Chemical Organization Theory

Welcome to

Chemical Organization Theory

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.

Publication

The Basic Theory

Peter Dittrich, Pietro Speroni di Fenizio (2007)
Chemical Organization Theory
Bull. Math. Biol., 69(4):119-1231, 2007, 10.1007/s11538-006-9130-8
abstract, old version: Anstract (arXiv 2005), old preprint (2005, short version) (supplement available on request)

Peter Dittrich, Pietro Speroni di Fenizio (2007)
Chemical Organization Theory
In: M. Al-Rubeai, M. Fussenegger (Eds.); Cell Engineering, Volume 5: Systems Biology, Springer (in print)

Peter Dittrich, Pietro Speroni di Fenizio (2005)
Chemical Organization Theory: Towards a Theory of Constructive Dynamical Systems
arXiv:q-bio.MN/0501016
Anstract, paper (pdf) (supplement available on request)

Pietro Speroni di Fenizio and Peter Dittrich (2002)
Artificial Chemistry's Global Dynamics. Movement in the Lattice of Organisation
The Journal of Three Dimensional Images, 16(4):160-163.
paper.pdf

Pietro Speroni di Fenizio, Peter Dittrich, Jens Ziegler and Wolfgang Banzhaf (2001)
Towards a Theory of Organizations
German Workshop on Artificial Life (GWAL 2000), Bayreuth, April 5-7, 2000 (in print)
preprint (ps), recent version (doc)

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
Journal home, preprint (pdf)

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
Workshop homepage, paper (pdf)

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)
preprint (pdf)

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

Application to Planetary Athmosphere Photo Chemistries

Florian Centler, Peter Dittrich (2006)
Chemical organizations in atmospheric photochemistries: a new method to analyze chemical reaction networks
Planet Space Sci. , doi:10.1016/j.pss.2006.08.002 (in print, corrected proof available online, 2006)
Journal home

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.
Conference homepage, preprint (pdf)

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 (in print)
Journal home, preprint (pdf)

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
Workshop homepage, paper (pdf)

Funding

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

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