Below is a more or less complete list of my peer reviewed publications. It does not include books (see the list on the right), theses, popular science, or conference proceedings. If you would like to get an advance print or do not have access to the journal in question, please drop me a line and I will send you a (re/pre)print. I have included links to movies & downloadble configurations, and additional material with some of the articles. The articles are in chronolgical order, with the just submitted ones appearing on top of the list.

1. Combined depeletion and electrostatic forces in polymer-induced membrane adhesion. A theoretical model
   Antonio Raudino, Martina Pannuzzo, and Mikko Karttunen, submitted

2. Mechanism of Inhibition of Calcium Oxalate Crystal Growthby an Osteopontin Phosphopeptide,
   Susanna Hug, Bernd Grohe, Jari Jalkanen, Brian Chan, Betty Galarreta, Krista Vincent, Francois Lagugne-Labarthet,Gilles Lajoie, Harvey A. Goldberg, Mikko Karttunen, Graeme K. Hunter, accepted for publication in Soft Matter.

3. Molecular Dynamics Simulations Indicate that Prothymosin Alpha and Nrf2 Bind to Keap1 via Preformed Structural Elements and Coupled Folding and Binding,
   Elio Cino, Jirasak Wong-ekkabut, Mikko Karttunen, Wing-Yiu Choy, accepted for publication in PLoS One

4. Matrix Gla Protein Inhibits Ectopic Calcification by a Direct Interaction with Hydroxyapatite Crystals
   Jason O'Young, Yinyin Liao, Yizhi Xiao, Jari Jalkanen, Gilles Lajoie, Mikko Karttunen, Harvey Goldberg, Graeme Hunter, accepted for publication in J. Am. Chem. Soc. [on-line]

5. A molecular dynamics implementation of the 3D Mercedes-Benz water model,
   T. Hynninen, C. L. Dias, A. Mkrtchyan, V. Heinonen, M. Karttunen, A. S. Foster, T. Ala-Nissila, Computer Physics Communications 183, 363-369 (2011). [on-line]

6. The Iceberg Model of hydration and its breakdown
   John Tatini Titantah, Mikko Karttunen, submitted

7. Molecular Dynamics Simulation of Thermal Accommodation Coefficients for Time-Resolved Laser-Induced Incandescence Sizing of Nickel Nanoparticles
   Kyle J. Daun, John Tatini Titantah, Mikko Karttunen, submitted

8. Molecular Dynamics Simulation of Accommodation Coefficients for Laser-Induced Incandescence Sizing of Metal Nanoparticles,
   Kyle J. Daun, Mikko Karttunen, John Tatini Titantah, submitted

9. Secondary stiffness transition in anistropic fiber networks -- stiffness gating for mechanosensitive smart materials.
   Jan Astrom, Sunil P.B. Kumar, Mikko Karttunen, submitted

10. Cationic DMPC/DOTAP Lipid Bilayers: Atomistic Insight for Structure and Dynamics,
    Wei Zhao, Andrey A> Gurtovenko, Ilpo Vattulainen, Mikko Karttunen, accepted for publication in J. Phys. Chem. B

11. Hydrophobic interactions in protein secondary stuctures,
    Cristiano Dias, Mikko Karttunen, Hue Sun Chan, Phys. Rev. E 84, 041931 (2011). [on-line]

12. Use of umbrella sampling to calculate the entrance/exit pathwayfor Z-pro-prolinal inhibitor in Prolyl Oligopeptidase,
    Jean-Francois St. Pierre, Normand Mousseau, Tomasz Rog, Mikko Karttunen, Alex Bunker, Journal of Chemical Theory and Computation 7, 1583-1594 (2011). [on-line]

13. Prolyl Oligopeptidase with Covalently Bound Inhibitors:Molecular Dynamics and Crystallographic Study,
    Karol Kaszuba, Tomasz Rog, Reinis Danne, Peter Canning, Vilmos Fulop, J-F. St. Pierre, Arturo Garcia-Horsman, P.T. Mannisto, Mikko Karttunen, Jyrki Hokkanen, Alex Bunker, submitted

14. Simulations of micellization of sodium hexyl sulfate,
    Maria Sammalkorpi, Samantha Sanders, Athanassios Panagiotopoulos, Mikko Karttunen, Mikko Haataja, J. Phys. Chem. B. 115, 1403-1410 (2011). [on-line]

15. A study of the surface structure of the PEGylated liposome in physiological conditions using all atom molecular dynamics simulation and Langmuir monolayer studies
    M. Stepniewski, M. Pasenkiewicz-Gierula, T. Rog, R. Danne, A. Orlowski, M. Karttunen, A. Urtti, M. Yliperttula, E. Vuorimaa, A. Bunker, Langmuir 27, 7788-7798 (2011). [on-line]

16. Hydrophobicity within the 3D Mercedes-Benz model: Potential of Mean Force,
    Cristiano L. Dias, Teemu Hynninen, Tapio Ala-Nissila, Adam S. Foster, and Mikko Karttunen, J. Chem. Phys. 134, 065106 (2011). [on-line]

17. Fluctuating lattice-Boltzmann model for complex fluids,
    Santtu T.T. Ollila, Colin Denniston, Mikko Karttunen, Tapio Ala-Nissila, J. Chem. Phys. 134, 064902 (2011). [on-line]

18. Low-density lipoprotein: Structure, dynamics, interactions of ApoB-100 with lipids,
    T. Murtola, T. Vuorela, M.T. Hyvönen, S.J. Marrink, M. Karttunen, I. Vattulainen, Soft Matter 7, 8135-8141 (2011) [on-line]

19. Static charges cannot drive a continuous flow of water molecules through a carbon nanotube,
    J. Wong-ekkabut, M. Miettinen, C. Dias, M. Karttunen, Nature Nanotechnology 5, 555-557 (2010). [on-line]

20. Myosin motor mediated contraction is enough to produce cytokinesis in the absence of polymerization,
    J. Astrom, S. von Alfthan, S.P.B. Kumar, M. Karttunen, Soft Matter 6, 5375-5381 (2010). [on-line]

21. Effects of the lipid bilayer phase state on the water membrane interface,
    M. Stepniewski, A. Bunker, M. Pasenkiewicz-Gierula, M. Karttunen, T. Rog, J. Phys. Chem. B 114, 11784-11792 (2010). [on-line]

22. Ab initio simulations of peptide-mineral interactions,
    Susanna Hug, Graeme K. Hunter, Harvey Goldberg, Mikko Karttunen, Physics Procedia 4, 51-60 (2010). [on-line]

23. Cutting Ice: Regelation at the Nanoscale,
    Teemu Hynninen, Vili Heinonen, Cristiano L. Dias, Mikko Karttunen, Adam S. Foster, Tapio Ala-Nissila, Phys. Rev. Lett. 105, 086102 (2010) [on-line]

24. Role of Lipids in Spheroidal High Density Lipoproteins,
    Timo Vuorela, Andrea Catte, Perttu S. Niemelä, Anette Hall, Marja T. Hyvönen, Siewert-Jan Marrink, Mikko Karttunen, Ilpo Vattulainen, PLoS Comput. Biol. 6, e1000964 (2010) [on-line]

25. The flexible polyelectrolyte hypothesis: a new paradigm of protein-crystal interaction in biomineralization,
    Graeme Hunter, Jason O'Young, Bernd Grohe, Mikko Karttunen and Harvey A. Goldberg, Langmuir 26, 18639-18646 (2010). [on-line]

26. Molecular docking, multiple sequence alignment and atomistic molecular dynamics simulations reveal residues associated with selective binding of beta-blockers to human beta-1 and beta-2-adrenergic receptors
    Karol Kaszuba, Tomasz Rog, Krzysztof Bryl, Ilpo Vattulainen, and Mikko Karttunen, J. Phys. Chem. B 114, 8374-8386 (2010). [on-line]

27. The Role of Glycolipids in Lipid Rafts: A View through Atomistic Molecular Dynamics Simulations with Galactosylceramide
    Anette Hall, Tomasz Rog, Mikko Karttunen, Ilpo Vattulainen,J. Phys. Chem. B 114, 7797-7807 (2010). [on-line]

28. Phosphorylation of Ser¹³⁶ is Critical for Potent Bone Sialoprotein-Mediated Nucleation of Hydroxyapatite Crystals
    Gurpreet S. Baht, Jason O'Young, Antonia Borovino, Coralee E. Tye, Mikko Karttunen, Graeme K. Hunter, and Harvey A. Goldberg, Biochemical Journal 428, 385-395 (2010). [on-line]

29. Molecular Dynamics Study of Prolyl Oligopeptidase with Inhibitor in Binding Cavity,
    K. Kaszuba, T. Rog, J.-F. St. Pierre, P.T. Männistö, M. Karttunen, A. Bunker, SAR and QSAR in Env. Res. 20, 595-609 (2009). [on-line]

30. Roles of Electrostatics and Conformation in Protein-Crystal Interactions,
    Paul V. Azzopardi, Jason O'Young, Gilles Lajoie, Mikko Karttunen, Harvey A. Goldberg and Graeme K. Hunter, PLoS One 5, e9330 (2010). [on-line].

31. Cholesterol Off-Plane Methyl Groups Induce Formation of Cholesterol- Rich Domains and Quasi-Long-Range Lateral Order in Cholesterol/Phospholipid Membranes ,
    Hector Martinez-Seara, Tomasz Róg, Mikko Karttunen, Ilpo Vattulainen, and Ramon Reigada,
    PLoS ONE 5 e11162 (2010). [on-line]

32. Mitochondrial Membranes with Mono- and Divalent Salt: Changes Induced by Salt Ions on Structure and Dynamics.
    S. Poyry, T. Róg, M. Karttunen, I. Vattulainen. J. Phys. Chem. B 113, 15513-15521 (2009). [on-line]

33. The hydrophobic e#ect and its role in cold denaturation,
    Cristiano L. Dias, Tapio Ala-Nissila, Jirasak Wong-ekkabut, Ilpo Vattulainen, Mikko Karttunen,Cryobiology 60, 91-99 (2010). [on-line]

34. Reply to the Comment by Graziano on "The hydrophobic effect and its role in cold denaturation"
    Cristiano L. Dias, Tapio Ala-Nissila, Jirasak Wong-ekkabut, Ilpo Vattulainen, Mikko Karttunen. Cryobiology 60, 356-357 (2010). [on-line]

35. Three-dimensional "Mercedes-Benz" model for water,
    Cristiano L. Dias, Tapio Ala-Nissila, Martin Grant, and Mikko Karttunen,
    J. Chem. Phys. 131, 054505 (2009). [on-line]

36. Ionic surfactant aggregates in saline solutions: Sodium dodecyl sulphate (SDS) in the presence of excess NaCl or CaCl2
    Maria Sammalkorpi, Mikko Karttunen, Mikko Haataja
    J. Phys. Chem. B 113, 5863-5870 (2009). [on-line]

37. Systematic coarse-graining from structure using internal states: application to phospholipid / cholesterol bilayer,
    Teemu Murtola, Mikko Karttunen, Ilpo Vattulainen
    J. Chem. Phys. 131, 055101 (2009). [on-line]

38. Ion Dynamics in Cationic Lipid Bilayer Systems in Saline Solutions,
    Markus S. Miettinen, Andrey A. Gurtovenko, Ilpo Vattulainen, and Mikko Karttunen
    J. Phys. Chem. B 113, 9226-9234 (2009). [on-line]

39. Why the sn-2 chain of monounsaturated glycerol-phospholipids is usually unsaturated while the sn-1 chain is saturated? Studies of SOPC and OSPC membranes with and without cholesterol
    H. Martinez-Seara, T. Rog, M. Karttunen, I. Vattulainen, R. Reigada
    J. Phys. Chem. B 113, 8347-8356 (2009). [on-line]

40. Agent-Based Modelling of Glucose Transport
    Rolina D. van Gaalen and Mikko Karttunen
    JCIS 1, 41-49 (2008). [PDF]

41. Multiscale modeling of emergent materials: biological and soft matter
    Teemu Murtola, Alex Bunker, Ilpo Vattulainen, Markus Deserno, and Mikko Karttunen
    PCCP 11, 1869-1892 (2009). [on-line]

42. Lipid domain morphologies in phosphatidylcholine-ceramide monolayers,
    Mikko Karttunen, Mikko P. Haataja, Matti Saily, Ilpo Vattulainen, and Juha M. Holopainen
    Langmuir 25, 4595-4600 (2009). [on-line]

43. Nonlinear Driven Response of a Phase-Field Crystal in a Periodic Pinning Potential
    C. V. Achim, J.A.P. Ramos, M. Karttunen, K.R. Elder, E. Granato, T. Ala-Nissila and S.C. Ying
    Phys. Rev. E 79, 011606 (2009).[on-line]

44. Aster formation and rupture transition in semi-flexible fiber networks with mobile cross-linkers,
    Jan A. Aström, P.B. Sunil Kumar, Mikko Karttunen
    Soft Matter 5, 2869-2874 (2009). [on-line]

45. Role of cardiolipins in the inner mitochondrial membrane: insight gained through atom-scale simulations
    Tomasz Róg, Hector Martinez-Seara, Nana Munck, Matej Oresic, Mikko Karttunen, Ilpo Vattulainen,
    J. Phys. Chem. B 113, 3413-3422 (2009). [on-line]

46. Water isotope effect on the bilayer properties: a molecular dynamics simulation study
    Tomasz Róg, Krzysztof Murzyn, Jeannine Milhaud, Mikko Karttunen, and Marta Pasenkiewicz-Gierula
    J. Phys. Chem. B 113, 97-121 (2009) [on-line]

47. Ordering effects of cholesterol and its analogues
    Tomasz Róg, Marta Pasenkiewicz-Gierula, Ilpo Vattulainen, Mikko Karttunen
    Biochim. Biophys. Acta 1788, 97-121 (2009). [on-line]

48. Phosphorylation of osteopontin peptides mediates adsorption to and incorporation into calcium oxalate crystals
    Jason O'Young, Sara Chirico, Nehal Al Tarhuni, Bernd Grohe, Mikko Karttunen, Harvey A. Goldberg and Graeme K. Hunter
    Cells, Tissues, Organs 189, 51-55 (2009). [On-line] [PDF]

49. Dynamical Scaling Exponents for Polymer Translocation through a Nanopore
    Kaifu Luo, Santtu T.T. Ollila, Ilkka Huopaniemi, Tapio Ala-Nissila, Pawel Pomorski, Mikko Karttunen, See-Chen Ying, Aniket Bhattacharya
    Phys. Rev. E. (Rapid Comm.) 78, 050901(R) (2008). [On-line]

50. Influence of cis double bond parameterization on lipid membrane properties: How seemingly insignificant details in force change even qualitative trends
    H. Martinez-Seara, T. Rog, M. Karttunen, R. Reigada, I. Vattulainen
    J. Phys. Chem. 129, 105103 (2008). [On-line]

51. Electrostatics in biomolecular simulations: Where are we now and where are we heading,
    Mikko Karttunen, Joerg Rottler, Ilpo Vattulainen, and Celeste Sagui,
    Current topics in membranes. Computational Modeling of Membrane Bilayers (edited by Scott Feller) (Elsevier). 60, 49-89 (2008). [on-line]

52. Strain hardening in dense actin networks
    Jan Astrom, P.B. Sunil Kumar, Ilpo Vattulainen, Mikko Karttunen
    Phys. Rev. E. 77, 051913 (2008) [On-line]

53. Micelle fission through surface instability and formation of an interdigitating stalk,
    Maria Sammalkorpi, Mikko Karttunen, Mikko Haataja
    J. Am. Chem. Soc. 130, 17977-17980 (2008). [On-line]

54. Interplay of Unsaturated Phospholipids and Cholesterol in Membranes: Effect of Double Bond Position ,
    Hector Martinez-Seara, Tomasz Róg, Marta Pasenkiewicz-Gierula, Ilpo Vattulainen, Mikko Karttunen, and Ramon Reigada,
    Biophysical Journal 95, 3295-3305 (2008). [On-line]

55. Comparison of cholesterol and its direct precursors along the biosynthetic pathway: Effects of cholesterol, desmosterol and 7-dehydrocholesterol on saturated and unsaturated lipid bilayers
    Tomasz Rog, Ilpo Vattulainen, Maurice Jansen, Elina Ikonen, and Mikko Karttunen
    J. Chem. Phys. 129, 154508 (2008). [on-line]

56. Significance of cholesterol methyl groups,
    S. Pöyry, T. Róg, M. Karttunen, I. Vattulainen,
    J. Phys. Chem. B 112, 2922 -2929, 2008. [On-line]

57. Extensive Molecular Dynamics simulations of the enzyme Catechol-O-Methyl Transferase: Methodological issues,
    A. Bunker, P.T. Männistöš, J.-F. St.-Pierre, T. Róg, P. Pomorski, and M. Karttunen,
    SAR and QSAR in Env. Res. 19, 179-189 (2008). [On-line]

58. Phase diagram of pinned lattices in the phase field crystal model
    C.V. Achim, Mikko Karttunen, K.R. Elder, E. Granato, T. Ala-Nissila, S.C. Ying
    J. Phys.: Conf. Series 100, 072001 (2008). [On-line]
    

59. Replacing the cholesterol hydroxyl group by the ketone group facilitates sterol flip-flop and promotes membrane fluidity
    Tomasz Rog, Lorna M. Stimson, Marta Pasenkiewicz-Gierula, Ilpo Vattulainen, Mikko Karttunen
    J. Phys. Chem. B. 112 1946-1952 (2008). [On-line]
    

60. Influence of Ethanol on Lipid Membranes: From Lateral Pressure Profiles to Dynamics and Partitioning,
    Emma Terämä, O.H. Samuli Ollilla, Emppu Salonen, Amy Rowat, Christa Trandum, Peter Westh, Michael Patra, Mikko Karttunen, Ilpo Vattulainen
    J. Phys. Chem. B 112, 4131-4139 (2008). [On-line]
    

61. Systematic approach to coarse-graining of molecular descriptions and interactions with applications to lipid membranes ,
    Teemu Murtola, Ilpo Vattulainen, Mikko Karttunen
    in , G. Voth (Ed.), CRC Press (Boca Raton, FL), 2008.

62. Comment to "Passage Times for Unbiased Polymer Translocation through a Narrow Pore",
    Kaifu Luo, Tapio Ala-Nissila, See-Chen Ying, Pawel Pomorski, and Mikko Karttunen
    submitted
    [preprint]

63. Microscopic mechanism for cold denaturation,
    C.L. Dias, T. Ala-Nissila, M. Karttunen, I. Vattulainen, and M. Grant
    Phys. Rev. Lett. 100, 118101 (2008).
    [On-line] [preprint]
    Selected for the April 1, 2008 issue of Virtual Journal of Biological Physics Research.

64. Structure of spheroidal HDL particles revealed by combined atomistic and coarse grained simulations ,
    Andrea Catte, James C. Patterson, Denys Bashtovyy, Martin K. Jones, Feifei Gu, Ling Li, Aldo Rampioni, Durba Sengupta, Timo Vuorela, Perttu Niemela, Mikko Karttunen, Siewert Jan Marrink, Ilpo Vattulainen, and Jere P. Segrest
    Biophys. J. 94, 2306-2319 (2008). [On-line]

65. Stearic acid spin labels in lipid bilayers: Insight through atomistic simulations ,
    Tomasz Róg, Lorna Stimson, Lei Dong, Anna Wisniewska, Magorzata Dutka, and Mikko Karttunen
    J. Phys. Chem. B 111, 12447-12453 (2007)
    [On-line]

66. Non-polar interactions between trans-membrane helical EGF peptide and phosphatidylcholines, sphingomyelins and cholesterol. Molecular dynamics simulation studies ,
    Tomasz Róg, Krzysztof Murzyn, Mikko Karttunen, and Marta Pasenkiewicz-Gierula
    J. Peptide Science 14 374-382 (2008). [On-line]

67. Glycolipid membranes through atomistic simulations: Effect of glucose and galactose head groups on lipid bilayer properties ,
    Tomasz Rog, Ilpo Vattulainen, Alex Bunker, Mikko Karttunen
    J. Phys. Chem. B 111, 10146-10154 (2007).
    [On-line]

68. Structural properties of ionic detergent aggregates: A large-scale molecular dynamics study of sodium dodecyl sulfate
    Maria Sammalkorpi, Mikko Karttunen, Mikko Haataja
    J. Phys. Chem. B 111, 11722-11733 (2007).
    [Online]

69. Control of calcium oxalate crystal growth by face-specific adsorption of an osteopontin phosphopeptide
    Bernd Grohe and Jason O'Young, Andrei Ionescu, Gilles Lajoie, Kem A. Rogers, Mikko Karttunen, Harvey A. Goldberg and, Graeme K. Hunter
    J. Am. Chem. Soc. 129, 14946-14951, 2007
    [On-line]

70. Molecular dynamics study of Sphingosine/POPC Bilayers: Ordering due to interplay of steric and electrostatic effects
    M. Patra and M. Karttunen
    submitted

71. Lateral diffusion in lipid membranes through collective flows,
    E. Falck, T. Rog, M. Karttunen, I. Vattulainen
    J. Am. Chem. Soc. 130, 44-45 (2008). [On-line]

72. Effect of double bond position on lipid bilayer properties: Insight through atomistic simulations,
    Hector Martinez-Seara, Tomasz Rog, Marta Pasenkiewicz-Gierula, Ilpo Vattulainen, Mikko Karttunen, and Ramon Reigada,
    J. Phys. Chem. B 111, 11162-11168 (2007).
    [on-line]

73. Enhanced dielectrophoresis of nanocolloids by dimer formation ,
    Emppu Salonen, Emma Terama, Ilpo Vattulainen, Mikko Karttunen
    Europhys. Lett.78 48004 (2007)
    [On-line] [preprint]

74. Role of phosphatidylglycerols in the stability of bacterial membranes ,
    Wei Zhao, Tomasz Rog, Andrey A. Gurtovenko, I. Vattulainen, Mikko Karttunen
    Biochimie 90, 930-938 (2008). [On-line]
    [Movies] [POPG parameters and configurations]

75. Reptational dynamics in dissipative particle simulations of polymer melts,
    P. Nikunen, I. Vattulainen, M. Karttunen,
    Phys. Rev. E (2007), 75, 036713 (2007).
    [online] [preprint]
    Selected for the April 1, 2007 issue of Virtual Journal of Biological Physics Research.

76. Role of sterol type on lateral pressure profiles of lipid membranes affecting membrane protein functionality: Comparison between cholesterol, desmosterol, 7-dehydrocholesterol and ketosterol
    S. Ollila, T. Rog, Mikko Karttunen, Ilpo Vattulainen
    J. Struct. Biol. 159, 311-323 (2007)
    [Online]

77. Coarse-Grained Model for Phospholipid/Cholesterol Bilayer Employing Inverse Monte Carlo with Thermodynamic Constraints.
    T. Murtola, E. Falck, M. Karttunen, and I. Vattulainen.
    J. Chem. Phys. 126, 075101 (2007).
    [Online]
    Selected for the Mar. 1, 2007 issue of the Virtual Journal of Biological Physics Research

78. Assessing the nature of lipid raft membranes ,
    P.S. Niemela, S. Ollila, M.T. Hyvonen, Mikko Karttunen, I. Vattulainen
    PLoS Computational Biology 3, e34 (2007).
    [Online] NOTE: Free on-line access!

79. What happens if cholesterol is made smoother: Importance of methyl substituents in cholesterol ring structure on phosphatidylcholinesterol interaction
    Tomasz Rog, Marta Pasenkiewicz-Gierula, Ilpo Vattulainen, and Mikko Karttunen
    Biophys. J. 92 3346-3357 (2007).
    [Online]

80. Insight into the Putative Specific Interactions between Cholesterol, Sphingomyelin and Palmitoyl-Oleoyl Phosphatidylcholine
    Jussi Aittoniemi, Perttu S. Niemela, M.T. Hyvonen, Mikko Karttunen, Ilpo Vattulainen
    Biophys. J. 92, 1125-1137 (2007)
    [Online]

81. Atomic-scale structure and electrostatics of anionic POPG lipid bilayers with Na+ counterions
    Wei Zhao, Tomasz Rog, Andrey A. Gurtovenko, Ilpo Vattulainen, and Mikko Karttunen
    Biophys. J. 92, 1114-1124 (2007).
    [Online]
    [Downloadable POPG & POPC configurations and parameters] [Movies]

82. Sterol tilt -- major determinant of sterol ordering capability in lipid membranes
    J. Aittoniemi, T. Róg, P. Niemela, M. Pasenkiewicz-Gierula, I. Vattulainen, Mikko Karttunen
    J. Phys. Chem. B (Letters) 110, 25562-25564 (2006).
    [Online]

83. Transient Ordered Domains in Pure Phospholipid Bilayers
    Teemu Murtola, Tomasz Rog, Emma Falck, Mikko Karttunen, Ilpo Vattulainen
    Phys. Rev. Lett. 97, 238102 (2006).
    [Online]
    Selected for the December 18, 2006 issue of the Virtual Journal of Nanoscale Science and Technology
    Selected for the December 15, 2006 issue of the Virtual Journal of Biological Physics Research

84. Dynamics of water at membrane surfaces: effect of headgroup structure ,
    K. Murzyn, W. Zhao, M. Karttunen, M. Kurdziel, and T. Rog
    BioInterphases 1, 98-105 (2006).
    [Online]

85. Phase Diagram and Commensurate-Incommensurate Transitions in the Phase Field Crystal Model with an External Pinning Potential
    C.V. Achim, M. Karttunen, K.R. Elder, E. Granato, T. Ala-Nissila, S.C. Ying,
    Phys. Rev. E 74, 021104 (2006).
    [Online]

86. Influence of pyrene-labeling on fluid lipid membrane
    J. Repakova, J. M. Holopainen, M. Karttunen, and I. Vattulainen
    J. Phys. Chem. B 110, 15403-15410 (2006).
    [Online]

87. Interaction of fusidic acid with lipid membranes: Implications to the mechanism of antibiotic activity
    E. Falck, J.T. Hautala, M. Karttunen, P.K.J. Kinnunen, M. Patra, H. Saaren-Seppala, I. Vattulainen, S.K. Wiedmer, and J.M. Holopainen
    Biophys. J. 91 1787-1799 (2006).
    [Online]
    

88. Long-range interactions & parallel scalability in molecular simulations
    Michael Patra, Marja T. Hyvönen, Emma Falck, Mohsen Sabouri-Ghomi, Ilpo Vattulainen, Mikko Karttunen
    Computer Physics Comm. 176, 14-22 (2006)
    [Online]
    [cond-mat/0410210]

89. Cell aggregation: Packing soft grains,
    Jan A. Åström and Mikko Karttunen
    Phys. Rev. E 73 062301 (2006).
    [Online]
    

90. Molecular dynamics study of charged dendrimers in salt-free solution: Effect of counterions
    A.A. Gurtovenko, S.V. Lyulin, M. Karttunen, I. Vattulainen
    J. Chem. Phys. 124, 094904 (2006).
    [preprint] [Online]
    Selected in the March 15, 2006 issue (vol. 11, issue 6) of the Virtual Journal of Biological Physics Research and also
    selected in the March 20, 2006 issue of the Virtual Journal of Nanoscale Science and Technology

91. Under the influence of alcohol: The effect of ethanol and methanol on lipid bilayers
    Michael Patra, Emppu Salonen, Emma Terama, Ilpo Vattulainen, Roland Faller, Bryan W. Lee, Juha Holopainen, and Mikko Karttunen
    Biophys. J. 90, 1121-1135 (2006).
    [cond-mat/0408122] [Online] [Movies of ethanol inteacting with a membrane]

92. Significance of Sterol Structural Specificity: Desmosterol cannot replace cholesterol in lipid rafts,
    Saara Vainio, Maurice Jansen, Mirkka Koivusalo, Tomasz Róg, Mikko Karttunen, Ilpo Vattulainen, and Elina Ikonen,
    J. Biol. Chem. 281, 348-355, (2006).
    [online]

93. Stencils with isoptropic discretisation error for differential operators,
    Michael Patra and Mikko Karttunen,
    Numerical Methods for Partial Differential Equations 22, 936-953 (2005).
    [Online] [Preprint] [Related Mathematica file]

94. Spatio-temporal dynamics in a Turing model
    T. Leppänen, M. Karttunen, R.A. Barrio, and K. Kaski
    InterJournal, Section: Complex Systems, Article number: 874
    [online]
    [Print]
    [Turing movies]

95. Dielectrophoresis of nanocolloids: a molecular dynamics study,
    E. Salonen and E. Terama and I. Vattulainen and Mikko Karttunen
    Eur. Phys. J. E 18, 133-142 (2005).
    [Online] [preprint]

96. Reply to "Comment on the use of the method of images for calculating electromagnetic responses of interacting spheres,
    J.P. Huang, K.W. Yu, G.Q. Gu, M. Karttunen, and L. Dong
    Phys. Rev. E 72, 023402 (2005)
    [Online]
    [Online]

97. Response to the Comment by Almeida et al.: Free Area Theories for Lipid Bilayers - Predictive or Not?
    E. Falck, M. Patra, M. Karttunen, M. T. Hyvonen, and I. Vattulainen
    Biophys. J. 89 745-752 (2005)
    [Online]

98. Exploring the effect of Xenon on biomembranes
    Lorna M. Stimson, Ilpo Vattulainen, Tomasz Róg, and Mikko Karttunen
    Cell. Mol. Biol. Lett. 10 563-565 (2005).
    [Online] [Movies of Xenon inteacting with a membrane]

99. Modeling glycolipids: Take one,
    Tomasz Róg, Ilpo Vattulainen and Mikko Karttunen
    Cell. Mol. Biol. Lett. 10 625-630 (2005).
    [Online]

100. Effect of Monovalent Salt on Cationic Lipid Membranes ,
     A. A. Gurtovenko, M. Miettinen, M. Karttunen, and I. Vattulainen
     J. Phys. Chem. B 109, 21126-21134 (2005).
     [Online] [DMTAP/DMPC Configurations and parameters]

101. Free Volume Properties of Sphingomyelin, DMPC, DPPC, and PLPC Bilayers ,
     M. Kupiainen, E. Falck, S. Ollila, P. Niemelä, A. A. Gurtovenko, M. T. Hyvönen, M. Patra, M. Karttunen, and I. Vattulainen
     Journal of Computational and Theoretical Nanoscience 2, 401-413 (2005)
     [PDF file] [Online] [DPPC and DMPC configurations]

102. Spectral representation of the effective dielectric constant of graded composites
     Lei Dong, Mikko Karttunen, and K. W. Yu
     Phys. Rev. E 72, 016613 (2005)
     [Online] [preprint]

103. Crumpling of a stiff tethered membrane,
     J.A. Åström, J. Timonen, and Mikko Karttunen
     Phys. Rev. Lett. 93, 244301 (2004).
     [Online] [cond-mat/0309506]

104. Impact of Cholesterol on Voids in Phospholipid Membranes
     Emma Falck, Michael Patra, Mikko Karttunen, Marja T. Hyvönen, and Ilpo Vattulainen
     J. Chem. Phys. 121, 12676 (2004)
     [cond-mat/0408380] [online]
     Selected for the December 15, 2004 issue of the Virtual Journal of Biological Physics Research

105. Morphological transitions and bistability in Turing systems
     Teemu Leppänen, Mikko Karttunen, R.A. Barrio, and Kimmo Kaski
     Phys. Rev. E 70, 066202 (2004).
     [Preprint] [online] [Turing movies]

106. Lessons of Slicing Membranes: Interplay of Packing, Free Area, and Lateral Diffusion in Phospholipid/Cholesterol Bilayers
     Emma Falck, Michael Patra, Mikko Karttunen, Marja T. Hyvönen, and Ilpo Vattulainen
     Biophys. J. 87, 1076-1091 (2004).
     [Online] [cond-mat/0402290]
     Selected in Sep. 2004 issue of Molecular Modeling & Computational Chemistry (MMCC).

107. Structural effects of small molecules on phospholipid bilayers investigated by molecular simulations
     B.W. Lee, R. Faller, A.K. Sum, I. Vattulainen, M. Patra, and M. Karttunen
     Fluid Phase Equilibria 225, 63-68 (2004)
     [Online] [preprint]

108. Coarse-Grained Model for Phospholipid/Cholesterol Bilayer
     Teemu Murtola, Emma Falck, Michael Patra, Mikko Karttunen, Ilpo Vattulainen
     J. Chem. Phys.121 9156-9165 (2004).
     [cond-mat/0406764] [online]
     Selected for the November 1, 2004 issue of the Virtual Journal of Biological Physics Research

109. Electrokinetic behavior of two touching inhomogeneous biological cells and colloidal particles: Effects of multipolar interactions,
     J.P. Huang, Mikko Karttunen, K.W. Yu, L. Dong, and G.Q. Gu
     Phys. Rev. E 69, 051402 (2004)
     [cond-mat/0306271] [online]
     Selected for the June 1, 2004 issue of the Virtual Journal of Biological Physics Research

110. Turing systems as models of complex pattern formation
     Teemu Leppänen, Mikko Karttunen, Kimmo Kaski, and Rafael A. Barrio
     Braz. J. Phys. 34, 368-372 (2004).
     [Turing movies] [online]

111. Anomalously slow phase transitions in self-gravitating systems
     Iaroslav Ispolatov and Mikko Karttunen
     Phys. Rev. E 70, 026102 (2004).
     [cond-mat/0403097] [online]

112. Nonlinear alternating current responses of dipolar fluids,
     J.P. Huang, K.W. Yu, and Mikko Karttunen
     Phys. Rev. E 70 011403 (2004).
     [online]     [cond-mat/0403019]

113. Modeling of biologically motivated soft matter systems
     Ilpo Vattulainen and Mikko Karttunen
     Handbook of Theoretical and Computational Nanotechnology, edited by M. Rieth and W. Schommers (American Scientific Publishers). [PDF]

114. Systematic comparison of force fields for microscopic simulations of NaCl in aqueous solutions: Diffusion, free energy of hydration and structural properties,
     Michael Patra and Mikko Karttunen,
     J. Comp. Chem 25, 678-689 (2004).
     [physics/0211059] [Online] [All RDFs from ion simulations]
     Selected in Apr. 2004 issue of Molecular Modeling & Computational Chemistry (MMCC).

115. Cationic DMPC/DMTAP Lipid Bilayers: Molecular Dynamics Study,
     A.A. Gurtovenko, Michael Patra, Mikko Karttunen, and Ilpo Vattulainen
     Biophys. J. 86, 3461-3472 (2004).
     [online] [cond-mat/0312400] [Download DMTAP / DMPC equilibrium configurations and parameters]
     Selected in July 2004 issue of Molecular Modeling & Computational Chemistry (MMCC)

116. Lipid bilayers driven to a wrong lane in molecular dynamics simulations by truncation of long-range electrostatic interactions
     Michael Patra, Mikko Karttunen, Marja T. Hyvönen, Emma Falck, and Ilpo Vattulainen
     J. Phys. Chem. B 108, 4485-4494 (2004).
     [Online] [Download equilibrium configurations]

117. Dimensionality effects in Turing pattern formation
     Teemu Leppänen, Mikko Karttunen, Kimmo Kaski, and Rafael A. Barrio
     Int. J. Mod. Phys. B 17, 5541-5553 (2003).
     [cond-mat/0306121] [Turing movies]

118. The effect of noise on Turing patterns,
     Teemu Leppänen, Mikko Karttunen, Rafael A. Barrio, and Kimmo Kaski,
     Prog. Theor. Phys. (suppl.) 150, 367-370 (2003).
     [Online] [Turing movies]

119. Electrorotation in graded colloidal suspensions,
     J.P. Huang, K.W. Yu, G.Q. Gu and Mikko Karttunen,
     Phys. Rev. E 67, 051405
     [Online] [Preprint]
     Selected for the June 1, 2003 issue of the Virtual Journal of Biological Physics Research

120. Collapses and explosions in self-gravitating systems
     Iaroslav Ispolatov and Mikko Karttunen
     Phys. Rev. E 68, 036117 (2003)
     [Online] [Preprint]

121. Molecular dynamics simulations of lipid bilayers: Major artifacts due to truncating electrostatic interactions
     Michael Patra, Mikko Karttunen, Marja T. Hyvönen, Emma Falck, Peter Lindqvist, and Ilpo Vattulainen
     Biophys. J. 84, 3636-3645 (2003)
     [Online] [Preprint] [Download equilibrium configurations]
     Selected in July 2003 issue of Molecular Modeling & Computational Chemistry (MMCC)

122. Characterization of Sphingosine-Phosphatidylcholine Monolayers: Effects of DNA,
     V. Matti J. Säily, Juha-Matti Alakoskela, Samppa J. Ryhänen, Mikko Karttunen, and Paavo K.J. Kinnunen
     Langmuir 19, 8956-8963 (2003)
     [Online]

123. How would you integrate the equations of motion in dissipative particle dynamics simulations?
     Petri Nikunen, Mikko Karttunen, and Ilpo Vattulainen
     Comp. Phys. Comm. 153, 407-423 (2003)
     [Online] [Preprint] [DPD movies]

124. Dielectrophoresis of charged colloidal suspensions,
     J.P. Huang, Mikko Karttunen, K. W. Yu, and L. Dong
     Phys. Rev. E 67, 021403 (2003)
     [Online] [Preprint]
     Selected for the Mar. 1, 2003 issue of the Virtual Journal of Biological Physics Research

125. Stability of charge inversion, Thomson problem and application to electrophoresis
     Michael Patra, Marco Patriarca, and Mikko Karttunen
     Phys. Rev. E 67, 031402 (2003)
     [Online] [Preprint]
     Selected for the Apr. 1, 2003 issue of the Virtual Journal of Biological Physics Research

126. On coarse-graining by the inverse Monte Carlo method: Dissipative Particle Dynamics simulations made to a precise tool in soft matter modeling,
     Alexander P. Lyubartsev, Mikko Karttunen, Ilpo Vattulainen, and Aatto Laaksonen
     Soft Materials 1, 121-137 (2003).
     [Online] [Preprint]

127. Integration schemes for dissipative particle dynamics simulations: From softly interacting systems towards hybrid models,
     Ilpo Vattulainen, Mikko Karttunen, Gerhard Besold, and James Polson,
     J. Chem. Phys., 116, pp. 3967-3979 (2002)
     [Online] [Preprint] [DPD movies]

128. A new dimension to Turing patterns, Teemu Leppänen, Mikko Karttunen, Kimmo Kaski, Rafael A. Barrio, and Limei Zhang, Physica D 168-169C, 35-44 (2002).
     [online] [preprint] [Turing movies]

129. Instabilities and resistance fluctuations in thin accelerated superconducting rings,
     Mikko Karttunen, K.R. Elder, Martin B. Tarlie, Martin Grant,
     Phys. Rev. E 66, 026115 (2002)
     [online] [preprint] [Movies of superconducting rings]
     Selected for the September 1, 2002 issue of the Virtual Journal of Applications of Superconductivity

130. Towards better integrators for dissipative particle dynamics simulations,
     Gerhard Besold, Ilpo Vattulainen, Mikko Karttunen, and James M. Polson,
     Phys. Rev. E, vol. 63, pp. R7611-R7614 (2000)
     [Online] [cond-mat preprint] [DPD movies]

131. Defects, Order, and Hysteresis in Driven Charge-Density Waves,
     Mikko Karttunen, Mikko Haataja, K. R. Elder, and Martin Grant,
     Phys. Rev. Lett., vol. 83, pp. 3518-3521 (1999)
     [Online] [preprint] [CDW movies]

132. Nucleation, growth, and scaling in slow combustion,
     Mikko Karttunen, Nikolas Provatas, Tapio Ala-Nissila, and Martin Grant,
     J. Stat. Phys. 90, 1401-1411 (1998).
     [Online] [cond-mat/9701209]

133. The Internet Pilot to Physics: An Open Information System for Physics Research and Education,
     Mikko Karttunen , Kenneth Holmlund, and Guenther Nowotny,
     Int. J. Mod. Phys. C 8 , 3-17 (1997).
     [TIPTOP is now part of PhysicsWeb.org]

134. Residual Stresses in Plastic Random Systems,
     Mikko Alava, Mikko Karttunen , and Kaarlo J.~Niskanen,
     Europhys. Lett. 32, 143-148 (1995).

135. Fracture in mesoscopic disordered systems,
     Mikko Karttunen , Kaarlo J. Niskanen, and Kimmo Kaski,
     Phys. Rev. B 49, 9453-9459 (1994).
     [Online]

136. Molecular dynamics of a microscopic droplet on a solid surface,
     Jouko A. Nieminen, Douglas B. Abraham, Mikko Karttunen, and Kimmo Kaski,
     Phys. Rev. Lett. 69, 124-127 (1992).
     [Online]