Abstract
We present a new approach or framework to model dynamic regulatory genetic activity. The framework is using a multi-scale analysis based upon generic assumptions on the relative time scales attached to the different transitions of molecular states defining the genetic system. At micro-level such systems are regulated by the interaction of two kinds of molecular players: macro-molecules like DNA or polymerases, and smaller molecules acting as transcription factors. The proposed genetic model then represents the larger less abundant molecules with a finite discrete state space, for example describing different conformations of these molecules. This is in contrast to the representations of the transcription factors which are—like in classical reaction kinetics—represented by their particle number only. We illustrate the method by considering the genetic activity associated to certain configurations of interacting genes that are fundamental to modelling (synthetic) genetic clocks. A largely unknown question is how different molecular details incorporated via this more realistic modelling approach lead to different macroscopic regulatory genetic models which dynamical behaviour might—in general—be different for different model choices. The theory will be applied to a real synthetic clock in a second accompanying article (Kirkilionis et al., Theory Biosci, 2011).
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The study in this article was partially supported by UniNet contract 12990 funded by the European Commission in the context of the VI Framework Programme.
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Kirkilionis, M., Janus, U. & Sbano, L. Multi-scale genetic dynamic modelling I : an algorithm to compute generators. Theory Biosci. 130, 165–182 (2011). https://doi.org/10.1007/s12064-011-0125-0
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DOI: https://doi.org/10.1007/s12064-011-0125-0