AUTOMATON: A Program That Combines a Probabilistic Cellular Automata and a Genetic Algorithm for Global Minimum Search of Clusters and Molecules

Osvaldo Yanez, Rodrigo Báez-Grez, Diego Inostroza, Walter A. Rabanal-León, Ricardo Pino-Rios, Jorge Garza, W. Tiznado

Resultado de la investigación: Article

4 Citas (Scopus)

Resumen

A novel program for the search of global minimum structures of atomic clusters and molecules in the gas phase, AUTOMATON, is introduced in this work. This program involves the following: first, the generation of an initial population, using a simplified probabilistic cellular automaton method, which allows easy control of the adequate distribution of atoms in space; second, the fittest individuals are selected to evolve, through genetic operations (mating and mutations), until the best candidate for a global minimum surfaces. In addition, we propose a simple way to build the descendant structures by establishing a ranking of genes to be inherited. Thus, by means of a chemical formula checker procedure, genes are transferred to the offspring, ensuring that they always have the appropriate type and number of atoms. It is worth noting that a fraction of the fittest group is subject to mutation operations. This program also includes algorithms to identify duplicate structures: one based on geometric similarity and another on the similar distribution of atomic charges. The effectiveness of the program was evaluated in a group of 45 molecules, considering organic and organometallic compounds (benzene, cyclopentadienyl anion, and ferrocene), Zintl ion clusters [Sn9-m-nGemBin](4-n)- (n = 1-4 and m = 0-(9-n)), star-shaped clusters (Li7E5 +, E = BH, C, Si, Ge) and a variety of boron-based clusters. The global minimum and the lowest-energy isomers reported in the literature were found for all the cases considered in this article. These results successfully prove AUTOMATON's effectiveness on the identification of energetically preferred structures of a wide variety of chemical species.

Idioma originalEnglish
PublicaciónJournal of Chemical Theory and Computation
DOI
EstadoAccepted/In press - 1 ene 2019

Huella dactilar

cellular automata
Cellular automata
genetic algorithms
Genes
Genetic algorithms
Organometallic Compounds
Atoms
Molecules
Boron
Organometallics
mutations
Benzene
Isomers
genes
Stars
Anions
molecules
Negative ions
Gases
Ions

ASJC Scopus subject areas

  • Computer Science Applications
  • Physical and Theoretical Chemistry

Citar esto

Yanez, Osvaldo ; Báez-Grez, Rodrigo ; Inostroza, Diego ; Rabanal-León, Walter A. ; Pino-Rios, Ricardo ; Garza, Jorge ; Tiznado, W. / AUTOMATON : A Program That Combines a Probabilistic Cellular Automata and a Genetic Algorithm for Global Minimum Search of Clusters and Molecules. En: Journal of Chemical Theory and Computation. 2019.
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abstract = "A novel program for the search of global minimum structures of atomic clusters and molecules in the gas phase, AUTOMATON, is introduced in this work. This program involves the following: first, the generation of an initial population, using a simplified probabilistic cellular automaton method, which allows easy control of the adequate distribution of atoms in space; second, the fittest individuals are selected to evolve, through genetic operations (mating and mutations), until the best candidate for a global minimum surfaces. In addition, we propose a simple way to build the descendant structures by establishing a ranking of genes to be inherited. Thus, by means of a chemical formula checker procedure, genes are transferred to the offspring, ensuring that they always have the appropriate type and number of atoms. It is worth noting that a fraction of the fittest group is subject to mutation operations. This program also includes algorithms to identify duplicate structures: one based on geometric similarity and another on the similar distribution of atomic charges. The effectiveness of the program was evaluated in a group of 45 molecules, considering organic and organometallic compounds (benzene, cyclopentadienyl anion, and ferrocene), Zintl ion clusters [Sn9-m-nGemBin](4-n)- (n = 1-4 and m = 0-(9-n)), star-shaped clusters (Li7E5 +, E = BH, C, Si, Ge) and a variety of boron-based clusters. The global minimum and the lowest-energy isomers reported in the literature were found for all the cases considered in this article. These results successfully prove AUTOMATON's effectiveness on the identification of energetically preferred structures of a wide variety of chemical species.",
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AUTOMATON : A Program That Combines a Probabilistic Cellular Automata and a Genetic Algorithm for Global Minimum Search of Clusters and Molecules. / Yanez, Osvaldo; Báez-Grez, Rodrigo; Inostroza, Diego; Rabanal-León, Walter A.; Pino-Rios, Ricardo; Garza, Jorge; Tiznado, W.

En: Journal of Chemical Theory and Computation, 01.01.2019.

Resultado de la investigación: Article

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T2 - A Program That Combines a Probabilistic Cellular Automata and a Genetic Algorithm for Global Minimum Search of Clusters and Molecules

AU - Yanez, Osvaldo

AU - Báez-Grez, Rodrigo

AU - Inostroza, Diego

AU - Rabanal-León, Walter A.

AU - Pino-Rios, Ricardo

AU - Garza, Jorge

AU - Tiznado, W.

PY - 2019/1/1

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N2 - A novel program for the search of global minimum structures of atomic clusters and molecules in the gas phase, AUTOMATON, is introduced in this work. This program involves the following: first, the generation of an initial population, using a simplified probabilistic cellular automaton method, which allows easy control of the adequate distribution of atoms in space; second, the fittest individuals are selected to evolve, through genetic operations (mating and mutations), until the best candidate for a global minimum surfaces. In addition, we propose a simple way to build the descendant structures by establishing a ranking of genes to be inherited. Thus, by means of a chemical formula checker procedure, genes are transferred to the offspring, ensuring that they always have the appropriate type and number of atoms. It is worth noting that a fraction of the fittest group is subject to mutation operations. This program also includes algorithms to identify duplicate structures: one based on geometric similarity and another on the similar distribution of atomic charges. The effectiveness of the program was evaluated in a group of 45 molecules, considering organic and organometallic compounds (benzene, cyclopentadienyl anion, and ferrocene), Zintl ion clusters [Sn9-m-nGemBin](4-n)- (n = 1-4 and m = 0-(9-n)), star-shaped clusters (Li7E5 +, E = BH, C, Si, Ge) and a variety of boron-based clusters. The global minimum and the lowest-energy isomers reported in the literature were found for all the cases considered in this article. These results successfully prove AUTOMATON's effectiveness on the identification of energetically preferred structures of a wide variety of chemical species.

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