Sergei Gavryushov, Ph.D.
email: sergei_gavryushov@yahoo.com
SUMMARY
Over 30 years Programming Experience, Applied Mathematics, Geophysics, Electrodynamics, Statistical Physics, Biophysics, and Computer Graphics.
WORK HISTORY
7/03-12/15 Researcher, Engelhardt Institute of Molecular Biology, Russ. Acad. Sci., Moscow, Russia
computer simulations of solvated macromolecules; development of a theory of electrostatics of DNA in the presence of multivalent ions; structural enzymology and mechanism of enzymatic reaction studies
7/03 - 11/04: leading researcher in a project of software development for rapid inversion of geophysical data of electromagnetic soundings; application of artificial neural network technique and parallel programming to magnetotelluric data processing
4/02-6/03 Postdoctoral Researcher, Physical Chemistry 1, Center for Chemistry and Chemical Engineering, Lund University, Lund, Sweden
computer simulations of solvated ions in a strong electric field; development of a theory of electrostatics of DNA in the presence of multivalent ions
1/00-3/02 Postdoctoral Researcher, Engelhardt Institute of Molecular Biology, Russ. Acad. Sci., Moscow, Russia
designed an advanced program for visualization and docking of biological macromolecules on PCs;
research project in the field of geophysics; technology and software development
1/99-12/99 Postdoctoral Researcher, Institute of Biocybernetics & Biomedical Engineering, Warsaw, Poland
1/97-12/98 Ph.D. student, Institute of Biochemistry and Biophysics (IBB) PAS, Warsaw, Poland
designed prototype of a package of software for advanced calculation of electrostatics of biological macromolecules on parallel supercomputers (Cray T3E)
1/96-12/96 Physicist, department of biophysics, IBB PAS, Warsaw
8/94-12/95 Fellow in biophysics, European Fellowship Fund, IBB PAS, Warsaw
1993-8/94 Researcher, Center of Bioengineering RAS, Moscow, Russia
designed an extremely high performance computer graphics program for visualization of biological macromolecules on PCs; Photorealistic quality of filling space model images together with the real time scale rotation were obtained for large macromolecules even on the Intel 386 processor
1990-1992 Programmer, computer graphics and animation on PCs, software firms, Moscow
created a package of high performance computer graphics utilities for design of computer games
1986-1990 Researcher, Moscow Geological Prospecting Institute, Geophysical faculty; numerical methods in electrodynamics
development of methods and software for solution of the inverse problems of electromagnetic soundings
EDUCATION
1/97-11/98 Ph.D. Biophysics Institute of Biochemistry and Biophysics, Polish Acad. Sci., Warsaw, Poland.
Dissertation: Electrostatics of Biological Macromolecules in Electrolyte Solutions. Application of the Modified Poisson-Boltzmann Theory.
1981-1986 M.S. Geophysics Moscow Geological Prospecting Institute, Geophysical faculty
PUBLICATIONS
Polyakov, K. M., Gavryushov, S. Mechanism of Thiocyanate Dehydrogenase Functioning Based on Structural Data. Mol. Biol. (Mosk) 59:123-134 (2025);
Gavryushov, S., Bashilov, A., Cherashev-Tumanov, K. V., Kuzmich, N. N., Burykina, T. I., Izotov, B. N. Interaction of Synthetic Cannabinoid Receptor Agonists with Cannabinoid Receptor I: Insights into Activation Molecular Mechanism. Int. J. Mol. Sci. 24, 19: 14874 (2023);
Gavryushov, S., Kuzmich, N. N., Polyakov, K. M. Quantum mechanical study of oxygen ligands protonation for the stable states of the laccase active site. Int. J. Mol. Sci. 24, 3: 2990 (2023);
Polyakov, K. M., Gavryushov, S., Fedorova, T. V., Glazunova, O. A., Popov, A. N. The subatomic resolution study of laccase inhibition by chloride and fluoride anions using single-crystal serial crystallography: insights into the enzymatic reaction mechanism. Acta Cryst. D 75:804-816 (2019);
Alexeev, C. S., Kulikova, I. V., Gavryushov, S., Tararov, V. I., Mikhailov, S. N. Quantitative Prediction of Yield in Transglycosylation Reaction Catalysed by Nucleoside Phosphorylases. Adv. Synth. Catal. 360:1-8 (2018);
Spada, S., Gavryushov, S., Bohinc, K. Uniformly charged nanoparticles between like-charged walls. J. Mol. Liq. 270:178-182 (2018);
Polyakov, K. M., Gavryushov, S., Ivanova, S., Fedorova, T. V., Glazunova, O. A., Popov, A. N., Koroleva, O. V. Structural study of the X-ray-induced enzymatic reduction of molecular oxygen to water by Steccherinum murashkinskyi laccase: insights into the reaction mechanism Acta Cryst. D 73:388-401 (2017);
Bohinc, K., Bossa, G. V., Gavryushov, S., May, S. Poisson-Boltzmann model of electrolytes containing uniformly charged spherical nanoparticles. J.Chem. Phys. 145:234901 (2016);
Znamenskaya, Y., Sotres, J., Gavryushov, S., Engblom, J., Arnebrant, T., Kocherbitov, V. Water Sorption and Glass Transition of Pig Gastric Mucin Studied by QCM-D. J. Phys. Chem. B 117:2554-2563 (2013);
Novikov, M. S., Valuev-Elliston, V., T., Babkov, D. A., Paramonova, M. P., Ivanov, A. V., Gavryushov, S. A., Khandazhinskaya, A. L., Kochetkov, S. N., Pannecouque, C., Andrei, G., Snoeck, R., Balzarini, J., Seley-Radtke, K. L. N1,N3-disubstituted uracils as nonnucleoside inhibitors of HIV-1 reverse transcriptase. Bioorg. and Med. Chem. B 21:1150-1158 (2013);
Gavryushov, S. Mediating Role of Multivalent Cations in DNA Electrostatics: An Epsilon-Modified Poisson-Boltzmann Study of B-DNA - B-DNA Interactions in Mixture of NaCl and MgCl2 Solutions J. Phys. Chem. B 113:2160-2169 (2009);
Gavryushov, S. Electrostatics of B-DNA in NaCl and CaCl2 Solutions: Ion Size, Interionic Correlation, and Solvent Dielectric Saturation Effects J. Phys. Chem. B 112:8955-8965 (2008);
Panova, N. G., Alexeev, C. S., Polyakov, K. M., Gavryushov, S. A., Kritzyn, A. M., Mikhailov, S. N. Substrate specificity of thymidine phosphorylase of E. coli: role of hydroxyl groups Nucleosides Nucleotides Nucleic Acids 27:1211-1214 (2008);
Gavryushov, S. Dielectric Saturation of the Ion Hydration Shell and Interaction between Two Double Helices of DNA in Mono- and Multivalent Electrolyte Solutions: Foundations of the e-Modified Poisson-Boltzmann Theory. J. Phys. Chem. B 111:5264-5276 (2007);
Shimelevich, M. I., Obornev, E. A., Gavryushov, S. Rapid neuronet inversion of 2D magnetotelluric data for monitoring of geoelectrical section parameters. Annals of Geophysics (It) 50:105-109 (2007);
Panova, N. G., Alexeev, C. S., Kuzmichov, A. S., Shcheveleva, E. V., Gavryushov, S. A., Polyakov, K. M., Kritzyn, A. M., Mikhailov, S. N., Esipov, R. S., Miroshnikov, A. I. Substrate specificity of Escherichia coli thymidine phosphorylase. Biochemistry (Mosc) 72:21-28 (2007);
Gavryushov, S. Efective Interaction Potentials for Alkali and Alkaline Earth Metal Ions in SPC/E Water and Polarization Model of Hydrated Ions. J. Phys. Chem. B 110:10888-10895 (2006);
Gavryushov, S., and P. Linse. Efective Interaction Potentials for Alkali and Alkaline Earth Metal Ions in SPC/E Water and Prediction of Mean Ion Activity Coefficients. J. Phys. Chem. B 110:10878-10887 (2006);
Shimelevich, M. I., Obornev, E. A., Gavryushov, S. A. Application of neuronet approximation to the solution of geo-electromonitoring problems. Izvestiya Vuzov, Geology and Prospecting 4:70-71 (in Russian) (2003);
Gavryushov, S., and P. Linse. Polarization Deficiency and Excess Free Energy of Ion Hydration in Electric Fields. J. Phys. Chem. B 107:7135-7142 (2003);
Shimelevich, M. I., Obornev, E. A., Gavryushov, S. A. A method of designing neural networks for solving multiparametric inverse problems of magnetotelluric sounding. Izvestiya Vuzov, Geology and Prospecting 6:129-137 (in Russian) (2001);
Gavryushov, S., and P. Zielenkiewicz. Electrostatics of a DNA-like Polyelectrolyte: Effects of Solvent Dielectric Saturation and Polarization of Ion Hydration Shells. J. Phys. Chem. B 103:5860-5868 (1999);
Gavryushov, S., and P. Zielenkiewicz. Electrostatic potential of B-DNA: Effect of Interionic Correlations. Biophys. J. 75:2732-2742 (1998);
Gavryushov, S., and P. Zielenkiewicz. Electrostatic potential and free energy of proteins: a comparison of the Poisson-Boltzmann and the Bogoliubov- Born-Green-Yvon equations. J. Phys.Chem. B 101:10903-10909 (1997);
Gavryushov, S., and P. Zielenkiewicz. Multivalent ion distribution around a cylindrical polyion: contribution of polarization effects due to difference between dielectric properties of the macromolecule's interior and the aqueous solvent. J. Phys. Chem. B 101:792-797 (1997)
Kolbanovskaia, E.I., Morozov, N.I., Gavriushov S.A., Il'in V.A., Beintmena, J., Vlodaver, A., Karpeiskii, M.I. Structure-activity analysis of ribonuclease A and related proteins. Mol Biol (Mosk). 27(6):1315-1334 (1993)
Gavryushov, S. A. and Shimelevich, M. I. Low-frequency asymptotic method of magnetotelluric sounding data processing. Izvestiya Vuzov, Geology and Prospecting 3 (in Russian) (1990)
Gavryushov, S. A. The variable stars V962 and V987 Ophiuchi. Variable Stars supp 4, 242-244 (in Russian) (1982)