By Roland Glowinski, Bernard Larrouturou, Roger Temam
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Each A-B-pair can decide to react, either according to rule x1 which reduces in the following manner: A | A | B | B → C1 | A | 0 | B → . . If alternatively rule x2 happened to be applied, one could observe: A|A|B|B → 0 | A | C2 | B → ... All channels are associated with a stochastic rate, that is either introduced by public declaration or the new operator. Such rates deﬁne exponential distributions that characterise the communication activity of the channel (see [33,34]). Communications over channels with infinite rate are executed instantaneously, as are conditionals and channel creations.
Molecular actors are connected by public channels in Fig. 14 that are declared and assigned stochastic rates in Fig. 15. The channel rnap is used both for Rnap docking to PRM and PR , and is assigned the rate Ka RNAP. Regulatory proteins establish connections to operator regions over the channel pro with Gene Regulation in the Pi Calculus PRM vacant rnap high rnap low inhibited PR vacant rnap inhibited OR1 , OR3 vacant cro rep blocked OR2 vacant cro rep high rep low blocked 39 Rep, Cro Rnap unbound unbound bound bound monomer Fig.
At the same time, interactions between Rep at OR2 and Rnap at PRM stimulate transcription of the gene cI, which allows for the production of new Rep. growth. The environmental signal upon induction leads to a massive destruction of Rep proteins. PR then becomes activated automatically, while transcription from PRM ceases. These are consequences of the network controlling transcription initiation. Repression of promoters by steric hindrance: The regulatory proteins Rep and Cro can bind to three neighboring operator regions OR1 , OR2 , and OR3 .