2000 , Volume 5, Special issue, p.87-99

A generalized chemical kinetic simulation method based on a block description of function dynamics of arbitrarily complex biological systems in terms of elementary processes is proposed. Biochemical reactions are considered as particular cases of elementary processes. An algorithm for constructing models of a complex molecular genetic system from individual blocks describing elementary processes is proposed. The generalized method was used to develop a dynamic model of [Java Applet] phage ontogenesis in the E. coli cell. The model [Java Applet] and [Java Applet] modes of replication; gene transcription; and mRNA translation as well as functions of [Java Applet], [Java Applet], [Java Applet], [Java Applet], [Java Applet], [Java Applet] promoters of constitutive terminator [Java Applet]; Q-regulated [Java Applet]-independent terminator [Java Applet], N-regulated, [Java Applet]-dependent terminators [Java Applet], [Java Applet], [Java Applet], [Java Applet], [Java Applet]; Nut sites; and functions of proteins exo, xis, beta, gamma, N, cI ([Java Applet] repressor), cII, cIII, cro (tof, antirepressor), O, P, Q, S, and R, which control all the major stages of the genetic program of phage development in the cell. The proposed algorithm for constructing models from submodels of "genes" according to a specified "genetic map" allows the function dynamics of virtually any genetic variant that might be constructed from [Java Applet] phage genes to be described.