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**37**.

## Article

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*, in pre
,

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.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, 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.
UNSPECIFIED.

## Other

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(Unpublished)

**Sun Jul 21 01:49:44 2019 BST**.