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**38**.

## Article

Atamas, Natalia, Bardik, Vitalii Y., Komisarenko, Serhiy, Makogonenko, Yevgen M., Lugovskoi, Edward V., Malomuz, Nikolai P., Nerukh, Dmitry and Solonin, Pavlo K.
(2019).
WATER DYNAMICS AND STABILITY OF MAJOR BLOOD PROTEINS AT PRE-DENATURATION STAGE.
*Atti della Accademia Peloritana dei Pericolanti*, 97
(Suppl ),

Zhuravlova, Z., Nerukh, D., Reut, V. and Vaysfel’d, N.
(2019).
Investigation of an Idealized Virus Capsid Model by the Dynamic Elasticity Apparatus.
*Journal of Mathematical Sciences (United States)*, 243
(1),
111–127.

Farafonov, Vladimir S. and Nerukh, Dmitry
(2019).
MS2 bacteriophage capsid studied using all-atom molecular dynamics.
*Interface Focus*, 9
(3),

Mchedlov-Petrossyan, Nikolay O., Farafonov, Vladimir S., Cheipesh, Tatyana A., Shekhovtsov, Sergey V., Nerukh, Dmitry A. and Lebed, Alexander V.
(2019).
In search of an optimal acid-base indicator for examining surfactant micelles:Spectrophotometric studies and molecular dynamics simulations.
*Colloids and Surfaces A: Physicochemical and Engineering Aspects*, 565
,
pp. 97-107.

Tarasova, Elvira and Nerukh, Dmitry
(2018).
All-Atom Molecular Dynamics Simulations of Whole Viruses.
*Journal of Physical Chemistry Letters*, 9
,
pp. 5805-5809.

Tarasova, Elvira, Farafonov, Vladimir, Taiji, Makoto and Nerukh, Dmitry
(2018).
Details of charge distribution in stable viral capsid.
*Journal of Molecular Liquids*, 265
,
pp. 585-591.

Tarasova, Elvira, Korotkin, Ivan, Farafonov, Volodymyr, Karabasov, Sergey and Nerukh, Dmitry
(2017).
Complete virus capsid at all-atom resolution:simulations using molecular dynamics and hybrid molecular dynamics/hydrodynamics methods reveal semipermeable membrane function.
*Journal of Molecular Liquids*, 245
,
pp. 109-114.

Tarasova, Elvira, Farafonov, Vladimir, Khayat, Reza, Okimoto, Noriaki, Komatsu, Teruhisa, Taiji, Makoto and Nerukh, Dmitry
(2017).
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.

Atamas, N., Bardik, V., Bannikova, A., Grishina, O., Lugovskoi, E., Lavoryk, S., Makogonenko, Y., Korolovych, V. and Nerukh, D.
(2017).
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
,

Korotkin, Ivan, Nerukh, Dmitry, Tarasova, Elvira, Farafonov, Vladimir and Karabasov, Sergey
(2016).
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.

Scukins, A., Nerukh, D., Pavlov, E., Karabasov, S. and Markesteijn, A.
(2015).
Multiscale molecular dynamics/hydrodynamics implementation of two dimensional “Mercedes Benz” water model.
*European Physical Journal*, 224
(12),
pp. 2217-2238.

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.

Korotkin, Ivan, Karabasov, Sergey, Nerukh, Dmitry, Markesteijn, Anton, Scukins, Arturs, Farafonov, Vladimir and Pavlov, Evgen
(2015).
A hybrid molecular dynamics/fluctuating hydrodynamics method for modelling liquids at multiple scales in space and time.
*Journal of Chemical Physics*, 143
(1),

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, 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, Jensen, Christian H. and Glen, Robert C.
(2010).
Identifying and correcting non-Markov states in peptide conformational dynamics.
*Journal of Chemical Physics*, 132
(8),
084104.

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),

Buts, V.A., Nerukh, A.G., Ruzhytska, N.N. and Nerukh, Dmitry
(2008).
Wave chaotic behaviour generated by linear systems.
*Optical and Quantum Electronics*, 40
(8),
pp. 587-601.

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),

Jensen, Christian H., Nerukh, Dmitry and Glen, Robert C.
(2007).
Calculating mean first passage times from Markov models of proteins.
*AIP Conference Proceedings*, 940
,
pp. 150-157.

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, 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.

## Book Section

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, A., Ruzhytska, N. and Nerukh, D.
(2006).
*Quasi-intermittency of waves and their complexity in modulated dielectric medium.*
IN: Conference Proceedings - 11th International Conference on Mathematical Methods in Electromagnetic Theory, MMET'06.
UKR: UNSPECIFIED.

## Other

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

**Thu Jan 23 02:48:13 2020 GMT**.