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Multi-scale genetic dynamic modelling I : an algorithm to compute generators
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Kirkilionis, Markus, 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. doi:10.1007/s12064-011-0125-0 ISSN 1431-7613.
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Official URL: http://dx.doi.org/10.1007/s12064-011-0125-0
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 | ||||
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Subjects: | Q Science > QA Mathematics Q Science > QR Microbiology |
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Divisions: | Faculty of Science, Engineering and Medicine > 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 | ||||
Official Date: | September 2011 | ||||
Dates: |
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Volume: | Vol.130 | ||||
Number: | No.3 | ||||
Page Range: | pp. 165-182 | ||||
DOI: | 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 |
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Funder: | European Commission (EC) | ||||
Grant number: | 12990 (EC) |
Data sourced from Thomson Reuters' Web of Knowledge
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