Department of physics <br/>of biological systems | IOP
Department of physics
of biological systems
Department of physics <br/>of biological systems | IOP
Head of Department

Doctor of sciences, professor
Galina Dovbeshko


The department of physics of biological systems was created in the Institute of physics in 1995 for studying the biological objects by the methods of theoretical and experimental physics. Prof. Valery KharkyanenThe department was founded by the famous theoretical physicist Prof. Valery Kharkyanen (28.06.1946 — 01.08.2013).

The major research area is the physical principles of functioning of the biological macromolecules (proteins, DNA), supramolecular assemblies (biological membranes) and nanostructures (nanostructured surfaces and nanoparticles), which contain biological molecules. Special attention is paid to non-linear dynamic effects (synergetic effects) and non-linear stochastic dynamics.

Enhanced infrared and Raman spectroscopy methods are used for experimental studies. The methods of computational modeling (molecular dynamics, quantum chemistry) are actively used to complement theoretical studies. Original computational techniques and software are being developed.

The physical principles of functioning of biological macromolecules and their assemblies are studied usina a combination of experimental, theoretical and computational methods. The experimental techniques include various methods of the surface-enhanced infrared and Raman spectroscopy. The theoretical studies are focused on slow conformational dynamics, stochastic dynamics and the phenomena of dynamic self-organization. The computational techniques involve quantum chemistry, and atomistic and coarse-grained molecular dynamics simulation. Data analysis techniques and innovative molecular modeling software are also being developed.

Experimental facilities: IR Fourier spectrometer Bruker IFS-66, surface plasmon resonance instrument Plasmon-4M and all required equipment for sample preparation.

Physical mechanisms of the functioning of biological macromolecules in non-equilibrium conditions

  • Modeling of the structural and dynamical properties of the asymmetric biological membranes and the processes of transmembrane permeation of various biological molecules.
  • Modeling of the transport of ions and biological molecules through the artificial nanopores and carbon nanotubes.
  • Development of the theory of multi-particle diffusion in the narrow pores.
  • Development of the theory of dichotomic signals from the single biological molecules, which reflect their functional properties.
  • Theoretical and experimental study of dynamic self-organization phenomena in the photoreaction centers of purple bacteria.
  • Study of the self-organization phenomena in the ion channels of biological membranes.
  • Development of the methods for identification of dynamic protein domains and modeling of their motions.

Enhanced spectroscopy of the biological molecules

  • Studies of conformational transitions in biological molecules caused by small dozes of electromagnetic radiation during their interaction with drugs and various nanostructures in vivo and in vitro.
  • Studies of structural features of nucleic acids and lipids from sensitive and resistant strains of tumor cells before and after treatment by anti-tumor drugs.
  • Development of the methodology of detection of small quantities of biological molecules based on SEIRA and SERS effects.
  • Development of the nanostructures metal surfaces for enhanced spectroscopy.
  • Detection of the nanoparticles of the heavy metals oxides in the air by SEIRA spectroscopy.
  • Studies of DNA condensation by the polyvalent metal ions.

Software development

  • The concept of dynamic protein domains, which are units of protein structure, but retain a distinct pattern of large-scale collective motions, was developed (S. O. Yesylevskyy, V. M. Kharkyanen).
  • The kinetics of electron recombination in the bacterial photosynthetic center was studied. A number of relaxation components, which are caused by the formation of “taxonomical” states in the system with separated charges the revealed (V. M. Kharkyanen).
  • A general analytical theory for the single-file diffusion of multiple strongly interacting particles in a one-dimensional pore was developed for application to the pores of ionic channels and artificial nanopores (V. M. Kharkyanen, S. O. Yesylevskyy).
  • A polarizable water model for the coarse-grained MARTINI force field was developed (S. O. Yesylevskyy).
  • A user-friendly and high-performance Pteros library for molecular simulation and analysis of molecular dynamics (MD) trajectories using the C++ and Python programming languages was developed (S. O. Yesylevskyy).
  • A methodology of MD simulation of asymmetric and highly curved biological membranes was developed. Methods for determining the shape and the curvature of an arbitrary membranes with topology were developed (S. O. Yesylevskyy).
  • A methodology for the separation of single carbon nanotubes from the bundles, their characterization and creation of hybrid nanotube-biomolecules systems was created (G. I. Dovbeshko, O. P. Gnatyuk).
  • Experimental methods for enhanced spectroscopy of biomolecules and their complexes onnanostructured metal surfaces were developed (G. I. Dovbeshko).
  • A model of interaction between anti-tumor drugs and nucleic acids was developed (G. I. Dovbeshko).
  • The SEIRA (Surface Enhanced Infrared Absorption) technique was applied to study the nucleic acids from tumor cells and the conformational properties of biological molecules adsorbed on carbon nanotubes, graphene and metal nanostructures. Conformational changes in the DNA caused by its interaction with carbon nanotubes were revealed (G. I. Dovbeshko).
  • Optical properties of photonic crystals infiltrated by biological molecules and living cells were studied. It was shown that DNA luminescence is enhanced in photonic crystals and its frequency is shifted to the visible range (G. I. Dovbeshko, V. V. Boiko).
  • The theory of the multi-particle single-file diffusion in the narrow pores in non-equilibrium conditions is developed. The theory is applied to the KcsA potassium channel.
  • The concept of dynamic domains in proteins is created. Dynamic domains are large-scale units of collective diffusive dynamics. The methods of identification of dynamic domains and modeling of their motions are developed. The dynamic domains of the large number of proteins are identified.
  • The kinetics of recombination of the photomobilized electron in the bacterial photosynthetic center is studied. The number of relaxation components, which are described by the fractional-power-law and could be caused by forming of “taxonomical” states in the system with separated charges is revealed.
  • The methodology of separation of single carbon nanotubes from the bundles, their characterization and creation of the hybrid nanotube-biomolecules systems is created.
  • The experimental techniques of enhanced spectroscopy of the biomolecules and their complexes on the metal nanostructured surfaces are developed.
  • The model of interaction of the anti-tumor drugs with nucleic acids is developed.
  • The SEIRA (Surface Enhanced Infrared Absorption) technique was applied to study the nucleic acids from the tumor cells, conformational properties of the biological molecules adsorbed at the carbon nanotubes and metal nanostructures. Conformational changes in the DNA caused by its interaction with carbon nanotubes are revealed.

2013

  • Leonid N. Christophorov, Valeriy N. Kharkyanen, Nataliya M. Berezetskaya. Molecular self-organization: A single molecule aspect // Chemical Physics Letters 583 (2013) 170–174
  • O. Posudievsky, O. A. Khazieieva, V. V.Cherepanov, G. I. Dovbeshko, A. G. Shkavro, V. G. Koshechko and V. D. Pokhodenko, J. Mater. Chem. C, 2013, DOI:10.1039/C3TC30856A.
  • V.V. Boiko, O.M. Fesenko, V.F. Gorchev, S.O. Karakhim, L. Dolgov, V. Kiisk, I. Sildos, V.S. Gorelik, G.I. Dovbeshko. Luminescent imaging of biological molecules and cells on the photonic crystal surface, In Book: Nanomaterials Imaging Techniques, Surface Studies, and Applications, Ed.: Olena Fesenko, Leonid Yatsenko, Mikhaylo Brodin, Springer, 2013. pp. 253-262.
  • Galyna Dovbeshko, Olena Fesenko , Olena Gnatyuk, Anna Rynder and Oleg Posudievsky. Comparative Analysis of the IR Signal Enhancement of Biomolecules Adsorbed on Graphene and Graphene Oxide Nanosheets, In Book: Nanomaterials Imaging Techniques, Surface Studies, and Applications, Ed.: Olena Fesenko, Leonid Yatsenko, Mikhaylo Brodin, Springer, 2013. pp. 25-34.
  • Yesylevskyy, S.O., Kraszewski, S., Picaud, F., and Ramseyer, C. (2013). Efficiency of the monofunctionalized C60 fullerenes as membrane targeting agents studied by all-atom molecular dynamics simulations. Molecular Membrane Biology 30, 338–345.
  • Yesylevskyy, S.O., Demchenko, A.P., Kraszewski, S., and Ramseyer, C. (2013). Cholesterol Induces Uneven Curvature of Asymmetric Lipid Bilayers. The Scientific World Journal 2013 .

2012

  • S.O. Yesylevskyy, Pteros: Fast and easy to use open-source C++ library for molecular analysis // Journal of Computational Chemistry, - 33(19). - P. 1632–1636.
  • Yesylevskyy, S.O., and Demchenko, A.P. (2012). How cholesterol is distributed between monolayers in asymmetric lipid membranes. Eur Biophys J 41, 1043–1054.
  • G. Dovbeshko, O.Fesenko, O. Gnatyuk, A. Rynder, O. Posudievsky "Enhancement of infrared absorption of biomolecules absorbed on single-wall carbon nanotubes and graphene nanosheets", J. Nanophotonics, 6(1), 061711 (Oct 22, 2012). http://dx.doi.org/10.1117/1.JNP.6.061711
  • Dovbeshko, G.; Fesenko, O.; Boyko, V.; Romanyuk, V.; Moiseyenko, V.; Gorelik, V.; Dolgov, L.; Kiisk, V.; Sildos, I. Vibrational spectra of opal-based photonic crystals // IOP Conference Series: Materials Science and Engineering, 38, (012008-1) - (012008-6) (2012).
  • G.I.Dovbeshko, O.M.Fesenko, V.V.Boyko, V.R.Romanyuk, V.S.Gorelik, V.N.Moiseyenko, V.B.Sobolev, V.V. Shvalagin. Secondary emission from synthetic opal infiltrated by colloidal gold and glycine // Ukrainian Journal of Physics. – 2012. – Vol. 57, №2. – P. 154-158.
  • G.I. Dovbeshko, O.M.Fesenko, V.V.Boyko, V.F. Gorchev, S.O. Karakhin, N.Ya. Gridina, V.S. Gorelik, V.N. Moiseenko. Novel photoluminescence-enhancing substrates for image formation of biological objects. UJP – 2012. V. 57, №7. P.732-739)
  • М.А. Заболотний, А.І. Момот, Г.І. Довбешко, О.П. Гнатюк, Г.І. Соляник, О.П. Дмитренко, М.П. Куліш, К.В. Федіна. Модифікація структури алкалоїдів препарату Conium фулеренами C60 // УФЖ – 2012. – т.57, №7. – с. 739-745

2011

  • A.P. Demchenko, S.O. Yesylevskyy, Interfacial Behavior of Fluorescent Dyes // Advanced fluorescence reporters in chemistry and biology III: Applications in sensing and imaging. - 2011. - N 10. - P. 3-64.
  • S.O. Yesylevskyy, A.P. Demchenko, Fluorescence probing in structurally anisotropic materials // Advanced fluorescence reporters in chemistry and biology III: Applications in sensing and imaging. - 2011. - N 10. - P. 119-160.
  • Jaroslaw J. Panek, Aneta Jezierska, Aleksander Koll, Galina Dovbeshko, Olena Fesenko. p-Nitrobenzoic acid adsorption on nanostructured Au surface investigated by combined experimental and computational approaches // ChemPhysChem. – 2011. – Vol.12, P. 1 – 12.
  • V. Cherpak, P. Stakhira, S. Khomyak, D. Volynyuk, Z. Hotra, L. Voznyak, G. Dovbeshko, O. Fesenko, V. Sorokin, A. Rybalochka, O. Oliynyk. Properties of 2,6-di-tert.-butyl-4-(2,5-diphenyl-3,4-dihydro-2H-pyrazol-3-yl)-phenol as hole-transport material for life extension of organic light emitting diodes // Optical Materials. – 2011. – Vol.33, №11. – P. 1727-1731.
  • G.Dovbeshko O.Gnatyuk, K. Yakovkin, M.V. Shuba, S.A. Maksimenko. Enhancement of the infrared absorption by biomolecules adsorbed on single wall carbon nanotubes. In Book: “Physics, chemistry and application of nanostructures” Ed. V.E.Borisenko, S.V.Gaponenko, V.S.Gurin, C.H.Kam., Word Scientific, New Jersey- London- Singapore, 2011, p.291-298.
  • С.Д. Ісаєв, Г.І. Довбешко, Г. Жалніна, О.П. Гнатюк, П.А. Іванченко. Застосування методу SEIRA для визначення малих концентрацій забруднювачів у повітрі // Наукові записки НАУКМа: Хімічні науки і технології. – 2011. – Том 118, с. 40-48.
  • Anthony J. Manzo, Alexander O. Goushcha, Nataliya M. Berezetska, Valery N. Kharkyanen and Gary W. Scott. Charge Recombination Time Distributions in Photosynthetic Reaction Centers Exposed to Alternating Intervals of Photoexcitation and Dark Relaxation.
  • The Journal of Physical Chemistry B. 115(26), P. 8534-8544.
  • Valeriy N. Kharkyanen, Yuri M. Barabash, Nataliya M. Berezetskaya, Eugene P. Lukashev, Peter P. Knox, Leonid N. Christophorov. Peculiarities of light-induced slow protein dynamics in the photosynthetic reaction center. Chemical Physics Letters. 512 (2011) P. 113–117.

2010

  • V.N. Kharkyanen, S.O. Yesylevskyy, N.M. Berezetskaya, Approximation of super-ions for single-file diffusion of multiple ions through narrow pores // Phys. Rev. E. - 2010. - V. 82. - N 5. - P. 051103.
  • S.O. Yesylevskyy, L.V. Schafer, D. Sengupta, S.-J. Marrink, Polarizable water model for the coarse-grained MARTINI force field // PLoS Comput. Biol. - 2010. - V. 6. - N 6. - P. E1000810.
  • Arakawa H. G. Dovbeshko, S.Diamantoglou, Heidar-Ali Tajmir Riahi Oxovanadium ions transfer RNA at multiple sites. DNA and cell biology. – 2010. -Vol. 29, №8. — P. 459-464.
  • G. Dovbeshko, O. Fesenko, O. Gnatyuk, Ya. Shtogun, L. Woods, S. Bertarione, A. Damin, D. Scarano, Adriano Zecchina, Nucleic acid interaction and interfaces with single-walled carbon nanotubes, “Carbon Nanotubes”, 2010, Ed. By Jose Mauricio Marulanda, In-Tech., 2010. pp.697-719.
  • G.I Dovbeshko, E. M. Fesenko, V.R.Romanyuk, V.I.Perekrestov, Yu.).Kosminska, S.I.Kshnyakina, Porous Al and Cu structures as infrared signal enhancers, Functional materials, 17, No1, 2010, p.1-5.
  • M. A. Zabolotny, E. S. Kobus, O. P. Dmitrenko, N. P. Kulish, N. M. Belyi, E. V. Stasyuk, Yu. M. Barabash, G. I. Dovbeshko, E. M. Fesenko, Yu. P. Piryatinskii, D. A. Grin’ko, Nonlinear optical properties of poly( N -vinylcarbazole)-C 60 nanocomposites, PHYS SOLID STATE , vol. 52, no. 4, pp. 884-888, 2010.
  • V.N. Kharkyanen, Yu.М. Barabash, N.М. Berezetskaya, М.V. Olenchuk, P.P. Knox, L.N. Christophorov. Deceleration of the electron transfer reaction in the photosynthetic reaction centre as a manifestation of its structure fluctuations. Biopolymers & Cell. 26, #4, 286-294 (2010)

2009

  • V.N. Kharkyanen, S.O. Yesylevskyy, Theory of single-file multiparticle diffusion in narrow pores. // Phys. Rev. E. - 2009. - V. 80. - P. 031118.
  • S.O. Yesylevskyy, S.-J. Marrink, A.E. Mark, Alternative mechanisms for the interaction of the cell-penetrating peptides penetratin and the TAT peptide with lipid bilayers. // Biophys. J. - 2009. - V. 97. - N 1. - P. 40-49.
  • G. Dovbeshko, O. Fesenko, K. Allahverdiev, A. Kaya. Conformational analysis of nucleic acids and proteins adsorbed on single walled carbon nanotubes. Journal of Structural Chemistry. – 2009. – Vol.50, №5. – P.991-999.
  • D.Kosenkov, Ya. Kholod, L.Gorb, O.Shishkin, G.M.Kuramshina, G.I.Dovbeshko, J.Leszczynsky Effect of a pH Change on the Conformational Stability of the Modified Nucleotide Queuosine Monophosphate. J. Phys. Chem. A. – 2009. –Vol. 113(33). –P. 9386–9395
  • G. Dovbeshko1, L. Woods, Ya. Shtogun, O. Fesenko. Modeling of DNA base interactions with carbon nanotubes: ab initio calculations and SEIRA data //AIP 2009. – Vol.2, №8.-рр. 416-420.
  • Anthony J. Manzo, Alexander O. Goushcha, Yuri M. Barabash, Valery N. Kharkyanen, Gary W. Scott. Equilibration kinetics in isolated and membrane-bound photosyntethic reaction centers upon illumination: a metod to determane the photoexcitation rate. Photosynth Res. DOI 10.1007/s 11120-009-9502-7.

2008

  • G. Dovbeshko, O. Fesenko, K. Yakovkin, S. Bertrione, A. Damin, D. Scarano, A. Zecchina, E. Obraztsova. The poly-A interaction and interfaces with carbon nanotubes. Molecular Crystals Liquid Crystals. – 2008. – Vol 496, №345331 – P. 170-185
  • G. Dovbeshko, O. Fesenko, V. Moiseyenko, V. Gorelik, V. Boyko and V. Sobolev. Multiscaled Ordered Carbon Nanotubes As a Model of Photonic Crystals. // Semiconductor physics, quantum electronics and optoelectronics. – 2008. -Vol.11, №4.-рр. 392-395.
  • D. Chubich, G. Dovbeshko, O. Fesenko, R. Fedorovich, T. Gavrilko, V. Cherepanov, A. Marchenko, A. Naumovets, V. Nechitaylo, G. Puchkovska, L. Viduta and A. Vitukhnovskii. Light-Emitting Diode of Planar Type Based on Nanocomposites Consisting of Island Au Film and Organic Luminofore Tb(thd)3 // Molecular Crystals Liquid Crystals. – 2008. – Vol 497, №346433. – pp. 186-195.
  • S. L. Bravina, N. V. Morozovsky, G. I. Dovbeshko, O. M. Fesenko, and E. D. Obraztsova. Carbon nanotubes based black absorbing coatings for pyroelectric and other thermal detector application. // Наносистеми, наноматеріали, нанотехнології. – 2008. – Т.4, 112-120.
  • D. Chubich, G. Dovbeshko, O. Fesenko, R. Fedorovich, T. Gavrilko, V. Cherepanov, A. Marchenko, A. Naumovets, V. Nechitaylo, G. Puchkovska, L. Viduta and A. Vitukhnovskii. Light-Emitting Diode of Planar Type Based on Nanocomposites Consisting of Island Au Film and Organic Luminofore Tb(thd)3 // Molecular Crystals Liquid Crystals. – 2008. – Vol 497, №346433. – pp. 186-195.
  • Maryna Olenchuk, Nataliya Berezetska. Study of the Recombination Process of Light-Induced Charge Separation in Reaction Centers of Purple Bacteria Under Long-Term Exposition. Mol. Cryst. Liq. Cryst. 2008, Vol. 497, pp. 121.

2007

  • Shtogun Ya.V. Woods L. M., Dovbeshko G.I. Adsorption of Adenine and Thymine and Their Radicals on Single-Wall Carbon Nanotubes. J. Phys. Chem. C. – 2007. – Vol. 111. –P. 18174–18181.
  • Ostapenko N.I. G. Dovbeshko, N. Kozlova, S. Suto, A. Watanabe Conformation change of nanosized silicon-organic polymer oriented into ordered nanoporous silicas. Thin Solid Films. –2007. TSF. – P.24204.
  • Christophorov, V.N. Kharkyanen. Discrete versus continuous schemes of conformational regulation. Chem. Phys. Res. J. 2007, 1, #1-3, pp. 1-14.
  • M.V. Olenchuk, Yu.M. Barabash, L.N. Christophorov, V.N. Kharkyanen. Peculiarities of light propagation through the media of molecules with long-lived photoexcited states. Chem.Phys.Letters. 2007. vol. 447, pp.358-363.

2006

  • Ю.М. Барабаш, Н.М. Березецька, В.М. Харкянен, Л.М. Христофоров. Синергетичні механізми структурної регуляції реакцій біологічних макромолекул. Фундаментальні орієнтири науки. 2006 р. 239-260.
  • Yesylevskyy, S.O., V.N. Kharkyanen, and A.P. Demchenko, Dynamic protein domains: identification, interdependence and stability. . Biophys. J., 2006. 91: p. 670-685.
  • Yesylevskyy, S.O., V.N. Kharkyanen, and A.P. Demchenko, The change of protein intradomain mobility on ligand binding, is it a commonly observed phenomenon? Biophys J, 2006. 91: p. 3002-3013.

  • Collective photo of department

Ongoing projects:

  • В/173 The study of structural and dynamic properties of natural and artificial nanosystems containing biological macromolecules and their complexes.
  • ВЦ-156 The study of condensed systems at the nanometer scale to clarify size-dependent physical effects and the development of physical foundations of new electronic and ionic technologies.
  • IncoNet EaP Twinning Grant “Controlling translocation of water-soluble anti-cancer drugs through cell membrane byphotoswitchable molecules: a computational study”.
  • Russian-Ukrainian project 27-02-14(5) “Trapping of electromagnetic radiation in resonance structures and in resonance photonic crystals with luminescence centers”.
  • Ukrainian-Poland project “Hybrid graphene nanomaterials for catalytic applications”.
  • Marie Curie action FP7-PEOPLE-2012-IRSES Fundamental and applied electromagnetics of nanocarbon.