The Chemical Metaphor as Programming Paradigm for Organic Computing

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
Journal home, preprint (pdf)

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
preprint (pdf), DOI: 10.1109/ICHIS.2007.4344021

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
paper (pdf), biomedcentral, poster presentation, doi:10.1186/1752-0509-1-S1-P26

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)

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
Workshop homepage, paper (pdf)

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)

(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
preprint (pdf),

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.
preprint (pdf), Proceedings

Other Related Publication

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)

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)

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)

Peter Dittrich, Wolfgang Banzhaf, Hilmar Rauhe, Jens Ziegler (1998)
Macroscopic and Microscopic Computation in an Artificial Chemistry
In: 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
abstract, full paper

Jens Ziegler, Peter Dittrich und Wolfgang Banzhaf (1997)
Towards a Metabolic Robot Controller
In: Information Processing in Cells and Tissues, Mike Holcombe and Ray Paton (eds.), Plenum Press, New York, pp. 305-318
abstract, full paper, IPCAT homepage

Wolfgang Banzhaf, Peter Dittrich and Hilmar Rauhe (1996)
Emergent Computation by Catalytic Reactions
Nanotechnology, 7 (1996) pp. 307 - 314
abstract, full paper (preprint): (256k)

Peter Dittrich and Wolfgang Banzhaf(1995)
The chemical computation metaphor and robot control
In Third European Conf. Artificial Life (ECAL'95) - Abstracts, page 45, Granada, Spain, June 4-6, 1995.

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)

abstract, full work:, da.pdf


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


Peter Dittrich
Bio Systems Analysis
Department of Mathematics and Computer Science
Friedrich-Schiller-University Jena
D-07743 Jena

"Nov 6 2007" Peter Dittrich