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)

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