使用定制DFTB方法的遗传算法搜索钠纳米簇的全局最小值

IF 2.5 4区 化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY
Nelson R. C. Junior, Maicon Pierre Lourenço, Breno R. L. Galvão
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引用次数: 0

摘要

由于纳米团簇的势能超表面存在大量的自由度和大量的局部极小值,因此在其上获取全局极小值是一项非常困难的任务。然而,这种极小值的发现提供了更可能发生的几何排列,这是计算这类粒子性质的关键一步。在此,我们开发了一种遗传算法(GA),其中包括在每个局部优化中进行梯度调整,以获得有效的遗传算法,当该算法与电子结构方法相结合时特别有用。这个想法首先得到了验证,然后用于预测多达100个原子的大型钠纳米团簇的最小值。方法为了验证算法的有效性,我们分析了该算法在求解Lennard-Jones聚类全局最小值时的效率。将新遗传算法与随机搜索和标准遗传算法进行了比较。为了探索钠簇的势能面,我们采用了密度-功能紧密结合(DFTB)方法,其参数已专门针对此类簇进行了调整,从而提高了其在此特定应用中的可靠性。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

A genetic algorithm search for the global minima of sodium nanoclusters using a tailored DFTB approach

A genetic algorithm search for the global minima of sodium nanoclusters using a tailored DFTB approach

A genetic algorithm search for the global minima of sodium nanoclusters using a tailored DFTB approach

Context

Obtaining the global minimum in the potential energy hypersurface of nanoclusters is a very difficult task, due to the large number of degrees of freedom and the vast number of local minima. However, the discovery of such minima provides the geometrical arrangement that is more likely to occur, which is a key step in computing the properties of such particles. Here we developed a genetic algorithm (GA) including a gradient adjustment in each local optimization, to obtain an efficient GA, which is particularly useful when the algorithm is coupled with electronic structure methods. The idea is first validated, and then used to predict the minima of large sodium nanoclusters up to one hundred atoms.

Methods

To validate the algorithm, we analyzed its efficiency in obtaining the global minima of Lennard–Jones clusters, whose solutions are well known and can be used as benchmark. The new GA is compared to a random search and a standard GA. For exploring the potential energy surface of sodium clusters, we employ the Density-Functional Tight-Binding (DFTB) method, with parameters that have been tuned specifically to such clusters, thus enhancing its reliability for this specific application.

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来源期刊
Journal of Molecular Modeling
Journal of Molecular Modeling 化学-化学综合
CiteScore
3.50
自引率
4.50%
发文量
362
审稿时长
2.9 months
期刊介绍: The Journal of Molecular Modeling focuses on "hardcore" modeling, publishing high-quality research and reports. Founded in 1995 as a purely electronic journal, it has adapted its format to include a full-color print edition, and adjusted its aims and scope fit the fast-changing field of molecular modeling, with a particular focus on three-dimensional modeling. Today, the journal covers all aspects of molecular modeling including life science modeling; materials modeling; new methods; and computational chemistry. Topics include computer-aided molecular design; rational drug design, de novo ligand design, receptor modeling and docking; cheminformatics, data analysis, visualization and mining; computational medicinal chemistry; homology modeling; simulation of peptides, DNA and other biopolymers; quantitative structure-activity relationships (QSAR) and ADME-modeling; modeling of biological reaction mechanisms; and combined experimental and computational studies in which calculations play a major role.
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