Endy:Computational modeling of demand/Species and reactions

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Transcription species

  • RNAP [P]
  • Promoter [D]
  • RNAP-Promoterclosed [PDc]
  • RNAP-Promoteropen [PDo]
  • RNAP-Promoterinit [PDi]
  • RNAPelong [Pe]
  • mRNA [M]

It should be possible to ignore some of these species as they don't affect the dynamics of the transcription model. TABASCO appears to skip the closed and open RNAP-Promoter species. Lumping the intermediate species together in this way makes some sense as I am unlikely to have access to rate constants for their formation and dissociation. The other advantage to this lumping is that transcription initiation is then analogous to a Michaelis-Menten enzyme reaction.

For a first iteration, I will consider the following species -

  • [P] - stable
  • [D] - stable
  • [PDi] abbreviated to [PD] - stable
  • [Pelong] - stable
  • [M] - unstable

Translation species

  • Ribosome [R]
  • RBS [M]
  • RBS-Ribosomeinit [RM]
  • Ribosomeelong [Relong]
  • Protein [O]


Polymerases (P), DNA (D) and Ribosomes (R) are all synthesized at a zeroth order rate. The synthesis rate was set by choosing a desired total number of the particular species per cell. The synthesis was set such that in the abscence of reactions other than dilution due to the growth, the species would reach that desired steady state level. The synthesis rate for species i was -
rsyn,i = Css,i

Where Css,i is the desired steady state number of species i per cell and μ is the rate constant for dilution due to growth.


  1. Record, M. T., Reznikoff, W. S., Craig, M. L., McQuade, K. L., and Schlax, P. J. Escherichia coli and Salmonella: Cellular and Molecular Biology, 2nd ed., vol. 1. ASM Press, 1996, ch. Escherichia coli RNA Polymerase (Eσ70), Promoters, and the Kinetics of the Steps of Transcription Initiation, pp. 792–821.