Alexander Lyubartsev. List of publications

    1987
  1. P.N.Vorontsov-Velyaminov, A.P.Lyubartsev. "Combining of the Monte Carlo and self consistent field methods in the theory of DNA and other polyelectrolutes". Vestnik LGU (Leningrad, USSR), v.4, p.13-19 (1987); in Rissian
  2. P.N.Vorontsov-Velyaminov, A.P.Lyubartsev. "Self consistent field - Monte Carlo method in the polyelectrolyte theory. Calculation of the electrostatic potential for the symmetrical polyions". Molekulyarnaya Biologia (Moscow), v.21, p.654-662 (1987); in Rissian (Engl. Transl: Molek.Biol, v.21,p.545 (1987))

    3. 1989

  3. P.N.Vorontsov-Velyaminov, A.P.Lyubartsev. "Monte Carlo - self consistent field method in the polyelectrolyte theory" J.Biomol.Struct.and Dyn., v.7., p.739-747 (1989)

    4. 1990

  4. A.P.Lyubartsev, P.N.Vorontsov-Velyaminov. "Monte Carlo simulation of flexible polyelectrolytes" Vysokomolekulyarnye Soedineniya (Moscow; in Russian), v.32A, p.721-726 (1990)
  5. A.P.Lyubartsev, V.P.Kurmi, P.N.Vorontsov-Velyaminov. "Monte Carlo - self consistent field simulation of the interaction of single- and divalent ions with DNA"Molekulyarnaya Biologia (Moscow), v.24, p.1533-1540 (1990) (in Russian)

    6. 1992

  6. A.P.Lyubartsev, A.A.Martsinovskii, S.V.Shevkunov, P.N.Vorontsov-Velyaminov. "New approach to Monte Carlo calculation of the free energy: Method of expanded ensembles". J.Chem.Phys., v.96, pp.1776-1783 (1992). Abstract and text
  7. A.P.Lyubartsev, V.P.Kurmi, P.N.Vorontsov-Velyaminov. "Study of ionic environment of symmetrical models of polyelectrolytes by computer experiment" Rus. J. Phys. Chem., v. 67, pp. 230-235 (1992).
  8. P.N.Vorontsov-Velyaminov, A.P.Lyubartsev. "Monte Carlo - self consistent field study of the symmetrical models of polyelectrolytes" Molecular Simulations, v.9, p.285-306 (1992).

    9. 1993

  9. A.P.Lyubartsev, A.A.Martsinovskii, P.N.Vorontsov-Velyaminov, T.V.Kuznetsova. "A new approach to the Monte Carlo Calculations of free energy with the use of expanded ensembles" Rus.J.Phys.Chem.,v.67,pp.230-235 (1993)
  10. A.P.Lyubartsev, P.N.Vorontsov-Velyaminov "Path Intergal Monte Carlo method in quantum statistics for a system of N identical fermions" Physical Review A, v.48(6), pp.4075-4083 (1993) Abstract and text

    11. 1994

  11. A.P.Lyubartsev, A. Laaksonen.,P.N.Vorontsov-Velyaminov. "Free Energy Calculations for Lennard-Jones Systems and Water Using the Expanded Ensemble Method. A Monte Carlo and Molecular Dynamics Simulation Study". Molecular Physics, v.82, pp.455-471 (1994) Abstract

    12. 1995

  12. A.P.Lyubartsev, L. Nordenskiold. "A Monte Carlo Simulation Study of Ion Distribution and Osmotic Pressure in Hexagonally Oriented DNA." J.Phys.Chem., v.99, p.10373 (1995). Abstract
  13. Alexander P. Lyubartsev and Aatto Laaksonen Calculation of Effective Interaction Potentials from Radial Distribution Functions: A Reverse Monte Carlo Approach Phys.Rev.E, v.52, p.3730 (1995). Abstract and text

    1996

  14. A. V. Broukhno, T. V. Kuznetsova, A. P. Lyubartsev and P. N. Vorontsov- Velyaminov "Calculation of the free energy of polymers within the framework of lattice and continuous models by molecular simulation methods using expanded statistical ensembles"Vysokomolekulyarnye soedinenia, v.38A, p.77-83 (1996).
  15. P.N. Vorontsov-Velyaminov, A.V.Broukhno, T.V.Kuznetsova and A.P.Lyubartsev. "Free Energy Calculations by Expanded Ensemble Method for Lattice and Continuous Polymers". J.Phys.Chem.,v.100(4),pp.1153-1158 (1996) Abstract ; Paper: PostScript file
  16. A. P. Lyubartsev, O. Førrisdahl, A. Laaksonen Calculations of solvation free energies by expanded ensemble method Proc. 2nd Int. Conf. on Natural gas Hydrates. Toulouse (France) June 2-6, 1996 pp. 311-318.
  17. Aatto Laaksonen and A. P. Lyubartsev Parallel molecular dynamics simulations of DNA system PDC Progress Report 1994-1996, p.121-126. Paralleldatorcentrum, Stockholm, 1996. Paper (PostScript file)
  18. A.P.Lyubartsev, A. Laaksonen.,P.N.Vorontsov-Velyaminov. "Determination of Free Energy from Chemical Potential. Application of the Expanded Ensemble Method". Molecular Simulations, v.18(1),pp.43-58 (1996). Abstract ; Paper (PostScript file)
  19. A. P. Lyubartsev and A. Laaksonen Concentration Effects in Aqueous NaCl Solutions. A Molecular Dynamics Simulation. J.Phys.Chem., v.100 (40), p.16410-18 (1996). Abstract and supporting information; Abstract and text from JPC Web site

    20. 1997

  20. A. P. Lyubartsev and A. Laaksonen "Osmotic and Activity Coefficients from Effective Potentials for Hydrated Ions" Phys.Rev.E., v.55 (5) p.5689 (1997) Abstract ; Abstract and text (APS Web site)
  21. A. P. Lyubartsev and L. Nordenskiöld "Monte Carlo Simulation Study of DNA Polyelectrolyte. Properties in the Presence of Multivalent Polyamines Ions". J. Phys. Chem. B, v.101, p.4335 (1997). Abstract and text
  22. L. Nordenskiöld, A.P. Lyubartsev, J. Tang and P. Janmey, " Electrostatically Induced Bundle Formation of Rodlike Polyelectrolytes. Comparison of Predictions from Monte Carlo Simulations with Experiments on FD and M13 virus particles" Materials Research Society Symposium Proceedings Series, v.489, section k2.8 (1997). Abstract.

    23. 1998

  23. A. P. Lyubartsev, O. Førrisdahl, A. Laaksonen " Solvation Free Energies of Methane and Alkali Halide Ion Pairs. An Expanded Ensemble Molecular Dynamics Simulation Study". J.Chem.Phys, v.108(1), pp. 227-233 (1998). Abstarct ; Paper (Postscript.gz).
  24. A. P. Lyubartsev, A. Laaksonen "Parallel Molecular Dynamics Simulations of Biomolecular Systems". Lecture Notes in Computer Science, No. 1541, 1998, pp 296-303. Paper (Postscript file).
  25. N. Korolev, A. P. Lyubartsev, L. Nordenskiöld. "Application of the polyelectrolyte theories for description of DNA melting in the presence of Na+- and Mg2+-ions". Biophys. J., v.75, pp.3041-3056 (1998) Abstract and text .
  26. A. P. Lyubartsev, J. X. Tang, P. A. Janmey, and L. Nordenskiöld "Electrostatically induced polyelectrolyte association of rodlike virus particles". Phys. Rev. Lett., v.81, p.5465-5468 (1998) Abstract and full PDF text from the AIP Web site
  27. L. van Dam, A.P.Lyubartsev, A.Laaksonen and L.Nordenskiöld " Self-diffusion and association of Li+, Cs+ and H 2O in oriented DNA fibers. An NMR and MD simulation study." J.Phys.Chem.B, v.102, pp.10636-10642 (1998) Abstract and text
  28. A.P.Lyubartsev and A.Laaksonen "Molecular Dynamics Simulations of DNA in Solution with Different Counterions." J.Biomol.Struct. and Dyn., v.16, pp.579-587 (1998) Abstract; Supplementary material

    29. 1999

  29. A.P.Lyubartsev, A.Laaksonen, "Quantum molecular dynamics simulations methods.", in "NSC Progress Report", p.35-37 (National Supercomputer Center, Linköping, 1999)
  30. D.L.Bergman, A.P.Lyubartsev, and A.Laaksonen, "Topological and spatial aspects of the hydration of solutes of extreme solvation entropy ", Phys. Rev. E, v. 60, pp. 4482-4495 (1999)
    31. Abstract and textfrom the APS Web site
  31. N.Korolev, A.P.Lyubartsev, A.Rupprecht and L.Nordenskiöld, "Experimental and Monte Carlo simulation studies on the competitive binding of Li+, Na+, and K+ ions to DNA in oriented DNA fibers", J. Phys. Chem. B, v.103, pp. 9008-9019 (1999) Abstract and text .
  32. N.Korolev, A.P.Lyubartsev, A.Rupprecht and L.Nordenskiöld, " Competitive binding of Mg2+, Ca2+, Na+, and K+ ions to DNA in oriented DNA fibers: Experimental and Monte Carlo simulation results", Biophys. J, v.77, pp. 2736-2749 (1999) Abstract and text.
  33. A.P.Lyubartsev, A.Laaksonen. "Reconstruction of pair interaction potentials from radial distribution functions." Computer Physics Communications, v. 121-122, p.57-59 (1999). Paper (postscript file)
  34. A.P.Lyubartsev, A.Laaksonen. "Effective Potentials for Ion-DNA Interactions" J. Chem. Phys., v.111, p.11207-11215 (1999). Abstract and full text from the AIP Web site

    35. 2000

  35. A.P.Lyubartsev and A. Laaksonen, MDynaMix - a scalable portable paralle MD simulation package for arbitrary molecular mixtures" Computer Physics Communications, v.128(3), pp.565-589 (2000) MDynaMix download page
  36. K. Kulinska, T.Kulinski, A.P.Lyubartsev, A.Laaksonen and R.W.Adamiak, Spatial distribution functions as a tool in the analysis of ribonucleic acids hydration - molecular dynamics studies Computers & Chemistry, v.24 (3-4), pp. 451-457 (2000)
  37. A.P.Lyubartsev and A.Laaksonen, "Determination of pair potentials from ab-initio simulations: Application to liqid water" Chem.Phys.Lett., v. 325, pp.15-21 (2000)
    38. Abstract and text from Elsevier Science
  38. P.G.Kusalik, A.P.Lyubartsev, D.L.Bergman and A.Laaksonen, Computer Simulation Study of Tert-butyl Alcohol. 1. Structure in the Pure Liquid" J. Phys. Chem. B, v. 104, pp.9526-9532 (2000) Abstract and text from the ACS Web site
  39. P.G.Kusalik, A.P.Lyubartsev, D.L.Bergman and A.Laaksonen, Computer Simulation Study of Tert-butyl Alcohol. Structure in Aqueous Solution" J. Phys. Chem. B, v. 104, pp.9533-9539 (2000). Abstract and text from the ACS Web site

    40. 2001

  40. N. Korolev, A.P.Lyubartsev, A.Rupprecht and L.Nordenskiöld, "Competitive Substitution of Hexammine Cobalt(III) for Na+ and K+ Ions in Oriented DNA Fibers" Biopolymers, v. 58, pp. 268-278 (2001)
    41. Abstract and text
  41. V. Lobaskin, A. Lyubartsev and P. Linse "Effective macroion-macroion potentials in asymmetric electrolytes" Phys. Rev. E, v. 63, 020401 (2001) Abstract and full text from the PRE Web site
  42. A.P Lyubartsev, K. Laasonen and A. Laaksonen "Hydration of Li+ ion. An ab-initio molecular Dynamics Simulation" J. Chem. Phys., v. 114, p.3120-3126 (2001) Abstract and full text from the JCP Web site
  43. A.Vishnyakov, A.P.Lyubartsev, A.Laaksonen "Molecular dynamics simulations of dimethylsulfoxide and dimethylsulfoxide-water mixtures" J. Phys. Chem. A, v. 105, pp. 1702-1710 (2001) Abstract and text from the ACS Web site
  44. A.Lyubartsev, M.Dahlberg and A.Laaksonen, "Modelling of gramicidin A ion-selective channel in a dmpc bilayer - A molecular dynamics simulation study"Proceedings of the 45 annual meeting of the Biophysical Society; Biophys. J., v.80, no.1 part 2, p.327a (2001)
  45. N. Korolev, A.P.Lyubartsev, L. Nordenskiöld and A. Laaksonen, "Spermine: An "invisible" component in the crystals of B-DNA: A grand canonical Monte Carlo and Molecular Dynamics simulation study" J. Mol. Biol., 308, 907-917 (2001) Abstract and text from Science direct
  46. R.Kjellander, A.P.Lyubartsev, and S.Marcelja, "McMillan Theory for Solvent Effects in Inhomogeneous Systems: Calculation of Interaction Pressure in Aqueous Electrical Double Layers" J. Chem. Phys., 114(21), 9565-9577 (2001) Abstract and full text from the JCP Web site
  47. A.P.Lyubartsev, S.P.Jacobsson, G. Sundholm and A. Laaksonen "Solubility of Organic Compounds in Water/Octanol System. An Expanded Ensemble Molecular Dynamics Simulation Study of log P parameters" J. Phys. Chem. B, v. 105, pp. 7775-7782 (2001) Abstract and ftext from the ACS Web site
  48. J.A.Nilsson, A.P.Lyubartsev, L.A.Eriksson and A.Laaksonen, "Molecular dynamics simulations of ubiquinone: a survey over torsional potentials and hydrogen bonds" Mol. Phys., v. 99 (21), pp. 1795-1804 (2001) Abstract and text from Taylor&Francis

    49. 2002

  49. A.P.Lyubartsev and L.Nordenskiöld "Computer Simulations of Polyelectrolytes", in Handbook of Polyelectrolytes and Their Applications, S. K. Tripathy, J. Kumar and H. S.Nalwa, Eds., American Scientific Publishers, Los Angeles (2002), Volume 3, Chapter 11, pp. 309-326.
  50. A. P. Lyubartsev and S. Marcelja Evaluation of effective ion-ion potentials in aqueous electrolytes  Phys.Rev.E, v.65(4), 041202 (2002) Abstract and full text from the APS Web site
  51. E. N. Brodskaya, A.P.Lyubartsev and A. Laaksonen Molecular dynamics simulations of water clusters with ions in atmospheric conditions. J.Chem.Phys, v.116, pp.7879-7892 (2002)  Abstract and full text from the AIP Web site
  52. N. Korolev, A.P.Lyubartsev, A. Laaksonen and L. Nordenskiöld On the competition between water, sodium ions and spermine in binding to DNA. A molecular dynamics computer simulation study"  Biophys. J., v.82,pp.2860-2875 (2002) Abstract and full text from the Biophys.J. Web site
  53. E. N. Brodskaya, A.P.Lyubartsev and A. Laaksonen "Investigation of Water Clusters Containing H+, OH-, and H3O+ Ions in Atomospheric Conditions", J.Phys.Chem., v.106 (25): pp. 6479-6487 (2002) Abstract and full text from the ACS Web site
  54. J. X.Tang, P.A.Janmey, A.P.Lyubartsev and L.Nordenskiöld, " Metal ion induced lateral aggregation of filamentous viruses fd and M13 ",  Biophys. J. ,v. 83: pp. 566-581 (2002) Abstract and full text from the Biophys.J. Web site.
  55. N. Korolev, A. P. Lyubartsev and L. Nordenskiöld Application of the Poisson-Boltzmann polyelectrolyte model for analysis of equilibtia between single-, double-, and triple-stranded polynucleotides in the presence of K+, Na+, and Mg2+ ions, J. Biomol. Struct. and Dynamics, v.20(2), pp.275-290 (2002) Abstract from the JBSD Web site

    56. 2003

  56. R.A.Lohikoski, J. Timonen, A.P.Lyubartsev and A. Laaksonen Internal Structure and Dynamics of the Decamer D(ATGCAGTCAG)2 in Li+ - H2O Solution: A Molecular Dynamics Simulation Study Molecular Simulations, v. 29(1), pp. 47-62 (2003)
  57. P.N.Vorontsov-Velyaminov and A.P.Lyubartsev, "Entropic sampling in the Path Integral Monte Carlo method", J. Phys. A: Math. Gen. v. 36, pp. 685-693 (2003)
    Abstract; Text (PDF).
  58. A.P.Lyubartsev, E.F.Heald and R.W.York, "Modeling a Boltzmann distribution: Simbo (simulated Boltzmann), a computer laboratory exercise" J. Chem. Education, v.80 (1), p. 109 Abstract    To get the program code for linux, send a e-mail request.
  59. A. P. Lyubartsev, M. Karttunen, I. Vattulainen and A. Laaksonen On coarse-graining by the inverse Monte Carlo method: Dissipative particle dynamics simulations made to a precise tool in soft matter modelling Soft Materials, v. 1(1), pp. 121-137 (2003) Abstract and text
  60. A.V. Egorov, A.V. Komolkin, V.I. Chizhik, P.V. Yushmanov, A.P.Lyubartsev and A.Laaksonen Temperature and concentration effects on Li$^+$-ion hydration. A molecular dynamics simulation study J. Phys. Chem. B, 107 (14), pp. 3234-3242 (2003) Abstract and full text (ACS)
  61. S.D.Ivanov, A.P.Lyubartsev and A.Laaksonen Bead-Fourier Path Integral Molecular Dynamics Phys. Rev. E, v.67, 066710 (2003) Abstract and full text (APS)
  62. N. Korolev, A. P. Lyubartsev and L. Nordenskiöld Application of the Poisson Boltzmann polyelectrolyte model for analysis of thermal denaturation of DNA in the presence of Na+ and polyamine cations Biophysical Chemistry, v.104, pp.55-66 (2003) Abstract and full text
  63. P. N. Vorontsov-Velyaminov and A. P. Lyubartsev Generalized ensemble methods in chemical physics Recent Research Developments in Chemical Physics, v. 4, pp. 63-78 (2003) Full text
  64. N. Korolev, A. P. Lyubartsev, A. Laaksonen and L. Nordenskiöld, A Molecular Dynamics Simulation Study of Oriented DNA with Polyamine and Sodium Counterions. Diffusion and Averaged Binding of Water and Cations Nucleic Acids Research, v. 31 (20), pp. 5971 - 5981 (2003) Abstract and full text
  65. E.N.Brodskaya, A.V.Egorov. A.P.Lyubartsev and A.Laaksonen Computer modeling of melting of ionized ice microcrystals J. Chem. Phys., v. 118, p. 10237 (2003) Abstract and full text from JCP

    66. 2004

  66. K. M. Åberg, A.P.Lyubartsev, S.P.Jacobsson and A.Laaksonen, Determination of solvation free energies by adaptive expanded ensemble molecular dynamics J. Chem. Phys., v. 120, pp. 3770-3776 (2004) Abstract and full text from JCP
  67. N. Korolev, A. P. Lyubartsev, A. Laaksonen and L. Nordenskiöld Molecular dynamics simulation study of oriented polyamine- and Na- DNA: Sequence specific interactions and effects on DNA structure Biopolymers, v. 73(5), pp. 542-555 (2004) Abstract and full text from Wiley Interscience
  68. A. P. Lyubartsev and A. Laaksonen "On the reduction of molecular degrees of freedom in computer simulations" Lecture Notes in Physics, v. 640 , pp. 219 - 244 (2004)   PDF text
  69. A. P. Lyubartsev "Molecular Simulations of DNA Counterion Distributions" Dekker Encyclopedia of Nanoscience and Nanotechnology, pp. 2131 - 2143 Dekker (2004)   Abstract PDF text
  70. N. Korolev, A. P. Lyubartsev and A. Laaksonen "Electrostatic Background of Chromatin Fiber Stretching" J. Biomol. Struct. and Dyn., v. 22(2), pp. 215-226 (2004)   Abstract PDF text
  71. F. Mocci, A. Laaksonen, A. Lyubartsev and G. Saba "Molecular dynamics investigation of Na-23 NMR relaxation in oligomeric DNA aqueous solution" J. Phys. Chem. B, v. 108(41), pp. 16295 - 16302 (2004)   Abstract and text
  72. A. P. Lyubartsev "Multiscale modeling of a lipid membrane bilayer" In: "Computational modeling and simulations of materials III", ed. P. Vincenzini and A. Lami, Techna Group, Faenza, Italy. Part A, pp. 53-60 (2004)
  73. N. Korolev, A. P. Lyubartsev, A. Laaksonen and L. Nordenskiöld "A molecular dynamics simulation study of polyamine and sodium DNA. Interplay between polyamine binding and DNA structure" Eur. Biophys. J., v. 33(8), pp. 671 - 682 (2004) Abstract and text
  74. J. M. Khalack and A. P. Lyubartsev "Car-Parrinello molecular dynamics simulations of Na+-Cl- ion pair in liquid water"Condensed Matter Physics, v. 7(4), p 683-698 (2004) Abstract and text

    75. 2005

  75. J. M. Khalack and A. P. Lyubartsev "Solvation structure of hydroxyl radical by Car-Parrinello molecular dynamics" J. Phys. Chem. A, v. 109(2), pp. 378 - 386 (2005)   Abstract and text
  76. A. P. Lyubartsev "Simulation of excited states and the sign problem in the path integral Monte Carlo method" J. Phys. A, v.38, pp. 6659-6674 (2005)  Abstract and text
  77. S. D. Ivanov and A. P. Lyubartsev "Simulations of one- and two-electron systems by Bead-Fourier path integral molecular dynamics" J. Chem. Phys., v. 123(3), 034105 (2005)   Abstract and text
  78. A. P. Lyubartsev "Multiscale modeling of lipids and lipid bilayers" Eur. Biophys. J., v. 35(1), pp. 53-61 (2005)   Abstract and text
  79. N. A. Volkov, A.A.Yurchenko, A.P.Lyubartsev and P.N.Vorontsov-Velyaminov "Entropic Sampling of Free and Ring Polymer Chains" Macromol. Theory and Simulations, v. 14(8), pp.491-504  Abstract and text

    80. 2006

  80. A. V. Egorov, A. V. Komolkin, A.P.Lyubartsev and A.Laaksonen "First and second hydration shell of Ni2+ studied by molecular dynamics simulations" Theor. Chem. Accounts, v. 115(2-3), pp.170-176 Abstract and text
  81. P.N.Vorontsov-Velyaminov, M.A.Voznesenski, D.V.Malakhov, A.P.Lyubartsev and A.V.Broukhno "Path Integral method in quantum statistics problems: generalized ensemble Monte Carlo and density functional approach" J. Phys. A: Math and Gen., v. 39, pp.4711-4716 (2006) Abstract and text
  82. N. Korolev, A.P.Lyubartsev and L.Nordenskiöld "Computer modeling demonstrate that electrostatic attraction of nucleosomal DNA is mediated by histone tails" Biophys. J., 90(6), 4305-4316 (2006) Abstract and text
  83. C.-J. Högberg and A.P.Lyubartsev "A Molecular Dynamics Investigation of the Influence of Hydration and Temperature on Structural and Dynamical Properties of a Dimyristoylphosphatidylcholine Bilayer" J. Phys. Chem. B, 110(29), 14326-14246 (2006) Abstract and text

    84. 2007

  84. J. Bunta, M. Dahlberg, L.Erikson, N.Korolev, A.Laaksonen, R.Lohikoski, A.Lyubartsev, M.Pinak, P.Schyman "Solvating, manipulating, damaging, and repairing DNA in a computer" Int.J.Quant.Chem., 107(2): 279-291 (2007) Abstract and text
  85. N.A.Volkov, P.N.Vorontsov-Velyaminov and A.P.Lyubartsev " Entropic sampling of flexible polyelectrolytes within the Wang-Landau algorithm" Phys. Rev. E, 75: 016705 (2007) Abstract and text
  86. C.-J. Högberg, A. Maliniak and A.P.Lyubartsev "Dynamical and structural properties of charged and uncharged lidocaine in a lipid bilayer" Biophys. Chem., 125, 416-424 (2007) Abstract and text
  87. A. P. Lyubartsev Interacting electrons in one dimension: A path integral Monte Carlo study" J. Phys. A., 40, 7151-7157 (2007) Abstract and text
  88. A. M. Nikitin, A. P. Lyubartsev "New six-site acetonitrile model for simulations of liquid acetonitrile and its aqueous mixtures" J. Comp. Chem., 28, 2020-2026 (2007) Abstract and text
  89. J. Thaning, C.-J. Högberg, B. Stevensson, A. P. Lyubartsev, and A. Maliniak "Molecular Conformations in a Phospholipid Bilayer Extracted from Dipolar Couplings: A Computer Simulation Study" J. Phys. Chem. B, 111, 13638 -13644 (2007) Abstract and text

    90. 2008

  90. C.-J. Högberg and A.P.Lyubartsev "Effect of Local Anesthetic Lidocaine on Electrostatic Properties of a Lipid Bilayer" Biophys. J., v. 94, pp. 525-531 Abstract and text; Preprint from Biofast; Open Access fulltext
  91. L. Nordenskiöld, N. Korolev, and A.P.Lyubartsev "DNA-DNA Interactions", In: "DNA interactions with polymers and surfactants", p. 209-238, Eds. R.Dias and B.Lindman, Willey InterScience, 2008.
  92. C.-J. Högberg, A.M.Nikitin and A.P.Lyubartsev "Modification of the CHARMM force field for DMPC lipid bilayer" J. Comp. Chem., v. 29 (14) , pp. 2359-2369 Abstract and text; PDF.
  93. V.Castro, B.Stevensson, S.V.Dvinskikh, C.-J. Högberg, A.P.Lyubartsev, H.Zimmermann, D. Sandström and A. Maliniak "NMR investigations of interactions between anesthetics and lipid bilayers" Biochim. Biophys. Acta, v. 1778, pp. 2604-2611. Abstract and text

    94. 2009

  94. Y. Yang, A. P. Lyubartsev, N. Korolev and Lars Nordenskiöld "Computer Modeling Reveals that Modifications of the Histone Tail Charges Define Salt-Dependent Interaction of the Nucleosome Core Particles" Biophys. J., v. 96, No. 6., pp. 2082-2094 Abstract and text
  95. A. Lyubartsev, Y. Tu and A.Laaksonen "Hierarchical Multiscale Modelling Scheme from First Principles to Mesoscale" J. Computational and Theoretical Nanoscience, v.6 (5), p. 951-959 Abstract and Text - a proof copy
  96. K. Dong, G. Zhou, X. Liu, X. Yao, S. Zhang and A.Lyubartsev "Structural Evidence for the Ordered Crystallites of Ionic Liquid in Confined Carbon Nanotubes" J. Phys. Chem. C, v. 113(23). p. 10013-10020 Abstract and Text
  97. Polyakov E.A., Vorontsov-Velyaminov P.N., Lyubartsev A.P. "Stochastic positive P-representation in problems of quantum statistics. Simulation of one-dimensional Bose-gas with delta-repulsion" Numerical Methods and Programming (Rus), v.10, p. 223-247 Abstract and Text.
  98. M.P.Ljungberg, A.P.Lyubartsev, A.Nilsson and L.G.M.Pettersson "Assessing the electric-field approximation to IR and Raman spectra of dilute HOD in D2O", J.Chem.Phys., v.131, 034501 ; doi:10.1063/1.3154144 Abstract and Text.
  99. C. Huang, K.T.Wikfeldt, T.Tokushima, D.Norlund, Y. Harada, U.Bergmann, M. Niebuhr, T.M.Weiss, Y. Horikawa, M. Leetmaa, M.P.Ljungberg, O. Takahashi, A.Lenz, L.Ojamae, A.P.Lyubartsev, S.Shin, L.G.M.Pettersson, A.Nilsson "The inhomogeneous structure of water at ambient conditions", Proc.Natl.Acad.Sci.USA, v.106 (36), 15214-15218 ; DOI: 10.1073/pnas.0904743106 Abstract and Text.
  100. A.Lyubartsev, A. Ben-Naim "One dimensional model for water and aqueous solutions. Part V. Monte Carlo simulation of dilute solutions of hard rod in waterlike particles" J. Chem. Phys., 131, 204507, doi:10.1063/1.3265948 Abstract and text
  101. M.A.Voznesenskiy, P.N.Vorontsov-Velyaminov and A.P.Lyubartsev "Path-integral - expanded-ensemble Monte Carlo method in treatment of the sign problem for fermions" Phys. Rev. E, 80, 066702, Doi: 10.1103/PhysRevE.80.066702 Abstract and text
  102. C.G.Jesudason, A.P.Lyubartsev and A.Laaksonen "Conformational characteristics of single flexible polyelectrolyte chain" Eur. Phys. J. E, 30, 341 - 350 (2009) DOI: 10.1140/epje/i2009-10532-5 Abstract and text

    103. 2010

  103. A. Lyubartsev, A.Mirzoev, L-J. Chen, A.Laaksonen "Systematic coarse-graining of molecular models by the Newton inversion method" Faraday Discuss., 2010, 144, 43 - 56, DOI: 10.1039/b901511f Abstract and text ; Open Access fulltext
  104. M. Leetmaa, M. P. Ljungberg, A.P.Lyubartsev, A. Nilsson and L. G. M. Pettersson "Theoretical approximations to X-ray absorption spectroscopy of liquid water and ice" J. Elect. Spectr and Related Phenomena, 2010, 177, 135 - 157, DOI: 10.1016/j.elspec.2010.02.004
  105. N. Korolev, A.P.Lyubartsev and L.Nordenskiöld "Cation-indiced polyelectrolyte-polyelectrolyte attraction in solutions of DNA and nucleosome core particles" J. Colloid and Interface Sci., 2010, 158, 32-47, DOI: 10.1016/j.cis.2009.08.002 Abstract and text
  106. N. Korolev, A. Allahverdi, Y. Yang, Y. Fan, A.P.Lyubartsev and L.Nordenskiöld "Electrostatic Origin of Salt-Induced Nucleosome Array Compaction" Biophys. J. , 2010, 99 (6),1896 - 1905 , DOI: 10.1016/j.bpj.2010.07.017 Abstract and text
  107. E. A. Polyakov, A. P. Lyubartsev, and P. N. Vorontsov-Velyaminov "Centroid molecular dynamics: Comparison with exact results for model systems" J. Chem. Phys., 2010, 133, 194103 , DOI: 10.1063/1.3484490 Abstract and text
  108. E. H. Mojumdar and A. P. Lyubartsev "Molecular Dynamics Simulations of Local Anesthetic Articaine in a Lipid Bilayer" Biophys. Chem., 2010, 153, 27-35. DOI:10.1016/j.bpc.2010.10.001 Abstract and text ; Open Access fulltext
  109. M. S. Santosh, Alexander P. Lyubartsev, Alexander A. Mirzoev, and D. Krishna Bhat "Molecular Dynamics Investigation of Dipeptide - Transition Metal Salts in Aqueous Solutions" J.Phys.Chem.B, 2010, 114, 16632-16640. DOI:10.1021/jp108376j Abstract and text
  110. P.N.Vorontsov-Velyaminov, N.A.Volkov, A.A.Yurchenko and A.P.Lyubartsev "Simulation of Polymers by the Monte Carlo Method using the Wang-Landau Algorithm" Polymer Sciense Ser. A, v.52(7), pp. 742-760 (2010); DOI: 10.1134/S0965545X10070096 Abstract and text

    111. 2011

  111. A.P.Lyubartsev and A.L.Rabinovich "Recent development in computer simulations of lipid bilayers" Soft Matter, v. 7, pp. 25-39 (2011) DOI: 10.1039/C0SM00457J, Review Abstract and text (RSC)
  112. A.A.Mirzoev and A.P.Lyubatsev "Effective solvent-mediated interaction potentials of Na+ and Cl- in aqueous solution: temperature dependence" Phys.Chem.Chem.Phys., v. 13, pp. 5722-5727 (2011) DOI: 10.1039/C0CP02397C Abstract and text (RSC)
  113. P.N.Vorontsov-Velyaminov, M.A.Voznesenskiy, E.A.Polyakov, and A.P.Lyubartsev "Calculation of Canonical Properties and Excited States by Path Integral Numerical Method" Contrib. Plasma Phys., v. 51(4), pp. 382-385, DOI: 10.1002/ctpp.201010112 (2011) Abstract and text (Wiley)
  114. M.S.Santosh, A.P.Lyubartsev, A.Mirzoev, and D.K.Bhat "Solute-Solvent Interactions in Aqueous Glycylglycine-CuCl(2) Solutions: Acoustical and Molecular Dynamics Perspective" J. Solution Chem., v. 40(9), pp. 1657-1671, DOI: 10.1007/s10953-011-9745-8 Abstract and text (Springer)
  115. N. A. Volkov, P.N.Vorontsov-Velyaminov and A.P.Lyubartsev "Two-Dimensional Wang-Landau Algorithm for Osmotic Pressure Calculations in a Polyelectrolyte-Membrane System" Macromolecular Theory and Simulations, v. 20(7), pp. 496 - 509, DOI: 10.1002/mats.201100015 (2011) Abstract and text (Wiley)
  116. A.V.Egorov, A.P. Lyubartsev and A. Laaksonen "Molecular Dynamics Simulation Study of Glycerol-Water Liquid Mixtures" J. Phys. Chem. B, 115(49), 14572-14581, DOI: 10.1021/jp208758r (2011) Abstract and text (ACS)

    117. 2012

  117. J.P.M. Jämbeck and A.P. Lyubartsev "Derivation and Systematic Validation of a Refined All-Atom Force Field for Phosphatidylcholine Lipids" J. Phys. Chem. B, 116(10), 3164-3179, DOI: 10.1021/jp212503e (2012) Abstract and Open Access text (ACS)
  118. N.Korolev, Y. Fan, A.P. Lyubartsev, L.Nordenskiöld "Modelling chromatin structure and dynamics: status and prospects" Current Opinion in Struct. Biol., 22(2), 151-159, DOI: 10.1016/j.sbi.2012.01.006 (2012) Abstract and text
  119. N. Volkov, A.Lyubartsev, L.Bergström "Phase transitions and thermodynamic properties of dense assemblies of truncated nanocubes and cuboctahedra" Nanoscale, 4 (15), 4765 - 4771. DOI: 10.1039/c2nr30411b (2012) Abstract and text
  120. N.Korolev, A.Allahverdi, A.P. Lyubartsev, L.Nordenskiöld "The polyelectrolyte properties of chromatin" Soft Matter, 8(36), 9322-9333, DOI: 10.1039/c2sm25662b (2012) Abstract and text
  121. A.Laaksonen, A.Lyubartsev and F. Mocci "MDynaMix studies of solvation, solubility and permeability" in: " Molecular Dynamics - Studies of Synthetic and Biological Macromolecules, Lichang Wang (Ed.), ISBN: 978-953-51-0444-5, InTech, DOI: 10.5772/35955. Open Access text
  122. J.P.M.Jämbeck, A.P. Lyubartsev "An Extension and Further Validation of an All-Atomistic Force Field for Biological Membranes" J. Chem. Theory and Computations, 8(8), 2938-2948, DOI: 10.1021/ct300342n (2012) Abstract and Open Access text

    123. 2013

  123. B. Faure, E. Wetterskog, K. Gunnarsson, E Josten, R.P. Hermann, T. Bruckel, J.W. Andreasen, JW (Andreasen, F. Meneau, M. Meyer, A. Lyubartsev, L. Bergström, G. Salazar-Alvarez, P. Svedlindh, "2D to 3D crossover of the magnetic properties in ordered arrays of iron oxide nanocrystals" Nanoscale, 5(3), 953-960 (2013). DOI: 10.1039/c2nr33013j Abstract
  124. J.P.M.Jämbeck, A.P. Lyubartsev "Another Piece of the Membrane Puzzle: Extending Slipids Further" J. Chem. Theory and Computations, 9(1), 774-784 (2013) DOI: 10.1021/ct300777p Abstract and Open Access text
  125. J.P.M.Jämbeck, F.Mocci, A.P. Lyubartsev, A.Laaksonen "Partial Atomic Charges and Their Impact on the Free Energy of Solvation" J. Comput.Chem., 34(3), 187-197 (2013) DOI: 10.1002/jcc.23117 Abstract
  126. Y. Fan, N.Korolev, A.P. Lyubartsev, L.Nordenskiöld "An Advanced Coarse-Grained Nucleosome Core Particle Model for Computer Simulations of Nucleosome-Nucleosome Interactions under Varying Ionic Conditions" PLoS One, 8 (2), e54228 (2013) DOI: 10.1371/journal.pone.0054228 Abstract and Open Access text
  127. J.P.M.Jämbeck, A.P. Lyubartsev "Implicit inclusion of atomic polarization in modeling of partitioning between water and lipid bilayers" Phys.Chem.Chem.Phys., 15(13), 4677-4686 (2013) DOI: 10.1039/c3cp44472d Abstract and Text
  128. Y-L. Wang, A. Lyubartsev, Z-Y. Lu, A. Laaksonen "Multiscale coarse-grained simulations of ionic liquids: comparison of three approaches to derive effective potentials" Phys.Chem.Chem.Phys., 15(20), 7701-7712 (2013) . DOI: 10.1039/c3cp44108c Abstract and Text
  129. A. Mirzoev, A.P.Lyubartsev "MagiC: Software Package for Multiscale Modeling" J. Chem. Theory and Computations, 9(3), 1512-1520 (2013) . DOI: 10.1021/ct301019v Abstract and Open Access Text; Software
  130. J.P.M.Jämbeck, A.P. Lyubartsev "Exploring the Free Energy Landscape of Solutes Embedded in Lipid Bilayers" J. Phys. Chem. Lett., 4(11), 1781-1787 (2013) DOI: 10.1021/jz4007993 Abstract and Open Access Text
  131. A.L.Rabinovich, A.P. Lyubartsev "Computer Simulation of Lipid Membranes: Methodology and Achievements " Polymer Science Serie C, 55(1), 162-180 (2013) DOI: 10.1134/S1811238213070060 Abstract and Text

    132. 2014

  132. J.P.M.Jämbeck, E.S.Eriksson, A.Laaksonen, A.P. Lyubartsev, L.A.Eriksson "Molecular Dynamics Studies of Liposomes as Carriers for Photosensitizing Drugs: Development, Validation, and Simulations with a Coarse-Grained Model" J. Chem. Theory and Computations, 10(1), 5-13 (2014) DOI: 10.1021/ct400466m Abstract and Text
  133. A.M.Nikitin, Yu.V.Milchevskiy, A.P.Lyubartsev "A new AMBER-compatible force field parameter set for alkanes" J. Molecular Modeling, 20(3), 2143 (2014) DOI: 10.1007/s00894-014-2143-6 Abstract and Text
  134. J.P.M.Jämbeck, A.P. Lyubartsev "Update to the General Amber Force Field for Small Solutes with an Emphasis on Free Energies of Hydration" J. Phys. Chem. B, 118(14), 3739-3804 (2014) DOI: 10.1021/jp4111234 Abstract and Text
  135. N. Korolev, D.Luo, A.P.Lyubartsev, L.Nordenskiöld "A Coarse-Grained DNA Model Parameterized from Atomistic Simulations by Inverse Monte Carlo" Polymers, 6(6), 1655-1675 (2014) DOI: 10.3390/polym6061655 Abstract and Text
  136. A.Mirzoev, A.P.Lyubartsev "Systematic Implicit Solvent Coarse Graining of Dimyristoylphosphatidylcholine Lipids" J. Comput. Chem., 35(16), 1208-1218 (2014) DOI: 10.1002/jcc.23610 Abstract and Text
  137. N. Korolev, H.Yu, A.P.Lyubartsev, L.Nordenskiöld "Molecular Dynamics Simulations Demonstrate the Regulation of DNA-DNA Attraction by H4 Histone Tail Acetylations and Mutations" Bioplymers, 101(10), 1051-1064 (2014) DOI: 10.1002/bip.22499 Abstract and Text
  138. A. L. Rabinovich and A. P. Lyubartsev "Bond orientation properties in lipid molecules of membranes: molecular dynamics simulations" J. Physics: Conference Series, 510, 012022 (2014) DOI: 10.1088/1742-6596/510/1/012022 Abstract and Text

    139. 2015

  139. C. A. K. Koppisetty, M. Frank, A. P. Lyubartsev, P.-G. Nyholm "Binding energy calculations for hevein-carbohydrate interactions using expanded ensemble molecular dynamics simulations" J. Computer-Aided Drug Design, 29(1), 13-21 (2015) DOI: 10.1007/s10822-014-9792-5 Abstract and Text
  140. A. P. Lyubartsev, N. Korolev, Y.P.Fan, L.Nordenskiöld "Multiscale modelling of nucleosome core particle aggregation" J. Phys.; Condensed Matter, 27(6), 064111 (2015) DOI: 10.1088/0953-8984/27/6/064111 Abstract and Text
  141. E. G. Brandt and A. P. Lyubartsev "Systematic Optimization of a Force Field for Classical Simulations of TiO2–Water Interfaces" J. Phys. Chem. C, 119(32), 18110-18125 (2015) DOI: 10.1021/acs.jpcc.5b02669 Abstract and Text
  142. E. G. Brandt and A. P. Lyubartsev "Molecular Dynamics Simulations of Adsorption of Amino Acid Side Chain Analogues and a Titanium Binding Peptide on the TiO2 (100) Surface" J. Phys. Chem. C, 119(32), 18126-18139 (2015) DOI: 10.1021/acs.jpcc.5b02670 Abstract and Text
  143. A. P. Lyubartsev, A. Naome, D. P. Vercauteren and A. Laaksonen "Systematic hierarchical coarse-graining with the inverse Monte Carlo method" J. Chem. Phys., 143, 243120 (2015) DOI: 10.1063/1.4934095 Abstract and Text
  144. A. Nikitin, Y. Milchevskiy, A. P. Lyubartsev "AMBER-ii: New Combining Rules and Force Field for Perfluoroalkanes" J. Phys. Chem. B, 119, 14563-14573 (2015) DOI: 10.1021/acs.jpcb.5b07233 Abstract and Text
  145. A. Botan, F. Favela-Rosales, P.F.J. Fuchs, M. Javanainen, M. Kanduc, W. Kulig, A. Lamber, C. Loison, A. Lyubartsev, M.S.Miettinen, L. Monticelli, J. Maatta, O.H.S.Ollila, M. Retegan, T. Rog, H. Santuz, J. Tynkkynen "Toward Atomistic Resolution Structure of Phosphatidylcholine Headgroup and Glycerol Backbone at Different Ambient Conditions" J. Phys. Chem. B, 119, 15075-15088 (2015) DOI: 10.1021/acs.jpcb.5b04878 Abstract and Text

    146. 2016

  146. E. G. Brandt, L. Agosta and A.P.Lyubartsev Reactive wetting properties of TiO2 nanoparticles predicted by ab initio molecular dynamics simulations Nanoscale, 8, 13385-13398 (2016) DOI: 10.1039/c6nr02791a Abstract and Text
  147. B. Vujic and A.P.Lyubartsev "Transferable force-field for modelling of CO2, N-2, O-2 and Ar in all silica and Na+ exchanged zeolites" Modellling and Simulation in Materials Science and Engineering, 24 (4), 045002 (2016). Abstract and Open Access Text
  148. N. Korolev, L. Nordenskiöld, A. P. Lyubartsev "Multiscale coarse-grained modelling of chromatin components: DNA and the nucleosome" Advances in Colloid and Interface Science, 232, 36-48 (2016). Abstract and Text
  149. A. P. Lyubartsev and A. L. Rabinovich "Force Field Development for Lipid Membrane Simulations" Biochim. Biophys. Acta - Biomembranes, 1858, 2483-2497 (2016). Abstract and Text
  150. H. Lopez, E. G. Brandt, A. Mirzoev, D. Zhurkin, A. Lyubartsev, V. Lobaskin "Multiscale Modelling of Bionano Interface" Modelling the toxicity of Nanoparticles (Eds. L. Tran et al), Advances in Experimental Medicine and Biology, vol 947 (2016). DOI: 10.1007/978-3-319-47754-1_7
  151. A. Atzori, S. Liggi, A. Laaksonen, M. Porcu, A.P.Lyubartsev, G.Saba, F. Mocci "Base sequence specificity of counterion binding to DNA: what can MD simulations tell us?" Canadian J. Chem., 94(12), 1181-1188 (2016). DOI: 10.1139/cjc-2016-0296
  152. I. Ermilova, A.P.Lyubartsev "Extension of the Slipids Force Field to Polyunsaturated Lipids" J. Phys. Chem. B., 120 (50), 12826-12842 (2016). DOI: 10.1021/acs.jpcb.6b05422 Abstract and Text

    153. 2017

  153. M. Rebic, F. Mocci, J. Ulichny, A.P.Lyubartsev, A.Laaksonen Coarse-Grained Simulation of Rodlike Higher-Order Quadruplex Structures at Different Salt Concentrations ACS Omega, 2(2), 386-396 (2017). DOI: 10.1021/acsomega.6b00419 Abstract and Text
  154. I.A.Silanteva, A.A.Yurchenko, P.N.Vorontsov-Velyaminov, A.P.Lyubartsev Equilibrium properties of 3-arm star-shaped polyions: an entropic sampling Monte Carlo study Nanosystems: Phys.Chem.Math., 8(1), 108-120 (2017). DOI: 10.17586/2220-8054-2017-8-1-108-120
  155. M. Saeedi, A.P.Lyubartsev, S. Jalili Anesthetics mechanism on a DMPC lipid membrane model: Insights from molecular dynamics simulations Biophys. Chem., 226, 1-13 (2017). DOI: 10.1016/j.bpc.2017.03.006 Abstract and text
  156. L. Agosta, E.G.Brandt, A.P.Lyubartsev Diffusion and reaction pathways of water near fully hydrated TiO2 surfaces from ab initio molecular dynamics J. Chem. Phys., 147(2), 024704 (2017). DOI: 10.1063/1.4991381 Abstract and text (Open Access)
  157. T. D. Sun, A. Mirzoev, N. Korolev, A.P.Lyubartsev, L.Nordenskiöld All-Atom MD Simulation of DNA Condensation Using Ab lnitio Derived Force Field Parameters of Cobalt(III)-Hexammine J. Phys. Chem. B., 121(33), 7761-7770 (2017). DOI: 10.1021/acs.jpcb.7b03793 Abstract and text
  158. I. Ermilova, S. Stenberg and A.P.Lyubartsev "Quantum chemical and molecular dynamics modelling of hydroxylated polybrominated diphenyl ethers" Phys.Chem.Chem.Phys., 19 (41), 28263-28274 (2017). DOI:10.1039/C7CP03471G Abstract and Text
  159. B. Vujic and A.P.Lyubartsev "Computationally based analysis of the energy efficiency of a CO2 capture process" Chemical Engineering Science, 174, 178-188 (2017). DOI: 10.1016/j.ces.2017.09.006 Abstract and Text

    160. 2018

  160. N. Korolev, A.P.Lyubartsev and L. Nordenskiöld "A systematic analysis of nucleosome core particle and nucleosome-nucleosome stacking structure" Scientific Reports, 8, 1543 (2018) DOI:10.1038/s41598-018-19875-0 Abstract and Open Access text
  161. A.L.Rabinovich, A.P.Lyubartsev , D.V.Zhurkin Unperturbed hydrocarbon chains and liquid phase bilayer lipid chains: a computer simulation study Eur. Biophys. J., 47(2), 109-130 (2018) DOI: 10.1007/s00249-017-1231-9 Abstract and Open Access text
  162. F.Elias-Wolff, M.Linden, A.P.Lyubartsev, E.G.Brandt Computing Curvature Sensitivity of Biomolecules in Membranes by Simulated Buckling J. Chem.Theory and Computations, 14(3), 1643-1655 (2018) DOI: 10.1021/acs.jctc.7b00878 Abstract and text
  163. F. Grote, I. Ermilova, A.P.Lyubartsev Molecular Dynamics Simulations of Furfural and 5-Hydroxymethylfurfural at Ambient and Hydrothermal Conditions J. Phys. Chem. B, 122 (35), 8416 - 8428 (2018) DOI: 10.1021/acs.jpcb.8b03350 Abstract and text
  164. E. Vitale, G. Zollo, L. Agosta, F. Gala, E.G.Branndt, A. Lyubartsev Stress Relief and Reactivity Loss of Hydrated Anatase (001) Surface J. Phys. Chem. C, 122 (39), 22407v - 22417 (2018) DOI: 10.1021/acs.jpcc.8b05646 Abstract and text
  165. A. P. Lyubartsev Inverse Monte Carlo Methods in: "Coarse-Grained Modeling of Biomolecules", pages 1-26, Ed. G. A. Papoian, CRC Press Taylor & Francis Group, Boka Raton, 2018 Chapter 1
  166. L. Nordenskiöld, A. P. Lyubartsev, N. Korolev Coarse-Grained Modeling of Nucleosomes and Chromatin in: "Coarse-Grained Modeling of Biomolecules", pages 297-340, Ed. G. A. Papoian, CRC Press Taylor & Francis Group, Boka Raton, 2018

    167. 2019

  167. I. Ermilova and A.P.Lyubartsev Cholesterol in phospholipid bilayers: positions and orientations inside membranes with different unsaturation degrees Soft Matter, 15 (1), 78 - 93 (2019) DOI: 10.1039/c8sm01937a Abstract and text
  168. F. Elias-Wolff, M. Linden, A. P. Lyubartsev, E. G. Brandt Curvature sensing by cardiolipin in simulated buckled membranes Soft Matter, 15 (4), 792 - 802 (2019) DOI: 10.1039/c8sm02133c Abstract and text
  169. A. Mirzoev, L. Nordenskiöld, A. P. Lyubartsev Magic v.3: An integrated software package for systematic structure-based coarse-graining Computer Physics Communications, 237, 263 - 273 (2019) DOI: 10.1016/j.cpc.2018.11.018 Abstract and text
  170. S. Mortezazadeh, Y. Jamali, H. Naderi-Manesh and A. P. Lyubartsev Implicit solvent systematic coarse-graining of dioleoylphosphatidylethanolamine lipids: From the inverted hexagonal to the bilayer structure PLOS ONE, 14(4), e0214673 (2019) DOI: 10.1371/journal.pone.0214673 Abstract and text
  171. T. D. Sun, A. Mirzoev, V. Minhas, N. Korolev, A. P. Lyubartsev and L. Nordenskiöld A multiscale analysis of DNA phase separation: from atomistic to mesoscale level Nucleic Acids Research, 47(11), 5550 - 5562 (2019) DOI: 10.1093/nar/gkz377 Abstract and text
  172. N. Ntarakas, I.Ermilova and A.P.Lyubartsev Effect of lipid saturation on amyloid-beta peptide partitioning and aggregation in neuronal membranes: molecular dynamics simulations Eur. Biophys. J., 48(8), 813-824 (2019) DOI: 10.1007/s00249-019-01407-x Full text
  173. D. Power, I. Rouse, S. Poggio, E. Brandt, H. Lopez, A. Lyubartsev, V. Lobaskin A multiscale model of protein adsorption on a nanoparticle surface Modelling and Simulation in Materials Science and Engineering, 27(8), 084003 (2019) DOI: 10.1088/1361-651X/ab3b6e Abstract and text

    174. 2020

  174. V. Minhas, T.D.Sun, A.Mirzoev, N. Korolev, A.P.Lyubartsev, L.Nordenskiöld Modeling DNA Flexibility: Comparison of Force Fields from Atomistic to Multiscale Levels J. Phys. Chem. B, 124(1), 38-49 (2020) DOI: 10.1021/acs.jpcb.9b09106 Abstract and text
  175. I.Ermilova and A.P.Lyubartsev Modelling of interactions between A beta(25-35) peptide and phospholipid bilayers: effects of cholesterol and lipid saturation RSC Advances, 10(7), 3902-3915 (2020) DOI: 10.1039/c9ra06424a Full text
  176. L. Agosta, E.G.Brandt, A.P.Lyubartsev Improved Sampling in Ab Initio Free Energy Calculations of Biomolecules at Solid-Liquid Interfaces: Tight-Binding Assessment of Charged Amino Acids on TiO2 Anatase (101) Computation, 8(1), 12 (2020) DOI:10.3390/computation8010012 Open access text
  177. F.Grote and A.P.Lyubartsev Optimization of Slipids Force Field Parameters Describing Headgroups of Phospholipids J. Phys. Chem. B, 124(40), 8784-8793 (2020) DOI: 10.1021/acs.jpcb.0c06386 Open access text
  178. H.Kokot, B.Kokot, A.Sebastijanovic, C.Voss,R.Podlipec, P.Zawilska, T.Berthing, C.B.Lopez, P.H.Danielsen, C.Contini, M.Ivanov, A.Kriselj, P.Cotar, Q.X.Zhou, J.Ponti, V.Zhernovkov, M.Schneemilch, Z,Doumandi, M.Pusnik, P.Umek, S.Pajk, Q.Joubert, O.Schmid, I.Urbancic, M.Irmler, J.Beckers, V.Lobaskin, S.Halappanavar, M.Quirke, A.P.Lyubartsev, U.Vogel, T.Koklic, T.Stoeger, J.Strancar Prediction of Chronic Inflammation for Inhaled Particles: the Impact of Material Cycling and Quarantining in the Lung Epithelium Adnanced Materials, 32(47), 2003913 (2020) DOI: 10.1002/adma.202003913 Open access text

    179. 2021

  179. M. Saeedimasine, E. G. Brandt and A.P.Lyubartsev Atomistic Perspective on Biomolecular Adsorption on Functionalized Carbon Nanomaterials under Ambient Conditions J. Phys. Chem. B, 125(1), 416 - 430 (2021) DOI: 10.1021/acs.jpcb.0c08622 Open access text
  180. P.H.B.B. Carvalho, A. Mace, O. Andersson, C.A.Tulk, J.Molaison, A.P.Lyubartsev, I.M.Nangoi, A.A.Leitao, U. Hausermann Pressure-induced amorphization of noble gas clathrate hydrates Phys. Rev. B, 103, 064205 (2021) DOI: 10.1103/PhysRevB.103.064205 Open access text
  181. A. Nikitin, V. Milchevskaya, A. Lyubartsev To the fast calculation of the solvation free energy. Combining expanded ensembles with L2MC J. Comput. Chem., 42(11), 787-792 (2021) DOI: 10.1002/jcc.26498 Abstract and text
  182. T.D.Sun, V.Minhas, N.Korolev, A.Mirzoev, A.P.Lyubartsev, L.Nordenskiöld Bottom-Up Coarse-Grained Modeling of DNA Fronties in Molecular Biosciences, 8, 645527 (2021) DOI: 10.3389/fmolb.2021.645527 Open access text
  183. J.Q.Yang, A.J.Pell, N.Hedin, A.Lyubartsev Computational insight into the hydrogenation of CO2 and carbamic acids to methanol by a ruthenium(II)-based catalyst: The role of amino (NH) ligand group Molecular Catalysis, 506, 111544 (2021) DOI: 10.1016/j.mcat.2021.111544 Abstract and text
  184. I. Rouse, D. Power, E.G.Brandt, M. Schneemilch, K. Kotsis, N.Quirke, A.P.Lyubartsev, V. Lobaskin First principles characterisation of bio-nano interface Phys. Chem. Chem. Phys., 23(24), 13473-13482 (2021) DOI: 10.1039/d1cp01116b Open Acess text
  185. M.Ivanov and A:P.Lyubartsev Atomistic Molecular Dynamics Simulations of Lipids Near TiO2 Nanosurfaces J. Phys. Chem. B, 125, 8048 (2021) DOI: 10.1021/acs.jpcb.1c04547 Open access text
  186. P.H.B.B.Carvaho,R.I.P.Moraes, A.A.Leitao, O.Andersson, C.A.Tulk, J.Molaison, A.P.Lyubartsev, U.Hausserman Structural investigation of three distinct amorphous forms of Ar hydrate RSC Advances, 11(49), 30744-30754 (2021) DOI: 10.1039/d1ra05697b Open Access Text

    187. 2022

  187. P.H.B.B.Carvaho, a.Mace, I.M.Nangoi, A.A.Leitao, C.A.Tulk, J.J.Molaison, O.Andersson, A.P.Lyubartsev, U.Hausserman Exploring High-Pressure Transformations in Low-Z (H-2, Ne) Hydrates at Low Temperatures Crystals, 12(1), 9 DOI: 10.3390/cryst12010009 Open Access Text
  188. X. F. Zhou, B. Shen, A. Lyubartsev, J. W. Zhai, N. Hedin Semiconducting piezoelectric heterostructures for piezo- and piezophotocatalysis Nano Energy, 96, 107141 (2022) DOI: 10.1016/j.nanoen.2022.107141 Open Access Text
  189. X. F. Zhou, F. Yan, A. Lyubartsev, B. Shen, J.W.Zhai, J. C. Conesa, N. Hedin Efficient Production of Solar Hydrogen Peroxide Using Piezoelectric Polarization and Photoinduced Charge Transfer of Nanopiezoelectrics Sensitized by Carbon Quantum Dots Advanced Science, 9 (18), 2105792 (2022) DOI: 10.1002/advs.202105792 Open access text
  190. T. D. Sun, V. Minhas, A. Mirzoev, N. Korolev, A. P. Lyubartsev, L.Nordenskiöld A Bottom-Up Coarse-Grained Model for Nucleosome-Nucleosome Interactions with Explicit Ions J. Chem. Theory and Computation, 18, 3948 - 3960 (2022) DOI: 10.1021/acs.jctc.2c00083 Open access text
  191. D. Menard, L. Blaschek, K. Kriechbaum, C.C.Lee, H. Serk, C.T.Zhu, A. Lyubartsev, Nuoendagula, Z. Bacsik, L. Bergström, A.Mathew, S. Kajita, E. Pesquet Plant biomechanics and resilience to environmental changes are controlled by specific lignin chemistries in each vascular cell type and morphotype Plant Cell, 34(12), 4877-4896 (2022) DOI10.1093/plcell/koac284 Open text
  192. F. Grote, A.P.Lyubartsev Water structure, dynamics and reactivity on a TiO2-nanoparticle surface: new insights from ab initio molecular dynamics Nanoscale, 14(44), 16536-16547 (2022) DOI10.1039/d2nr02354g Open text

    193. 2023

  193. F.Grote, A.Lyubartsev, S.V.Dvinskikh, V.Rinwa, J.Holmbaeck Phase equilibrium, dynamics and rheology of phospholipid-ethanol mixtures: a combined molecular dynamics, NMR and viscometry study Phys. Chem. Chem. Phys., 25(13), 15905-15915 (2023) DOI: 10.1039/d3cp00425b Text
  194. P.H.B.B. Carvalho, M. Ivanov, O. Andersson, T. Loerting, M. Bauer, C. A. Tulk, B. Haberl, L. L. Daemen, J. J. Molaison, K. Amann-Wonkel, A. P. Lyubartsev, C. L. Bull, N. P. Funnel, U. Haussermann Neutron scattering study of polyamorphic THF center dot 17(H2O) - toward a generalized picture of amorphous states and structures derived from clathrate hydrates Phys. Chem. Chem. Phys., 25(21), 14981-14991 (2023) DOI: 10.1039/d3cp00539a Text
  195. M. Saeedimasine, F. Grore, A. P. Lyubartsev Ab Initio Derived Classical Force Field for Molecular Dynamics Simulations of ZnO Surfaces in Biological Environment J. Phys. Chem. A, 127(25), 5446-5457 (2023) DOI: 10.1021/acs.jpca.3c00424 Text
  196. R. Rahmani , A.P.Lyubartsev "Biomolecular Adsorprion at ZnS Nanomaterials: A Molecular Dynamics Simulation Study of the Adsorption Preferences, Effects of the Surface Curvature and Coating" Nanomateroals, 13(15), 2239 (2023) DOI: 10.3390/nano13152239 Text
  197. M. Ivanov, M. Posysoev, A.P.Lyubartsev "Coarse-Grained Modeling Using Neural Networks Trained on Structural Data" J. Chem. Theory and Comput., 19(19), 6704-6717 (2023) DOI: 10.1021/acs.jctc.3c00516 Text

    198. 2024

  198. M. Ivanov, A.P.Lyubartsev "Development of a bottom-up coarse-grained model for interactions of lipids with TiO2 nanoparticles" J. Comput. Chem., 19(19), 6704-6717 (2023) DOI: 10.1002/jcc.27310 Text
  199. M. Saeedimasine, R.Rohmani and A.P.Lyubartsev "Biomolecular Adsorption on Nanomaterials: Combining Molecular Simulations with Machine Learning" J. Chem. Inf. and Modelling, 64(9), 3799-3811 (2024) Text
  200. L. Agosta, L. Fiore, N. Colozza, G. Perez-Ropero, A. Lyubartsev, F. Arduini, K. Hermansson "Adsorption of Glycine on TiO2 in Water from On-the-fly Free-Energy Calculations and In Situ Electrochemical Impedance Spectroscopy" Langmuir, 40(23), 12009-12016 (2024) Text
  201. T. Sun, N. Korolev, V. Minhas, A. Mirzoev, A. P. Lyubartsev, L. Nordenskiöld Multiscale modeling reveals the ion-mediated phase separation of nucleosome core particles Biophys. J. , 123(11), 1414-1434 (2024) DOI10.1016/j.bpj.2023.10.030 Text
  202. R. Herboth, A.P.Lyubartsev Exploring Carbamazepine Polymorph Crystal Growth in Water by Enhanced Sampling Simulations ACS Omega, 9 (34), 36718-36731 (2024) DOI10.1021/acsomega.4c05458 Text
  203. F. Grote, M. Saeedimasine, A.P.Lyubartsev Polarizable force field for TiO2 based on the Drude oscillator model AIP Advances, 14(11), 115123 (2024) DOI10.1063/5.0242166 Text
  204. I. Ermilova, A. Lyubartsev, V. Kocherbitov Sucrose versus Trehalose: Observations from Comparative Study Using Molecular Dynamics Simulations ACS Omega, 9(46), 46323-46338 (2024) OI10.1021/acsomega.4c07314 Text

    205. 2025

  205. T.D.Sun, N. Korolev, A.P.Lyubartsev, L.nordenskiöld CG modeling of nucleosome arrays reveals the salt-dependent chromatin fiber conformational variability J. Chem. Phys., 162(2), 024101 (2025) DOI10.1063/5.0242509 Text

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