Artificial chemistry
Encyclopedia
An artificial chemistry is a computer model used to simulate various types of system
s. Artificial chemistry is in some ways similar to a chemical reaction, hence the name. The field of artificial chemistry originated in artificial life
but has shown to be a versatile method with applications in many fields such as chemistry
, economics
, sociology
and linguistics
.
, in particular from strong artificial life. The idea behind this field was that if one wanted to build something alive, it had to be done by a combination of non-living entities. For instance, a cell is itself alive, and yet is a combination of non-living molecules. Artificial chemistry enlists, among others, researchers that believe in an extreme bottom-up approach to artificial life.
then took up the work developing the AlChemy model. The model was presented at the second International Conference of Artificial Life. In his first papers he presented the concept of organization
, as a set of molecules that is algebraically closed and self-maintaining.
Two main schools of artificial chemistries have been in Japan and Germany. In Japan the main researchers have been Takashi Ikegami, Hideaki Suzuki and Yasuhiro Suzuki. In Germany
, it was Wolfgang Banzhaf, who, together with his students Peter Dittrich and Jens Ziegler, developed various
artificial chemistry models. Their 2001 paper 'Artificial Chemistries - A Review' became a standard in the field. Jens Ziegler, as part of his PhD thesis, proved that an artificial chemistry could be used to control a small Khepera robot. Among other models, Peter Dittrich developed the Seceder model which is able to explain group formation in society through some simple rules. Since then he became a professor in Jena
where he investigates artificial chemistries as a way to define a general theory of constructive dynamical systems.
and biology
.
A further motivation to study artificial chemistries is the interest in constructive dynamical systems. Yasuhiro Suzuki has modeled various systems such as membrane systems, signaling pathways (P53), ecosystems, and enzyme systems by using his method, abstract rewriting system on multisets (ARMS).
System
System is a set of interacting or interdependent components forming an integrated whole....
s. Artificial chemistry is in some ways similar to a chemical reaction, hence the name. The field of artificial chemistry originated in artificial life
Artificial life
Artificial life is a field of study and an associated art form which examine systems related to life, its processes, and its evolution through simulations using computer models, robotics, and biochemistry. The discipline was named by Christopher Langton, an American computer scientist, in 1986...
but has shown to be a versatile method with applications in many fields such as chemistry
Chemistry
Chemistry is the science of matter, especially its chemical reactions, but also its composition, structure and properties. Chemistry is concerned with atoms and their interactions with other atoms, and particularly with the properties of chemical bonds....
, economics
Economics
Economics is the social science that analyzes the production, distribution, and consumption of goods and services. The term economics comes from the Ancient Greek from + , hence "rules of the house"...
, sociology
Sociology
Sociology is the study of society. It is a social science—a term with which it is sometimes synonymous—which uses various methods of empirical investigation and critical analysis to develop a body of knowledge about human social activity...
and linguistics
Linguistics
Linguistics is the scientific study of human language. Linguistics can be broadly broken into three categories or subfields of study: language form, language meaning, and language in context....
.
Formal definition
An artificial chemistry is defined in general as a triple (S,R,A). In some cases it is sufficient to define it as a tuple (S,I).- S is the set of possible molecules S={s1...,sn}, where n is the number of elements in the set, possibly infinite.
- R is a set of n-aryArityIn logic, mathematics, and computer science, the arity of a function or operation is the number of arguments or operands that the function takes. The arity of a relation is the dimension of the domain in the corresponding Cartesian product...
operationOperation (mathematics)The general operation as explained on this page should not be confused with the more specific operators on vector spaces. For a notion in elementary mathematics, see arithmetic operation....
s on the molecules in S, the reaction rules R={r1...,rn}. Each rule ri is written like a chemical reaction a+b+c->a*+b*+c*. Note here that ri are operators, as opposed to +. - A is an algorithmAlgorithmIn mathematics and computer science, an algorithm is an effective method expressed as a finite list of well-defined instructions for calculating a function. Algorithms are used for calculation, data processing, and automated reasoning...
describing how to apply the rules R to a subsetSubsetIn mathematics, especially in set theory, a set A is a subset of a set B if A is "contained" inside B. A and B may coincide. The relationship of one set being a subset of another is called inclusion or sometimes containment...
P
S. - I are the interaction rules of the molecules in S.
Types of artificial chemistries
- depending on the space of possible molecules
- finite
- infinite
- depending on the type of reactions
- catalytic systems
- reactive systems
- depending on the space topology
- well stirred reactor
- topologically arranged (1,2,3 dimensional)
Important concepts
- Organizations: An organization is a set of molecules that is closed and self-maintaining. As such, it is a set that does not create anything outside itself, and such that any molecule inside the set can be generated within the set.
- Closed sets
- Self-maintaining sets
- Hasse diagram of organizations
History of artificial chemistries
Artificial chemistries emerged as a sub-field of artificial lifeArtificial life
Artificial life is a field of study and an associated art form which examine systems related to life, its processes, and its evolution through simulations using computer models, robotics, and biochemistry. The discipline was named by Christopher Langton, an American computer scientist, in 1986...
, in particular from strong artificial life. The idea behind this field was that if one wanted to build something alive, it had to be done by a combination of non-living entities. For instance, a cell is itself alive, and yet is a combination of non-living molecules. Artificial chemistry enlists, among others, researchers that believe in an extreme bottom-up approach to artificial life.
Important contributors
The first reference about artificial Chemistries come from a Technical paper written by John McCaskill. Walter Fontana working with Leo BussLeo Buss
Leo W. Buss is a Professor in Yale University's departments of geology, geophysics, and ecology and evolutionary biology.-Life:He graduated from Johns Hopkins University with a B.A., M.A., and Ph.D in 1979....
then took up the work developing the AlChemy model. The model was presented at the second International Conference of Artificial Life. In his first papers he presented the concept of organization
Organization
An organization is a social group which distributes tasks for a collective goal. The word itself is derived from the Greek word organon, itself derived from the better-known word ergon - as we know `organ` - and it means a compartment for a particular job.There are a variety of legal types of...
, as a set of molecules that is algebraically closed and self-maintaining.
Two main schools of artificial chemistries have been in Japan and Germany. In Japan the main researchers have been Takashi Ikegami, Hideaki Suzuki and Yasuhiro Suzuki. In Germany
Germany
Germany , officially the Federal Republic of Germany , is a federal parliamentary republic in Europe. The country consists of 16 states while the capital and largest city is Berlin. Germany covers an area of 357,021 km2 and has a largely temperate seasonal climate...
, it was Wolfgang Banzhaf, who, together with his students Peter Dittrich and Jens Ziegler, developed various
artificial chemistry models. Their 2001 paper 'Artificial Chemistries - A Review' became a standard in the field. Jens Ziegler, as part of his PhD thesis, proved that an artificial chemistry could be used to control a small Khepera robot. Among other models, Peter Dittrich developed the Seceder model which is able to explain group formation in society through some simple rules. Since then he became a professor in Jena
Jena
Jena is a university city in central Germany on the river Saale. It has a population of approx. 103,000 and is the second largest city in the federal state of Thuringia, after Erfurt.-History:Jena was first mentioned in an 1182 document...
where he investigates artificial chemistries as a way to define a general theory of constructive dynamical systems.
Applications of artificial chemistries
Artificial Chemistries are often used in the study of protobiology, in trying to bridge the gap between chemistryChemistry
Chemistry is the science of matter, especially its chemical reactions, but also its composition, structure and properties. Chemistry is concerned with atoms and their interactions with other atoms, and particularly with the properties of chemical bonds....
and biology
Biology
Biology is a natural science concerned with the study of life and living organisms, including their structure, function, growth, origin, evolution, distribution, and taxonomy. Biology is a vast subject containing many subdivisions, topics, and disciplines...
.
A further motivation to study artificial chemistries is the interest in constructive dynamical systems. Yasuhiro Suzuki has modeled various systems such as membrane systems, signaling pathways (P53), ecosystems, and enzyme systems by using his method, abstract rewriting system on multisets (ARMS).
See also
- Cellular automataCellular automatonA cellular automaton is a discrete model studied in computability theory, mathematics, physics, complexity science, theoretical biology and microstructure modeling. It consists of a regular grid of cells, each in one of a finite number of states, such as "On" and "Off"...
- Computational chemistryComputational chemistryComputational chemistry is a branch of chemistry that uses principles of computer science to assist in solving chemical problems. It uses the results of theoretical chemistry, incorporated into efficient computer programs, to calculate the structures and properties of molecules and solids...
- the use of simplified models to simulate chemical interactions
External links and references
- Artificial chemistries--a review(pdf file)
- Tim Hutton's Papers & Talks - includes several papers on artificial chemistries for artificial life
- the ARTIFICIAL CHEMISTRY webpage of Peter Dittrich's workgroup.
- the protobiology.org website