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Chemical Organization Theory

Chemical organization theory offers a new way to anlyze complex dynamical networks. It aims espically at constructive chemical reaction systems, but can also be applied to chemical-like systems found in domains like popluation dynamics and infection biology.

 

Contact:

Pietro Speroni di Fenizio  (Phd student)
Florian Centler  (Phd student)
Peter Dittrich  (PI)

In order to understand complex dynamical production systems (such as chemical systems) where new components can appear and disappear, we are developing a theory of (chemical) organizations, which is inspired by works by Fontana and Buss. The theory allows to view production networks from a different, more global perspective and allows to decompose the network into a hierarchy. The central element of such a decomposition is a so called organization, which we define simply as a closed and self-maintaining set of components.

Currently we (a) extent the theory by dynamical components and (b) apply it to biological dynamical networks in order to demonstrate its feasibility.

Software

Publications

The Basic Theory

Peter Dittrich, Pietro Speroni di Fenizio (2007)
Chemical Organization Theory
Bull. Math. Biol., 69(4):1199-1231, 2007
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Peter Dittrich, Pietro Speroni di Fenizio (2007)
Chemical Organization Theory
In: M. Al-Rubeai, M. Fussenegger (Eds.); Cell Engineering, Volume 5: Systems Biology, p. 361-393, Springer
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Peter Dittrich, Pietro Speroni di Fenizio (2005)
Chemical Organization Theory: Towards a Theory of Constructive Dynamical Systems
arXiv:q-bio.MN/0501016 (supplement available on request)
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  Pietro Speroni di Fenizio, Peter Dittrich (2002)
Artificial Chemistry's Global Dynamics. Movement in the Lattice of Organisation
The Journal of Three Dimensional Images, 16(4):160-163.

Pietro Speroni di Fenizio, Peter Dittrich, Jens Ziegler, Wolfgang Banzhaf (2001)
Towards a Theory of Organizations
German Workshop on Artificial Life (GWAL 2000), Bayreuth, April 5-7, 2000 (in print)
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Application to Immunsystem-HIV Dynamics

Naoki Matsumaru, Florian Centler, Pietro Speroni di Fenizio, Peter Dittrich (2006)
Chemical organization theory applied to virus dynamics
it - Information Technology, 48(3), 154-160
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Naoki Matsumaru, Pietro Speroni di Fenizio, Florian Centler, Peter Dittrich (2005)
A Case Study of Chemical Organization Theory Applied to Virus Dynamics
in: J. T. Kim (Ed.), Systems Biology Workshop at ECAL 2005, Workshop Proceedings CD-ROM, 5-9 Septmebner 2005, Kent, UK
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Application to Biochemical Networks (E. Coli)

Florian Centler, Pietro Speroni di Fenizio, Naoki Matsumaru, Peter Dittrich (2006)
Chemical organizations in the central sugar metabolism of Escherichia Coli
In: Modeling and Simulation in Science Engineering and Technology, Post-proceedings of ECMTB 2005 (in print)

Christoph Kaleta, Florian Centler, Peter Dittrich (2006)
Analyzing Molecular Reaction Networks: From Pathways to Chemical Organizations
Mol. Biotechnol., 34(2): 117-123


Application to Planetary Athmosphere Photo Chemistries

Florian Centler, Peter Dittrich (2007)
Chemical organizations in atmospheric photochemistries: a new method to analyze chemical reaction networks
Planet. Space Sci. , 55(4): 413-428, 2007
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Application to Chemical Computing

(Results from our organic computing project CHEMORG).

Naoki Matsumaru, Florian Centler, Peter Dittrich (2005)
Chemical Organization Theory as a Theoretical Base for Chemical Computing
in: C. Teuscher, A. Adamatzky (Eds.), Workshop on Unconventional Computing, p. 71-82, Luniver Press, Beckington.
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Naoki Matsumaru, Florian Centler, Pietro Speroni di Fenizio, Peter Dittrich (2007)
Chemical Organization Theory as a Theoretical Base for Chemical Computing
International Journal of Unconventional Computing, 3(4), 285-309
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Naoki Matsumaru, Peter Dittrich (2006)
Organization-oriented chemical programming for the organic design of distributed computing systems
Proc. of BIONETICS'06, Cavalese, December 11-13, IEEE
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Funding

Basic funding has been provided by the BMBF (Federal Ministry of Education and Research of Germany), grant 0312704A, as part of the Jena Centre for Bioinformatics. The work on chemical computing has been funded by the DFG (German Research Foundation).