MSBP
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Contents |
General Information
- Application's name: Modeling of some biochemical processes with the purpose of realization of their thin and purposeful synthesis
- Virtual Research Community: Life Sciences VC
- Scientific contact: Jumber Kereselidze, Ramaz Kvatadze ramaz@grena.ge
- Technical contact: George Mikuchadze gmikuchadze@gmail.com
- Developers: Scientific groups of biophysical chemistry of the Tbilisi State University and the Sokhumi State University
- Web site: http://tobefilledin/
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 ab initio 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. Researches will farther develop their experience in participation in European programmes and will contribute to the integration of the Georgian research potential to the European Research Area.
Collaborations and Beneficiaries
Tobefilledin
Technical Features and HP-SEE Implementation
- Primary programming language: Tobefilledin
- Parallel programming paradigm: Tobefilledin
- Main parallel code: Tobefilledin
- Pre/post processing code: Tobefilledin
- Application tools and libraries: Enumerate (comma separated)
- Number of cores required: Tobefilledin
- Minimum RAM/core required: Tobefilledin
- Storage space during a single run: Tobefilledin
- Long-term data storage: Tobefilledin
Usage Example
Tobefilledin, text and (maybe) images.
Publications
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