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Encyclopedia of Complexity and Systems Science pp 326–344Cite as

Artificial Chemistry

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Definition of the Subject

Artificial chemistries are chemical‐like systems or abstract models of chemical processes. They are studied in order to illuminate andunderstand fundamental principles of chemical systems as well as to exploit the chemical metaphor as a design principle for information processingsystems in fields like chemical computing or nonlinear optimization.

An artificial chemistry (AC) is usuallya formal (and, more seldom, a physical) system that consists of objects called molecules, which interact according to rules calledreactions. Compared to conventional chemical models, artificial chemistries are more abstract in the sense that there is usually not a one-to-onemapping between the molecules (and reactions) of the artificial chemistry to real molecules (and reactions). An artificial chemistry aims at capturing thelogic of chemistry rather than trying to explain a particular chemical system. More formally, an artificial chemistry can be...

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Notes

  1. 1.

    For general reaction systems, this definition has to be refined. When Acontains species that are part of the inflow, like a and b inFig. 1, but which are not produced in a catalytic way, we might want them to be part of anautocatalytic set. Assume, for example, the set \( { A = \{ a , b, aa, ba \} }\) from Fig. 1, where aa catalyzes theproduction of aa and ba, while using up “substrate” a and b, which are not catalytically produced.

Abbreviations

Molecular species:

A molecular species is an abstract class denoting an ensemble of identical molecules. Equivalently the terms “species”, “compound”, or just “molecule” are used; in some specific context also the terms “substrate” or “metabolite”.

Molecule:

A molecule is a concrete instance of a molecular species. Molecules are those entities of an artificial chemistry that react. Note that sometimes the term “molecule” is used equivalently to molecular species.

Reaction network:

A set of molecular species together with a set of reaction rules. Formally, a reaction network is equivalent to a Petri network. A reaction network describes the stoichiometric structure of a reaction system.

Order of a reaction:

The order of a reaction is the sum of the exponents of concentrations in the kinetic rate law (if given). Note that an order can be fractional. If only the stoichiometric coefficients of the reaction rule are given (Eq. (1)), the order is the sum of the coefficients of the left-hand side species. When assuming mass‐action kinetics, both definitions are equivalent.

Autocatalytic set:

A (self‐maintaining) set where each molecule is produced catalytically by molecules from that set. Note that an autocatalytic may produce molecules not present in that set.

Closure:

A set of molecules A is closed, if no combination of molecules from A can react to form a molecule outside A. Note that the term “closure” has been also used to denote the catalytical closure of an autocatalytic set.

Self‐maintaining:

A set of molecules is called self‐maintaining, if it is able to maintain all its constituents. In a purely autocatalytic system under flow condition, this means that every molecule can be catalytically produced by at least one reaction among molecule from the set.

(Chemical) Organization:

A closed and self‐maintaining set of molecules.

Multiset:

A multiset is like a set but where elements can appear more than once; that is, each element has a multiplicity, e. g., \( { \{a, a, b, c, c, c \} } \).

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  1. Department of Mathematics and Computer Science, Friedrich Schiller University Jena, Jena, Germany

    Peter Dittrich

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    Robert A. Meyers Ph. D. (Editor-in-Chief) (Editor-in-Chief)

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Dittrich, P. (2009). Artificial Chemistry . In: Meyers, R. (eds) Encyclopedia of Complexity and Systems Science. Springer, New York, NY. https://doi.org/10.1007/978-0-387-30440-3_23

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