochemical reactions: System consistency, data needs, and rate formulations",
abstract = "This paper intends to lay-out a foundation of protocols for planning and analyzing biogeochemical experiments. It presents critical theoretical issues that must be considered for proper application of reaction-based biogeochemical models. The selection of chemical components is not unique and a decomposition of the reaction matrix should be used for formal selection. The decomposition reduces the set of ordinary differential equations governing the production-consumption of chemical species into three subsets of equations: mass action; kinetic-variable; and mass conservation. The consistency of mass conservation equations must be assessed with experimental data before kinetic modeling is initiated. Assumptions regarding equilibrium reactions should also be assessed. For a system with M chemical species involved in N reactions with NI linearly-independent reactions and NE linearly-independent equilibrium reactions, the minimum number of chemical species concentration vs. time curves that must be measured to evaluate the kinetic suite of reactions using a reaction-based model will be (NI-NE). However, for a partial assessment of system consistency, at least one more species must be measured [i.e. (NI-NE+1)]. For a complete assessment of system consistency, (NI-NE+NC) additional species would have to be measured, where NC is the number of chemical components. Reaction rates for kinetic reactions that are linearly independent of other kinetic reactions can be determined based on only one profile of a kinetic-variable concentration vs. time for each kinetic reaction. Reaction rates for parallel kinetic reactions that are linearly dependent on each other cannot be uniquely segregated when they result in production of the same species, however, they must be included for simulation purposes. Kinetic reactions that are linearly dependent only on equilibrium reactions are redundant and do not have to be modeled. The bioreduction of ferric oxide is used as an example to functionally demonstrate these points, and shows that Henri-Michaelis-Benton-Monod kinetics should be applied with care to coupled abiotic and biotic systems.",
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Modeling and measuring biogeochemical reactions : System consistency, data needs, and rate formulations. / Yeh, Gour Tsyh; Burgos, William D.; Zachara, John M.

In: Advances in Environmental Research, Vol. 5, No. 3, 01.08.2001, p. 219-237.

Research output: Contribution to journalArticle

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