Using next generation computers and algorithms for modelling the dynamics of large biomolecular systems

Publications

  1. V.A. Semiletov and S.A. Karabasov,
    CABARET scheme for Computational Aero Acoustics: extension to asynchronous time stepping and 3D flow modelling,
    Int. J. Aeroacoustics, in press.
  2. A.P. Markesteijn and S.A. Karabasov,
    Acoustic wave focusing by non-uniform mean flow in a rectangular duct with viscous walls,
    Int. J. Aeroacoustics, in press.
  3. Anton Markesteijn, Sergey Karabasov, Arturs Scukins, Dmitry Nerukh, Vyacheslav Glotov, and Vasily Goloviznin,
    Concurrent multiscale modelling of atomistic and hydrodynamic processes in liquids,
    Phil. Trans. R. Soc., A 372 (2021), 20130379 (2014).
  4. Evgen Pavlov, Makoto Taiji, Arturs Scukins, Anton Markesteijn, Sergey Karabasov, and 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 Discussions, DOI:10.1039/C3FD00159H (2014).
  5. A.P. Markesteijn and S.A. Karabasov,
    Time Asynchronous Relative Dimension in Space method for multi-scale problems in fluid dynamics,
    J. Comp. Phys., 258, 137-164 (2014).
  6. A.P. Markesteijn, S.A. Karabasov, V.Yu. Glotov, and V.M.Golovznin,
    A New Non-Linear Two-Time-Level Central Leapfrog Scheme in Staggered Conservation-Flux Variables for Fluctuating Hydrodynamics Equations with GPU Implementation,
    under review.
  7. V.Yu. Glotov, V.M. Goloviznin, S.A. Karabasov, and A.P. Markesteijn,
    New Two Level Leapfrog Scheme for Modeling the Stochastic Landau–Lifshitz Equations,
    Zhurnal Vychislitel'noi Matematiki i Matematicheskoi Fiziki, 54 (2), 298–317 (2014),
    (translated: ISSN 09655425, Computational Mathematics and Mathematical Physics, 2014, Vol. 54, No. 2, pp. 315–334. © Pleiades Publishing, Ltd., 2014).
  8. G.A. Faranosov, V.M. Goloviznin, S.A. Karabasov, V.G. Kondakov, V.F. Kopiev, M.A. Zaitsev,
    CABARET method on unstructured hexahedral grids for jet noise computation,
    Computers and Fluids, 88, 165-179 (2013).
  9. V.A. Semiletov and S.A. Karabasov,
    CABARET scheme with conservation-flux asynchronous time-stepping for nonlinear aeroacoustics problems,
    Journal of Computational Physics, 253, 157-165 (2013).
  10. Dmitry Nerukh and Sergey Karabasov,
    Water-Peptide Dynamics during Conformational Transitions,
    The Journal of Physical Chemistry Letters, 4 (5), 815-819 (2013).
  11. S.A. Karabasov, C. Bogey and T.P .Hynes,
    An investigation of the mechanisms of sound generation in initially laminar, subsonic jets using the Goldstein acoustic analogy,
    J. Fluid Mech, 714, 24–57 (2013).
  12. V.M. Goloviznin, S.A. Karabasov, V.G. Kondakov,
    Generalization of CABARET scheme for two-dimensional orthogonal computational grid,
    Com. Math, 25 (7), 103-136 (2013).
  13. A. Obabko, P. Fischer, T. Tautges, V. Goloviznin, M. Zaitsev, V. Chudanov, V. Pervichko, A. Aksenova, S. Karabasov,
    Large Eddy Simulation of thermo-hydraulic mixing in a T-junction,
    in electronic book "Nuclear Reactor Thermal Hydraulics", ISBN 980-953-307-668-8 (2013).
  14. V. Semiletov, S. Karabasov,
    A 3D frequency-domain linearised Euler solver based on the Goldstein acoustic analogy equations for the study of nonuniform meanflow propagation effects,
    AIAA-2013-2019, 19th AIAA/CEAS Conference, Berlin 27-29 May (2013).
  15. V. Semiletov, S. Karabasov, D. Lyubimov, G. Faranosov, V. Kopiev,
    On the effect of flap deflection on jet flow for a jet-pylon-wing configuration: near-field and acoustic modelling results,
    AIAA-2013-2215, 19th AIAA/CEAS Conference, Berlin 27-29 May (2013).
  16. V. Kondakov, S. Karabasov, V. Goloviznin,
    On the effect of Mach number on subsonic jet noise sources in the Goldstein acoustic analogy model,
    AIAA-2013-2275, 19th AIAA/CEAS Conference, Berlin 27-29 May (2013).
  17. G. Faranosov, S. Karabasov, V. Kopiev,
    Application of Azimuthal Decomposition Technique for validation of CAA methods,
    AIAA-2013-2238, 19th AIAA/CEAS Conference, Berlin 27-29 May (2013).
  18. Alexander G. Nerukh and Dmitry A. Nerukh,
    Time-spatial drift of decelerating electromagnetic pulses,
    Opt. Express, 21 (14), 17366-17371 (2013).
  19. Dmitry Nerukh,
    Non-Markov state model of peptide dynamics,
    Journal of Molecular Liquids, 176, 65-70 (2012).
  20. Dmitry Nerukh, Noriaki Okimoto, Atsushi Suenaga, and Makoto Taiji,
    Ligand Diffusion on Protein Surface Observed in Molecular Dynamics Simulation,
    The Journal of Physical Chemistry Letters, 3 (23), 3476-3479 (2012).
  21. Vitaliy Bardik, Vladimir Gotsulskii, Evgen Pavlov, Nikolai Malomuzh, Dmitry Nerukh, Igor Yanchuk, and Serhiy Lavoryk,
    Light scattering study of human serum albumin in pre-denaturation: Relation to dynamic transition in water at 42C,
    Journal of Molecular Liquids, 176 (0), 60-64 (2012),
    (Special Issue Dynamics and Phase Transition: Selected Papers on Molecular Liquids presented at the EMLG/JMLG 2011 Annual Meeting 11 - 15 September 2011).
  22. V.Yu. Bardik, D. Nerukh, E.V. Pavlov, and M.S. Vlasyuk,
    Free energy functional expansion as the generalized approach to the equation of state of dense fluids,
    Ukrainian Journal of Physics, 57 (6), 612-618 (2012).
  23. V.Yu. Bardik, D. Nerukh, E.V. Pavlov, M.S. Vlasyuk, and I.V. Zhyganiuk,
    Equation of state for water in the small compressibility region,
    Ukrainian Journal of Physics, 57 (1), 49-53 (2012).
  24. Vladimir Ryabov and Dmitry Nerukh,
    Statistical complexity of low and high dimensional systems,
    Journal of Atomic, Molecular, and Optical Physics, 2012, 589651 (2012).
  25. V.M. Goloviznon, M.A. Zaitsev, S.A. Karabasov, and I.A. Korotkin,
    New computational hydrodynamics algorithms for multi-process numerical simulations,
    Moscow University Press, 2012, 480 p, ISBN 978-5-211-06426-3.
  26. V.M Goloviznin, V.Yu. Glotov, A.V. Danilin, I.A. Korotkin, and S.A. Karabasov,
    Computational modelling of incompressible turbulent flows in multiple dimensions with the CABARET scheme,
    (in “Basic problems of multiphase and turbulent flows”, Moscow, Nauka).
  27. L.Y. Gomzikov, S.A. Karabasov, V.G. Latyshev, A.M. Sipatov,
    Advanced heat analysis of turbine rotor blades coupled with combustion chamber simulation,
    TsAGI Science Journal, 43 (5).
  28. S.A. Karabasov and V.M Goloviznin,
    Direct numerical simulations of compressible vortical flow problems,
    (in “Fluid Dynamics/ Book 1”, INTECH, 2012, ISBN 979-953-307-111-3).
  29. N. Depuru Mohan, O. Graham, S. Karabasov, H. Xia, A. Dowling, P. Tucker, T. Hynes,
    Reduced-order Jet Noise Modelling for Chevrons,
    AIAA-2012-2083.
  30. A. Markesteijn, S. Karabasov,
    Acoustic Wave Focusing by Non-uniform Mean Flow in a Rectangular Duct with Viscous Walls,
    AIAA-2012-2091.
  31. V. Semiletov, S. Karabasov, G. Faranosov, M. Zaitsev,
    Airfoil Flow and Noise Computation Using Monotonically Integrated LES and Acoustic Analogy,
    AIAA-2012-2108.
  32. G. Faranosov, V. Goloviznin, S. Karabasov, V. Kondakov, V. Kopiev, M. Zaitsev,
    CABARET Method on Unstructured Hexahedral Grids for Jet Noise Computation,
    AIAA-2012-2146.
  33. S. Karabasov, R. Sandberg,
    On the effect of Mach number and coflow for turbulent jet noise sources,
    AIAA-2012-2298.