Ivannikov Institute for System Programming of the RAS


Development of parallel algorithm for computer simulation of water-ion DNA cover.

Authors

Avetisyan A.I., Gaissaryan S.S., Kalugin M.D., Teplukhin A.V.

Abstract

In this paper a parallel program for simulating water-ion cover of DNA fragments using Monte-Carlo method is presented. A cubic cell filled with water molecules and natrium and chloride ions is simulated. ParJava system, which allows instruments for developing parallel programs in Java language with MPI library, was used in our work.

Physical features of investigated system are calculated on statistically significant sample of molecular configuration in elementary cell, which is carried out with Monte-Carlo method in the classical scheme of Metropolis algorithm.

The process of computer simulation consists of 3 stages. On the first stage water cover is prepared with an independent parallel program. On the second stage a DNA fragment is placed in the center of a cell and Na+ and Cl- ions are inserted with the use of pseudorandom number generator. After finishing preparative stages, thermal motion of water molecules and ions around DNA fragment is simulated.

Results for simulating DNA fragment consisting of 150 base pairs (15 loops of duplex DNA, 9555 atoms) are presented also. Calculations were performed on ISP RAN cluster (12 nodes, 2 CPU Intel(R) Xeon(R) X5355 each, Myrinet-2000 interconnect). For simulation 80 cores of total 96 were used, each core handled 1 MPI-process. It took 9 hours to perform 10000 of experiments with each molecule in the system and first stage – preparation or water cover took about 3 hours.

Full text of the paper in pdf (in Russian)

Keywords

numerical simulation, DNA, water-ion interaction, parallel computing

Edition

Proceedings of XIII Baikal Conference on Information and Mathematical Technologies in Science and Management. 2008.

Research Group

Compiler Technology

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