MSBP

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(Foreseen Activities)
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== Foreseen Activities ==
== Foreseen Activities ==
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* Until now simulations are performed for the small fragments of the DNA. The main goal is stabile operation of application with reasonably large fragments of the DNA on HP-SEE infrastructure.  
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* DNA tendency to denaturation is stipulated by the elevation of ethanol’s concentration in the ambient. The proton transfer between nucleobases of DNA (Adenine-Thimine, Guanine-Cytosine) causes rare tautomeric transformation of the nucleobases pair, which in turn increases both probability of denaturation and frequency of mutation. In the next runs we will increase number of nucleobases (from 4 to 8) in the molecular structures.  
* Preparation of publication based on results of simulations on HP-SEE infrastructure.
* Preparation of publication based on results of simulations on HP-SEE infrastructure.

Revision as of 12:10, 24 September 2012

Contents

General Information

  • Application's name: Modeling of some biochemical processes with the purpose of realization of their thin and purposeful synthesis
  • Application's acronym: MSBP
  • Virtual Research Community: Life Sciences
  • Scientific contact: Jumber Kereselidze, Ramaz Kvatadze ramaz[at]grena.ge
  • Technical contact: George Mikuchadze gmikuchadze[at]gmail.com
  • Developers: Scientific groups of biophysical chemistry of the Tbilisi State University and the Sokhumi State University
  • Web site: http://wiki.hp-see.eu/index.php/MSBP

Short Description

One of the priority directions of modern natural sciences is the research and creation of an opportunity of realization of thin end purposeful synthesis of nucleotide bases. Solution of this problem is directly connected to application of modern methods of quantum chemistry (DFT- Density Function Theory) and molecular mechanics. The scientific groups of biophysical chemistry of the Tbilisi State University and the Sokhumi State University during last years are engaged in research of modeling of transformations of biochemical macromolecular systems (amino acids, proteins and DNA) with the use of the appropriate computer programs (program package „ PRIRODA – 04“, P6, P32 - Moscow State University). The main characteristics of the PRIRODA quantum-chemical program designed for the study of complex molecular systems by the density functional theory, at the MP2, MP3, and MP4 levels of multiparticle perturbation theory, and by the coupled-cluster single and double excitations method (CCSD) with the application of parallel computing.

Problems Solved

The energy characteristics of the tautomeric transformations of cytosine, thymine, and uracil have been calculated within the framework of the quantum chemistry theory of functional density. It was obtained that the directions of the tautomeric conversions are characterized by energies of activation calculated according to the theory of functional density. The published data on the prototropic tautomerism of some carbonyl and nitrogen-containing acyclic and heterocyclic compounds are systematized. Mechanisms of the intramolecular and intermolecular proton transfer in tautomerisation reactions was considered. On the basis of the results of semiempirical and quantum-chemical calculations, preference is given to an intermolecular collective (dimeric, trimeric, tetrameric or oligomeric) mechanism. A new approach to the description of the solvent effect on the prototropic tautomeric equilibrium was proposed.

Scientific and Social Impact

The solution of this problem is directly connected to application of modern methods of quantum chemistry (DFT- Density Function Theory) and molecular mechanics. Obtained results will be important for the prediction of denaturation of DNA. Working on this project will significantly improve research capacity of the scientists involved and will rise educational level in biophysical chemistry at the Tbilisi State University and Sokhumi State University. Researches will improve their experience in participation in European Programmes and will contribute to the integration of the Georgian research potential to the European Research Area.

Collaborations

  • Tbilisi Statae University, Georgia
  • Sokhumi State University, Georgia
  • Moscow State University, Russia

Beneficiaries

Primary beneficiaries will be research groups from Tbilisi, Sokhumi and Moscow State Universities, however obtained results can be used by all scientists working on realization of thin end purposeful synthesis of nucleotide bases. Students involved in this research will gain experience in scientific collaboration.

Number of users

9

Development Plan

  • Concept: Done before the project started.
  • Start of alpha stage: M1
  • Start of beta stage: M6
  • Start of testing stage: M8
  • Start of deployment stage: M11
  • Start of production stage: M15

Resource Requirements

  • Number of cores required for a single run: From 24 to up to 200
  • Minimum RAM/core required: 1 GB/24
  • Storage space during a single run: 200 - 500 MB
  • Long-term data storage: not required
  • Total core hours required: not clear yet

Technical Features and HP-SEE Implementation

  • Primary programming language: C, Fortran
  • Parallel programming paradigm: MPI/OpenMP
  • Main parallel code: OpenMPI/OpenMP
  • Pre/post processing code: in-house development, C
  • Application tools and libraries: Intel C/Fortran compilers, GCC/GFortran, PGI Fortran

Usage Example

Infrastructure Usage

  • Home system: NCIT-Cluster
    • Applied for access on: 04.2011
    • Access granted on: 05.2011
    • Achieved scalability: 64 cores
  • Accessed production systems:
  1. HPC centre in Debrecen (Debrecen SC)
    • Applied for access on: 07.2012
    • Access granted on: 08.2012
    • Achieved scalability: 64 cores
  • Porting activities: The application has been successfully ported at NCIT-Cluster. George Mikuchadze was assisted by Mihnea Dulea and then by Emil Slusanschi Associate Professor of the Department of Computer Science and Engineering of University Politehnica of Bucharest. In August 2012 application was successfully ported at HPC centre in Debrecen.
  • Scalability studies: Tests on 8, 16, 33 and 64 cores.

Running on Several HP-SEE Centres

  • Benchmarking activities and results: After successful deployment on 8 cores benchmarking was initiated for 16, 32 and 64 cores.
  • Other issues: Further study for higher scaling is still required.

Achieved Results

  • The quantum-chemical modeling of a proton transfer in nitrogen containing biological active compounds using the modern non empirical method - Density Function Theory. As a result of calculations of the energetic, electronic and structural characteristics of protons transfer in the nucleotide bases the mutation processes in DNA are quantitatively described. The quantum-chemical model of the stacking and pentameric mechanisms of the tautomeric transformations of the heterocyclic compounds is constructed.

Publications

  • T. Zarqua, J. Kereselidze and Z. Pachulia. Quantum-chemical description of the influenceof electronic effects of proton transfer in guanine-cytosine base pairs. J.Biol. Phys. Chem., v.10, pp.71-73 (2010).
  • J. Kereselidze, T. Zarqua, Z. Paculia, M. Kvaraia. Quantum Chemical Modeling of the Mechanism of Formation of the Peptide Bond.International Conference on Computational Biology. Tokyo, Japan May 26-28, 2010.WASET, 65, p.1469 (2010).
  • M. Kvaraia, J. Kereselidze, Z. Pachulia and T. Zarqua. Quantum-Chemical Study of the Solvent Effect on Process of a Proton Transfer in Nucleotide Bases. Proceed. Georgian NA Sciences, v. 36, pp 306-308 (2010).
  • J. Kereselidze, Z. Pachulia and M. Kvaraia. Quantum-chemical modeling of tendency of DNA to denaturetion. J.Biol. Phys. Chem., 11, 51-53 (2011).


Foreseen Activities

  • DNA tendency to denaturation is stipulated by the elevation of ethanol’s concentration in the ambient. The proton transfer between nucleobases of DNA (Adenine-Thimine, Guanine-Cytosine) causes rare tautomeric transformation of the nucleobases pair, which in turn increases both probability of denaturation and frequency of mutation. In the next runs we will increase number of nucleobases (from 4 to 8) in the molecular structures.
  • Preparation of publication based on results of simulations on HP-SEE infrastructure.
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