I'm just getting to grips with using ode function and have used the
examples and vignettes to produce a small model of a one-pool,
michaelis-menten, enzyme kinetic reaction. The rate of flux of substrate
into pool A is constant (fluxoa) however the rate of flux out of pool A
is controlled by the HMM equation (v = Vmax/ ( 1 + (Km / Concentration A
)) ). This function works fine and gives correct answers for the
size of the pool of quantity of substrate in pool A at all times,
however if possible I'd like to also extract the values of interim
variables at each time t. Could anyone give me a clue of how to include
the value of CA at each time t, along with QA in the results?
Thanks
Jim
R code
==================
parameters <- c(vola = 17.3629, vmax = 4.7, mmk = 0.5435, fluxoa =
2.389)
state <- c(QA=9.437)
MM <- function(t, state, parameters) {
with(as.list(c(state, parameters)),{
## concentration of substrate in pool A, quantity
## divided by the volume of the solvent pool
CA <- QA/vola
## output of substrate from pool A
fluxao <- vmax / (1 + (mmk/CA))
## rate of change of quantity of substrate
## in pool A
dA <- fluxoa - fluxao
## return the rate of change
list(dA)
})
}
times <- seq(0, 100, by = 5)
library(deSolve)
out1 <- ode(y = state, times = times, func = MM, parms = parameters)
head(out1)
--
Dr. Jim Maas
University of East Anglia
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