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WP 1 : Cell Biology , Autopoiesis and Biological Design Patterns D 1 . 4 : Mathematical Models of Gene Expression Computing
| Content Provider | Semantic Scholar |
|---|---|
| Author | Dini, Paolo Egri-Nagy, Attila Nehaniv, Chrystopher L. Schilstra, Maria J. Leeuwen, Ingeborg Van Munro, A. Laín, Sonia Lain, Bullet S. Hollick, Jonathan James Campbell, John S. Staples, O. D. Higgins, Matt Aoubala, M. McCarthy, Alex Appleyard, Vera Murray, Kelly E. Baker, Loyd Thompson, Aaron C. Mathers, Jeremiah Holland, S. J. Stark, Michael J. R. Pass, Greg Woods, Jorden Lane, D. P. Westwood, Nicholas James |
| Abstract | Project funded by the European Community under the " Information Society Technology " Programme. Short Description: This report further develops the framework for linking biological behaviour to software behaviour specification, at an abstract level, and reports on the latest exciting experimental findings on the p53-mdm2 regulatory pathway. We argue that symbolic dynamics and algebraic automata theory are essential elements of this link. We discuss these two fields in some detail and show their relevance to the p53-mdm2 system. In particular, we show that it exhibits homoclinic behaviour, and is therefore amenable to a horseshoe map-type of analysis through symbolic dynamics, and that even at a fairly coarse discretisation the automaton derived from it harbours a simple non-abelian group in its holonomy decomposition. Dependencies Achievements* Done: Aligned our epistemological perspective on interaction computing with the meta-theoretical framework developed in D12.10. Advanced experimental understanding of p53-mdm2 system. Greatly extended the computational power of the SgpDec semigroup decomposition computational algebra program. Discovered a simple non-abelian group in the automaton derived from the p53-mdm2 system. Identified oscillatory behaviour of p53-mdm2 system as homoclinic. Strengthened the plausibility of the theoretical framework for interaction computing based on category theory transformations and adjunctions, postulating the link between structure and behaviour to be related to the link between a Krohn-Rhodes and a symbolic dynamics view of finite-state automata, respectively. Not done: Did not have time to study symbolic dynamics to a sufficient depth to reach concrete conclusion about its links with algebraic automata theory. Did not, therefore, attempt to define a mathematical model for interaction computing. Although the plausibility of the approach has been strengthened, a few more years of work are likely to be needed before conclusive mathematical results in this area are reached. • Attila Egri-Nagy and Chrystopher L. Nehaniv. SgpDec software package for hierarchical coordinatization of groups and semigroups, implemented in the GAP computer algebra system, Version 0. |
| File Format | PDF HTM / HTML |
| Alternate Webpage(s) | http://www.lse.ac.uk/media@lse/research/OPAALS/D01.4_Mathematical_Models_of_Gene_Expression_Computing.pdf |
| Language | English |
| Access Restriction | Open |
| Content Type | Text |
| Resource Type | Article |
