PARALLEL OPTIMIZATION TECHNOLOGY FOR ATOMIC-MOLECULAR MORSE CLUSTERS

В статье рассматриваются специализированные вычислительные технологии и алгоритмы, используемые для поиска низкопотенциальных атомно-молекулярных кластеров. Проведенные вычислительные эксперименты продемонстрировали достаточно высокую конкурентоспособность новых алгоритмов по сравнению с классическими для функций рассматриваемого типа. С использованием разработанного программного комплекса получены рекордные результаты оптимизации атомно-молекулярных кластеров Морса рекордных размерностей. The paper deals with specialized computing technology and algorithms used for finding low-potential atomic-molecular clusters. The performed computational experiments demonstrated a rather high competitiveness of the new algorithms in comparison with the classical methods for the considerable functions. Using the developed software, the applied problem of molecular docking was solved. Using the developed software package, record results for optimization of atomic-molecular Morse clusters of large dimensions have been obtained.

PSO-CGO

In this paper the authors present PSO-CGO, a novel particle swarm algorithm for cluster geometry optimization. The proposed approach combines a steady-state strategy to update solutions with a structural distance measure that helps to maintain population diversity. Also, it adopts a novel rule to update particles, which applies velocity only to a subset of the variables and is therefore able to promote limited modifications in the structure of atomic clusters. Results are promising, as PSO-CGO is able to discover all putative global optima for short-ranged Morse clusters between 30 and 50 atoms. A comprehensive analysis is presented and reveals that the proposed components are essential to enhance the search effectiveness of the PSO.

ANALYSIS OF THE MELTING PROCESS OF THE 14-PARTICLE MORSE CLUSTER THROUGH THE ATOMIC EQUIVALENCE INDEXES

In this paper, by using the standard microcanonical molecular-dynamics simulations, the melting processes of the 14-particle Morse clusters are investigated. The three steps melting process found in 2004 by one of the authors of this paper are analyzed further by the atomic equivalence indexes. The properties of the structure of the cluster in different melting processes are explored by the atomic equivalence indexes. It is found that in the melting process for most of the time the cluster keeps the basic structure frame similar to that in the solid-like state while there are very short time periods when the particles of the cluster exchange their locations.