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1

[IEEE 2013 IEEE 12th International Conference on Laser and Fiber-Optical Networks Modeling (LFNM) - Sudak, Ukraine (2013.09.11-2013.09.13)] 2013 IEEE 12th International Conference on Laser and Fiber-Optical Networks Modeling (LFNM 2013) - Generation of drifting optical pulses

Nerukh, Alexander G., Nerukh, Dmitry A.

Year:

2013

Language:

english

File:

PDF, 3.67 MB

english, 2013

2

Structural insight into TNF-Î± inhibitors through combining pharmacophore-based virtual screening and molecular dynamic simulation

Qaiser, Hina, Saeed, Maria, Nerukh, Dmitry, Ul-Haq, Zaheer

Journal:

Journal of Biomolecular Structure and Dynamics

Year:

2020

File:

PDF, 4.70 MB

2020

3

MS2 bacteriophage capsid studied using all-atom molecular dynamics

Farafonov, Vladimir S., Nerukh, Dmitry

Journal:

Interface Focus

Year:

2019

Language:

english

File:

PDF, 1.29 MB

english, 2019

4

Time-spatial drift of decelerating electromagnetic pulses

Nerukh, Alexander G., Nerukh, Dmitry A.

Journal:

Year:

2013

Language:

english

File:

PDF, 5.71 MB

english, 2013

5

Identification of metastable states in peptide’s dynamics

Ruzhytska, Svitlana, Jacobi, Martin Nilsson, Jensen, Christian H., Nerukh, Dmitry

Journal:

The Journal of Chemical Physics

Year:

2010

Language:

english

File:

PDF, 766 KB

english, 2010

6

IR and NMR studies of hydrogen bonding in hexan-1-ol?tetrabutylammonium iodide solutions in the temperature range 28?145 �C and in tetrachloromethane

Kalugin, Oleg N., Nerukh, Dmitry A., Vyunnik, Ivan N., Otlejkina, Elena G., Surov, Yurij N., Pivnenko, Nikolaj S.

Journal:

Journal of the Chemical Society Faraday Transactions

Year:

1994

Language:

english

File:

PDF, 584 KB

english, 1994

7

The application of theoretical models of complex shape to the fitting of experimental spectra having closely overlapping bands

Griffiths, Trevor R., Nerukh, Dmitry A., Eremenko, Sergey A.

Journal:

Physical Chemistry Chemical Physics

Year:

1999

Language:

english

File:

PDF, 266 KB

english, 1999

8

Dynamical frustration of protein's environment at the nanoseconds time scale

Journal:

Journal of Molecular Liquids

Year:

2009

Language:

english

File:

PDF, 600 KB

english, 2009

9

Non-Markov state model of peptide dynamics

Journal:

Journal of Molecular Liquids

Year:

2012

Language:

english

File:

PDF, 873 KB

english, 2012

10

Statistical Complexity of Low- and High-Dimensional Systems

Ryabov, Vladimir, Nerukh, Dmitry

Journal:

Journal of Atomic Molecular and Optical Physics

Year:

2012

Language:

english

File:

PDF, 8.79 MB

english, 2012

11

[IEEE 2006 International Conference on Transparent Optical Networks - Nottingham (2006.6.18-2006.6.18)] 2006 International Conference on Transparent Optical Networks - Complexity and ¿ Quasi-Intermittency¿ of Electromagnetic Waves in Regular Time-Varying Medium

Nerukh, Alexander, Ruzhytska, Nataliya, Nerukh, Dmitry

Year:

2006

Language:

english

File:

PDF, 212 KB

english, 2006

12

Light scattering study of human serum albumin in pre-denaturation: Relation to dynamic transition in water at 42°C

Bardik, Vitaliy, Gotsulskii, Vladimir, Pavlov, Evgen, Malomuzh, Nikolai, Nerukh, Dmitry, Yanchuk, Igor, Lavoryk, Serhiy

Journal:

Journal of Molecular Liquids

Year:

2012

Language:

english

File:

PDF, 557 KB

english, 2012

13

Complexity of classical dynamics of molecular systems. II. Finite statistical complexity of a water–Na[sup +] system

Nerukh, Dmitry, Karvounis, George, Glen, Robert C.

Journal:

The Journal of Chemical Physics

Year:

2002

Language:

english

File:

PDF, 311 KB

english, 2002

14

Sensitivity of peptide conformational dynamics on clustering of a classical molecular dynamics trajectory

Jensen, Christian H., Nerukh, Dmitry, Glen, Robert C.

Journal:

The Journal of Chemical Physics

Year:

2008

Language:

english

File:

PDF, 807 KB

english, 2008

15

All-Atom Molecular Dynamics Simulations of Whole Viruses

Tarasova, Elvira, Nerukh, Dmitry

Journal:

The Journal of Physical Chemistry Letters

Year:

2018

Language:

english

File:

PDF, 3.12 MB

english, 2018

16

[AIP THEORETICAL AND COMPUTATIONAL NANOPHOTONICS (TACONA-PHOTONICS 2009): Proceedings of the 2nd International Workshop - Bad Honnef (Germany) (28–30 October 2009)] AIP Conference Proceedings - Evolution of Waves Induced by Time Change of Medium Permittivity in a Sphere

Nerukh, A., Remayeva, T., Sakhnenko, N., Chigrin, Dmitry N.

Year:

2009

File:

PDF, 625 KB

2009

17

In search of an optimal acid-base indicator for examining surfactant micelles: Spectrophotometric studies and molecular dynamics simulations

Mchedlov-Petrossyan, Nikolay O., Farafonov, Vladimir S., Cheipesh, Tatyana A., Shekhovtsov, Sergey V., Nerukh, Dmitry A., Lebed, Alexander V.

Journal:

Colloids and Surfaces A: Physicochemical and Engineering Aspects

Year:

2019

Language:

english

File:

PDF, 2.38 MB

english, 2019

18

Water network dynamics at the critical moment of a peptide’s β-turn formation: A molecular dynamics study

Karvounis, George, Nerukh, Dmitry, Glen, Robert C.

Journal:

The Journal of Chemical Physics

Year:

2004

Language:

english

File:

PDF, 1.12 MB

english, 2004

19

Complexity of classical dynamics of molecular systems. I. Methodology

Nerukh, Dmitry, Karvounis, George, Glen, Robert C.

Journal:

The Journal of Chemical Physics

Year:

2002

Language:

english

File:

PDF, 499 KB

english, 2002

20

21-residue peptide's dynamics at and between elementary structural transitions

Dmitry Nerukh, Makoto Taiji

Journal:

Journal of Molecular Liquids

Year:

2009

Language:

english

File:

PDF, 375 KB

english, 2009

21

[AIP COMPLIFE 2007: The Third International Symposium on Computational Life Science - ()] AIP Conference Proceedings - Calculating Mean First Passage Times from Markov Models of Proteins

Jensen, Christian H., Nerukh, Dmitry, Glen, Robert C., Siebes, Arno P. J. M., Berthold, Michael R., Glen, Robert C., Feelders, Ad J.

Year:

2007

Language:

english

File:

PDF, 274 KB

english, 2007

22

Computational mechanics of molecular systems: Quantifying high-dimensional dynamics by distribution of Poincaré recurrence times

Ryabov, Vladimir, Nerukh, Dmitry

Journal:

Chaos An Interdisciplinary Journal of Nonlinear Science

Year:

2011

Language:

english

File:

PDF, 1.50 MB

english, 2011

23

Complete virus capsid at all-atom resolution: Simulations using molecular dynamics and hybrid molecular dynamics/hydrodynamics methods reveal semipermeable membrane function

Tarasova, Elvira, Korotkin, Ivan, Farafonov, Vladimir, Karabasov, Sergey, Nerukh, Dmitry

Journal:

Journal of Molecular Liquids

Year:

2017

Language:

english

File:

PDF, 970 KB

english, 2017

24

Details of charge distribution in stable viral capsid

Tarasova, Elvira, Farafonov, Vladimir, Taiji, Makoto, Nerukh, Dmitry

Journal:

Journal of Molecular Liquids

Year:

2018

Language:

english

File:

PDF, 4.07 MB

english, 2018

25

Accurate modelling of pulse transformation by adjustable-in-time medium parameters

Natalia N. Ruzhitskaya, Alexander G. Nerukh, Dmitry Nerukh

Journal:

Optical and Quantum Electronics

Year:

2003

Language:

english

File:

PDF, 644 KB

english, 2003

26

Ligand Diffusion on Protein Surface Observed in Molecular Dynamics Simulation

Nerukh, Dmitry, Okimoto, Noriaki, Suenaga, Atsushi, Taiji, Makoto

Journal:

The Journal of Physical Chemistry Letters

Year:

2012

Language:

english

File:

PDF, 1.01 MB

english, 2012

27

All-Atom Molecular Dynamics Simulations of Entire Virus Capsid Reveal the Role of Ion Distribution in Capsid’s Stability

Tarasova, Elvira, Farafonov, Vladimir, Khayat, Reza, Okimoto, Noriaki, Komatsu, Teruhisa S., Taiji, Makoto, Nerukh, Dmitry

Journal:

The Journal of Physical Chemistry Letters

Year:

2017

Language:

english

File:

PDF, 813 KB

english, 2017

28

AIP Conference Proceedings [AIP THE FOURTH INTERNATIONAL WORKSHOP ON THEORETICAL AND COMPUTATIONAL NANOPHOTONICS: TaCoNa-Photonics 2011 - Bad Honnef, (Germany) (26–28 October 2011)] - Accurate Analysis of Transient Processes in Coupled WGM Microcavities with Time Varying Refractive Index

Sakhnenko, Nataliya, Nerukh, Alexander, Chigrin, Dmitry N.

Year:

2011

Language:

english

File:

PDF, 192 KB

english, 2011

29

Quantifying long time memory in phase space trajectories of molecular liquids

Vladimir Ryabov, Dmitry Nerukh

Journal:

Journal of Molecular Liquids

Year:

2011

Language:

english

File:

PDF, 2.47 MB

english, 2011

30

Multidimensional quantum dynamics with trajectories: a novel numerical implementation of Bohmian mechanics

Dmitry Nerukh, John H. Frederick

Journal:

Chemical Physics Letters

Year:

2000

Language:

english

File:

PDF, 483 KB

english, 2000

31

Quantifying the complexity of chaos in multibasin multidimensional dynamics of molecular systems

Dmitry Nerukh, George Karvounis, Robert C. Glen

Journal:

Year:

2004

Language:

english

File:

PDF, 152 KB

english, 2004

32

Controlling protein molecular dynamics: How to accelerate folding while preserving the native state

Jensen, Christian H., Nerukh, Dmitry, Glen, Robert C.

Journal:

The Journal of Chemical Physics

Year:

2008

Language:

english

File:

PDF, 596 KB

english, 2008

33

Identifying and correcting non-Markov states in peptide conformational dynamics

Nerukh, Dmitry, Jensen, Christian H., Glen, Robert C.

Journal:

The Journal of Chemical Physics

Year:

2010

Language:

english

File:

PDF, 525 KB

english, 2010

34

Association of novel monomethine cyanine dyes with bacteriophage MS2: A fluorescence study

Vus, Kateryna, Tarabara, Uliana, Balklava, Zita, Nerukh, Dmitry, Stich, Michael, Laguta, Anna, Vodolazkaya, Natalya, Mchedlov-Petrossyan, Nikolay O., Farafonov, Vladimir, Kriklya, Nika, Gorbenko, Galy

Journal:

Journal of Molecular Liquids

Year:

2020

Language:

english

File:

PDF, 2.30 MB

english, 2020

35

Erratum to “Computational mechanics reveals nanosecond time correlations in molecular dynamics of liquid systems” [Chem. Phys. Lett. 457 (2008) 439]

Journal:

Chemical Physics Letters

Year:

2008

Language:

english

File:

PDF, 114 KB

english, 2008

36

Two-phase flow analogy as an effective boundary condition for modelling liquids at atomistic resolution

Korotkin, Ivan, Nerukh, Dmitry, Tarasova, Elvira, Farafonov, Vladimir, Karabasov, Sergey

Journal:

Journal of Computational Science

Year:

2016

Language:

english

File:

PDF, 4.98 MB

english, 2016

37

Computational mechanics reveals nanosecond time correlations in molecular dynamics of liquid systems

Journal:

Chemical Physics Letters

Year:

2008

Language:

english

File:

PDF, 317 KB

english, 2008

38

Complex vibrational correlation functions extracted from the resolved ν2 band of liquid acetonitrile

Nerukh, Dmitry, Griffiths, Trevor R.

Journal:

Physical Chemistry Chemical Physics

Year:

2001

Language:

english

File:

PDF, 196 KB

english, 2001

39

Molecular phase space transport in water: Non-stationary random walk model

Dmitry Nerukh, Vladimir Ryabov, Makoto Taiji

Journal:

Physica A: Statistical Mechanics and its Applications

Year:

2009

Language:

english

File:

PDF, 991 KB

english, 2009

40

Molecular Dynamics implementation of BN2D or ‘Mercedes Benz’ water model

Scukins, Arturs, Bardik, Vitaliy, Pavlov, Evgen, Nerukh, Dmitry

Journal:

Computer Physics Communications

Year:

2015

Language:

english

File:

PDF, 566 KB

english, 2015

41

MS2 bacteriophage capsid studied using all-atom molecular dynamics

Farafonov, Vladimir S., Nerukh, Dmitry

Journal:

Interface Focus

Year:

2019

File:

PDF, 1.29 MB

2019

42

Complex temporal patterns in molecular dynamics: A direct measure of the phase-space exploration by the trajectory at macroscopic time scales

Nerukh, Dmitry, Ryabov, Vladimir, Glen, Robert C.

Journal:

Physical Review E

Year:

2008

Language:

english

File:

PDF, 1.59 MB

english, 2008

43

A hybrid molecular dynamics/fluctuating hydrodynamics method for modelling liquids at multiple scales in space and time

Korotkin, Ivan, Karabasov, Sergey, Nerukh, Dmitry, Markesteijn, Anton, Scukins, Arturs, Farafonov, Vladimir, Pavlov, Evgen

Journal:

The Journal of Chemical Physics

Year:

2015

Language:

english

File:

PDF, 4.67 MB

english, 2015

44

Real and imaginary parts of the vibrational relaxation of acetonitrile in its electrolyte solutions: new results for the dynamics of solvent molecules

Dmitry Nerukh, Trevor R. Griffiths

Journal:

Journal of Molecular Liquids

Year:

2004

Language:

english

File:

PDF, 486 KB

english, 2004

45

Simple One-electron Invariants of Molecular Chirality

A. V. Luzanov, Dmitry Nerukh

Journal:

Journal of Mathematical Chemistry

Year:

2007

Language:

english

File:

PDF, 276 KB

english, 2007

46

Water–Peptide Dynamics during Conformational Transitions

Nerukh, Dmitry, Karabasov, Sergey

Journal:

The Journal of Physical Chemistry Letters

Year:

2013

Language:

english

File:

PDF, 1.91 MB

english, 2013

47

Visualising and controlling the flow in biomolecular systems at and between multiple scales: from atoms to hydrodynamics at different locations in time and space

Pavlov, Evgen, Taiji, Makoto, Scukins, Arturs, Markesteijn, Anton, Karabasov, Sergey, Nerukh, Dmitry

Journal:

Faraday Discussions

Year:

2014

Language:

english

File:

PDF, 3.59 MB

english, 2014

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