CHNOSZ (version 0.8)

transfer: Mass Transfer Calculations

Description

Simulate a mass transfer process such as mineral weathering or sequential formation of proteins.

Usage

transfer(nsteps = 500, dmode = "coupled", devmax = 0.1, plot = NULL,
    ibalance = 1, fmode = "one", buffers = NULL, alphamax = -2,
    alphastart = -10, T = 25, P = "Psat", do.title = TRUE, beta = 0)
  draw.transfer(t, ylim = c(-10, 1), ylimbasis = c(-12, -2), 
    logprogress = FALSE)
  feldspar(which = "closed", do.plot = FALSE)
  apc(which = "open", basis = "CO2", do.plot = FALSE)

Arguments

nsteps

numeric, maximum number of steps to run simulation.

dmode

character, destruction mode.

devmax

numeric, maximum deviation of logarithm of activity of basis species in any step.

plot

numeric, which basis species to use as plotting and coupling variables.

ibalance

numeric, which basis species is the primary conservant.

fmode

character, formation mode.

buffers

list, basis species to be buffered during the simulation.

alphamax

numeric, maximum value of the destruction exponent.

alphastart

numeric, initial value of the destruction exponent.

T

numeric, temperature.

P

numeric, pressure.

do.title

logical, plot a title?

beta

numeric, alpha + beta = buffer transfer exponent.

t

list, the output of transfer.

ylim

numeric, y-axis limits.

ylimbasis

numeric, y-axis limits for the logarithms of activities of basis species.

logprogress

logical, put reaction progress on a logarithmic scale?

which

character, type of system to simulate.

do.plot

logical, summarize the results using draw.transfer?

basis

character, type of basis definition to use.

Value

• transfer returns a list containing information about the conditions at each step: basis, data frame of the logarithms of activities of basis species, species, data frame of the logarithms of activities (moles for solids) of species, alphas, numeric vector of the values of the destruction exponent, dmodes, character vector of the destruction mode, istables, numeric vector of the index of the most stable product, myaffs, list of the affinities of the formation reactions of species, didwork, logical vector indicating whether the steps succeeded or failed.

Details

The transfer function calculates a reaction path that is generated by incrementally reacting a starting composition into an aqueous system. Before calling this function, set up a system and define the starting material using species.

At each step, a small amount ($10^{\alpha}$) of the starting composition is provisionally reacted and a relatively more stable product may be formed. The amount of product formed is such that the activity of the primary conservant (the basis species given in ibalance) is not changed. The changes in the activities of the other basis species are calculated, and the process is iterated until nsteps is reached or the value of $\alpha$ is driven to a very low value (logpresent, which is a constant set in the code to $-50$).

If at a given step the most stable product is different from the one before, either the previous products are ignored (for cmode equal to none, i.e. an open system) or the reaction of the starting material is coupled to that of the existing products (for cmode equal to coupled, i.e. a closed system) through a secondary conservation constraint. The basis species that are candidates for the secondary conservation are identified in iplot.

The initial value of alpha is given by alphastart. After successful steps, the function increases the value of alpha by $1$, and after failed steps to decrease the value of alpha by $1$. One condition that can lead to a failed step is that the logarithm of activity of any basis species changes by more than devmax. Therefore, throughout the simulation the value of $\alpha$ dynamically adjusts to the devmax set by the user.

buffers is a list with elements basis indicating the basis species to be buffered and buffer naming the buffers to use for that basis species. If this argument is given, at each step the activity of the basis species in the buffer is calculated. The difference between this activity and the current activity of the basis species in the system is then multiplied by 10 raised to the ( alpha + beta ) and this quantity added to the current activity of the basis species in the system. As a result, the value of beta modifies the strength of the buffer relative to the incremental reaction progress.

draw.transfer is used to plot the logarithms of activities of basis species, and logarithms of activities (moles for solid species, molalities for aqueous species) of the minerals or proteins as a function of reaction progress, or logarithm of reaction progress if logprogress is set to TRUE. The y-limits of the plots can be set using ylim and ylimbasis.

feldspar and apc encode examples for feldspar weathering and the reaction among proteins in the anaphase-promoting complex of yeast. Equivalent code for two selected examples is shown below.

References

Helgeson, H. C., Garrels, R. M. and Mackenzie, F. T., 1969. Evaluation of irreversible reactions in geochemical processes involving minerals and aqueous solutions. II. Applications. Geochim. Cosmochim. Acta, 33, 455-481.

Steinmann, P., Lichtner, P. C. and Shotyk, W., 1994. Reaction path approach to mineral weathering reactions. Clay Clay Min., 42, 197-206.

Examples

data(thermo)

  ## react potassium feldspar in a closed system
  ## after Steinmann et al., 1994
  ## and Helgeson et al., 1969
  basis(c('Al+3','H4SiO4','K+','H2O','H+','O2'),c(0,-6,-6,0,0,0))
  species(c('k-feldspar','muscovite','pyrophyllite','kaolinite','gibbsite'))
  a <- affinity(H4SiO4=c(-6,-2),'K+'=c(-3,8))
  diagram(a)
  basis('pH',4)
  species(1:5,c(-4,rep(-999,4)))
  t <- transfer(550,dmode='coupled',plot=c(2,3),devmax=0.2)
  # plot the output from transfer
  draw.transfer(t)
  # reset the plot layout
  layout(matrix(1))
  # note, the same calculation can be performed using
  # feldspar("closed")

  ## react APC2 from Saccharomyces cerevisiae
  ## to other proteins in the anaphase-promoting complex
  ## (closed system)
  basis(c("CO2","H2O","NH3","H2","H2S"),c(-10,0,-4,-10,-7))
  basis("H2","aq")
  species(c("APC1","APC2","APC5","CDC16","APC10","SWM1"),"YEAST")
  a <- affinity(CO2=c(-10,0),H2=c(-10,0))
  diagram(a,residue=TRUE,as.residue=TRUE)
  species(1:nrow(species()),-999)
  species("APC2_YEAST",0)
  t <- transfer(510,ibalance="PBB",plot=c(1,4),dmode="coupled",devmax=0.15)
  # this calculation is also available with
  # apc("closed")