Biomedical Engineering Reference
In-Depth Information
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ellipses correspond to the state elements (primary and complex components);
•
boxes represent the elementary processes (transformations and transportations);
•
dotted lines declare the reading connections that forward the intensive parameters
(e.g. concentrations) from the output slots of the state elements to the input slots
of the transition elements;
dashed lines define the modifying connections that forward the decreasing
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changes of the extensive characteristics (e.g. moles of components) from the
output slots of the transition elements to the input slots of the state elements;
solid lines define the modifying connections that forward the increasing changes
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of the extensive characteristics (e.g. moles of components) from the output slots
of the transition elements to the input slots of the state elements.
Description of the model means that the automatically generated. DOT file is
extended with the detailed definition of the process model. As an example, we use
a small part of the extended script, related to the decomposition of ee_NV_L_D_R
(only the characteristic parts will be shown).
The ee_NV_L_D_R complex refers to NV_L_D_R being in the inner side of the
plasma membrane, in compartment of early endosome. The respective state
element is defined by the declaration
'ee_NV_L_D_R' [
shape='ellipse'
model='component'
data='[]'
inp='[i(comp,dl,[d(ee,[0.01],nd),d(quant,[0],nd)])]'
out='[]' ]
where model of 'component' refers to the respective prototype, declared at another
state element, as
newprototype='component'
program='m(y,component,[],[i(comp,dl,Extenziv)],[o(conc,dl,Intenziv)])
:-calculate_intensive(Extenziv,Intenziv),!.'
while the calculate_intensive() predicate calls for the general clause, determining
the concentrations of the components in the compartments.
The list “inp” contains the initial values for the mass of the compartment ee
( = 0.01) and for the respective component NV_L_D_R ( = 0).
The decomposition of this complex, accompanied by “returning” of the receptor
to the plasma membrane is declared, as follows:
'r4' [shape='box'
newprototype='decomp&transport'
data='[c(par,dl,[d(kin,[0.1],nd),d(eq,[100000],nd)])]'
program='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,[w],nd),d(quant,[C3],nd)])],
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