Constructing Biological Pathway Models with Hybrid Functional Petri Nets - Biological Petri Nets - page 99

Table 2
Places having non-zero initial values in Fig. 7

Name Variable Initial value Comment

CAP m4 5 concentration of CAP

cAMP m5 100 concentration of cAMP

glucose m6 50 concentration of glucose

AMP m11 200 concentration of AMP

ADP m12 200 concentration of ADP

LacZ m20 5 concentration of LacX

LacY m24 2.5 concentration of LacY

LacA m28 1 concentration of LacA

lactose outside of a cell m29 50 lactose outside of a cell

Fig. 5. Negative regulation mechanism: This figure contains the HFPN model of Fig. 4.

Initial values of places

The places which have initial values greater than zero are listed in Table 3.

Transcription control switch

We will sketch how places, transitions and arcs are determined in the process of modeling.
Figure 2 shows the structure of the lac operon.
In the absence of lactose, a repressor is bound to the operator. The repressor prevents RNA polymerase
from starting RNA synthesis at the promoter. On the other hand, in the presence of lactose and the absence