Registration Number
0214U006777,
0113U004534
, R & D reports
Title
Hardware-software system for modeling and analysis of natural and synthetic nano-systems in a Grid environment.
popup.stage_title
Head
Yatsenko Leonid Petrovich,
Registration Date
21-02-2014
Organization
Institute of physics NASU
popup.description2
Grid technology is actively and fruitfully used for modeling of natural and artificial nanosystems. In particular it is useful for investigation of biological macromolecules and synthetic nanoclusters. Methods of molecular dynamics and quantum chemistry are widely used for modeling of structure and dynamics of complex supramolecular systems and obtaining paths of all atoms in the system over time. Any such modeling consists of three steps: 1) constructing a model system 2) calculation of paths or equilibrium geometry 3) an analysis of the trajectories or equilibrium geometry and interpretation of results. Till now, only the second stage of this process has been successfully integrated in the Grid environment, whereas systems design and analysis are carried out locally. During the execution of the project a stable API of Pteros library was created. Library code has been spared from unnecessary dependencies and was reduced to common standards in formatting. A detailed documentation was developed, and a tutorial for working with the library was created. Complete instructions for installing the library on computing clusters of Ukrainian Grid segment were written, and the library itself was installed on computer clusters included in VO MolDynGrid. Complitly new system of analytic plugins was developed and it was demonstrated the ability to use plugins written in both C + + and Python language. The most probable structure of clusters consisting of 2-10 atoms of germanium terminated with iodine was determined by quantum-chemical calculations. It was found that the smallest clusters are possessed linear structures, medium ones (7-8 atoms Ge) are possessed rings forms, in the transition region, and the biggest ones with 9-10 atoms of germanium have bulk structure. Vibrational spectra (IR and RS) were calculated for all the characteristic clusters of size of 2-10 atoms. These results may be useful for the further identification of the clusters in experiments. The results presented in this work are contributed to Phys. Rev. B.
Product Description
popup.authors
Єсилевський Семен Олександрович
Березецька Наталя Михайлівна
Блонський Іван Васильович
Дмитрук Ігор Миколайович
Дмитрук Андрій Миколайович
Рябцев Андрій Володимирович
Шинкаренко Євген Вікторович
Яценко Леонід Петрович
popup.nrat_date
2020-04-02
