equilibrate {CHNOSZ} | R Documentation |
Calculate equilibrium chemical activities of species from the affinities of formation of the species at unit activity.
equilibrate(aout, balance=NULL, loga.balance=NULL, ispecies=1:length(aout$values), normalize=FALSE, as.residue=FALSE, method=c("boltzmann", "reaction")) equil.boltzmann(Astar, n.balance, loga.balance) equil.reaction(Astar, n.balance, loga.balance)
aout |
list, output from |
balance |
character or numeric, how to balance the transformations |
ispecies |
numeric, which species to include |
normalize |
logical, normalize the molar formulas of species by the balancing coefficients? |
as.residue |
logical, report results for the normalized formulas? |
Astar |
numeric, affinities of formation reactions excluding species contribution |
n.balance |
numeric, number of moles of conserved component in the formation reactions of the species of interest |
loga.balance |
numeric, logarithm of total activity of balanced quantity |
method |
character, equilibration method to use |
equilibrate
calculates the chemical activities of species in metastable equilibrium, for constant temperature, pressure and chemical activities of basis species, using specified balancing constraints on reactions between species.
It takes as input aout
, the output from affinity
, which may be calculated from a multidimensional grid of conditions.
The equilibrium chemical activities of species are calculated using either the equil.reaction
or equil.boltzmann
functions, the latter only if the balance is on one mole of species.
aout
contains the chemical affinities of formation reactions of each species of interest.
equilibrate
needs to be provided constraints on how to balance the reactions representing transformations between the species.
balance
indicates the balancing constraints, according to the following scheme:
NULL: autoselect
name of basis species: balance on this basis species
length: balance on length of proteins
1: balance on one mole of species
numeric vector: user-defined constraints
The default value of NULL for balance
indicates to use the coefficients on the basis species that is present (i.e. with non-zero coefficients) in all formation reactions, or if that fails, to set the balance to 1.
However, if all the species (as listed in code aout$species
) are proteins (have an underscore character in their names), the default value of NULL for balance
indicates to use length as the balance.
NOTE: The summation of activities assumes an ideal system, so ‘molality’ is equivalent to ‘activity’ here.
loga.balance
gives the logarithm of the total activity of balance
(which is total activity of species for 1 or total activity of amino acid residue-equivalents for length).
If loga.balance
is missing, its value is taken from the activities of species listed in aout
; this default is usually the desired operation.
normalize
if TRUE indicates to normalize the molar formulas of species by the balance coefficients.
This operation is intended for systems of proteins, whose conventional formulas are much larger than the basis speices.
The normalization also applies to the balancing coefficients, which as a result consist of 1s.
After normalization and equilibration, the equilibrium activities are then re-scaled (for the original formulas of the species), unless as.residue
is TRUE.
equil.boltzmann
is used to calculate the equilibrium activities if balance
is 1 (or when normalize
or as.residue
is TRUE), otherwise equil.reaction
is called.
The default behavior can be overriden by specifying either boltzmann or reaction in method
.
Using equil.reaction
may be needed for systems with huge (negative or positive) affinities, where equil.boltzmann
produces a NaN result.
ispecies
can be supplied to identify a subset of the species to include in the calculation.
equil.reaction
and equil.boltzmann
each return a list with dimensions and length equal to those of Astar
, giving the log10
of the equilibrium activities of the species of interest.
equilibrate
returns a list, containing first the values in aout
, to which are appended m.balance
(the balancing coefficients if normalize
is TRUE, a vector of 1s otherwise), n.balance
(the balancing coefficients if normalize
is FALSE, a vector of 1s otherwise), loga.balance
, Astar
, and loga.equil
(the calculated equilibrium activities of the species).
The input values to equil.reaction
and equil.boltzmann
are in a list, Astar
, all elements of the list having the same dimensions; they can be vectors, matrices, or higher-dimensionsal arrays.
Each list element contains the chemical affinities of the formation reactions of one of the species of interest (in dimensionless base-10 units, i.e. A/2.303RT), calculated at unit activity of the species of interest.
The equilibrium activities (in base-10 log units) of the species of interest returned by either function satisfy the constraints that 1) the final chemical affinities of the formation reactions of the species are all equal and 2) the total activity of the conserved component is equal to (loga.balance
).
The first constraint does not impose a complete equilibrium, where the affinities of the formation reactions are all equal to zero, but allows for a metastable equilibrium, where the affinities of the formation reactions are equal to each other.
In equil.reaction
(the algorithm described in Dick, 2008 and the only one available prior to CHNOSZ_0.8), the calculations of relative abundances of species are based on a solving a system of equations representing the two constraints stated above.
A close approximation of the solution is found using uniroot
.
Prior to CHNOSZ_0.9-9, the values in the Astar
were used to generate initial guesses of the logarithms of activities of species; values of loga.balance
that were hugely different from these guesses could generate errors from uniroot
such as "f() values at end points not of opposite sign".
Now (from version 0.9-9), a more flexible method for generating guesses is in place.
In equil.boltzmann
(algorithm available beginning with CHNOSZ_0.8), the chemical activities of species are calculated using the Boltzmann distribution.
This calculation is faster than the algorithm of equil.reaction
, but is limited to systems where the transformations are all balanced on one mole of species.
If equil.boltzmann
is called with balance
other than 1, it stops with an error.
Dick, J. M. (2008) Calculation of the relative metastabilities of proteins using the CHNOSZ software package. Geochem. Trans. 9:10. https://doi.org/10.1186/1467-4866-9-10
diagram
has examples of using equilibrate
to make equilibrium activity diagrams. revisit
can be used to perform further analysis of the equilibrium activities.
palply
is used by both equil.reaction
and equil.boltzmann
to parallelize intensive parts of the calculations.
## equilibrium in a simple system: ## ionization of carbonic acid basis("CHNOS+") species(c("CO2", "HCO3-", "CO3-2")) # set unit activity of the species (0 = log10(1)) species(1:3, 0) # calculate Astar (for unit activity) res <- 100 Astar <- affinity(pH=c(0, 14, res))$values # the logarithms of activity for a total activity # of the balanced quantity (C or CO2) equal to 0.001 loga.boltz <- equil.boltzmann(Astar, c(1, 1, 1), 0.001) # calculated another way loga.react <- equil.reaction(Astar, c(1, 1, 1), 0.001) # probably close enough for most purposes stopifnot(all.equal(loga.boltz, loga.react)) # the first ionization constant (pKa) ipKa <- which.min(abs(loga.boltz[[1]] - loga.boltz[[2]])) pKa.equil <- seq(0, 14, length.out=res)[ipKa] # calculate logK directly logK <- subcrt(c("CO2","H2O","HCO3-","H+"), c(-1, -1, 1, 1), T=25)$out$logK # we could decrease tolerance here by increasing res stopifnot(all.equal(pKa.equil, -logK, tolerance=1e-2))