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The Chemical Metaphor as Programming Paradigm for Organic Computing

In this project we develop a theoretical and practical framework to exploit the bio-chemical information processing metaphor as a programming paradigm for organic computing. By doing so, we expect to make available a technology that allows to create computational systems with the properties of their biological counterpart.

 

Contact:
Naoki Matsumaru (Phd student)
Peter Dittrich (PI),

All known life forms process information on a bio-molecular level. Examples are: signal processing in bacteria (e.g., chemotaxis), gene expression and morphogenesis, defense coordination and adaptation in the immune system, broadcasting information by the endocrine system, or finding a short route to a food source by an ant colony. This kind of information processing is known to be robust, self-organizing, adaptive, decentralized, asynchronous, fault-tolerant, and evolvable. Computation emerges out of an orchestrated interplay of many decentralized relatively simple components (molecules). This project will develop a theoretical and practical framework to exploit this bio-chemical information processing metaphor as a programming paradigm for organic computing. By doing so, we expect to make available a technology that allows to create computational systems with the properties of their biological counterpart.

A couple of approaches are already using the chemical metaphor (e.g., Gamma, MGS, amorphous computing, and reaction-diffusion processors), but in accordance with Conrad's tradeoff principle, programming a chemical computer appears to be difficult. Therefore, we will focus -- beside implementing a workbench for chemical computing -- on developing and evaluating different techniques of ``chemical programming''. Furthermore, we will develop analysis methods based on our chemical organization theory. Finally, we will evaluate the new techniques quantitatively and compare them to conventional approaches. As a demonstrator application domain we aim at sensor networks, systems biology, and virtual actors.

Publication (Results)

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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Peter Dittrich, Naoki Matsumaru (2007)
Organization-Oriented Chemical Programming
Hybrid Intelligent Systems, 2007. HIS 2007. 7th International Conference on (HIS 2007), 17-19 Sept. 2007, pages 8-23, IEEE DL
other links:
Naoki Matsumaru, Thorsten Lenser, Thomas Hinze, Peter Dittrich (2007)
Designing a chemical program using chemical organization theory
BMC Systems Biology, 1(Suppl 1):P26, 2007 - poster presentation, doi:10.1186/1752-0509-1-S1-P26
other links:
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
other links:
Naoki Matsumaru, Pietro Speroni di Fenizio, Florian Centler, Peter Dittrich (2006)
On the Evolution of Chemical Organizations
in: S. Artmann, P. Dittrich (Eds.), Proc. 7th German Workshop on Artificial Life, p. 135-146
other links:
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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(the following papers have been published before funding was available)

Peter Dittrich (2005)
Chemical Computing
in: J.-P. Banatre, J.-L. Giavitto, P. Fradet, O. Michel (Eds.), Unconventional Programming Paradigms (UPP 2004), LNCS 3566, p. 19 - 32, Springer, Berlin, 2005

Peter Dittrich (2005)
The Chemical Information Processing Metaphor as a Programming Paradigm for Organic Computing
In: Proc. of the Workshop Self-Organization and Emergence, 18th International Conference on Architecture of Computing Systems (ARCS 2005), U. Brinkschulte et al. (Eds.), VDE Verlag, Innsbruck, Austria, March 14-17, p. 95-100, 2005.
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Other Related Publications

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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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)

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
other links:
Peter Dittrich, Wolfgang Banzhaf, Hilmar Rauhe, Jens Ziegler (1998)
Macroscopic and Microscopic Computation in an Artificial Chemistry
Proceedings of the Second German Workshops on Artificial Life (GWAL'97), P. Dittrich, H. Rauhe, and W. Banzhaf (Eds.), SYS Report, No. SYS-5/98, ISSN 0941-4568, Univ. of Dortmund, p. 19-22, 1998
other links:
Jens Ziegler, Peter Dittrich, Wolfgang Banzhaf (1997)
Towards a Metabolic Robot Controller
Information Processing in Cells and Tissues, Mike Holcombe and Ray Paton (eds.), Plenum Press, New York, pp. 305-318
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Wolfgang Banzhaf, Peter Dittrich, Hilmar Rauhe (1996)
Emergent Computation by Catalytic Reactions
Nanotechnology, 7 (1996) pp. 307 - 314
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Peter Dittrich (1995)
Selbstorganisation in einem System von Binärstrings mit algorithmischen Sekundärstrukturen
Diplomarbeit im Fachbereich Informatik der Universität Dortmund, Lehrstul fuer Systemanalyse (LS XI) (Diplomathesis, Dept. of Computer Science, University of Dortmund)
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Funding

German Research Foundation (DFG) Grant Di 852/4-1, start: September 2005

Contact

Peter Dittrich
Biosystem Analysis Research Group
Department of Mathematics and Computer Science
Friedrich Schiller University Jena
D-07743 Jena
Germany