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Key publications:

Personal publications: Medvedev N.N., Naberukhin Y.I., Efimov Y.Y., Voloshin V.P., Anikeenko A.V.Kim A.V.

Book: "Voronoi-Delaunay method for non-crystalline structures"

Corrections: Erratum


Key publications

2012, 2011, 2010, 2009, 2008, 2007, 2006, 2005, 2004

2019

A.V. Kim, E.A. Shelepova,  O.Y. Selyutina, E.S. Meteleva, A.V. Dushkin, N.N. Medvedev, N.E. Polyakov, N.Z. Lyakhov. Glycyrrhizin-assisted transport of praziquantel anthelmintic drug through the lipid membrane: an experiment and MD simulation // Molecular Pharmaceutics, 16(7), 2019, 3188-3198. DOI

2018

E.A. Shelepova, A.V. Kim, V.P. Voloshin, N.N. Medvedev. Intermolecular Voids in Lipid Bilayers in the Presence of Glycyrrhizic Acid // The Journal of Physical Chemistry B, 122.43 (2018): 9938-9946. DOI

 V.P. Voloshin, A.V. Kim, E.A. Shelepova, N.N. Medvedev. Determination of the boundary surface between the lipid bilayer and water.// Journal of Structural Chemistry  2018, 59 (1), P. 96-105. DOI PDF

2017

 A.V.Anikeenko, E.D.Kadtsyn, N.N.Medvedev. Statistical geometry characterization of global structure of TMAO and TBA aqueous solutions. // Journal of Molecular Liquids, 2017, 245, 35-41. DOI PDF

● Smolin N, Voloshin VP, Anikeenko AV, Geiger A, Winter R, Medvedev NN. TMAO and urea in the hydration shell of the protein SNase. // Phys Chem Chem Phys. 2017, 19(9):6345-6357. DOI PDF

● B. Fabian, M. Sega, V.P. Voloshin, N.N. Medvedev, P. Jedlovszky. Lateral Pressure Profile and Free Volume Properties in Phospholipid Membranes Containing Anesthetics // J. Phys. Chem. B 2017, 121, 2814 −2824. DOI PDF

● Anikeenko, A.V., Zelikman, M.V., Kadtsyn, E.D. Medvedev N.N. Simulation of glycyrrhizic acid associates with cholesterol in methanol Journal of Structural Chemistry (2017) 58 (2), 268–275. DOI PDF

2016

 E.D. Kadtsyn, A.V. Anikeenko, N.N. Medvedev. Molecular dynamics simulation of a DNA duplex labeled with triarylmethyl spin radicals // Journal of Molecular Liquids, 2016. DOI PDF

 M.V. Zelikman, A.V. Kim, N.N. Medvedev, Structure of Small Associates of Glycyrrhizic Acid with Cholesterol in an Aqueous Solution: Molecular Dynamics Simulation // Journal of Structural Chemistry. 2016, 57 (5), pp. 940-946. DOI PDF

2015

V.P. Voloshin, N.N. Medvedev, N. Smolin, A. Geiger, R. Winter. Exploring volume, compressibility and hydration changes of folded proteins upon compression. Phys. Chem. Chem. Phys., 17, 8499-8508, 2015. DOI PDF

2014

V.P. Voloshin, A.V. Kim, N.N. Medvedev, R. Winter, A. Geiger. "Calculation of the volumetric characteristics of bio-macromolecules in solution by the Voronoi-Delaunay technique". Biophysical Chemistry, 192, 1-9, 2014. DOI PDF

Kim, A.V., Medvedev, N.N., A. Geiger. Molecular dynamics study of the volumetric and hydrophobic properties of the amphiphilic molecule C8E6// Journal of Molecular Liquids, 189, pp 74–80, 2014. DOI PDF

V.P. Voloshin, N.N. Medvedev, and A.Geiger. Fast Calculation of the Empty Volume in Molecular Systems by the use of Voronoi-Delaunay Subsimplexes // Trans. on Comput. Sci. XXII, LNCS 8360,  p.156, 2014. DOI PDF

2013

A.V. Anikeenko, N.N. Medvedev, N.F. Uvarov, Molecular dynamics study of ion migration mechanism in rubidium nitrate// Solid State Ionics, 251, 13-17, 2013. DOI

Kim, A.V., Voloshin, V.P., Medvedev, N.N., A. Geiger. "Decomposition of a protein solution into Voronoi shells and Delaunay layers: calculation of the volumetric properties". Transactions on Computational Science XX , Springer, Volume 8110, pp 56-71, 2013. DOI PDF

A.S. Roik, A.V. Anikeenko, N.N. Medvedev, "Polytetrahedral order and chemical short-range order in metallic melts”, Journal of Structural Chemistry, Volume 54, Issue 2, pp. 332-340, 2013. DOI PDF

Medvedev, N.N., Voloshin, V.P., Kim, A.V., Anikeenko, A.V., Geiger, A. Calculation of the partial molar volume and its components on the molecular dynamics models of dilute solutions. // Zh. Struct. Khimii 2013,  Vol 54 (Supplement no.2), S276-S297 (in Russian). URL PDF

2012

 Kim, A.V., Voloshin, V.P.,  Medvedev, N.N.,  Geiger, A. "Decomposition of a Protein Solution into Voronoi Shells and Delaunay Layers". Voronoi Diagrams in Science and Engineering (ISVD), 2012 Ninth International Symposium on, pp. 95-102. DOI

2011

V.P. Voloshin, N.N. Medvedev, M.N. Andrews, R.R. Burri, R. Winter, A. Geiger,  Volumetric Properties of Hydrated Peptides: Voronoi-Delaunay Analysis of Molecular Simulation Runs, J. Phys. Chem. B,  2011, 115 (48), pp 14217–14228. DOI

Yu.I. Naberukhin, V.P. Voloshin. Structure of ice Ih and ice Ic as described in the language of Delaunay simplices. Acta Crystallographica Section A. 2011, A67, 507–511. DOI, PDF

V.P. Voloshin, A.V. Anikeenko, N.N. Medvedev, A. Geiger, "An algorithm for the calculation of volume and surface of unions of spheres. Application for solvation shells", Proceedings of Eighth International Symposium on Voronoi Diagrams in Science and Engineering (ISVD 2011), Qingdao, China, June 28th - 30th, 2011, pp. 170-176. DOI

A.V. Anikeenko, N.N. Medvedev, "On the high density of liquid cyclohexane", Journal of Structural Chemistry, Volume 52, Number 3, pp. 497-504, 2011. DOI

A.S. Roik, A.V. Anikeenko, N.N. Medvedev, "Investigation of the particular features of the structure factor of liquid Al-based alloys", Journal of Molecular Liquids, 2011, Volume 161, Issue 2, pp. 78-84. DOI

N.F. Uvarov, A.S. Ulikhin, A.A. Iskakova, N.N. Medvedev, A.V. Anikeenko, "Ionic conductivity in orientationally disordered phases", Russian Journal of Electrochemistry, Volume 47, Number 4, pp. 404-409, 2011. DOI

N.F. Uvarov, A.A. Iskakova, A.S. Ulihin, N.N. Medvedev, A.V. Anikeenko, "Ion transport in salts orientationally disordered in anionic sublattice", Solid State Ionics, Volume 188, Issue 1, pp. 78-82, 2011. DOI

2010

A.V. Anikeenko, A.V. Kim, N.N. Medvedev, "Molecular dynamics simulation of the structure of C6 alkanes", Journal of Structural Chemistry, Volume 51, Number 6, pp. 1090-1096, 2010. PDF DOI

V.P. Voloshin, A.V. Anikeenko, N.N. Medvedev, A. Geiger, D. Stoyan, "Hydration Shells in Voronoi Tessellations", Proceedings of Seventh International Symposium on Voronoi Diagrams in Science and Engineering (ISVD 2010), 28-30 June 2010, Quebec, Canada, pp. 254-259. DOI

2009

A.V. Anikeenko, A.V. Kim, N.N. Medvedev, "Delaunay simplexes in liquid cyclohexane", proceedings of Sixth International Symposium on Voronoi Diagrams in Science and Engineering (ISVD 2009), 23-26 July 2009, Technical University of Denmark, Kongens Lyngby, Municipality of Lyngby-Taarbæk, Denmark; published by IEEE Computer Society. pp. 271-277.

2008

Alexey V. Anikeenko, Marina L. Gavrilova, Nikolai N. Medvedev.  Shapes of Delaunay Simplexes and Structural Analysis of Hard Sphere Packings . In book:  Generalized Voronoi Diagram: A Geometry-Based Approach to Computational Intelligence.  Ed. Marina L. Gavrilova, Springer-Verlag Berlin Heidelberg.  In serial: Studies in Computational Intelligence,Volume 158,  pp 13-45, 2008. PDF

A. V. Anikeenko and N. N. Medvedev, T. Aste. Structural and entropic insights into the nature of the random-close-packing limit. // Physical Review E 77, 031101 (2008). PDF

2007

A.V. Anikeenko and N. N. Medvedev. Polytetrahedral Nature of the Dense Disordered Packings of Hard Spheres. PRL 98, 235504 (2007). PDF

A.V. Anikeenko, N.N. Medvedev, A. Bezrukov, D.Stoyan, "Observation of fivefold symmetry structures in computer models of dense packing of hard spheres", Journal of Non-Crystalline Solids, 353, pp. 3545-3549, 2007. DOI

A.V. Anikeenko, N.N. Medvedev, "Structural features of dense hard-sphere packings. Critical densities", Zhurnal Strukturnoi Khimii , V. 48, No. 4, pp. 823-830, 2007 (in russian).

2006

Medvedev N.N., Voloshin V.P., Luchnikov V.A., Gavrilova M.L. An algorithm for three-dimensional Voronoi S-network . J. of Comput. Chem. Vol. 27, (14) , pp. 1676 - 1692 (2006). PDF

Lochmann K., Anikeenko A.V, Elsner A., Medvedev N.N., Stoyan D. Statistical verification of crystallization in hard sphere packings under densification. Eur. Phys. J. B 53, 67-76 (2006). PDF

A.V. Anikeenko, M.L. Gavrilova and N.N. Medvedev. A novel delaunay simplex technique for the detection of crystalline nuclei in dense packings of spheres. Journal of Ceramic Processing Research. Vol. 7, No. 3, pp.195-200 (2006). PDF

Yu. I. Naberukhin, V. P. Voloshin. Sructure of large noncrystalline Lennard-Jones models. // Journal of Structural Chemistry , 47, Supplement, pp S126-S140, 2006. PDF, Doc(Rus)

Anikeenko A. V., Medvedev N. N. Homogeneous crystallization of the Lennard-Jones liquid. Structural analysis based on Delaunay simplices method. Journal of Structural Chemistry, Vol.47, (2) 267-276 (2006). PDF, PDF (Russian)

M. G. Alinchenko, A. V. Anikeenko, V. P. Voloshin, N. N. Medvedev, D. Paschek, A. Appelhagen, and A. Geiger. Spatial correlations of interatomic voids in molecular liquids studied using delaunay simplices. Journal of Structural Chemistry, Vol. 47, Supplement, pp. S119-S125, 2006. PDF, PDF (Russian)

A.V. Kim and N.N.Medvedev. Melting and homogeneous crystallization of a Lennard-Jones systems. Journal of Structural Chemistry, vol.47, Supplement, pp.S141-S150, 2006. PDF, Doc (Russian)

Anikeenko A.V., Medvedev N.N. and Gavrilova M.L. Application of Procrustes Distance to Shape Analysis of Delaunay Simplexes. Proceedings of the 3rd International Symposium on Voronoi Diagrams in Science and Engineering 2006. Ed. B.Werner, IEEE Computer Society, 148-152, (2006). abstract, PDF

Anikeenko A.V., Medvedev N.N., Elsner A., Lochmann K., and Stoyan D. Critical densities in hard sphere packings. Delaunay simplex analysis. Proceedings of the 3rd International Symposium on Voronoi Diagrams in Science and Engineering 2006. Ed. B.Werner, IEEE Computer Society, 153-158, (2006). abstract, PDF

2005

Anikeenko A.V., Gavrilova M.L., Medvedev N.N. The coloring of the Voronoi network: investigation of structural heterogeneity in the packings of spheres". // Japan J.Indust. Appl. Math., 22, 151-165 (2005). PDF

Rabinovich A. L., Balabaev N. K., Alinchenko M. G., Voloshin V. P., Medvedev N. N., Jedlovszky P., "Computer simulation study of intermolecular voids in unsaturated phosphatidylcholine lipid bilayers", // J. Chem. Phys. 122 Article No. 084906 (2005). PDF

Anikeenko A.V., Gavrilova M.L., Medvedev N.N., A novel Delaunay simplex technique for detection of crystalline nuclei in dense packings of spheres. // Lecture Notes in Computer Science (LNCS). 3480, 816 - 826 (2005). PDF

Alinchenko M.G., Voloshin V.P., Medvedev N.N., Mezei M., Partay L., and Jedlovszky P. Effect of cholesterol on the properties of phospholipid membranes. 4. Interatomic voids. // J. Phys. Chem. B, 109 (34), 16490 -16502 (2005). PDF

Voloshin V.P., Naberukhin Yu.I. Structure of the interparticle space in big noncrystalline packings of the Lennard-Jones atoms and its influence on the diffusion mobility of admixed particles.// Zhurnal Strukturnoi Khimii46(2)273 - 283 (2005) PDF(in Russian)

Voloshin V.P., Medvedev N.N., Investigation of the prepeak in the structure factor . The study of inhomogeneous packings of  Lennard-Jones atoms.// Zhurnal Strukturnoi Khimii, Vol.46, (1), 96-100 (2005). PDF(Russian)

Medvedev N.N., Voloshin V.P., Intermolecular voids for structure investigation  of computer model of liquids and glasses.// Zhurnal Strukturnoi Khimii, Vol.46, (1), 98 - 101. abstractPDF(Russian)

Voloshin V.P., Medvedev N.N., Naberukhin Yu.I., Geiger A., Klene M. Radial Distribution Functions of Atoms and Voids in Large Computer Models of Water.// Journal of Structural Chemistry 46(3), 438-445 (2005) PDF, PDF(Russian)

N.N.Medvedev. Concept of navigation map for empty interatomic space and its applications. In Proceedings of The 2nd International Symposium on Voronoi Diagrams in Science and Engineering. Oct. 10-13, 2005, Hynyang University, Seoul, Korea. pp.72-73.

Yu.Ya.Efimov, Yu.I.Naberukhin, Thermodynamic functions of liquid water calculated from the temperature evolution of the vibration spectrum contour // Spectrochimica Acta, Part A: Mol. & Biomolecular Spectroscopy, 2005, Volume/Issue 61/8, pp. 1789-1794.

  Yu.Ya.Efimov, N.N.Medvedev, Yu.I.Naberukhin. New Aspects of Water Structure: Molecular Spectroscopy and Computer Simulation Analysis. In Proceedings of the nternational Symposium of the Association of Academies of Science in Asia on Science and Technology of Water in memory of the late Prof. Mu Shik Jhon., Oct.12, 2005, Seoul, Korea. pp.45-52. PDF

2004

M.G. Alinchenko and A. V. Anikeenko, N. N. Medvedev and V. P. Voloshin, M. Mezei, P. Jedlovszky. Morphology of Voids in Molecular Systems. A Voronoi-Delaunay Analysis of a Simulated DMPC Membrane. J. Phys. Chem. B, 108 (49), 19056 -19067, 2004. PDF

  A. V.Anikeenko, M. G. Alinchenko, V. P. Voloshin, N. N. Medvedev, M. L. Gavrilova and P. Jedlovszky. Implementation of the Voronoi-Delauney Method for Analysis of Intermolecular Voids. A. Lagana et al. (Eds.): ICCSA 2004, LNCS 3045, pp. 217-226. PDF

Medvedev, N., Bezrukov, A.; Shtoyan, D. From amorphous solid to defective crystal. A study of structural peculiarities in close packings of hard spheres.Journal of Structural Chemistry, Volume 45, Supplement 1, January 2004, pp. S23-S30. PDF. Jurnal Strukturnoi Khimii, 45 (Application) pp.24 - 31, 2004. PDF(Russian)

Yu.Ya.Efimov, Yu.I.Naberukhin, Fluctuation theory of hydrogen bonding applied to vibration spectra of HOD molecules in liquid water. II. Infrared spectra: contour shape, integrated intensity, temperature dependence. // Molecular Physics, 2004, v. 102, p. 1407-1414.

Yu.Ya.Efimov, Yu.I.Naberukhin. Description of spectroscopic and thermodynamic properties of liquid water and of potential of H-bonding on a basis of fluctuation concept. // International Conference of Hydrogen Bonding, Moscow, Klaz'ma, 2004, p.O5 (Oral contribution).

  N.N.Medvedev, V.P.Voloshin, A.L.Rabinovich, N.K.Balabaev, P.Jedlovszky. Free space distribution and percolation in computer models of lipidic bilayers. R.S.Vartapetian & others (editors). "Structure and dynamics of molecular systems", 2004, Publication IX, part 1,112 - 115. Kazan. (in Russian)

A.L.Rabinovich, N.K.Balabaev, V.P.Voloshin, N.N.Medvedev, P.Jedlovszky. Phosphathidilholin bilayers, computer modeling and intermolecular voids research//Structure and dynamics of molecular systems, 2004. Collected lectures thesises and reports of XI All-Russian conference (Yalchik - 2004). Moscow - Yoshkar-Ola - Ufa - Kazan, Publisher Moscow State Technical University, 2004. P.213. (in Russian)


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