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第15行： − − *S is the [[Set (mathematics)|set]] of possible molecules S={s<sub>1</sub>...,s<sub>n</sub>}, where n is the number of elements in the set, possibly infinite. − *R is a set of [[arity|n-ary]] [[operation (mathematics)|operation]]s on the molecules in S, the reaction rules R={r<sub>1</sub>...,r<sub>n</sub>}. Each rule r<sub>i</sub> is written like a chemical reaction a+b+c->a*+b*+c*. Note here that r<sub>i</sub> are operators, as opposed to +. − *A is an [[algorithm]] describing how to apply the rules R to a [[subset]] P<math>\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. − 第32行：
第21行： − ==Types of artificial chemistries== − − ==Types of artificial chemistries== − + 第62行：
第48行： − + − + − − − + − + − + − − − − + − + − − − 第96行：
第74行： − The first reference about Artificial Chemistries come from a Technical paper written by [[John McCaskill]]+ − .<ref>J.S.McCaskill. Polymer chemistry on tape: A computational model for emergent genetics. Technical report, MPI for Biophysical Chemistry, 1988.</ref> − [[Walter Fontana]] working with [[Leo Buss]] then took up the work developing the [[AlChemy model]] − − .<ref name="FB1994">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.</ref> − 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 − − .<ref>P. Speroni di Fenizio. Chemical Organization Theory. PhD thesis, Friedrich Schiller University Jena, 2007.</ref> − − − 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]] − ,<ref>T. Ikegami and T. Hashimoto. Active mutation in self-reproducing networks of machines and tapes. Artificial Life, 2(3):305–318, 1995.</ref> − <ref>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.</ref> − [[Hideaki Suzuki]] − <ref>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.</ref> − <ref>H. Suzuki. A network cell with molecular agents that divides from centrosome signals. Biosystems, 94(1-2):118–125, 2008.</ref> − and <nowiki>Yasuhiro Suzuki</nowiki> − <ref>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.</ref> − .<ref>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.</ref> − 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' <ref name="DZB2001" /> 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 − .<ref>J.Ziegler and W.Banzhaf. Evolving control metabolisms for a robot. ArtificialLife, 7(2):171–190, 2001.</ref> − 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 system]]s. − + − 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。+ + − − 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). − 第140行：
第88行： − + − 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。
无编辑摘要
== 形式定义 ==
== 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。
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是可能分子的集合S={s<sub>1</sub>...,s<sub>n</sub>}，其中 n 是集合中元素的个数，它可能是无限的。
* S是可能分子的集合S={s<sub>1</sub>...,s<sub>n</sub>}，其中 n 是集合中元素的个数，它可能是无限的。
* I是S中分子间相互作用的规则。
* I是S中分子间相互作用的规则。
= = 人工化学的种类 = =
== 人工化学的种类 ==
* depending on the space of possible molecules
* depending on the space of possible molecules
* 依据可能分子的空间划分
* 依据可能分子的空间划分
*
** 有限
* 有限
** 无限
*
* 无限
* 依据反应类型划分
* 依据反应类型划分
*
** 催化系统
* 催化系统
** 活化系统
*
** 抑制系统
* 活化系统
*
* 抑制系统
* 依据空间拓扑划分
* 依据空间拓扑划分
*
** 搅拌良好的反应器
* 搅拌良好的反应器
** 拓扑排列(1、2、3维)
*
* 拓扑排列(1、2、3维)
== 重要贡献者 ==
== 重要贡献者 ==
关于人工化学的第一篇参考文献来自John McCaskill的一篇技术论文。<ref>J.S.McCaskill. Polymer chemistry on tape: A computational model for emergent genetics. Technical report, MPI for Biophysical Chemistry, 1988.</ref>沃尔特·丰塔纳（Walter Fontana）与Leo Buss合作，随后开发了AlChemy模型<ref>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.</ref>。<ref name="FB1994">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.</ref>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。Dittrich和Speroni di Fenizio将这一概念进一步发展为化学组织理论<ref>P. Dittrich, P. Speroni di Fenizio. [https://dx.doi.org/10.1007/s11538-006-9130-8 Chemical Organization Theory]. Bulletin of Mathematical Biology (2007) 69: 1199:1231.</ref>。<ref>P. Speroni di Fenizio. Chemical Organization Theory. PhD thesis, Friedrich Schiller University Jena, 2007.</ref>
<ref>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.</ref>
<ref>P. Dittrich, P. Speroni di Fenizio. [https://dx.doi.org/10.1007/s11538-006-9130-8 Chemical Organization Theory]. Bulletin of Mathematical Biology (2007) 69: 1199:1231.</ref>
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Takashi Ikegami、<ref>T. Ikegami and T. Hashimoto. Active mutation in self-reproducing networks of machines and tapes. Artificial Life, 2(3):305–318, 1995.</ref>
<ref>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.</ref>Hideaki Suzuki<ref>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.</ref>
<ref>H. Suzuki. A network cell with molecular agents that divides from centrosome signals. Biosystems, 94(1-2):118–125, 2008.</ref>和Yasuhiro Suzuki。<ref>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.</ref><ref>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.</ref>在德国，在德国，Wolfgang Banzhaf与他的学生Peter Dittrich和Jens Ziegler一起开发了各种人工化学模型。他们2001年的论文《Artificial Chemistries - A Review》<ref name="DZB2001" />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。<ref>J.Ziegler and W.Banzhaf. Evolving control metabolisms for a robot. ArtificialLife, 7(2):171–190, 2001.</ref>在其他模型中，Peter Dittrich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 ==
== 人工化学的应用 ==
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。
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 ==
== 大众文化中的人工化学 ==
在1994年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。