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Department of Prospective Information Technologies
Group for Computer Modelling of Nanostructures and Biosystems
Major Research Areas
- investigations of various nano-molecular structures, of dynamics in their atom and molecular changes, phase and structural changes, and adjoint processes of reconstruction and charge transport in them, including biological structures;
- investigations of non-linear qualities and processes in molecular, ordered, biological and related non-linear systems, including qualities in the neighbourhood of critical points; calculations of their specific physical parameters;
- working out and application of modern computer methods, complexes and means for digital and graphic investigations of properties of molecular nanostructures and biomolecular systems; carrying out of mathematical and computer modelling of their structure and dynamics of their behavior under various conditions, and in varying parameters of the environment.
Main Objects
- ordered non-linear nano-molecular, organic and biological systems with critical points, structural and phase changes;
- proton subsystems of molecular, ordered and biological nanostructures, including systems of hydrogen bonds in various structures;
- ion channels of excitable biological membranes, their structural components, lipid bilayers and their interactions;
- structures of hydroxyapatyte and artificial bone tissues, their formation and interactions; growth of hydroxyapatyte nanocrystals on various substrates and under various conditions;
- polymeric ultrathin ferroelectric Langmuir-Blodgett films (including films, based on vinylidene fluoride copolymer with trifluoroethylene, and films with fluorine replaced by other components) and nanocrystals based on them;
- self-organizing molecular nanostructures based on diphenylalanine-like (FF) amino acids and their peptide nanotubes (PNT); nanocrystal-like nanostructures based on other amino acids (glycine, etc.);
- DNA components, including nucleic bases (thymin, adenine, guanine, cytosine) and corresponding base pairs, mono- and multipeptide structures;
- ferroelectric and bioferroelectric systems and related structures, including nanocomposite materials with nanobiomolecular embeddings (lipids, peptides, proteins, DNA fragments), and also biomembrane and cell components (microtubules, receptors, fibrillae, etc.);
- cardiac rhythm (pulse), variability of cardiac rhythm and peculiarities of cardiac rhythm control, including non-linear models and their application in the framework of the functional system theory, and also for the entire organism.
Main Methods
- methods of molecular mechanics and molecular dynamics;
- methods of quantum chemistry, and quantum mechanics, including calculations by various ab initio methods and methods of density functional theory (DFT);
- methods of condensed media theory, solid state physics, thin-film physics and surface physics;
- methods of non-linear dynamics and continuous medium dynamics;
- methods of thermodynamics and statistical physics;
- methods of the theory of complex systems, functional system theory and theory of self-organization.
Means
- mathematical and computer means for resolution of systems of non-linear differential equations, analysis and investigation of multi-dimensional functionals (including the inherent means of the IMPB - like TRAX, expansion in special functions, functional minimization programs, etc.),
- mathematical and computer means and methods of multivariate statistics, including sets of standard means Origin, M/ANOVA, and so on.
- mathematical methods for optimization/minimization of complex functionals and resolution of non-linear algebraic and differential equations.
- software packages for molecular modeling: calculations by methods of molecular mechanics, molecular dynamics and quantum-chemical calculations: HyperChem 7.0, 7.5, 8.0 for Windows PC and the recent version for Linux clusters (constant update of new versions of software is being made by Hypercube Inc., USA).
- software package MOPAC2009 ( including PM6 method) for Windows PC and the version for Linux clusters (constant update of new versions of software is being made by J.Stewart ?Stewart Computational Chemistry?, USA).
- software package Gaussian98 (update of new versions of software Gaussian09 + GaussView is being made).
- software packages (PP) based on density functional theory (DFT) with direct operating output on Linux University cluster of
Aveiro (UA), Portugal (under the Agreement on scientific cooperation "IMPB-UA"). 1) PP AIMPRO with restricted access
(http://aimpro.ncl.ac.uk/restricted), Newcastle University developing for DFT in the local density approximation (LDA); 2) PP VASP
(Vienna Ab initio Simulation Package, https://www.vasp.at)
for DFT accompanying in generalized gradient approximation (GGA).
- software package ?Varicard? for cardiogram processing, and a new original software package for forming and graphic analysis of complex patterns of variability of cardiac rhythm.
Technical Support
- 132-processor Linux cluster of the IMPB/RAS with a software complex (including Gaussian-98 with the Linda program for parallel processors, software package MOPAC2009 with PM6 method),
- series of personal computers of various levels, including notebooks, (on the base of processors of Intel-Pentium-IV type, including multi-core complexes),
- permanent remote access to interactive work on a multi-core Linux cluster at the University of Aveiro (Portugal) with ab initio software packages
AIMPRO and the VASP (in the framework of joint projects and cooperation Agreement "IMPB-UA").
- computer systems of a number of laboratories for joint projects within the framework of the agreement on mutual cooperation: Center for Research in
Ceramics and Composite Materials (CICECO) of the University of Aveiro (Portugal), Institute of Electrical Engineering Physics of the University of
Saarland (Federal Republic of Germany), Institute of Biomedical Engineering and Nanotechnologies of the Riga Technical University (Latvia); as well as
the Centre "Modern Nanotechnologies" of the Ural Federal University and the Department of Physics, Faculty of Physics Southern Federal University (Russia).
Grants and Projects
- 2019 - 2024
- Russian Foundation for Basic Research (RFBR) PROJECT 19-01-00519_À «Computer modeling and study of the structures and properties of new nanomaterials based on amino acids and other biomolecular structures» (2019-2021)
- Russian Foundation for Basic Research (RFBR) PROJECT 20-51-52-014_GFEN_a “Ferroelectric composites based on two-dimensional graphene/graphene-like structures, dichalcogenides, and polymer ferroelectrics” (2020-2021)
- 2014 - 2018
- Russian Foundation for Basic Research (RFBR) PROJECT 16-51-53-017 GFEN_a "Investigation of the molecular mechanisms of the polarization switching in the polymer PVDF/P(VDF-TrFE) ferroelectric ultrathin films at the nanoscale" (2016-2017)
- Russian Foundation for Basic Research (RFBR)) PROJECT 15-01-04924_A " Computational study of the ferroelectric properties of new nanobiomaterials and biomolecular structures" (2015-2017)
- Russian Foundation for Basic Research (RFBR) PROJECT 14-31-50605 mol_nr "Computer study of polarization switching in PVDF and P (VDF-TrFE)" (2014)
- 2004-2012
- INTAS 03-51-3967 "Ferroelectricity on the molecular level"(2004-2006);
- NMP3-CT-2003-504937 "PERCERAMICS" (FP6 of EC) "Multifunctional percolated nanostructured ceramics fabricated from hydroxylapatyte" (2005-2008)
- Russian Foundation for Basic Research (RFBR) PROJECT 05-02-16871 «Ferroelectricity on the molecular level in ultrathin films, jointly with the A.V.Shubnikov Institute of Crystallography (IC RAS) (2005-2007)
- DAAD (German Academic Exchange Service) grant No 325 «Ferroelectricity on the molecular level» (2006)
- DFG (German Research Foundation) grant KL 654/25-1 AOBJ: 539404 «Modelling of Ferroelectricity in thin PVDF-copolymer films» (2007)
- DFG (German Research Foundation) grant KL 654/29-1 AOBJ: 550297 «Modeling of Ferroelectric properties of PVDF-copolymer films between metallic electrodes» (2008)
- DAAD (German Academic Exchange Service) grant No 325-A09/03515 «Modeling of PVDF chain dipole interactions with electrodes and influence of electrodes on PVDF Ferroelectric properties» (2009)
- Foundation of Science and Technology of Portugal - Fundacao para a Ciencia e a Tecnologia (FCT, Portugal) grant SFRH/ BPD/22230 /2005 «Development of polar nano-materials, based on polymer ferroelectric films and self-assembled molecules for biological and memory applications» (2006 ? 2012)
- 1999-2003
- International Project "Ion Channels" (jointly with the City University of New York, USA), (1999 ? 2001),
- Russian Foundation for Basic Research (RFBR) PROJECT 00-02-16682 Research of ferroelectric systems with hydrogen bonds and embedded biomolecular components (2000-2002),
State-Financed Project
- Computer simulation of biomolecular nanostructures and processes.
- Number of state. Registration 01201373458. The period 2016 - 2018.
- Computer simulation of biomolecular nanostructures and processes.
- Number of state. Registration 01201373458. The period 2013 - 2015. The work has been finished, and the report on it has been rendered.
- Mathematical Modelling of Ion Channels in Excitable Biological Membranes. State Registration Number 01.200 409640. Years 2006-2008. The work has been finished, and the report on it has been rendered.
- Modelling of Formation and Dynamics of Behavior of Polar Biomolecular Nanostructures and Composite Materials?. Years 2009-2012. Number 01 200 952314.
Staff of the Group
The Group is a part of the DPIT of the IMPB/RAS
- Bystrov, Vladimir S., Dr. Sc. (Physics and Mathematics), principal researcher ? the head of the Group
- Paramonova, Yekaterina V., Cand. Sc. (Physics and Mathematics) researcher
- Baumuratova, Tatiana R., Cand. Sc. (Physics and Mathematics), researcher
- Bystrova, Anna V., junior researcher
- Gevorgyan Varsenik Ervandovna, junior researcher at the RFBR grants (undergraduate student, Southern Federal University)
- Avakyan Leon A. Ph.D., a research fellow at the RFBR grants o (Associate Professor, Southern Federal University)
- Kamyshlov, Vladimir V., former post-graduate student of the Pushchino State Institute for Science (non-staff)
- Sapronova, Alla V., Cand. Sc. (Physics and Mathematics), researcher (non-staff)
- Filippov, Sergey V., researcher of the DPIT (part-time worker)
- Zaitsev, Aleksandr Yu., researcher of the Interinstitute Department of Computing and Informational Resources of the IMPB/RAS (part-time worker)
- Bystrova, Natalya K., Cand. Sc. (Biology), senior researcher of the Instutute of Theoretical and Experimental Biophysics (ITEB RAS)
(part-time worker, working period from 2000 up to 2009)
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