人工化学

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An artificial chemistry is a chemical-like system that usually consists of objects, called molecules, that interact according to rules resembling chemical reaction rules. Artificial chemistries are created and studied in order to understand fundamental properties of chemical systems, including prebiotic evolution, as well as for developing chemical computing systems. Artificial chemistry is a field within computer science wherein chemical reactions—often biochemical ones—are computer-simulated, yielding insights on evolution, self-assembly, and other biochemical phenomena. The field does not use actual chemicals, and should not be confused with either synthetic chemistry or computational chemistry. Rather, bits of information are used to represent the starting molecules, and the end products are examined along with the processes that led to them. The field originated in artificial life but has shown to be a versatile method with applications in many fields such as chemistry, economics, sociology and linguistics.

An artificial chemistryW. Banzhaf and L. Yamamoto. Artificial Chemistries, MIT Press, 2015. P. Dittrich. Artificial chemistry (AC) In A. R. Meyers (ed.), Computational Complexity: Theory, Techniques, and Applications, pp. 185-203, Springer, 2012.P. Dittrich, J. Ziegler, and W. Banzhaf. Artificial chemistries — A review. Artificial Life, 7(3):225–275, 2001.

is a chemical-like system that usually consists of objects, called molecules, that interact according to rules resembling chemical reaction rules. Artificial chemistries are created and studied in order to understand fundamental properties of chemical systems, including prebiotic evolution, as well as for developing chemical computing systems. Artificial chemistry is a field within computer science wherein chemical reactions—often biochemical ones—are computer-simulated, yielding insights on evolution, self-assembly, and other biochemical phenomena. The field does not use actual chemicals, and should not be confused with either synthetic chemistry or computational chemistry. Rather, bits of information are used to represent the starting molecules, and the end products are examined along with the processes that led to them. The field originated in artificial life but has shown to be a versatile method with applications in many fields such as chemistry, economics, sociology and linguistics.

人工化学是一种类化学系统，通常由名为分子的主体组成，它们会根据类似化学反应的规则相互作用。人工化学的创立和研究是为了理解化学系统的基本性质，包括生命起源前的进化，以及开发化学计算系统。人工化学是计算机科学中的一个领域，其中的化学反应——通常是生化反应——是计算机模拟的，提供了关于进化、自组装和其他生化现象的洞见。该领域不使用实际的化学物质，不应与合成化学或计算化学混淆。更确切地说，是将比特信息代表起始分子，并检验反应终产物和产生它们过程。该领域起源于人工生命，但已被证明是一种多用途的方法，在化学、经济学、社会学和语言学等许多领域都有应用。

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).

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).

= = 形式定义 = = 人工化学一般定义为三元组 (S,R,A)。在某些情况下，将它定义为元组(S,I)就足够了。

• S is the set of possible molecules S={s₁...,s_n}, where n is the number of elements in the set, possibly infinite.
• R is a set of n-ary operations on the molecules in S, the reaction rules R={r₁...,r_n}. Each rule r_i is written like a chemical reaction a+b+c->a*+b*+c*. Note here that r_i are operators, as opposed to +.
• A is an algorithm describing how to apply the rules R to a subset P[math]\displaystyle{ \subset }[/math]S.
• I are the interaction rules of the molecules in S.

• 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-ary operations 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 algorithm describing how to apply the rules R to a subset P\subsetS.
• I are the interaction rules of the molecules in S.

• S是可能分子的集合S={s₁...,s_n}，其中 n 是集合中元素的个数，它可能是无限的。
• R是S中分子的n元运算的集合，即反应规则R={r₁...,r_n}。每个反应规则r_i的写法类似于一个化学反应 a+b+c->a*+b*+c*。请注意，r_i是操作符，而不是 + 。
• A是一个描述如何将规则R应用于子集P[math]\displaystyle{ \subset }[/math]S的算法。
• I是S中分子间相互作用的规则。

= 人工化学的种类 =

• depending on the space of possible molecules
  • finite
  • infinite
• depending on the type of reactions
  • catalytic systems
  • reactive systems
  • inhibitive systems
• depending on the space topology
  • well stirred reactor
  • topologically arranged (1-, 2-, and 3-dimensional)

• depending on the space of possible molecules
  • finite
  • infinite
• depending on the type of reactions
  • catalytic systems
  • reactive systems
  • inhibitive systems
• depending on the space topology
  • well stirred reactor
  • topologically arranged (1-, 2-, and 3-dimensional)

• 依据可能分子的空间划分
• 有限
• 无限
• 依据反应类型划分
• 催化系统
• 活化系统
• 抑制系统
• 依据空间拓扑划分
• 搅拌良好的反应器
• 拓扑排列(1、2、3维)

Important concepts

• The field is heavily reliant on mathematics, to include mathematical modeling. It in fact relies more on a mathematics background than a chemistry background.
• 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

• The field is heavily reliant on mathematics, to include mathematical modeling. It in fact relies more on a mathematics background than a chemistry background.
• 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

= = 重要概念 =

• 该领域严重依赖于数学，包括数学建模。事实上，它更多地依赖于数学背景，而不是化学背景。
• 组织: 组织是一组封闭的、自我维持的分子。因此，它是一个集合，不会创造任何自身之外的存在，任何该集合内部的分子都能在该集合中被生成。
• 闭集
• 自我维持集
• 组织的哈斯图

= 人工化学的历史 =

Artificial chemistries emerged as a sub-field of artificial life, 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. In artificial life, bits of information were used to represent bacteria or members of a species, each of which moved, multiplied, or died in computer simulations. In artificial chemistry bits of information are used to represent starting molecules capable of reacting with one another. The field has pertained to artificial intelligence by virtue of the fact that, over billions of years, non-living matter evolved into primordial life forms which in turn evolved into intelligent life forms.

Artificial chemistries emerged as a sub-field of artificial life, 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. In artificial life, bits of information were used to represent bacteria or members of a species, each of which moved, multiplied, or died in computer simulations. In artificial chemistry bits of information are used to represent starting molecules capable of reacting with one another. The field has pertained to artificial intelligence by virtue of the fact that, over billions of years, non-living matter evolved into primordial life forms which in turn evolved into intelligent life forms.

人工化学作为人工生命的子领域而出现，特别是源自强人工生命。这个领域背后的观念是，若想要构建一个有生命的存在，则必须由非生命实体的组合来完成。例如，一个细胞本身是有生命的，但却是非生命分子的组合。此外，人工化学还吸引了另一批研究者，他们相信一种极端的自下而上的人工生命方法。在人工生命中，比特信息被用来表示细菌或物种个体，在计算机模拟中，每个细菌或物种都会移动、繁殖或者死亡。在人工化学中，比特信息则被用来表示能彼此反应的起始分子。该领域与人工智能有关，因为数十亿年的演化过程中，非生命物质进化为原始生命形式，而原始生命形式又进化为智能生命形式。

= 重要贡献者 =

The first reference about Artificial Chemistries come from a Technical paper written by John McCaskill . Walter Fontana working with Leo Buss 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. This concept was further developed by Dittrich and Speroni di Fenizio into a theory of chemical organizations .

The first reference about Artificial Chemistries come from a Technical paper written by John McCaskill .J.S.McCaskill. Polymer chemistry on tape: A computational model for emergent genetics. Technical report, MPI for Biophysical Chemistry, 1988. Walter Fontana working with Leo Buss then took up the work developing the AlChemy model W. Fontana. Algorithmic chemistry. In C. G. Langton, C. Taylor, J. D. Farmer, and S. Rasmussen, editors, Artificial Life II, pages 159–210. Westview Press, 1991. .W. Fontana and L. Buss. “The arrival of the fittest”: Toward a theory of biological organization. Bulletin of Mathematical Biology, 56(1):1–64, 1994. 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. This concept was further developed by Dittrich and Speroni di Fenizio into a theory of chemical organizations P. Dittrich, P. Speroni di Fenizio. Chemical Organization Theory. Bulletin of Mathematical Biology (2007) 69: 1199:1231. .P. Speroni di Fenizio. Chemical Organization Theory. PhD thesis, Friedrich Schiller University Jena, 2007.

关于人工化学的第一篇参考文献来自约翰 · 麦卡斯基尔（John McCaskill）的一篇技术论文。沃尔特·丰塔纳（Walter Fontana）与利奥·巴斯（Leo Buss）合作，随后开发了AlChemy模型。该模型发表于第二届国际人工生命大会。在他的第一篇论文中，他提出了组织的概念，即一组代数封闭且自我维持的分子。迪特里奇（Dittrich）和斯佩罗尼·迪·费尼齐奥（Speroni di Fenizio）将这一概念进一步发展为化学组织理论。

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.

Two main schools of artificial chemistries have been in Japan and Germany. In Japan the main researchers have been Takashi Ikegami ,T. Ikegami and T. Hashimoto. Active mutation in self-reproducing networks of machines and tapes. Artificial Life, 2(3):305–318, 1995. T. Ikegami and T.Hashimoto. Replication and diversity in machine-tape coevolutionary systems. In C. G. Langton and K. Shimohara, editors, Artificial Life V, pages 426–433. MIT Press, 1997. Hideaki Suzuki H.Suzuki. Models for the conservation of genetic information with string-based artificial chemistry. In W. Banzhaf, J. Ziegler, T. Christaller, P. Dittrich, and J. T. Kim, editors, Advances in Artificial Life, volume 2801 of Lecture Notes in Computer Science, pages 78–88. Springer, 2003. H. Suzuki. A network cell with molecular agents that divides from centrosome signals. Biosystems, 94(1-2):118–125, 2008. and Yasuhiro Suzuki Y. Suzuki, J. Takabayashi, and H. Tanaka. Investigation of tritrophic interactions in an ecosystem using abstract chemistry. Artificial Life and Robotics, 6(3):129–132, 2002. .Y. Suzuki and H. Tanaka. Modeling p53 signaling pathways by using multiset processing. In G. Ciobanu, G. Pa ̆un, and M. J. Pérez-Jiménez, editors, Applications of Membrane Computing, Natural Computing Series, pages 203–214. Springer, 2006. 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 .J.Ziegler and W.Banzhaf. Evolving control metabolisms for a robot. ArtificialLife, 7(2):171–190, 2001. 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.

人工化学的两个主要流派在日本和德国。在日本，主要的研究人员是池上隆（Takashi Ikegami）、铃木英代木（Hideaki Suzuki）和铃木康弘（Yasuhiro Suzuki）。在德国，在德国，沃尔夫冈·班扎夫（Wolfgang Banzhaf）与他的学生彼得·迪特里奇（Peter Dittrich）和延斯·齐格勒（Jens Ziegler）一起开发了各种人工化学模型。他们2001年的论文《人工化学——一篇综述》成为该领域的标准。作为博士论文的一部分，延斯·齐格勒证明了人工化学可以用来控制小型Khepera机器人。在其他模型中，彼得 · 迪特里希发展了离群者模型，该模型能通过一些简单的规则来解释社会中的群体形成。从那时起，他成为耶拿的教授，并在那里研究将人工化学用于定义构造性动力学系统的一般理论。

= 人工化学的应用 =

Artificial Chemistries are often used in the study of protobiology, in trying to bridge the gap between chemistry 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).

Artificial Chemistries are often used in the study of protobiology, in trying to bridge the gap between chemistry 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).

人工化学常用于原生物学的研究，试图弥合化学和生物学之间的鸿沟。进一步研究人工化学的另一个动机是对构造性动力学系统的兴趣。铃木康弘利用他的方法建立了各种系统的模型，即基于多重集的抽象重写系统(ARMS)，如膜系统、信号通路(P53)、生态系统和酶系统。

= 大众文化中的人工化学 =

In the 1994 science-fiction novel Permutation City by Greg Egan, brain-scanned emulated humans known as Copies inhabit a simulated world which includes the Autoverse, an artificial life simulator based on a cellular automaton complex enough to represent the substratum of an artificial chemistry. Tiny environments are simulated in the Autoverse and filled with populations of a simple, designed lifeform, Autobacterium lamberti. The purpose of the Autoverse is to allow Copies to explore the life that had evolved there after it had been run on a significantly large segment of the simulated universe (referred to as "Planet Lambert").

In the 1994 science-fiction novel Permutation City by Greg Egan, brain-scanned emulated humans known as Copies inhabit a simulated world which includes the Autoverse, an artificial life simulator based on a cellular automaton complex enough to represent the substratum of an artificial chemistry. Tiny environments are simulated in the Autoverse and filled with populations of a simple, designed lifeform, Autobacterium lamberti. The purpose of the Autoverse is to allow Copies to explore the life that had evolved there after it had been run on a significantly large segment of the simulated universe (referred to as "Planet Lambert").

在1994年格雷格·伊根（Greg Egan）的科幻小说《置换城市》（Permutation City）中，大脑扫描的模拟人类复制体居住在一个包含自动宇宙（Autoverse）的模拟世界中。自动宇宙是一个人工生命模拟器，它基于一个复杂到足以将人工化学作为底层的元胞自动机。在自动宇宙中模拟的微环境，充满了一种设计简单的生命形式，即名为朗伯自动菌（Autobacterium lamberti）的种群。自动宇宙的目的是让复制品探索在模拟宇宙(称为朗伯行星)上的相当大区域运转之后而演化的生命。

See also

• Avida Digital Evolution
• Cellular automata
• Computational chemistry - the use of simplified models to simulate chemical interactions

• Avida Digital Evolution
• Cellular automata
• Computational chemistry - the use of simplified models to simulate chemical interactions

Avida数字进化

元胞自动机

计算化学 - 使用简化模型模拟化学相互作用

External links

• Artificial Chemistries website
• Tim Hutton's Papers & Talks - includes several papers on artificial chemistries for artificial life
• the protobiology.org website

• Artificial Chemistries website
• Tim Hutton's Papers & Talks - includes several papers on artificial chemistries for artificial life

• the protobiology.org website

= = 外部链接 =

• 人工化学网站
• Tim Hutton 的论文与讲座-包括几篇关于将人工化学用于人工生命的论文
• protobiology.org 网站

References

Category:Artificial life

类别: 人工生命

This page was moved from wikipedia:en:Artificial chemistry. Its edit history can be viewed at 人工化学/edithistory