Molecular Dynamics Study of Complex Systems

The parallel molecular dynamics simulation of complex system consisting of surfactant/polymer mixtures is planning to carry out. The self –assembling of surfactant systems is also planning to study. The molecular dynamics results together with experimental finding will help to understand the mechanism of interactions in physical point of view and, which is most important, will give us an important information concerning the conformation and localization of system components (polymer, surfactant, water, ect.). The main research method is the molecular dynamics simulation, as well as for comparison the GPS measurement and X-ray methods are planning to use. The application based on NAMD and GROMACS packages, which are designed for high-performance simulation of large molecular systems.

The 50ns molecular dynamics simulation run of SDS/water/oil system in presence of polyampholyte at pH=9 have been done. It is planned to continue the additional 50ns simulation run of mentioned system at pH=4. The analysis of molecular dynamics data is done for the system at pH=9. The self-organization of surfactant/water system is in progress (currently at ~16ns run point).

The investigations will help to understand the mechanism of interaction of anionic SDS and cationic/anionic/noncharged polymer and to receive important information on the dynamical and structural features of mentioned systems. The results of the proposed investigations will make an important contribution to basic researches in Colloid Physics.

Application's name: Molecular Dynamics Study of Complex Systems (MDSCS)
Scientific contact: Dr. Armen Poghosyan (sicnas at sci.am)
Technical contact: Dr. Hrachya Astsatryan(hrach at sci.am)
Developers: National Academy of Sciences of the Republic of Armenia
Web site: Bioinformatics Group

For more information visit HP-SEE Wiki Page.

Scientific Papers

• A. Poghosyan, L. Arsenyan, H. Astsatryan, M. Gyurjyan, H. Keropyan and A. Shahinyan
  "Package Benchmarking on the Base of Armenian Grid Infrastructure"
  Journal of Communications and Network, Scientific Research Publishing, Vol. 4 No. 1, 2012, pp. 34-40,
  DOI:10.4236/cn.2012.41005
• A.H. Poghosyan, L. H. Arsenyan, H.V. Astsatryan
  "NAMD Benchmarking of Complex System on Bulgarian BlueGene/P"
  IEEE Proceedings of MIPRO 2012 - Jubilee 35th International Convention, Opatija, Croatia (accepted).
• A.H.Poghosyan, L.H. Arsenyan and A.A. Shahinyan
  "Molecular dynamics study of long chain alkyl sulfonate/water system"
  JCIS in review