Kirkilionis, Markus, 1962-, Janus, Ulrich and Sbano, Luca. (2011) Multi-scale genetic dynamic modelling I : an algorithm to compute generators. Theory in Biosciences, Vol.130 (No.3). pp. 165-182. ISSN 1431-7613

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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).

Item Type:	Journal Article
Subjects:	Q Science > QA Mathematics Q Science > QR Microbiology
Divisions:	Faculty of Science > Mathematics
Library of Congress Subject Headings (LCSH):	Genetic algorithms, Genetic programming (Computer science), Multiscale modeling, Markov processes, Escherichia coli, DNA microarrays
Journal or Publication Title:	Theory in Biosciences
Publisher:	Springer
ISSN:	1431-7613
Date:	September 2011
Volume:	Vol.130
Number:	No.3
Page Range:	pp. 165-182
Identification Number:	10.1007/s12064-011-0125-0
Status:	Peer Reviewed
Publication Status:	Published
Access rights to Published version:	Restricted or Subscription Access
Description:	Special Issue: ECCS'09 From Molecules to Living Systems
Funder:	European Commission (EC)
Grant number:	12990 (EC)
URI:	http://wrap.warwick.ac.uk/id/eprint/38392

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