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

  4. 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)
  5. 1990

  6. A.P.Lyubartsev, P.N.Vorontsov-Velyaminov. "Monte Carlo simulation of flexible polyelectrolytes" Vysokomolekulyarnye Soedineniya (Moscow; in Russian), v.32A, p.721-726 (1990)
  7. 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)
  8. 1992

  9. 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
  10. 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).
  11. 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).
  12. 1993

  13. 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)
  14. 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
  15. 1994

  16. 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
  17. 1995

  18. 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
  19. 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

  20. 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).
  21. 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
  22. 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.
  23. 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)
  24. 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)
  25. 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
  26. 1997

  27. 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)
  28. 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
  29. 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.
  30. 1998

  31. 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).
  32. 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).
  33. 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 .
  34. 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
  35. 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
  36. 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
  37. 1999

  38. A.P.Lyubartsev, A.Laaksonen, "Quantum molecular dynamics simulations methods.", in "NSC Progress Report", p.35-37 (National Supercomputer Center, Linköping, 1999)
  39. 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)
  40. Abstract and textfrom the APS Web site
  41. 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 .
  42. 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.
  43. 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)
  44. 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
  45. 2000

  46. 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
  47. 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)
  48. 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)
  49. Abstract and text from Elsevier Science
  50. 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
  51. 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
  52. 2001

  53. 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)
  54. Abstract and text
  55. 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
  56. 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
  57. 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
  58. 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)
  59. 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
  60. 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
  61. 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
  62. 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
  63. 2002

  64. 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.
  65. 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
  66. 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
  67. 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
  68. 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
  69. 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.
  70. 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
  71. 2003

  72. 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)
  73. 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).
  74. 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.
  75. 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
  76. 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)
  77. 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)
  78. 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
  79. 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
  80. 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
  81. 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
  82. 2004

  83. 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
  84. 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
  85. 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
  86. A. P. Lyubartsev "Molecular Simulations of DNA Counterion Distributions" Dekker Encyclopedia of Nanoscience and Nanotechnology, pp. 2131 - 2143 Dekker (2004)   Abstract PDF text
  87. 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
  88. 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
  89. 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)
  90. 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
  91. 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
  92. 2005

  93. 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
  94. 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
  95. 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
  96. A. P. Lyubartsev "Multiscale modeling of lipids and lipid bilayers" Eur. Biophys. J., v. 35(1), pp. 53-61 (2005)   Abstract and text
  97. 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
  98. 2006

  99. 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
  100. 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
  101. 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
  102. 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
  103. 2007

  104. 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
  105. 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
  106. 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
  107. A. P. Lyubartsev Interacting electrons in one dimension: A path integral Monte Carlo study" J. Phys. A., 40, 7151-7157 (2007) Abstract and text
  108. 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
  109. 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
  110. 2008

  111. 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
  112. 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.
  113. 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.
  114. 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
  115. 2009

  116. 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
  117. 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
  118. 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
  119. 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.
  120. 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.
  121. 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.
  122. 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
  123. 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
  124. 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
  125. 2010

  126. 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
  127. 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
  128. 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
  129. 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
  130. 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
  131. 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
  132. 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
  133. 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
  134. 2011

  135. 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)
  136. 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)
  137. 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)
  138. 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)
  139. 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)
  140. 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)
  141. 2012

  142. 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)
  143. 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
  144. 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
  145. 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
  146. 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
  147. 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
  148. 2013

  149. 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
  150. 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
  151. 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
  152. 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
  153. 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
  154. 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
  155. 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
  156. 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
  157. 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
  158. 2014

  159. 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
  160. 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
  161. 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
  162. 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
  163. 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
  164. 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
  165. 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
  166. 2015

  167. 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
  168. 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
  169. 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
  170. 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
  171. 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
  172. 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
  173. 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
  174. 2016

  175. 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
  176. 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
  177. 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
  178. 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
  179. 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
  180. 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
  181. 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
  182. 2017

  183. 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
  184. 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
  185. 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
  186. 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)
  187. 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

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