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Information × Registration Number 0212U002468, 0111U008777 , R & D reports Title Upgrade hardware-software system for molecular modeling and analysis of nanosystems in a Grid environment. popup.stage_title Head Yatsenko Leonid Petrovich, Registration Date 01-03-2012 Organization Institute of physics NASU popup.description2 Grid technology is increasingly used for modeling of natural and artificial nanosystems, in particular of biological molecules and synthetic nano-clusters. The most widely used methods of molecular dynamics MD) and quantum chemistry, which allows to simulate the structure and dynamics of complex supramolecular systems and obtain the trajectories of all atoms of the system over time. The size of a typical trajectory of molecular dynamics for protein of medium size can exceed tens of gigabytes, and its treatment can take several hours. This makes the analysis stage rather complicated technically and numerically intensive. Integration analysis of molecular dynamics trajectories with a grid environment is very challenging due to the fact that it is necessary: 1) create new software for the analysis of the trajectories, 2) to optimize its performance on individual computing clusters, and 3) provide access to local and remote resources where the trajectories are physically stored, and 4) create an interface for user interaction with the system analysis. At this stage of the project, the module for molecular analysis, based on the MD trajectories of asynchronous processing was created. A system for interpretation of the command-line options for interactive analysis programs for running on computer clusters and processing parameters in JSON format to communicate with a Web interface for remote execution was created. PTEROS library and analysis programs were installed on the computer cluster of IoPh NAS and virtual laboratory MolDynGrid. Quantum-chemical methods of calculation assist in investigations of nano-objects, the physical experiments which are extremely difficult due to their inaccessible quantity, as well as a significant distribution of particles in the samples by size, shape, structure and chemical composition. However, the complexity of the calculations dramatically increases with the number of atoms that make up the object under study (cluster). Here parallel computing techniques come to the aid. Such problems can be solved effectively in a grid concept. Our work focuses on the study of nanoscale clusters of binary semiconductors A2B6 and A4V7 relevant to nano-and opto-electronics, biology and medicine, particularly in determining their structures by numerical methods. Product Description popup.authors Єсилевський Семен Олександрович Березецька Наталя Михайлівна Блонський Іван Васильович Дмитрук Ігор Миколайович Дмитрук Андрій Миколайович Негрійко Анатолій Михайлович Романенко Віктор Іванович Рябцев Андрій Володимирович Харкянен Валерій Миколайович Яценко Леонід Петрович popup.nrat_date 2020-04-02 Close