Biomedical Engineering Reference
In-Depth Information
[o(minus_1,dl,[d(Compartment1,[DComp1],nd),d(quant,[DM1],nd)]),
o(plus_1,dl,[d(Compartment2,[DComp2],nd),d(quant,[DM2],nd)]),
o(plus_2,dl,[d(Compartment1,[DComp1],nd),d(quant,[DM3],nd)])]):-
g(dt,DT), DComp1 is 0.0, DComp2 is 0.0,
Rate is Kin*(C1-(1/Eq)*C2*C3)*Comp1*DT,
DM1 is (−1)*Rate, DM2 is Rate, DM3 is Rate.' ]
It is a transition prototype with two (kinetic and equilibrium) parameters, as well
as three input and three output slots, corresponding to the formulation of the “1-2”
kinetic (mass action) expression. The three input slots correspond to the reading of
concentration of the components, while the three output slots refer to the decrease
of ee_NV_L_D_R, as well as to the increase of ee_NV_L_D and pm_R. The
method makes possible also the change of the compartments' mass, but right now
it is neglected (DComp1 = DComp2 = 0).
The rate of the process prototype is calculated by the bold italics signed part of
the program, declared in the given Prolog clause. These brief program parts can be
edited freely through a general interface. Accordingly, the open program code can
be adapted to the various special hybrid and multiscale problems, easily.
An example for a reading connection is the following:
'ee_NV_L_D_R'→'r4' [
style='dotted'
sendop='read'
sendslot='conc'
receiveop='write'
receiveslot='inp_1' ]
This declares reading of ee_NV_L_D_R concentration for the above discussed
elementary process. The shown, significant definitions determine the sending slot
and operator, as well as the receiving slot and operator, respectively. When running,
the connection will carry the actual sign from the sending to the receiving element.
As another example the modifying connection
'r4'→'ee_NV_L_D' [
style='solid'
sendop='read'
sendslot='plus_2'
receiveop='add'
receiveslot='comp' ]
declares increasing of ee_NV_L_D concentration caused by the given transition.
The shown significant definitions determine the respective sending and receiving
slots and operators. When running, the connection will carry the actual molar
change from the sending to the receiving slots.
Having started from this temporary input file, the general DCM process
simulator first interprets the script and prepares the GNU-Prolog declarations of the
expert and user modules. In the user's module, there are four types (partitions) of
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