chemical computing peter dittrich bio systems analysis department. of mathematics and computer...
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Chemical Computing
Peter Dittrich
Bio Systems AnalysisDepartment. of Mathematics and Computer Science
Friedrich-Schiller-University Jena
Friedrich-Schiller-Universität Jena Jena Centre for Bioinformatics
BMBF Grant No. 0312704A
UPP2004, Mt. S. Michel, 15.09.04 P. Dittrich - FSU & JCB Jena 4
Bio Systems Analysis Group
Jena Centre for Bioinformatics
CS, Jena University
UPP2004, Mt. S. Michel, 15.09.04 P. Dittrich - FSU & JCB Jena 5
Chemical Computing
1. Computing helps Chemistry
2. Chemistry helps Computing
UPP2004, Mt. S. Michel, 15.09.04 P. Dittrich - FSU & JCB Jena 6
What is Chemistry?
• Deals with– Substances composed of molecules– Reactions that transform substances, such
that the composition of molecules changes– Dynamics
UPP2004, Mt. S. Michel, 15.09.04 P. Dittrich - FSU & JCB Jena 7
Where does Chemical Computing Occur in Nature?
UPP2004, Mt. S. Michel, 15.09.04 P. Dittrich - FSU & JCB Jena 8
Principles of Chemical Computing
• Pattern recognition
• Formation of (spatial) structures
• Change of conformation
• Optical activity
• Chemical kinetics
• Energy minimization
UPP2004, Mt. S. Michel, 15.09.04 P. Dittrich - FSU & JCB Jena 9
Chemistry Helps Computing
1. Real chemical computing
2. Artificial chemical computing
UPP2004, Mt. S. Michel, 15.09.04 P. Dittrich - FSU & JCB Jena 10
Examples Where the Chemical Metaphor is Used in Computing
• Real Chemical Computing(Liberman 1972, 1979), (Conrad 1972) (Seelig & Rössler 1972) and others
– Enzymes– DNA/RNA-Comp – Optical– Reaction-Diffusion– Programmed Self-Assembly
UPP2004, Mt. S. Michel, 15.09.04 P. Dittrich - FSU & JCB Jena 11
Examples Where the Chemical Metaphor is Used in Computing
Artificial Chemical Computing• Abstract Molecular Machine (Liang)• Rewriting systems
(e.g., GAMMA, CHAM, P-Systgems, ARMS, …)• Hormone systems in distributed robot control systems (e.g.
COG)• Chemical-like systems to control the behavior and emotions in
artificial agents (e.g. Creatures or PSI (D. Dörner)• Control of morpho-genetic systems (control of artificial gene
expression and morphogenesis)• Control of growth of artificial neural networks (e.g., Astor/
Adami)• Control of amorphous computers• Communication among neurons in an ANN where neurons
have spatial coordinates (e.g., neural gas by P. Husbands)
UPP2004, Mt. S. Michel, 15.09.04 P. Dittrich - FSU & JCB Jena 12
Example for Microscopic Chemical Computing
DNA Computing (Adleman)
UPP2004, Mt. S. Michel, 15.09.04 P. Dittrich - FSU & JCB Jena 13
Example for Macroscopic Chemical Computing Chemical Neuron
[see Hjelmfelt, Weinberger, Ross 1991]
UPP2004, Mt. S. Michel, 15.09.04 P. Dittrich - FSU & JCB Jena 14
Example for Macroscopic Chemical
Computing: Simple Hyper-cyclic Associative Memory
[Dittrich 1995]
Hypercycle of replicating catalysts
Query
(Input)
Answer
(Output)
UPP2004, Mt. S. Michel, 15.09.04 P. Dittrich - FSU & JCB Jena 16
Fine Grained Parallelism
Usually:• Distributed• Robust • Asynchronous• Emergent • Self-organizing
→ soft computing, organic computing, computational intelligence
UPP2004, Mt. S. Michel, 15.09.04 P. Dittrich - FSU & JCB Jena 19
“Invisible Networks”
• A network larger than the neural network of the human brain:
• M = {2, 3, …, 10E30}
• A + B + X -> A + B + C with
C = A/B if A mod B = 0, C = C otherwise.
UPP2004, Mt. S. Michel, 15.09.04 P. Dittrich - FSU & JCB Jena 20
Self-modification
• Self-modification(s. higher-order & generative programming)
• Strange loop
• Dualism of – structure and function – data and program– Tape and machine
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Challenges
• Efficiency
• Scalability
• Programmability
• Adaptability
UPP2004, Mt. S. Michel, 15.09.04 P. Dittrich - FSU & JCB Jena 24
Wolfgang BanzhafUniversity of Newfoundland
Evolving Artificial Chemistries by Genetic Programming
UPP2004, Mt. S. Michel, 15.09.04 P. Dittrich - FSU & JCB Jena 25
Andrew AdamatzkyUniversity of the West of England
Programming Reaction- Diffusion Computers
UPP2004, Mt. S. Michel, 15.09.04 P. Dittrich - FSU & JCB Jena 26
Tetsuya AsaiGraduate School of Informaton Science and Technology, Sapporo
Reaction Diffusion Processors
UPP2004, Mt. S. Michel, 15.09.04 P. Dittrich - FSU & JCB Jena 27
Klaus-Peter ZaunerUniversity of Southampton
From Prescriptive Programming of Solid-State Devices to Orchestrated Self-Organization of Informed Matter
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Winfried KurthUniversity of Cottbus
Relational Growth Grammars
UPP2004, Mt. S. Michel, 15.09.04 P. Dittrich - FSU & JCB Jena 29
Yann RadenacIRISA, Rennes
High-order Chemical Programming Style
UPP2004, Mt. S. Michel, 15.09.04 P. Dittrich - FSU & JCB Jena 30
Questions for discussion
• How to program a chemical computer (whatever it is)?• How do chemical computing paradigms scale up?• Can the chemical metaphor lead to new computational
systems with abilities superior to conventional approaches?
• Or even to systems that can not be realized by conventional approaches?
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Growing Artificial NNs
[J. S. Astor, Christophs Adami: A Developmental Model for the Evolution of Artificial Neural Networks., Artificial Life 6(3), 189-218, 2000 http://norgev.alife.org/]
[Astor/Adami]
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