ABCluster: the artificial bee colony algorithm for cluster global optimization

Physical Chemistry Chemical Physics : PCCP
Jun Zhang, Michael Dolg

Abstract

Global optimization of cluster geometries is of fundamental importance in chemistry and an interesting problem in applied mathematics. In this work, we introduce a relatively new swarm intelligence algorithm, i.e. the artificial bee colony (ABC) algorithm proposed in 2005, to this field. It is inspired by the foraging behavior of a bee colony, and only three parameters are needed to control it. We applied it to several potential functions of quite different nature, i.e., the Coulomb-Born-Mayer, Lennard-Jones, Morse, Z and Gupta potentials. The benchmarks reveal that for long-ranged potentials the ABC algorithm is very efficient in locating the global minimum, while for short-ranged ones it is sometimes trapped into a local minimum funnel on a potential energy surface of large clusters. We have released an efficient, user-friendly, and free program "ABCluster" to realize the ABC algorithm. It is a black-box program for non-experts as well as experts and might become a useful tool for chemists to study clusters.

References

Jan 1, 1992·Proceedings of the National Academy of Sciences of the United States of America·R ZwanzigB Bagchi
Jul 1, 1993·Physical Review. B, Condensed Matter·F Cleri, V Rosato
Feb 20, 1995·Physical Review Letters·T Erber, G M Hockney
Jul 10, 1995·Physical Review Letters·D M Deaven, K M Ho
Aug 28, 1999·Science·D J Wales, H A Scheraga
Nov 1, 1994·Chemical Reviews·M J Elrod, R J Saykally
Apr 24, 2002·Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics·M A MillerD J Wales
Sep 30, 2008·Angewandte Chemie·Elke PahlPeter Schwerdtfeger
May 23, 2012·Nature Chemistry·Hannu Häkkinen
Nov 28, 2012·The Journal of Chemical Physics·Christoph WehmeyerDaniel Sebastiani
Feb 8, 2013·Physical Chemistry Chemical Physics : PCCP·Mark T OakleyDavid J Wales
Mar 14, 2013·Journal of Computational Chemistry·Zhanghui ChenLinwang Wang
Dec 18, 2013·The Journal of Chemical Physics·D Schebarchov, D J Wales
Mar 20, 2014·Angewandte Chemie·Emil RodunerMichael Hunger
Nov 7, 2014·Physical Review Letters·D Schebarchov, D J Wales
May 15, 2015·Physical Chemistry Chemical Physics : PCCP·D Schebarchov, D J Wales
May 10, 2011·Journal of Chemical Theory and Computation·Christoph Schiffmann, Daniel Sebastiani
Nov 4, 2004·The Journal of Physical Chemistry. a·Yuhong XiangXueguang Shao

❮ Previous
Next ❯

Citations

Jan 8, 2016·Physical Chemistry Chemical Physics : PCCP·Jun Zhang, Michael Dolg
Aug 16, 2016·Journal of the American Chemical Society·Jilai LiHelmut Schwarz
Oct 11, 2016·Physical Chemistry Chemical Physics : PCCP·Alhadji MalloumNejm-Eddine Jaidane
Mar 3, 2017·The Journal of Chemical Physics·Andreas GrüneisSeiichiro Ten-No
Apr 12, 2017·Physical Chemistry Chemical Physics : PCCP·Gao-Lei HouXue-Bin Wang
Jun 19, 2018·Physical Chemistry Chemical Physics : PCCP·Ling LiuXiuhui Zhang
Sep 25, 2018·Journal of Physics. Condensed Matter : an Institute of Physics Journal·Junjian MiaoYi Gao
Nov 15, 2018·Physical Chemistry Chemical Physics : PCCP·Alhadji MalloumJeanet Conradie
Oct 1, 2019·Journal of Computational Chemistry·Alhadji MalloumJeanet Conradie
Nov 27, 2019·Proceedings of the National Academy of Sciences of the United States of America·Ling LiuXiao Cheng Zeng
Apr 4, 2020·Physical Chemistry Chemical Physics : PCCP·Shuang NiXiu-Mei Pan
Jun 6, 2020·Physical Chemistry Chemical Physics : PCCP·Alhadji MalloumJeanet Conradie
Jul 17, 2018·The Journal of Chemical Physics·Alhadji MalloumJeanet Conradie
Dec 12, 2019·The Journal of Chemical Physics·Kailiang YuLinjun Wang
Apr 10, 2020·The Journal of Chemical Physics·Alex M MaldonadoJohn A Keith
Jul 3, 2017·The Journal of Chemical Physics·E AriasJ F Pérez-Torres
Jan 3, 2019·The Journal of Chemical Physics·Alhadji MalloumJeanet Conradie
Apr 1, 2019·The Journal of Chemical Physics·Alhadji MalloumJeanet Conradie
Aug 30, 2018·Chemical Science·Yasemin Basdogan, John A Keith
Oct 16, 2019·Frontiers in Chemistry·Maya KhatunAnakuthil Anoop
Sep 19, 2020·Chemical Communications : Chem Comm·Amlan J KalitaAnkur K Guha
Jan 7, 2021·Physical Chemistry Chemical Physics : PCCP·Sourav GhoshalPranab Sarkar
Feb 6, 2021·Science·Xu-Cheng HeMikko Sipilä
Jan 9, 2021·The Journal of Chemical Physics·John J KreinbihlChristopher J Johnson
May 5, 2020·Journal of Chemical Theory and Computation·Jun ZhangManh-Thuong Nguyen
Mar 24, 2021·The Journal of Physical Chemistry. a·Rui WangTianlei Zhang
Mar 23, 2021·Physical Chemistry Chemical Physics : PCCP·Jiarong LiuXiuhui Zhang
Mar 30, 2021·Frontiers in Chemistry·Ruby Srivastava

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.