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Information × Registration Number 0211U000793, 0110U005450 , R & D reports Title Hardware-software system for modeling and analysis of natural and synthetic nanosystems in a Grid environment. popup.stage_title Head Yatsenko Leonid Petrovich, Registration Date 24-02-2011 Organization Institute of physics NASU popup.description2 Grid environment allows to increase in several times the volume and speed of calculations for modeling the dynamics of complex systems, but it is difficult to adapt existing software products. The aim of this project is to develop hardware and software, which allows to simply and effectively develop, test and use unconventional methods of modeling and analysis of nanosystems in the Grid environment. Similar complex is unique not only in Ukraine but also in the world. Library Pteros permits in the grid design of complex molecular systems and analyzing the results of their modeling, which significantly accelerates the computations compared to using local resources. It is implemented in C++ using the high-level tools, that makes its interface very simple and understandable for non-programmers. During execution of the project the next tasks were fulfilled: a library of data analysis of molecular dynamics of macromolecules Pteros was filled with basic functionality, namely: developed common data structure for describing macromolecular systems, created a parser for the selection of groups of atoms in the structure of a language selection which is an extension of VMD language pack; implemented standard algorithms for translation of atom groups and their rotation around arbitrary axes, implemented algorithms for calculating the RMS distances between structures and algorithms for structural alignment of these structures, the algorithm of the model of elastic nets GNM; implemented the calculation of normal modes and the correlation matrices in the model GNM; algorithms HCC, HCCP and HIEROT for detection and analysis of dynamic domains in proteins and model of their motions, added support for type potentials DFIRE and automatic adaptation of a framework for their use; implemented reading and writing formats PDB, GRO, XTC and TRR. Work has begun on the possibility of interpreting the topologies in packet format GROMACS. Work on educational materials that will be replenished with the development of the library. Selection and validation of methods of quantum-mechanical calculations were carried out on example of the problem of numerical optimization of the structure of the cluster isomers (ZnO)78 by quantum-chemical methods using computational cluster of the Institute of Physics. Computer simulation of cluster isomers (ZnO)78 using the package Avogadro, built and optimized by the semiempirical AM1 using a package of quantum chemical calculations Firefly model isomers (ZnO) 78, calculated binding energy, the problem of optimizing the geometry of stable isomers of (ZnO), 78 of first principles has been tested on the computational cluster of the Institute of Physics NASU, put on by and ready to run in Grid environment. Develop a program to parallel computing was carried out to calculate the evolution of the populations of three-level atom interacting with ultrashort laser pulses of high intensity. The interaction of atoms with ultrashort laser pulses is of interest to study a wide range of issues. This, in particular, the management of population of atomic states, atomic motion in light fields, their cooling, control of chemical processes, etc. The developed program can significantly increase the speed of such calculations. Product Description popup.authors Єсилевський Семен Олександрович Березецька Наталя Михайлівна Блонський Іван Васильович Гергель Олег 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