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LECTURES AND POSTERS AT CONFERENCES |
- Dmitry Nerukh,
Molecular Dynamics modelling of biomolecular systems: potentials and perspectives,
Granovsky readings 2023 (St Petersburg, Russia) (invited lecture) (2023)
- Vladimir Farafonov, Maryna Bakumenko, Artemii Yanushevskyi, Vitaly Bardik, Aleksiy Pozhilenkov, Andrey Kalachev, Nataly Vaysfeld, Michael Stich, and Dmitry Nerukh,
All-atom MD of entire virus with genome in solution at physiological conditions,
WATOC 2020, 12th Triennial Congress of the World Association of Theoretical and Computational Chemists (Vancouver, Canada) (lecture) (2022)
- Vladimir S. Farafonov, Michael Stich, and Dmitry Nerukh,
Reconstruction and validation of entire virus model with complete genome from mixed resolution cryo-EM density,
Faraday Discussion: Challenges in biological cryo electron microscopy (Sheffield, UK) (lecture) (2022)
- Vladimir Farafonov, Natalya Vodolazkaya, Marina Nikolskaya, Anna Laguta, Zita Balklava, Michael Stich, Nikolay Mchedlov-Petrossyan, and Dmitry Nerukh,
All-atom structure and dynamics of entire virus with genome in solution at physiological conditions,
Faraday joint interest group conference (online) (2021)
- Dmitry Nerukh,
Multiscale Molecular Dynamics modelling of large biomolecular systems,
Modern problems in biomedical sciences (Saint Petersburg, Russia) (plenary lecture) (2021)
- Sergey Karabasov, Dmitry Nerukh, Xinjian Liu, Fan Li, Ivan Korotkin, and Vladimir Farafonov,
Combining Molecular Dynamics and Computational Fluid Dynamics: when are the Hybrid Continuum-Atomistic Multiscale Models useful?,
CRC 1114 Scaling Cascades in Complex Systems (online) (2020)
- Tetiana Kornylova, Hanna Shokhina, Nataly Vaysfeld, and Dmitry Nerukh,
A variational approach for finding equations of motion for a discretised Navier-Stokes system,
Midlands Computational Chemistry Meeting (online) (2020)
- Hanna Shokhina, Tetiana Kornylova, Nataly Vaysfeld, and Dmitry Nerukh,
Construction of the Lagrangian for the equations of motion for the SDPD model,
Midlands Computational Chemistry Meeting (online) (2020)
- James E Sullivan, Dmitry Nerukh, and Jens Christian Claussen,
NK Fitness Landscapes Interpolated between K=2 and K=3,
DPG Spring Meeting of the Condensed Matter Section (Regensburg, Germany) (lecture) (2019)
- Natalya Vodolazkaya, Marina Nikolskaya, Anna Laguta, Vladimir Farafonov, Zita Balklava, Michael Stich, Nikolay Mchedlov-Petrossyan, and Dmitry Nerukh,
Experimentally measured hydrophobicity and charge distribution on MS2 virus surface,
EMLG2019 (Kutna Hora, Czech Republic) (lecture) (2019)
- Dmitry Nerukh,
Multiscale modelling of complex biomolecular systems,
Royal Society Theo Murphy Meeting 2018 (invited lecture) (2018)
- Dmitry Nerukh, Elvira Tarasova, Vladimir Farafonov, Nikita~Visencuk Visenko, Aleksey Pozhilenkov, Sergey Karabasov, Ivan Korotkin, Marina Bakumenko, and Elizaveta Berezovska,
Multiscale multiphysics of liquid solutions of complex molecular systems,
EMLG2018 (Nagoya, Japan) (lecture) (2018)
- Dmitry Nerukh, Sergey Karabasov, Elvira Tarasova, Ivan Korotkin, and Vladimir Farafonov,
Hybrid Molecular Dynamics - hydrodynamics modelling of liquid solutions: whole virus at atomistic resolution,
11th Triennial Congress of the World Association of Theoretical and Computational Chemists (WATOC 2017) (Munich, Germany, 2017)
(lecture, abstract)
- Z. Zhuravlova, D. Kozachkov, D. Pliusnov, V. Radzivil, V. Reut, O. Shpynarov, E. Tarasova, D. Nerukh, N. Vaysfel’d,
Modelling of virus vibrations with 3-D dynamic elasticity theory,
23rd International Conference Engineering Mechanics (Svratka, Czech Republic, 2017)
(abstract)
- Dmitry Nerukh, Sergey Karabasov, Elvira Tarasova, Ivan Korotkin, Vladimir Farafonov,
Hybrid Molecular Dynamics/hydrodynamics modelling of liquid solutions of complex molecular systems: whole virus at atomistic resolution,
Joint EMLG/JMLG Annual Meeting (Platanias - Chania, Crete, Greece, 2016)
(lecture, abstract)
- Sergey Karabasov, Ivan Korotkin, Dmitry Nerukh, Elvira Tarasova, Vladimir Farafonov, Anton Markesteijn,
Hybrid modelling based on two-phase flow analogy: advances and challenges,
Hybrid Simulation Methods in Fluid Dynamics: Models, Software and Applications (TU Munich, Germany, 2015)
(lecture, PDF)
- S.Karabasov, I.Korotkin, A.Markesteijn, D.Nerukh,
Two-phase-flow analogy as an effective boundary condition for modelling of liquids at atomistic resolution,
24th Discrete Simulation of Fluid Dynamics (DSFD) Conference (Edinburgh, UK, 2015)
(lecture, abstract)
- Sergey Karabasov, Dmitry Nerukh, Ivan Korotkin, and Anton Markesteijn,
An Eulerian-Lagrangian framework for multi-scale/multi-physics (continuum-atomistic) modelling of liquids based on a hydrodynamic analogy,
CECAM workshop "Molecular hydrodynamics meets fluctuating hydrodynamics" (Madrid, Spain, 2015)
(lecture, PDF)
- Dmitry Nerukh, Sergey Karabasov, Arturs Scukins, Evgen Pavlov, Ivan Korotkin, Vladimir Farafonov, and Makoto Taiji,
Hybrid molecular dynamics–hydrodynamics approach for multiscale modelling of liquid molecular systems,
10th Congress of the World Association of Theoretical and Computational Chemists (WATOC 2014) (Santiago, Chile, 2014)
(lecture, PDF)
- Dmitry Nerukh, Sergey Karabasov, Arturs Scukins, Evgen Pavlov, Ivan Korotkin, Vladimir Farafonov, and Makoto Taiji,
Hybrid molecular dynamics–hydrodynamics framework for modelling liquid molecular systems,
EMLG - JMLG annual meeting 2014 (Rome, Italy, 2014)
(lecture, PDF)
- Dmitry Nerukh, Arturs Scukins, Evgen Pavlov, Sergey Karabasov, Anton Markesteijn,
Hybrid molecular dynamics - hydrodynamics framework for modelling liquids,
Liquids 2014 (Lisbon, Portugal, 2014)
(poster, PDF)
- Evgen Pavlov, Makoto Taiji, Arturs Scukins, Ivan Korotkin, Anton Markesteijn, Sergey Karabasov, Dmitry Nerukh,
Visualising and controlling the flows in biomolecular systems at and between multiple scales: from atoms to hydrodynamics at different locations in time and space,
Faraday Discussion 169: Molecular Simulations and Visualization (Nottingham, UK, 2014)
(lecture, PDF)
- Sergey Karabasov, Dmitry Nerukh, Arturs Scukins, Evgen Pavlov, Anton Markesteijn, Pardis Tabaee, Makoto Taiji,
Modelling solutions of biomolecules at atomistic and continuum representation at the same time: hybrid MD/hydrodynamics framework,
CCPBioSim / CCP5 Multiscale Modelling Conference (Manchester, UK, 2014)
(lecture, PDF)
- Alexander G. Nerukh, Dmitry A. Nerukh,
Generation of drifting optical pulses,
6th International Conference on Advanced Optoelectronics and Lasers CAOL*2013 (Sudak, Ukraine, 2013)
(Poster, PDF)
- Dmitry Nerukh, Arturs Scukins, Evgen Pavlov, Sergey Karabasov, Anton Markesteijn, and Vitaliy Bardik,
Modelling liquid solutions at atomistic and continuum representation at the same time: hybrid MD/hydrodynamics implementation of two dimensional water model,
Methods and Applications of Computational Chemistry (Kharkov, Ukraine, 2013)
(Lecture, PDF)
- Dmitry Nerukh, Arturs Scukins, Evgen Pavlov, Vladimir Ryabov, Sergey Karabasov, and Anton Markesteijn,
Molecular dynamics/hydrodynamics hybrid description of liquids and biomolecular solutions,
EMLG - JMLG annual meeting 2013 (Lille, France, 2013)
(Lecture, PDF)
- Dmitry Nerukh,
Dynamics of water and conformational transitions in proteins,
Theory and Applications of Computational Chemistry (Pavia, Italy, 2012)
(Lecture, PDF)
- Dmitry Nerukh, Sergey Karabasov,
Combined peptide-water energy landscape: the dynamics of rare conformational transitions,
Energy Landscapes (Obergurgl, Austria, 2012)
(Poster, PDF)
- A. Nerukh, D. Zolotariov, D. Nerukh, and T. Benson,
Reflection of a spatial-temporal Airy pulse from a layer,
ICTON 2012 (Warwick, UK, 2012)
(Lecture, PDF)
- Dmitry Nerukh, Sergey Karabasov,
The flow of MD trajectories in peptide-water systems at the moments of conformational transitions,
Computational Molecular Science 2012 (Cirencester, UK, 2012)
(Lecture, PDF)
- A. Nerukh, D. Zolotariov, D. Nerukh,
Interaction of time-varying Airy pulses with a layer,
European Microwave Week 2012 (Amsterdam, Netherlands, 2012)
(Poster, PDF)
- Dmitry Nerukh,
The decisive role of water in elementary conformational transitions of a peptide,
29th EMLG/JMLG (European/Japan Molecular Liquids Group) annual meeting (Warsaw, Poland, 2011)
(Lecture, PDF)
- Dmitry Nerukh and Vladimir Ryabov,
The structure of chaos in liquid water,
8th Liquid Matter Conference (Vienna, Austria, 2011)
(Poster, PDF)
- Dmitry Nerukh,
The role of water in conformational transitions of peptides,
32nd International Conference on Solution Chemistry (Montpellier, France, 2011)
(Lecture, PDF)
- Dmitry Nerukh,
Dissecting peptide conformational transitions: unique water dynamics,
Ninth Triennial Congress of the World Association of Theoretical and Computational Chemists (Santiago de Compostella, Spain, 2011)
(Lecture, PDF)
- Dmitry Nerukh,
Phase space dynamics of biomolecular systems: the structure of chaos and role of water in conformational transitions,
The Complexity of Dynamics and Kinetics in Many Dimensions (Telluride, USA, 2011)
(Lecture, PDF)
- Alexander G. Nerukh, Denis A. Zolotariov, Dmitry A. Nerukh,
Decelerating non-diffractive electromagnetic Airy pulses,
Loughborough Antennas & Propagation Conference 2011 (Loughborough, UK, 2011)
(Abstract, PDF)
- V.B. Ryabov, D. Nerukh,
Quantifying dynamic traps in high-dimensional phase space of molecular ensembles,
2nd International Symposium Rare Attractors and Rare Phenomena in Nonlinear Dynamics RA’11 (Riga – Jurmala, Latvia, 2011)
(Abstract, PDF)
- Vitaliy Bardik, Evgen Pavlov, Igor Zhyganiuk, Dmitry Nerukh,
Generalized approach to the equation of state of dense fluids and dilute gases,
Thermodynamics 2011 (Athens, Greece, 2011)
(Abstract, PDF)
- V. Bardik, E. V. Pavlov, A.V. Kcleshonok, D.A. Nerukh, I.V. Zhyganiuk,
Equation of state of dense fluids in the high pressure – high temperature region,
International Conference on Statistical Physics (Larnaca, Cyprus, 2011)
(Abstract, PDF)
- A. Nerukh, D. Zolotariov, D. Nerukh,
Time-varying Airy Pulses,
13th International Conference on Transparent Optical Networks, ICTON 2011 (Stockholm, Sweden, 2011) (lecture)
(Abstract, PDF)
- Dmitry Nerukh, Vladimir Ryabov, and Makoto Taiji,
Non-stationary diffusion in the phase space diffusion of molecular liquids,
EMLG/JMLG Annual Meeting "Intermolecular Interactions and Liquid Structure" (Salzburg, Austria, 2009) (lecture)
(Abstract, PDF)
- Dmitry Nerukh and Vladimir Ryabov
Phase space diffusion in molecular liquids: non-stationary random walk model,
Mathematical Challenges of Molecular Dynamics, Second Annual Conference (Bath, UK, 2009) (lecture)
(Abstract, PDF)
- Dmitry Nerukh, Christian H Jensen, and Robert C Glen,
The Markovian time scale of peptide conformational dynamics,
Molecular Kinetics 2009 (Berlin, Germany, 2009)
(Abstract, PDF)
- Dmitry Nerukh, Vladimir Ryabov, and Makoto Taiji,
Diffusion in the phase space of molecular liquids,
Dynamics and structure in physics and chemistry (Kharkov, Ukraine, 2009)
(Abstract, PDF)
- Dmitry Nerukh and Vladimir Ryabov,
Single molecular signals reveal microsecond long time correlations in bulk liquids,
XI. Annual Linz Winter Workshop (Linz, Austria, 2009)
(Abstract, PDF)
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Christian H. Jensen, Dmitry Nerukh and Robert C. Glen,
Statistical complexity of classical molecular dynamics systems: a measure of phase space exploration and non-Markovian behaviour of molecular conformations,
Physics of Living Matter, Symposium II (Cambridge, UK, 2007)
(Poster, PDF)
- Dmitry Nerukh and Makoto Taiji,
Peptide's dynamics between structural transitions,
Joint Conference of JMLG/EMLG Meeting 2007 and 30th Symposium on Solution Chemistry of Japan Molecular Approaches to Complex Liquids System (Fukuoka, Japan, 2007)
(Abstract, PDF)
- Christian H. Jensen, Dmitry Nerukh, and Robert C. Glen,
Calculating Mean First Passage Times from Markov Models of Proteins,
CompLife 2007 (Utrecht, the Netherlands, 2007)
(Abstract, PDF)
- Dmitry Nerukh, Maxim Fedorov, Christian Jensen, and Robert C Glen,
Physical chemistry of aqueous solutions of macromolecules: the emergence of self-organised structures,
Modern Physical Chemistry for Advanced Materials (Kharkov, Ukraine, 2007)
(Abstract, DOC)
- Dmitry Nerukh, Christian Jensen, and Vladimir Ryabov,
Statistical complexity of classical molecular dynamics systems: a measure of phase space exploration and non-Markovian behaviour of molecular conformation,
XIV Annual Seminar Nonlinear Penomena in Complex Systems (Minsk, Belorussia, 2007)
(Abstract, PDF)
- Dmitry Nerukh, George Karvounis, and Robert Glen,
The dynamic complexity of bio-molecules: quantifying emergent behaviour,{new}
Computational Life Science (Cambridge, UK, 2006)
(Lecture, Macromedia flash, 6.3Mb)
[no borders version]
- Yuriy Chesnokov, Dmitry Nerukh, Robert Glen,
Individually Adaptable Automatic QT Detector,
Computers in Cardiology (Valencia, Spain, 2006)
(Abstract, DOC)
- Alexander Nerukh, Nataliya Ruzhytska, Dmitry Nerukh,
Hurst's Index and Complexity of Wave in Modulated Dielectric Medium,
8th International Conference on Transparent Optical Networks (ICTON 2006) (Nottingham, UK, 2006)
(Abstract, PDF, Lecture, PPT)
- A. Nerukh, N. Ruzhytska, and D. Nerukh,
Quasy-intermittency of waves and their complexity in modulated dielectric medium,
International Conference on Mathematical Methods in Electromagnetic Theory (MMET*06) (Kharkov, Ukraine, 2006)
(Abstract, PDF)
- Yuriy Chesnokov, Dmitry Neruh, Robert Glen,
HRV analysis of patients prone to atrial fibrillation using a Neural Network approach,
Measurement & Modelling of Autonomic Function (London, UK, 2006)
(Poster, PPT; Abstract, DOC)
- Robert Glen and Dmitry Nerukh,
Why do proteins fold?,
The First European Conference On Chemistry For Life Sciences (Rimini, Italy, 2005)
(Lecture, PPT)
- F. Fedotov, N. Ruzhytska, D. Nerukh,
Complexity of Electromagnetic Pulse Passing a Layer of Nonlinear Medium,
7th International Conference on Transparent Optical Networks (ICTON 2005) (Barcelona, Spain, 2005)
(Abstract, PDF)
- Dmitry Nerukh, George Karvounis, and Robert C Glen,
Dynamic complexity of protein folding: computational mechanics on classical molecular trajectories,
2nd International Conference on Cybernetics and Information Technologies, Systems and Applications (CITSA 2005) and the 11th International Conference on Information Systems Analysis and Synthesis (ISAS 2005) (Orlando, USA, 2005) (invited lecture)
(Abstract, PDF)
- Dmitry Nerukh, George Karvounis, and Robert C Glen,
Loss of chaoticity during beta-turn transition: dynamic complexity of protein folding,
International Workshop on Theoretical and Computational Chemistry of Complex Systems (Hong Kong, China, 2005)
(Abstract, PDF)
- Ruzhytska N.N., Nerukh A.G., and Nerukh D.A.,
Changing of complexity and spectrum of different signals in time-varying medium,
10-th International Conference on Mathematical Methods in Electromagnetic Theory (MMET*04) (Dnepropetrovsk, Ukraine, 2004)
(Abstract, PDF)
- N. Ruzhytska, A. Nerukh, and D. Nerukh,
Sharpening of the Signal Spectrum with the Change of its Complexity,
6th International Conference on Transparent Optical Networks (ICTON 2004) (Wroclaw, Poland, 2004)
(Proceeding, PDF)
- Dmitry Nerukh, George Karvounis, and Robert C. Glen,
Statistical complexity of protein folding: application of computational mechanics to molecular dynamics,
International Conference on Complex Systems (ICCS2004) (Boston, USA, 2004)
(Lecture, Macromedia flash, 6.3Mb)
[no borders version]
- N. Ruzhytska, A. Nerukh, D. Nerukh,
Parallel Evolution of Electromagnetic Signal Complexity with the Medium Change,
12th International Workshop on Optical Waveguide Theory and Numerical Modelling (Ghent, Belgium, 2004)
(Abstract, PDF)
- Dmitry Nerukh, George Karvounis, and Robert C. Glen,
Dynamic Complexity during Folding in molecular systems,
Frontiers in Chemical Biology: Biomolecular dynamics and force generation (Manchester, UK, 2003)
(Poster, PDF, 1.8Mb)
- Natalia N. Ruzhytska, Alexander G. Nerukh, and Dmitry Nerukh,
Dependence of electromagnetic signal complexity on medium disturbances,
International Workshop on Optical Waveguide theory and numerical modelling (Prague, Czech Republic, 2003)
- Natalia N. Ruzhytska, Alexander G. Nerukh, and Dmitry Nerukh,
Calculation of complexity of a pulse transformation in time-varying medium,
Mathematical Methods in Electromagnetic Theory - MMET*02 (Kiev, Ukraine, 2002)
(Proceedings (MS Word))
- Dmitry Nerukh,
Real and imaginary parts of the vibrational correlation function extracted from the highly overlapping Raman bands of liquid electrolyte solutions,
Sixth Liblice Conference on the Statistical Mechanics of Liquids (Spindleruv Mlyn, Czech Republic, 2002)
(Poster, Corel Draw file)
(Poster, PDF)
- Dmitry Nerukh, Clemens Woywod, and John H. Frederick,
Multidimensional de Broglie - Bohm dynamics: the quantum motion with trajectories,
TSRC Workshop on "Theory of nonadiabatic processes", (Telluride, CO, USA, 2000) (lecture)
- Dmitry Nerukh, Clemens Woywod, and John H. Frederick,
Multidimensional Bohmian mechanics: quantum dynamics on one and two potential surfaces,
Pitzer memorial symposium on theoretical chemistry, (Berkeley, CA, USA, 2000)
- Eremenko S.A., Kalugin O.N., and Nerukh D.A.,
Resolution of vibrational spectra of liquids having overlapping bands of complex shape: uniqueness of solution and method of fitting,
7th European Conference on Spectroscopy of Biological Molecules, (El Escorial, Madrid, Spain, 1997)
- Eremenko S.A., Kalugin O.N., and Nerukh D.A.,
Influence of ions and temperature on the dynamics of solvent molecules in acetonitrile electrolyte solutions,
40th Hungarian Conference on Spectrochemistry (Debrecen, Hungary, 1997)
- Kalugin O.N., Nerukh D.A., Eremenko S.A., Volobuev M.N. and Vyunnik I.N.,
Spectroscopic studies of molecular dynamics of acetonitrile molecules in electrolyte solutions,
VI International Conference "Problems of solvation and complex formation in solutions", (Institute of Non-aqueous Solution Chemistry Ivanovo, Russia, 1995) (lecture)
- Kalugin O.N., Nerukh D.A., Vyunnik I.N., Vankevich A.V. and Eremenko S.A.,
Interparticle interactions and dynamics of molecules in acetonitrile solutions of NaI, NaBPh4, Bu4NI according Raman spectroscopy,
XII International Seminar on Interparticle Interactions and Molecular
Conformations, XII International Seminar on Interparticle Interactions and Molecular Conformations, (Institute of Mono-crystals
Kharkov, Ukraine)
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