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Scukins, Arturs; Bardik, Vitaliy; Pavlov, Evgen and Nerukh, Dmitry (2015). Molecular Dynamics implementation of BN2D or 'Mercedes Benz' water model. Computer Physics Communications, 190 , pp. 129-138.

Karabasov, Sergey; Nerukh, Dmitry; Hoekstra, Alfons; Chopard, Bastien and Coveney, Peter V. (2014). Multiscale modelling:approaches and challenges. Philosophical Transactions A, 372 (2021),

Pavlov, Evgen; Taiji, Makoto; Scukins, Arturs; Markesteijn, Anton; Karabasov, Sergey and Nerukh, Dmitry (2014). Visualising and controlling the flow in biomolecular systems at and between multiple scales:from atoms to hydrodynamics at different locations in time and space. Faraday Discussions, 169 , pp. 285-302.

Nerukh, Alexander G. and Nerukh, Dmitry A. (2013). Time-spatial drift of decelerating electromagnetic pulses. Optics Express, 21 (14), pp. 17366-17372.

Nerukh, Dmitry and Karabasov, Sergey (2013). Water-peptide dynamics during conformational transitions. Journal of Physical Chemistry Letters, 4 (5), pp. 815-819.

Bardik, Vitaliy; Gotsulskii, Vladimir; Pavlov, Evgen; Malomuzh, Nikolai; Nerukh, Dmitry; Yanchuk, Igor and Lavoryk, Serhiy (2012). Light scattering study of human serum albumin in pre-denaturation:relation to dynamic transition in water at 42°C. Journal of Molecular Liquids, 176 , pp. 60-64.

Nerukh, Dmitry (2012). Non-Markov state model of peptide dynamics. Journal of Molecular Liquids, 176 , pp. 65-70.

Nerukh, Dmitry; Okimoto, Noriaki; Suenaga, Atsushi and Taiji, Makoto (2012). Ligand diffusion on protein surface observed in molecular dynamics simulation. Journal of Physical Cemistry Letters, 3 (23), 3476–3479.

Bardik, V.Yu; Nerukh, D.; Pavlov, E.V. and Vlasyuk, M.S. (2012). Free energy functional expansion as the generalized approach to the equation of state of dense fluids. Ukrainian Journal of Physics, 57 (6), pp. 612-618.

Bardik, V.Yu.; Nerukh, D.; Pavlov, E. and Zhyganiuk, I. (2012). Equation of state for water in the small compressibility region. Ukrainian Journal of Physics, 57 (1), pp. 47-51.

Ryabov, Vladimir and Nerukh, Dmitry (2011). Computational mechanics of molecular systems:quantifying high-dimensional dynamics by distribution of Poincaré recurrence times. Chaos, 21 (3),

Nerukh, Dmitry and Ryabov, Vladimir (2011). Quantifying long time memory in phase space trajectories of molecular liquids. Journal of Molecular Liquids, 159 (1), pp. 99-104.

Fedorov, Maxim V.; Goodman, Jonathan M.; Nerukh, Dmitry and Schumm, Stephan (2011). Self-assembly of trehalose molecules on a lysozyme surface: the broken glass hypothesis. Physical Chemistry Chemical Physics, 13 (6), pp. 2294-2299.

Ruzhytska, Svitlana; Jacobi, Martin N.; Jensen, Christian H. and Nerukh, Dmitry (2010). Identification of metastable states in peptide's dynamics. Journal of Chemical Physics, 133 (16), p. 164102.

Nerukh, Dmitry; Ryabov, Vladimir and Taiji, Makoto (2009). Molecular phase space transport in water:non-stationary random walk model. Physica A, 388 (22), pp. 4719-4726.

Nerukh, Dmitry and Taiji, Makoto (2009). 21-residue peptide's dynamics at and between elementary structural transitions. Journal of Molecular Liquids, 147 (1-2), pp. 124-127.

Nerukh, D. (2009). Dynamical frustration of protein's environment at the nanoseconds time scale. Journal of Molecular Liquids, 145 (3), pp. 139-144.

Jensen, Christian H.; Nerukh, Dmitry and Glen, Robert C. (2008). Controlling protein molecular dynamics:how to accelerate folding while preserving the native state. Journal of Chemical Physics, 129 (22),

Nerukh, D. (2008). Computational mechanics reveals nanosecond time correlations in molecular dynamics of liquid systems. Chemical Physics Letters, 457 (4-6), pp. 439-443.

Nerukh, Dmitry; Ryabov, Vladimir and Glen, Robert C. (2008). Complex temporal patterns in molecular dynamics:a direct measure of the phase-space exploration by the trajectory at macroscopic time scales. Physical Review E, 77 (3),

Jensen, Christian H.; Nerukh, Dmitry and Glen, Robert C. (2008). Sensitivity of peptide conformational dynamics on clustering of a classical molecular dynamics trajectory. Journal of Chemical Physics, 128 (11),

Luzanov, A.V. and Nerukh, Dmitry (2007). Simple one-electron invariants of molecular chirality. Journal of Mathematical Chemistry, 41 (4), pp. 417-435.

Luzanov, A.V. and Nerukh, D. (2005). Complexity and chirality indices for molecular informatics::differential geometry approach. Functional Materials, 12 (1), pp. 55-64.

Nerukh, Dmitry; Karvounis, George and Glen, Robert C. (2004). Quantifying the complexity of chaos in multibasin multidimensional dynamics of molecular systems. Complexity, 10 (2), pp. 40-46.

Karvounis, George; Nerukh, Dmitry and Glen, Robert C. (2004). Water network dynamics at the critical moment of a peptide's ß-turn formation:a molecular dynamics study. Journal of Chemical Physics, 121 (10), pp. 4925-4935.

Nerukh, Dmitry and Griffiths, Trevor R. (2004). Real and imaginary parts of the vibrational relaxation of acetonitrile in its electrolyte solutions:new results for the dynamics of solvent molecules. Journal of Molecular Liquids, 109 (2), pp. 83-97.

Ruzhytska, Natalia N.; Nerukh, Alexander G. and Nerukh, Dmitry (2003). Accurate modelling of pulse transformation by adjustable-in-time medium parameters. Optical and Quantum Electronics, 35 (4-5), pp. 347-364.

Nerukh, Dmitry; Karvounis, George and Glen, Robert C. (2002). Complexity of classical dynamics of molecular systems. I. Methodology. Journal of Chemical Physics, 117 (21), pp. 9611-9617.

Nerukh, Dmitry; Karvounis, George and Glen, Robert C. (2002). Complexity of classical dynamics of molecular systems. II. Finite statistical complexity of a water-Na+ system. Journal of Chemical Physics, 117 (21), pp. 9618-9622.

Atamas, N.; Bardik, V.; Bannikova, A.; Grishina, O.; Lugovskoi, E.; Lavoryk, S.; Makogonenko, Y.; Korolovych, V. and Nerukh, D. The effect of water dynamics on conformation changes of albumin in pre-denaturation state:photon correlation spectroscopy and simulation. Journal of Molecular Liquids, In pre ,

Buts, V.A.; Nerukh, A.G.; Ruzhytska, N.N. and Nerukh, Dmitry Wave chaotic behaviour generated by linear systems. Optical and Quantum Electronics, 40 (8), pp. 587-601.

Korotkin, Ivan; Karabasov, Sergey; Nerukh, Dmitry; Markesteijn, Anton; Scukins, Arturs; Farafonov, Vladimir and Pavlov, Evgen A hybrid molecular dynamics/fluctuating hydrodynamics method for modelling liquids at multiple scales in space and time. Journal of Chemical Physics, 143 (1),

Korotkin, Ivan; Nerukh, Dmitry; Tarasova, Elvira; Farafonov, Vladimir and Karabasov, Sergey Two-phase flow analogy as an effective boundary condition for modelling liquids at atomistic resolution. Journal of Computational Science, 17 (part 2), pp. 446-456.

Markesteijn, Anton; Karabasov, Sergey; Scukins, Arturs; Nerukh, Dmitry; Glotov, Vyacheslav and Goloviznin, Vasily Concurrent multiscale modelling of atomistic and hydrodynamic processes in liquids. Philosophical Transactions A, 372 (2021),

Nerukh, Dmitry; Jensen, Christian H. and Glen, Robert C. Identifying and correcting non-Markov states in peptide conformational dynamics. Journal of Chemical Physics, 132 (8), 084104.

Scukins, A.; Nerukh, D.; Pavlov, E.; Karabasov, S. and Markesteijn, A. Multiscale molecular dynamics/hydrodynamics implementation of two dimensional “Mercedes Benz” water model. European Physical Journal, 224 (12), pp. 2217-2238.

Tarasova, Elvira; Farafonov, Vladimir; Khayat, Reza; Okimoto, Noriaki; Komatsu, Teruhisa; Taiji, Makoto and Nerukh, Dmitry All-atom molecular dynamics simulations of entire virus capsid reveal the role of ion distribution in capsid’s stability. Journal of Physical Chemistry Letters, 8 (4), pp. 779-784.

Book Section

Nerukh, Alexander G. and Nerukh, Dmitry A. (2013). Generation of drifting optical pulses. IN: Conference Proceedings : 12th international conference on Laser and Fiber-Optical Networks Modeling, LFNM 2013. Piscataway, NJ (US): IEEE.

Nerukh, Alexander G.; Zolotariov, D.A.; Nerukh, D.A. and Georgiev, Georgi N. (2012). Green's function for paraxial equation. IN: PIERS proceedings Moscow. Progress in electromagnetics research symposium . Electromagnetics Academy.

Nerukh, A.; Zolotariov, D. and Nerukh, D. (2012). Interaction of time-varying airy pulses with a layer. IN: European Microwave Week 2012: "Space for Microwaves", conference proceedings. IEEE.

Nerukh, A.; Zolotariov, D.; Nerukh, D. and Benton, T. (2012). Reflection of a spatial-temporal airy pulse from a layer. IN: 14th International Conference on Transparent Optical Networks. IEEE conference publications . IEEE.

Nerukh, A.G.; Zolotariov, D.A. and Nerukh, D.A. (2011). Decelerating Airy pulses. IN: Conference proceedings - 11th International Conference on Laser and Fiber-Optical Networks Modeling, LFNM 2011. Sukhoivanov, I.A. and Shulika, O.V. (eds) Piscataway, NJ (US): IEEE.

Nerukh, A.G.; Zolotariov, D.A. and Nerukh, D.A. (2011). Generation of decelerating Airy pulses. IN: 2011 VIII International Conference on Antenna Theory and Techniques. IEEE.

Nerukh, A.; Zolotariov, D. and Nerukh, D. (2011). Time-varying airy pulses. IN: 2011 13th International Conference on Transparent Optical Networks. IEEE Conference Publications . IEEE.

Nerukh, Dmitry (2010). Why are MD simulated protein folding times wrong? IN: Advances in Computational Biology. Arabnia, Hamid R. (ed.) Advances in Experimental Medicine and Biology, Part 3 . Springer.

Nerukh, Dmitry; Karvounis, George and Glen, Robert C. (2006). Dynamic complexity of chaotic transitions in high-dimensional classical dynamics:Leu-Enkephalin folding. IN: Computational life sciences II. Berthold, Michael R.; Glen, Robert C. and Fischer, Ingrid (eds) Lecture notes in computer science . Berlin (DE): Springer.

Nerukh, Dmitry and Ryabov, Vladimir Computational mechanics of molecular systems. IN: Computational mechanics research trends. Berger, Hans P. (ed.) Computer Science, Technology and Applications . Nova science.

Other

Nerukh, Alexander G.; Zolotariov, Denis A. and Nerukh, Dmitry (2011). Bifurcating trajectory of non-diffractive electromagnetic airy pulse. UNSPECIFIED. (Unpublished)