Biology Reference
In-Depth Information
Table 1, continued
From
To
Name
Type
Delay/Speed
Variable
Weight
Type
Variable
Weight
Comment
T69
D
1.254
m22
1
N
m23
1
transription rate of lacY
m25
1
T70
C
m23/2
m23
1
T
m24
-
translation rate of lacY
T71
D
0.065
m25
1
N
m26
1
moving rate of RNA polymerase
T72
D
0.682
m26
1
N
m27
1
transription rate of lacA
T73
C
m27/5
m27
1
T
m28
-
translation rate of lacA
T74
C
m 24 × m 29
m29
0
N
m9
-
transforming rate of into a cell
m 29 + m 24 × 10
m24
2.5
T
T75
C
m 20 × m 9
m9
0
N
m30
-
decomposing rate of lactose to
galactose and glucose
m 9+ m 20 × 10
m20
5
T
m6
-
T76
C
m9/5
m9
1
T
m8
-
producing rate of allolactose from
lactose inside of a cell
T77
D
0.5
m3
1
N
m10
1
conformation
rate
of
repressor
and all llolactose
m8
1
N
m16
1
N
T79
C
m5/10
m5
0
N
m11
-
reaction rate: cAMP to AMP
T80
C
m11/10
m11
0
N
m5
-
reaction rate: AMP to cAMP
m6
5
I
T81
C
m11/10
m11
0
N
m12
-
reaction rate: AMP to ADP
T82
C
m12/10
m12
0
N
m11
-
reaction rate: ADP to AMP
m8 - producing rate of allolactose from
lactose outside of a cell
All transitions in this figure are listed in the “Name” column. The symbol D or C in “Type” column represents the type of
transition, discrete transition or continuous transition, respectively. In the “Delay/Speed” column, the firing speed of continuous
transition or the delay time of discrete transition is described according to the type of transition. The column “From”, which
represents incoming arc(s) to a transition, is divided into three sub-columns, “variable” (variable names of the places attached to
the incoming arcs), “weight” (weight of the incoming arcs), and “type” (N, T, and I represent normal, test, and inhibitory arcs,
respectively). The column “To”, which represents outgoing arcs from a transition, is divided into two sub-columns, “variable”
(variable names of the places attached to the outgoing arcs) and “weight” (weight of the outgoing arcs).
T94
C
m29/10
m29
0
T
to the underlying biological knowledge. (See the explanation in the subsection “Hydrolyzing lactose to
glucose and galactose” for the transitions T66-T73).
Functional continuous transition
A functional continuous transition is used for T 59 , which describes a reaction converting four
monomers to one tetramer (Fig. 6(a)). Recall that HPN can not have functions as parameters of the
transitions. We can not model this type of reaction with HPN, since, a reaction speed of this type is
always assigned to a transition as a function of values of the places as shown in the above. In contrast, it
is possible to model this reaction with the HDN as shown in Fig. 6(b). However, as is shown in Fig. 6(b),
the constructed HDN model is not natural or intuitive. Recall that a functional continuous transition of
HFPN allows us to assign any functions to arcs and transitions for controlling the speed/condition of
consumption, production, or firing. From Fig. 6(c), we can see that this reaction can be modeled naturally
and intuitively with a functional continuous transition. At an arc of HFPN, two kinds of parameters
“threshold” and “speed” are assigned. The continuous transition attached at the head of the arc can not
fire unless the content of the place attached at the tail of the arc exceeds the “threshold” of the arc. On
the other hand, “speed” is a value or a function, defining the amount flowing through the arc.
 
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