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The Laboratory of Information Technologies

Research in progress


JINR EXPERIENCE IN DEVELOPMENT OF GRID MONITORING AND ACCOUNTING SYSTEMS

Sergey Belov, Vladimir Korenkov, Alexander Uzhinsky
Laboratory of Information Technologies, JINR


Different monitoring systems are now extensively used to keep an eye on real time state of each service of distributed grid infrastructures and jobs running on the Grid. Tracking current services' state as well as the history of state changes allows rapid error fixing, planning future massive productions, revealing regularities of Grid operation and so on. LIT has a longstanding experience in successful development and design of Grid monitoring and accounting systems for global grid segments and for local national grid projects in Russia.

NANOSTRUCTURE SIMULATION BY METHODS OF DISCRETE DYNAMICS

V.V. Kornyak
Laboratory of Information Technologies, JINR

Many nanostructures, in particular, certain carbon and hydrocarbon molecules, are highly symmetric discrete formations. We study discrete dynamical systems of different types, deterministic and non-deterministic ones, defined on such structures. Many of the most important properties and peculiarities of behavior of the systems under consideration are direct results of their symmetries. One of the main tools for our study is a program in C we are developing now. The program is based on the computer algebra and computational group theory methods.

DISTRIBUTED COMPUTATIONS IN BIOINFORMATICS

T.P. Akishina, P.V. Zrelov, V.V. Ivanov
Laboratory of Information Technologies, JINR, Dubna

R.V. Polozov
Institute of Theoretical and Experimental Biophysics RAS

V.S. Sivozhelezov
Institute of Cell Biophysics RAS


Computational biosensor nanotechnology [1] can only be implemented if it comprises development of a database of immobilized enzymes. Such a database will contain all modes of enzyme immobilization such as self-assembly, Langmuir films, electrostatic immobilization etc., and enable selection, within a specialized expert system, of the optimal mode of immobilization from modes of immobilization available for all enzymes binding the specified ligand or a family of ligands. Therefore, a task emerges of searching a large number of variants of enzyme immobilization, which requires solving many similar problems of data recalculation among various enzymes, modes of their immobilization, and possibly various ligands. Results of such recalculation must be obtained in real time to enable interactive correction of the characteristics and parameters of the developed biosensor by the software user / biosensor developer. This brings about the need in distributed computations where each of the many analogous problems will be solved on different processors incorporated into a distributed computation medium.

Such a computational technology will be elaborated, with the above-mentioned physical bioinformatics tasks relevant to biosensor development as its first application. Further, the technology will be adopted and applied to several other physical bioinformatics tasks, including:
  • ribosomal protein biosynthesis, where subnanometer-precision calculation of the electrostatic field of the ribosome are necessary to model the process of amino acid delivery to the active site of protein biosynthesis, as well as to account for the influence of electrostatic field of the ribosome to the folding of the nascent polypeptide chain into the functional (native) protein structure,
  • calculations of physicochemical properties such as electrostatic potentials, distributions of hydrophobic regions, etc., of long (thousands basepairs) of the regulatory fragments of genomic DNA, especially promoters/operators, signal sequences, etc., and recognition of those DNA fragments by proteins,
  • comparative analysis and classification of large protein families according to their physicochemical properties and structures,
  • calculation of physicochemical properties of the collagen molecule and modeling of collagen packing into fibrils and higher-level structures,
  • calculation of physicochemical properties of the beta layers of amyloid peptide molecules and modeling of formation of senile plaques and transmembrane channels by amyloid peptides.
This work was supported by grant RFBR 07-07-00234.

INVESTIGATION OF THERMAL AND THERMALELASTIC PROCESSES AT THE INTERACTION OF HEAVY IONS WITH MATERIALS IN THE FRAME OF THERMAL SPIKE MODEL

I.V. Amirkhanov, D.Z. Muzafarov, I.V. Puzynin, T.P. Puzynina, N.R. Sarker, I. Sarkhadov, Z. A. Sharipov
Laboratory of Information Technologies, JINR,

A.Yu. Didyk
Flerov Laboratory of Nuclear Reactions, JINR

In the last years with increasing interest the experimental researches on the impacts of heavy charged particles on materials have been conducted. Such investigations concern, in particular, the studying of features of a radiative sputtering, formation of tracks and change of mechanical properties of materials irradiated by high energy heavy ions. We will note that in spite of quite long-term periods of investigations, the conditions of "tracks" formation in solid bodies are not clear in details yet. Two models which explain the causes of the occurrence of "track" in dielectrics were suggested about fifty years ago, namely: a thermal spike model and a mechanism of Coulomb explosion. The thermal spike model is featured with a system of two bound equations of partial differential coefficients for temperature of electrons Te and lattice Ti.

The generalization of the thermal spike model considering the motion of ion within the material have been worked out. Computer program SRIM-2007 allows one to calculate the losses of energy of heavy ions at its passage through condensed matter. The carried out calculations (with the using of the results of program SRIM-2007) have shown the time of passage by an ion of uranium of a nickel target makes tion ~ 4?10-12 s. In the previous investigations, the motion of an ion in a material was not taken into account consideration and the radiant activities t ~ 10-14 s was offered in due course. We suggested a thermal spike model with a new radiant considering the motions of an ion within a material. Some results of calculations are given at irradiation of nickel by ions of uranium with the energy of 700 MeV and the comparative analysis with the previous results where the motion of an ion in a material was not taken into account.

A nonlinear thermal spike model at pyrolytic graphite under irradiation by 86Kr and 209Bi heavy ions with high energies was studued.

The use of the nonlinear thermal spike model for calculations of temperature effects at two layer structures under their irradiation by high energy heavy ions was presented. Temperatures at two layer structures, presenting a massive substrate and a surface cover by a relatively thin layer from another material under irradiation by swift heavy ions with high ionizing energy loss in frames of the thermal spike model at three dimensional case were calculated. The temperature changes near the separate boundary of such two layer structure on the example of Ni-W of the convective warm exchanging coefficient are studied in detail. Parameter characterizes the changes of the temperature gradient near the separate boundary, i.e. determines the type of heat contact. It was established that calculated temperatures of electronic and lattice subsystems for nonlinear model (characterizing by thermal physical coefficients depending on the temperature) was much less than those in the linear model (characterizing by thermal physical coefficients without dependence on the temperature). It was shown that the transition from a nonideal case of heat contact to an ideal case of heat contact takes place at increasing coefficient.

The numerical simulation of thermoelastic effects in metals irradiated by pulsed ion beems in frames of a thermal spike model are carried out in the present work. Solving the system of thermoelasticity equations in frames of the thermal spike model and the thermoelasticity equations, a comparative analysis of solutions is carried out. It is shown that in the solution of the system of thermoelasticity equations in frames of the thermal spike model the temperature in the sample is less in comparison with the solution of thermoelasticity equations. A dependence of the properties of a thermoelastic wave (the shape of amplitude and the maximum absolute value) on the velocity of insert of radiant is established.

NUMERICAL STUDY OF THE DYNAMICS OF POLARON STATES

I.V. Amirkhanov*, E.V. Zemlyanaya*, V.D. Lakhno**, D.Z. Muzafarov*, I.V. Puzynin*, T.P. Puzynina*, Z.A. Sharipov*

*Joint Institute for Nuclear Research, Laboratory of Information Technologies,
**Istitute of Mathematics Problems of Biology RAS

A numerical scheme for solving a system of the nonlinear differential equations describing the evolution of polaron in a homogeneous environment has been investigated. An accuracy of the computational scheme is analyzed. The obtained results allows us to conclude that if in an initial state polaron was in a particular state (basic or excited one), it remains in this state irrespective of the presence or absence of damping in the system. It is shown that the initial charge distributions given by some superpositions at presence in the system of damping eventually evolve to a basic state. No evolution to a basic state is observed at the absence of damping in the system.

NUMERICAL SIMULATION OF HEATMASS TRANSFER PROCESS IN THE POROUS MATERIALS

I.V. Amirkhanov, T.P. Puzynina, I.V. Puzynin, I. Sarhadov
Laboratory of Information Technologies, JINR,

E. Pavlushova
ENERGO-CT s.r.o., Kosice, Slovak Republic,

M. Pavlush
Department of Quantitative Methods, University of Presov, Presov, Slovak Republic

The solution of inverse diffusion problems for the definition of a transport coefficient of moisture in porous materials with the use of experimental data of a spatial distribution of moisture during the different moments of time represents major interest. In the present work the modeling equations featuring transport of heat, moisture and an air in porous materials are formulated. Numerical investigations of these equations for the cases of penetration of moisture from the outside in a material and its drying and also the comparative analysis of the obtained results with the results of other works are carried out.

MATHEMATICAL MODELING OF ELECTROMAGNETIC RESPONSE OF NON-METALLIC NANOPARTICLES FOR APPLICATION AS BIOLABLES

I.V. Molodtsova, D.V. Podgainy
Laboratory of Information Technologies, JINR ,

S.I. Bastrukov, H.-K. Chang
Institute of Astronomy, National Tsing Hua University, Hsinchu, Taiwan,

P.-Y. Lai
Department of Physics and Center for Complex Systems, National Central University, Chungli, Taiwan



Current increasing interest in the pecularities of electromagnetic response of ultrafine particles (nano- and nicro-dimensions) of different materials is motivated by their practical utilization for biomedical purposes.

The well-know example is the nanoparticles of noble metals, like gold and silver, whose capability of responding by surface plasmon resonances (optically induced oscillations ofvalence electrons against immobile ions well-recognizable in the optical spectra of resonant photoabsorption) is of practical interest in the usage of these metallic nanoparticles as biolabels. The optically induced oscillatory response of a spherical two-component, shell-core structured, nanoparticle by nodeless elastic vibrations of soft peripheral shell against hard and dynamically immobile inner core is considered in paper [1]. The eigenfrequencies of the even-parity, spheroidal and odd-parity torsional vibrational modes trapped in the finite-depth shell are obtained which are of practical interest for modal specification of individual resonances in spectra of the resonant scattering of long wavelength ultrafine particles.

The electromagnetic response of a nanoparticle of an ion-doped polymeric elastic insulator, commonly called as an electret, is considered in the continuum model of a uniformly charged elastic sphere [2]. The prime purpose was to elucidate stability of such nanoparticles to optically induced distortions. This issue is of crucial importance to utilization of uniformly charged polymeric ultra fine particles which are used as a biolabes in in-vivo experiments with live tissues.

[1] S.I. Bastrukov, P.-Y. Lai, I.V. Molodtsova, H.-K. Chang, D.V. Podgainy, Surface response of spherical core-shell structured nanoparticle by optically induced elastic oscillations of soft shell against hard core, Surface Review and Letters, Vol. 16 (2009), p. 5.

[2] S.I. Bastrukov, I.V. Molodtsova, P.-Y. Lai, Optically induced electrostriction modes in a nanoparticle of a uniformly charged electret, International Journal of Nanoscience, Vol. 7 (2008), p. 291.

OPTICAL CONTROL OF COLOR ALTERNATION IN THE MAGNETICALLY ALIGNED NEMATIC LIQUID CRYSTAL

I.V. Molodtsova, D.V. Podgainy
Laboratory of Information Technologies, JINR,

S.I. Bastrukov
Institute of Astronomy, National Tsing Hua University, Hsinchu, Taiwan,

P.-Y. Lai
Department of Physics and Center for Complex Systems, National Central University, Chungli, Taiwan


The magnetic-field-induced transient periodic structures in nematic liquid crystals are the subject of intensive investigations in view of a variety of technological applications. In work [1] it was shown that uniformly magnetized nematic liquid crystals with positive diamagnetic anisotropy, often referred to as ferronematics, can transmit a transverse wave in which the velocity and director undergo coupled oscillations. This conclusion is inferred from the model of long wavelength hydrodynamic response whose reactive force is dominated by antisymmetric stresses originating from polarizability of ferronematic medium. The dispersion equation characterizing low-frequency oscillatory behavior of a ferronematic liquid crystal is obtained, followed by a brief discussion of possible experimental identification of the magnetotorsion mode predicted. The predicted effect has been independently confirmed in experiments of Prof. Yin group, University of California [2]. In these experiments the nanostructured superparamagnetic Fe3O4 colloids have been assembled into ordered arrays in various solvents in response to external magnetic fields. It was found that macgentically alighened ferronematic changes its color with alternating of intensity of constant magnetic field in accord with predictions of work [1].

[1] S.I. Bastrukov, P.-Y. Lai, D.V. Podgainy, I.V. Molodtsova, Optical response of magnetically aligned nematic soft matter by transverse nemato-magnetic waves, Journal of Magnetism and Magnetic Materials, Vol. 304 (2006), p. e353.

[2] Ge, J. and Yin. Y., Magnetically Responsive Colloidal Photonic Crystals, Journal of Materials Chemistry, Vol. 18 (2008), p. 5041.

DETECTING CAVITIES IN THE MACROMOLECULES STRUCTURES USING ENVELOPING TRIANGULATION

J. Busha, J. Skiivanek
Dept. of Mathematics, Technical University, Koshice, Slovak Republic

E. Hayryan
Laboratory of Information Technologies, JINR

Sh. Hayryan, Chin-Kun Hu, Ming-Chya Wu
Institute of Physics, Academia Sinica, Nankang, Taipei, Taiwan


The solvent environment plays a crucial role in the structure and function of biological macromolecules, such as DNA, RNA and proteins. Exact determination of direct interactions between the macromolecules and the solvent molecules still remains a very hard mathematical and computational problem. For this reason different kinds of approximations are usually done which allow one to describe these extremely complicated interactions through physically averaged macroscopic parameters. Such effective parameters include, for example, a solvent accessible area of the solute molecule and the so called excluded volume. Computation of these parameters requires evaluation of complicated algorithms. For this reason, any effort to develop effective analytical methods is always welcomed.

The existence of cavities should be taken into account by solving different problems connected to the molecular properties. In the presented work some special triangulation which includes inside possible cavities points is considered. An algorithm of the construction of such triangulation is discussed. Examples of using this triangulation for making a decision about the point location and for calculation of the solvent accessible surface area and the inaccessible volume of a molecule are given.

QUANTUM-CHEMICAL CLUSTER CALCULATIONS FOR TRANSITION METAL OXIDES

L. Siurakshina
Laboratory of Information Technologies, JINR

V. Yushankhai
Bogoliubov Laboratory of Theoretical Physics, JINR


Recently we have initiated developing ab initio quantum chemical cluster calculations of local electronic and magnetic properties of new functional materials based on transition metal oxides. For instance, nanostructured porous materials synthesized in the form of complex cobalt oxides like RBaCo2O5+x (R=rare earth) are promising for their application as electrode components in Solid Oxide Fuel Cells (SOFC) in hydrogen energetics. In the present study the quantum chemical cluster calculations are performed to provide a basis for a theoretical analysis of the thermally induced spin state transitions of cobalt ions in the complex cobalt oxide RBaCo2O5.5(R=Ho, Gd).

MATHEMATICAL MODELING OF QUANTUM WELL POTENTIALS IN NANOELECTRONICS

A.Suzko
Laboratory of Information Technologies, JINR

I. Tralle
Institute of Physics, University of Rzeszow, Poland

E.P. Velicheva
Dzhelepov Laboratory of Nuclear Problems


We apply the intertwining operator technique to the generalized Schrodinger equation with a position-dependent effective mass with linearly energy-dependent potentials and show how to construct the quantum well potentials in nanoelectronics with a given spectrum.

COHERENT SPIN DYNAMICS IN MAGNETIC NANOMOLECULES AND NANOCLUSTERS

V.I. Yukalov *, E.P. Yukalova**, V.K. Henner***, and P.V. Kharebov***

* Bogolubov Laboratory of Theoretical Physics Joint Institute for Nuclear Research, Dubna 141980, Russia
** Laboratory of Information Technologies Joint Institute for Nuclear Research, Dubna 141980, Russia
*** Department of Physics, Perm State Unirersity, Perm 614000, Russia


The peculiarities of coherent spin radiation by magnetic nanomolecules is investigated by means of numerical simulation. The consideration is based on a microscopic Hamiltonian taking into account realistic dipole interactions. Superradiance can be realized only when the molecular sample is coupled to a resonant electric circuit. The feedback mechanism allows one to reach a fast spin reversal time and a large radiation intensity. The influence on the level of radiation, caused by the sample shape and orientation, is analysed. The most powerful coherent radiation is found to occur for an elongated sample directed along the resonator magnetic field.

NANOTECH APPLICATION: BIOSENSOR DEVELOPMENT

V. V. Ivanov, P. V. Zrelov
Laboratory of Information Technologies, Joint Institute for Nuclear Research, Dubna 141980, Moscow region, Russia

V. S. Sivozhelezov
Chair of Biophysics, University of Genoa, Italy

R. V. Polozov
Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino 142290, Moscow Region, Russia


Nowadays the biosensor technologies, in particular those constructed on the basis of enzymes, are the basic tool in such areas as medical diagnostics, ecology and food industry. In these and a number of other scopes there is a necessity of defining the presence and measuring the concentration of the substances whose natural sensors are enzymes.

The basis of the biosensor technology is the immobilization of enzymes, i.e. the addition of the enzyme to a chemically inert insoluble material, the so-called "substrate", in the form of a film consisting of one or several monomolecular layers (nanolayers). Numerous experimental data on the enzymes immobilization, also for the biosensor development, have been accumulated in the world. However, they are disorder and therefore there is a need to classify them.

The database will allow one to use within the expert system all the data on the proteins immobilization available in the sources worldwide. The data being definitely ordered what will provide a way for effectively choice of only those from them which most exactly correspond to the predetermined characteristics of the biosensor. The software of the expert system should process simultaneously hundreds data arrays in real time, so the software should be adapted for work in a distributed computing environment.

References
[1]. V.V. Ivanov, P.V. Zrelov, R.V. Polozov, A.A. Kataev, V.S. Sivozhelezov: Toward computational biosensor nanotechnology: electrostatic properties of enzymes and polyelectrolytes, In Nuclear physics and nanotechnologies: Nuclear-physics aspects of formation, investigation, and application of nanostructures / A.N.Sisakian, Chief Editor, pp. 293-311, Dubna, 2008.

MOLECULAR CARTOGRAPHY OF DNA, RNA AND PROTEINS IN THE DISTRIBUTED COMPUTING INFRASTRUCTURE

O. A. Afanasyev, V. V. Ivanov, V. A. Stepanenko and P. V. Zrelov,
Laboratory of Information Technologies, Joint Institute for Nuclear Research, Dubna 141980, Moscow region, Russia

Y. N. Chirgadze
Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Moscow Region, Russia

R. V. Polozov
Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino 142290, Moscow Region, Russia


The problem of binding between DNA and specific functional protein factors faces very complex atomic surface interactions which presents both the relief of molecular surface and specific features of atomic functions. Usually, solution of this problem is based on a direct calculation of atomic interactions which allows learning the most important interactions. However, a systematic approach and analysis of numerous data requires the use of molecular cartography which is more representative than the lists of atomic pair interactions, and enables scientists of different professions to study the problem. In this communication we present first results on the use of a novel approach to analyzing molecular surface of biological molecules that have the shape of elongated helixes. In the case of the complex of operator DNA with transcription factor, the surface maps represent the surface of the recognizing alpha-helix of the protein factor and the surface of the specific binding groove of a double-chained DNA molecule.

A software program complex for investigation of the surface of biopolymer molecule proteins and nucleic acids is worked out. It includes three program codes: SURFACE-2008, PROT-Z and DNA/RNA-Z. These codes are based on the known program SURFACE [1, 2] designed earlier for the surface cartography of globular proteins in frames of MS DOS. New codes are realized in the DELPHI language in the framework of OC Windows, they have similar graphical interfaces for setting the control parameters and for presenting the computational results.

The code SURFACE-2008 is a modification of SURFACE for OC Windows together with both changing the coloring of atoms of amino acids and nucleotide bases in the Aitov-Hummer projections and including the compact saving of protein maps in the JPG-format.

New algorithms, not used earlier in the SURFACE code, are included into PROT-Z and DNA/RNA-Z codes. The PROT-Z code is intended for construction of maps of helical protein molecules, and the DNA/RNA-Z code - for helical DNA and RNA molecules. An original scheme of the cylindrical projection for the fragments of helical molecule on a plane is implemented in both codes. In this scheme, an axis Z of helical fragment of the molecule is directed along the vertical axis of the cylinder projection. The atoms are represented as spheres with the given van-der-Waals radii. Definite problems inherent, both to specificity of cylindrical projection and peculiarity of double-chained helical structures of DNA and RNA, were overcome.

The software complex involves the codes PROT-Zcompact and DNA/RNA-Zcompact which represent the modified Linux versions of codes PROT-Z and DNA/RNA-Z and are destined for organization of massive calculations of the map parameters in the distributed computing media. These parameters are used in full versions of corresponding programs for graphical presentation and further analysis of maps.

There are also additional service programs for the selecting definite chains and their segments of DNA or RNA from atomic coordinates of PDB-files (Protein Data Bank).

References:
[1.] Yu. Chirgadze, N. Kurochkina, S. Nikonov. Molecular cartography of proteins: surface relief analysis of the calf eye lens protein gamma-crystallin. Protein Engineering, 3, 105-110, 1989.
[2.] S. R. Aglyamov, Y. N. Chirgadze. Manual instruction of program SURFACE for calculation maps of molecular surface of globular proteins, ed. Institute of Protein Research RAS, 1999.

TeV Muon Reconstruction: from Data Handling to New Physics Phenomena

I.Golutvin*, V.Karzhavin*, P.Moissenz*, V.Palichik**, V.Perelygin*, S.Shmatov*

* - VBLHEP JINR; ** - LIT JINR

  • It is expected to start data taking at the LHC experiments in November, 2009 .
  • Multi-purpose physical program at these experiments makes high demands of their detecting systems.
  • The essential part of these physical tasks are the processes with reconstruction of muons.
  • Studies with TeV muons at the CMS experiment can lead to discoveries of new physical phenomena and also become a tool for testing the reconstruction algorithms on their efficiency and measurement accuracy.


Postal address:
LIT JINR, 141980 Dubna,
Moscow region, Russia
Phone: (7-49621) 64-019
Telefax: (7-49621) 65-145
E-mail: KTR@jinr.ru