scholarly journals How to Program Artificial Chemistries

2003 ◽  
pp. 20-30
Author(s):  
Jens Busch ◽  
Wolfgang Banzhaf
Keyword(s):  
Artificial Chemistries

Wet Artificial Chemistries

2015 ◽  
pp. 405-438 ◽  
Author(s):  
Wolfgang Banzhaf ◽  
Lidia Yamamoto
Keyword(s):  
Artificial Chemistries

Modular combinations of Artificial Chemistries

2018 ◽  
Author(s):  
Penelope Faulkner Rainford ◽  
Angelika Sebald ◽  
Susan Stepney
Keyword(s):  
Artificial Chemistries

Artificial Chemistries

2015 ◽  
Author(s):  
Wolfgang Banzhaf ◽  
Lidia Yamamoto
Keyword(s):  
Artificial Chemistries

Evolving Reaction-Diffusion Ecosystems with Self-Assembling Structures in Thin Films

1998 ◽  
Vol 4 (1) ◽  
pp. 25-40 ◽  
Author(s):  
Jens Breyer ◽  
Jörg Ackermann ◽  
John McCaskill
Keyword(s):  
Self Assembly ◽  
Flexible Structures ◽  
Reaction Diffusion ◽  
In Vitro Evolution ◽  
Spatially Resolved ◽  
Self Assembling ◽  
Artificial Dna ◽  
Additional Stabilization ◽  
Artificial Chemistries

Recently, new types of coupled isothermal polynucleotide amplification reactions for the investigation of in vitro evolution have been established that are based on the multi-enzyme 3SR reaction. Microstructured thin-film open bioreactors have been constructed in our laboratory to run these reactions spatially resolved in flow experiments. Artificial DNA/RNA chemistries close to the in vitro biochemistry of these systems have been developed, which we have studied in computer simulations in configurable hardware (NGEN). These artificial chemistries are described on the level of individual polynucleotide molecules, each with a defined sequence, and their complexes. The key feature of spatial pattern formation provides a weak stabilization of cooperative catalytic properties of the evolving molecules. Of great interest is the step to include extended self-assembly processes of flexible structures—allowing the additional stabilization of cooperation through semipermeable, flexible, self-organizing membrane boundaries. We show how programmable matter simulations of experimentally relevant molecular in vitro evolution can be extended to include the influence of self-assembling flexible membranes.

Artificial Chemistries – Towards Constructive Dynamical Systems

2004 ◽  
Vol 97-98 ◽  
pp. 43-50 ◽  
Author(s):  
Wolfgang Banzhaf
Keyword(s):  
Dynamical Systems ◽  
Artificial Chemistry ◽  
Artificial Chemistries

In this contribution we consider constructive dynamical systems, taking one particular Artificial Chemistry as an example. We argue that constructive dynamical systems are in fact widespread in combinatorial spaces of Artificial Chemistries.

Modeling Molecular Computing Systems by an Artificial Chemistry—Its Expressive Power and Application

2007 ◽  
Vol 13 (3) ◽  
pp. 223-247 ◽  
Author(s):  
Kazuto Tominaga ◽  
Tooru Watanabe ◽  
Keiji Kobayashi ◽  
Masaki Nakamura ◽  
Koji Kishi ◽  
...  
Keyword(s):  
Dna Computing ◽  
Expressive Power ◽  
Molecular Computing ◽  
Levels Of Abstraction ◽  
Computing Systems ◽  
Artificial Chemistry ◽  
Biochemical Systems ◽  
String Pattern ◽  
Artificial Chemistries ◽  
Elementary Chemical

Artificial chemistries are mainly used to construct virtual systems that are expected to show behavior similar to living systems. In this study, we explore possibilities of applying an artificial chemistry to modeling natural biochemical systems—or, to be specific, molecular computing systems—and show that it may be a useful modeling tool for molecular computation. We previously proposed an artificial chemistry based on string pattern matching and recombination. This article first demonstrates that this artificial chemistry is computationally universal if it has only rules that have one reactant or two reactants. We think this is a good property of an artificial chemistry that models molecular computing, because natural elementary chemical reactions, on which molecular computing is based, are mostly unimolecular or bimolecular. Then we give two illustrative example models for DNA computing in our artificial chemistry: one is for the type of computation called the Adleman-Lipton paradigm, and the other is for a DNA implementation of a finite automaton. Through the construction of these models we observe preferred properties of the artificial chemistry for modeling molecular computing, such as having no spatial structure and being flexible in choosing levels of abstraction.

Computing with Artificial Chemistries

2015 ◽  
pp. 345-372
Author(s):  
Wolfgang Banzhaf ◽  
Lidia Yamamoto
Keyword(s):  
Artificial Chemistries

Basic Concepts of Artificial Chemistries

2015 ◽  
pp. 11-44
Author(s):  
Wolfgang Banzhaf ◽  
Lidia Yamamoto
Keyword(s):  
Basic Concepts ◽  
Artificial Chemistries

Sub-Symbolic Artificial Chemistries

2017 ◽  
pp. 287-322 ◽  
Author(s):  
Penelope Faulkner ◽  
Mihail Krastev ◽  
Angelika Sebald ◽  
Susan Stepney
Keyword(s):  
Artificial Chemistries

Evolving Control Metabolisms for a Robot

2001 ◽  
Vol 7 (2) ◽  
pp. 171-190 ◽  
Author(s):  
Jens Ziegler ◽  
Wolfgang Banzhaf
Keyword(s):  
Information Processing ◽  
Metabolic Pathways ◽  
Robot Navigation ◽  
New Method ◽  
Control Programs ◽  
Processing Pathways ◽  
Efficient Information ◽  
Small Robot ◽  
Artificial Chemistries ◽  
Selection Of

This article demonstrates a new method of programming artificial chemistries. It uses the emerging capabilities of the system's dynamics for information-processing purposes. By evolution of metabolisms that act as control programs for a small robot one achieves the adaptation of the internal metabolic pathways as well as the selection of the most relevant available exteroceptors. The underlying artificial chemistry evolves efficient information-processing pathways with most benefit for the desired task, robot navigation. The results show certain relations to such biological systems as motile bacteria.

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