Define the basis species of a chemical system.
character, names or formulas of species, or numeric, indices of species
character, physical states or names of buffers
numeric, logarithms of activities or fugacities
logical, delete the current basis species definition?
The basis species represent the possible range of chemical compositions for all the species of interest. Any valid set of basis species used here must meet two conditions: 1) the number of basis species is the same as the number of chemical elements (including charge) in those species and 2) the square matrix representing the elemental stoichiometries of the basis species has a real inverse.
To create a basis definition, call
basis with the names or formulas of the basis species in the first argument.
Alternatively, the first argument may consist of numeric values indicating the species indices (rownumbers in
thermo$obigt), but a mixture of character and numeric values will generate an error.
The special names pH, pe and Eh can be included in the
species argument; they get translated into the names of the proton (H+) and electron (e-) as appropriate.
The physical states or logarithms of activities of species in the basis definition can be changed by calling
basis with the formulas of species that are in the basis set, or their species indices.
If either of the second or third arguments to
basis is of type character, it refers to the name of a state (if present in
thermo$obigt$state) or to the name of a chemical activity
buffer (if present in
If either of these arguments is numeric it specifies the logarithms of activities (or fugacities for gases) of the basis species.
In case pH, pe or Eh is named, the logarithm of activity of the basis species is converted from these values.
For example, a value of 7 for pH is stored as a logarithm of activity of -7.
basis is called with NULL values of both
logact, the new set of species, if they are a valid basis set, completely replaces any existing basis definition.
If this occurs, any existing species definition (created by the
species function) is deleted.
delete set to TRUE or
species set to "" to clear the basis definition.
This also deletes the
species list, if any.
If the value of
basis is one of the keywords in the following table, the corresponding set of basis species is loaded, and their activities are given preset values.
This approach is used by many of the examples in the package.
The basis species identified by these keywords are aqueous except for \H2O (liq), \O2 (gas) and \Fe2O3 (hematite).
||\CO2, \H2O, \NH3, \H2S, \O2|
||\CO2, \H2O, \NH3, \H2S, \O2, \Hplus|
||\CO2, \H2O, \NH3, \H2S, \eminus, \Hplus|
||\CO2, \H2O, \NH3, \H3PO4, \H2S, \eminus, \Hplus|
||\Mgplus2, \CO2, \H2O, \NH3, \H3PO4, \H2S, \eminus, \Hplus|
||\Fe2O3, \CO2, \H2O, \NH3, \H2S, \O2|
||\Fe2O3, \CO2, \H2O, \NH3, \H2S, \O2, \Hplus|
||cysteine, glutamic acid, glutamine, \H2O, \O2|
||cysteine, glutamic acid, glutamine, \H2O, \O2|
||cysteine, glutamic acid, glutamine, \H2O, \O2, \Hplus|
The logarithms of activities of amino acids in the QEC4 basis are -4 (i.e., basis II in Dick, 2016); those in QEC and QEC+ are set to approximate concentrations in human plasma (see Dick, 2017).
Returns the value of
thermo$basis after any modifications; or, if
delete is TRUE, its value before deletion (invisibly).
Dick, J. M. (2016) Proteomic indicators of oxidation and hydration state in colorectal cancer. PeerJ 4:e2238. https://doi.org/10.7717/peerj.2238
Dick, J. M. (2017) Chemical composition and the potential for proteomic transformation in cancer, hypoxia, and hyperosmotic stress. PeerJ 5:e3421 https://doi.org/10.7717/peerj.3421
info to query the thermodynamic database in order to find what species are available.
makeup is used by
basis to generate the stoichiometric matrix from chemical formulas.
swap.basis is used to change the chemical compounds (species formulas) used in the basis definition while keeping the chemical potentials of the elements unaltered.
species for setting up the formation reactions from basis species.
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## define basis species # one, two and three element examples basis("O2") basis(c("H2O", "O2")) basis(c("H2O", "O2", "H+")) ## clear the basis species basis("") ## Not run: ## marked dontrun because they produce errors # fewer species than elements basis(c("H2O", "H+")) # more species than elements basis(c("H2O", "O2", "H2", "H+")) # non-independent species basis(c("CO2", "H2O", "HCl", "Cl-", "H+")) ## End(Not run) ## specify activities and states basis(c("H2O", "O2", "CO2"), c(-2, -78, -3), c("liq", "aq", "aq")) # change logarithms of activities/fugacities basis(c("H2O", "O2"), c(0, -80)) # change state of CO2 basis("CO2", "gas")
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