Simulation Based Analysis of Nanocarrier Internalization: Exciting Challenges with a New Computational Tool - Intracellular Delivery: Fundamentals and Applications - page 140

predicates, describing the state and transition elements, as well as the reading and
modifying (increasing, decreasing or overwriting) connections.
The user module contains altogether 34 p() states, 40 a() transitions, 96 x() reading
and 96 y() modifying connections. Its smaller part, generated by the above example
script is the following:

p(y,ee_NV_L_D_R,[],component,[],[i(comp,dl,[d(ee,[0.01],nd),d(quant,[0],
nd)])],[],[],[],[]).
a(y,r4,[],decomp&transport, [c(par,dl,[d(kin,[0.1],nd),d(eq,[100000],nd)])],
[i(inp_1,dl,[d(ee,[],nd),d(quant,[],nd)]),
i(inp_2,dl,[d(pm,[],nd),d(quant,[],nd)]),
i(inp_3,dl,[d(ee,[],nd),d(quant,[],nd)])],[],[],[],[]).
x(y,read,ee_NV_L_D,[],conc,write,r4,[],inp_3,dl,[],nd,[],[],[]).
y(y,read,r4,[],plus_2,addinc,ee_NV_L_D,[],comp,dl,[],nd,[],[],[]).

In the expert's module there are altogether 1 m() state functioning and 8 v()
transition clauses for the declaration of functioning of the state and transition ele-
ments, respectively. Two clauses, generated by the above example script are the
followings:

m(y,component,[],[i(comp,dl,Extenziv)],[o(conc,dl,Intenziv)]):-
ujintenziv(Extenziv,Intenziv),!.
v(y, decomp&transport,[c(par,dl,[d(kin,[Kin],nd),d(eq,[Eq],nd)])],[
i(inp_1,dl,[d(Compartment1,[Comp1],nd),d(quant,[C1],nd)]),
i(inp_2,dl,[d(Compartment2,[Comp2],nd),d(quant,[C2],nd)]),
i(inp_3,dl,[d(Compartment1,[Comp1],nd),d(quant,[C3],nd)])],[
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.

During simulation, the general purpose DCM kernel consults the expert's and
user's files, and organizes the simulation of the model. The prescribed output is
automatically saved in a file that can be shown in runtime or afterwards.

3.3 Example for the Simulated Results

First, we will show an example for the input data and output results of a typical
simulation. The state elements and the respective initial concentrations are sum-
marized in Table 2 . In Table 2 , the columns refer to the various compartments with
their reference measures (which express the estimated ratios of the compartments).
The components are listed in the rows, and the blue colored cells represent the pos-
sible compartmental components. As indicated in Table 2 , there are only five non-
zero initial concentrations, as follows:

ext_NV_L_D