[SOSlib-devel] variable compartment bug: example

[Stefan M. <ste...@oe...>]

andrew:

for the SBML system
	S1 in C
	S1->junk : k * [S1]
	dC/dt = 1

the right math is:
	dS1/dt = k * [S1] / C(0) * C
	dC/dt = 1
with initial cond:
	S1(0) = [S1](0) * C(0)
	C(0)

notation:
	S1 ... substance
	[S1] ... conc

the "proposed solution" (who proposed this?) has the right units,
but is wrong otherwise... :)

as rainer and me already discussed, everything would be much clearer,
if the kinetic law included the compartment explicitly:
	S1 in C
	S1->junk : C * r * [S1]
	dC/dt = 1

with:
	r ... the "real" chemical rate constant.

rainer:

chemists always knew that rate constants are not constant with respect to pH, 
T, ... as a physicist i have to be fair! :)

to conclude: the math is not really tricky.
odes for substances are better suited to handle both multiple and variable 
compartments. of course, we have to take care of many implementation 
details...

cheers,
stefan.