SoftSimu - Publications

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Publications and theses

If you want a paper copy/reprint of any of the articles below, please contact
Mikko Karttunen (mkarttu [at] uwo.ca).

We also provide some related software and downloadable configurations for (bio)molecular simulations on our 'Downloads' page (on the upper panel).

Extras:

2009:

  1. 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

  2. Phosphorylation of Ser136 is Critical for Potent Bone Sialoprotein-Mediated Nucleation of Hydroxyapatite Crystals
    Gurpreet S. Bahta, Jason O'Young, Antonia Borovino, Coralee E. Tye, Mikko Karttunen, Graeme K. Huntera, and Harvey A. Goldberg, submitted

  3. 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., in press

  4. 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, submitted

  5. The hydrophobic effect and its role in cold denaturation,
    Cristiano L. Dias, Tapio Ala-Nissila, Jirasak Wong-ekkabut, Ilpo Vattulainen, Mikko Karttunen. Cryobiology, in press. [on-line]

  6. 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]

  7. 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]

  8. 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]

  9. 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]

  10. 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]

  11. 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]

  12. 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]

  13. 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]

  14. 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]

  15. 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]

  16. 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]

  17. 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]

  18. 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]

2008:

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

  2. 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]

  3. 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]

  4. Systematic approach to coarse-graining of molecular descriptions and interactions with applications to lipid membranes ,
    Teemu Murtola, Ilpo Vattulainen, Mikko Karttunen,
    in "Coarse-Graining of Condensed Phase and Biomolecular Systems", G. Voth (Ed.), CRC Press (Boca Raton, FL), 2008.

  5. 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 Róg, Ilpo Vattulainen, Maurice Jansen, Elina Ikonen, and Mikko Karttunen
    J. Chem. Phys. 129, 154508 (2008). [on-line]

  6. 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]

  7. Strain hardening in dense actin networks
    Jan A. Åström, P.B. Sunil Kumar, Ilpo Vattulainen, Mikko Karttunen
    Phys. Rev. E 77, 051913 [On-line]

  8. 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]

  9. Nano-sized fullerene clusters permeate lipid membranes, ,
    Jirasak Wong-ekkabut, Svetlana Baoukina, Wannapong Triampo, I-Ming Tang, D. Peter Tieleman, and Luca Monticelli
    Nature Nanotechnology 3, 363-368 (2008). [on-line]

  10. Point defects in pure amorphous silicon and their role in structural relaxation: A tight-binding molecular-dynamics study,
    Xavier Urli, Cristiano L. Dias, Laurent J. Lewis, and Sjoerd Roorda
    Phys. Rev. B 77, 155204 (2008). [On-line]

  11. 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]
    Selected for the April 1, 2008 issue of Virtual Journal of Biological Physics Research.

  12. 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]

  13. 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]

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

  15. 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]

  16. 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,
    submitted

  17. 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]

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

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

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

  21. 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]

  22. Role of phosphatidylglycerols in the stability of bacterial membranes ,
    Wei Zhao, Tomasz Róg, Andrey A. Gurtovenko, I. Vattulainen, Mikko Karttunen
    Biochimie 90, 930-938 (2008). [On-line]

2007:

   See also: 2007 | 2006 | 2005 | 2004 | 2003 | 2002 | 2001 | Popular science | Theses | Old | Top

  1. 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]

  2. 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]

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

  4. 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]

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

  6. 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]

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

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

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

  10. Atomic-scale structure and electrostatics of anionic POPG lipid bilayers with Na+ counterions
    Wei Zhao, Tomasz Róg, Andrey A. Gurtovenko, Ilpo Vattulainen, and Mikko Karttunen
    Biophys. J. 92, 1114-1124 (2007).
    [Online]

  11. 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]

  12. 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. Róg, Mikko Karttunen, Ilpo Vattulainen
    J. Structural Biology, 159, 311-323 (2007)
    [Online]

  13. 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!

  14. 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).
    Selected for the March 1, 2007 issue of Virtual Journal of Biological Physics Research
    [Online]

  15. 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 (2007)
    [Online] [ cond-mat/0410210]

2006:

   See also: 2007 | 2006 | 2005 | 2004 | 2003 | 2002 | 2001 | Popular science | Theses | Old | Top

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

  2. 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]

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

  4. The influence of lateral and terminal substitution on the structure of a liquid crystal dendrimer: A computer simulation study
    Mark R. Wilson, Lorna M. Stimson and Jaroslav M. Ilnytskyi,
    accepted for publications in Liquid Crystals

  5. 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]

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

  7. 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]

  8. 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]

  9. Ab initio band bending, metal-induced gap states, and Schottky barriers of a carbon and a boron nitride nanotube device
    Khorgolkhuu Odbadrakh, Pawel Pomorski, and Christopher Roland.
    Phys. Rev. B 73, 233402 (2006).
    [Online]

  10. Cholesterol-sphingomyelin interactions: A molecular dynamics simulation study
    T. Róg and M. Pasenkiewicz-Gierula
    Biophys. J. 91 3756-3767 (2006). [online].

  11. Cholesterol effects on the unsaturated phosphatidylcholine bilayer: a molecular dynamics simulation study,
    Tomasz Róg, Marta Pasenkiewicz-Gierula
    Biochimie 88, 449-460 (2006). [online]

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

  13. 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 for the March 15, 2006 issue (vol. 11, issue 6) of the Virtual Journal of Biological Physics Research, and Selected for the March 20, 2006 issue of the Virtual Journal of Nanoscale Science and Technology

  14. 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]

  15. 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]

  16. Influence of the disulfide bond configuration on the dynamics of the spin label attached to cytochrome c,
    Krzysztof Murzyn, Tomasz Róg, Wojciech Blicharski, Malgorzata Dutka, Janusz Pyka, Sebastian Szytula, Wojciech Froncisz
    Proteins 62, 1088-1100 (2006). online]

  17. Effective ac response of graded colloidal suspensions,
    En-Bo Wei, L. Dong and K. W. Yu,
    J. Appl. Phys. 99, 054101 (2006).

  18. Giant enhancement of optical nonlinearity in multilayer metallic films,
    J. P. Huang, L. Dong and K. W. Yu,
    J. Appl. Phys. 99, 053503 (2006).

  19. Systematic coarse-graining of multicomponent lipid bilayers,
    T. Murtola, E. Falck, T. Róg, M. Karttunen, and I. Vattulainen,
    Biophys. J. 90, 289A (2006). (Biophys. Soc. Conf. Proc.)

  20. Diffusion mechanisms of lipids in bilayers,
    E. Falck, T. Róg, M. Karttunen, and I. Vattulainen,
    Biophys. J. 90, 367A (2006). (Biophys. Soc. Conf. Proc.)

  21. Specific interactions between cholesterol, sphingomyelin, and POPC,
    J. Aittoniemi, P. Niemela, M. T. Hyvonen, M. Karttunen, and I. Vattulainen,
    Biophys. J. 90, 371A (2006). (Biophys. Soc. Conf. Proc.)

  22. Dynamics, kinetics and partitioning of alcohols in lipid membranes,
    E. Terama, M. Patra, A. Rowat, C. Trandum, P. Westh, E. Salonen, M. Karttunen, and I. Vattulainen,
    Biophys. J. 90, 508A (2006). (Biophys. Soc. Conf. Proc.)

2005:

   See also: 2007 | 2006 | 2005 | 2004 | 2003 | 2002 | 2001 | Popular science | Theses | Old | Top

  1. 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]

  2. Coarse-grained simulation studies of a liquid crystal dendrimer: towards computational predictions of nanoscale structure through microphase separation,
    Zak E. Hughes, Mark R. Wilson and Lorna M. Stimson
    Soft Matter 1, 436-443 (2005)
    [Online]

  3. Molecular dynamics simulations of side chain liquid crystal polymer molecules in isotropic and liquid-crystalline melts,
    Lorna M. Stimson and Mark R. Wilson
    J. Chem. Phys 123 034908 (2005)
    [Online]
    Selected for the August 1, 2005 issue of the Virtual Journal of Biological Physics Research

  4. 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]

  5. 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]
    Selected for the August 15, 2005 issue of the Virtual Journal of Biological Physics Research

  6. 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]

  7. 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]    

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

  9. 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]

  10. Multipole polarizability of a graded spherical particle, ,
    L. Dong, J.P. Huang, K.W. Yu and G.Q. Gu,
    Eur. Phys. J. B 48, 439-444 (2005).

  11. 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]

  12. 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]

  13. Molecular dynamics modeling of polymer fragment dielectrophoresis ,
    E. Salonen, E. Terämä, I. Vattulainen, and M. Karttunen
    Biophys. J. 88, 404A (2005). (Biophys. Soc. Conference)

  14. Characterization of the effects of ethanol and methanol on lipid bilayers ,
    E. Terämä, E. Salonen, I. Vattulainen, J. Holopainen, R. Faller, M. Patra, and M. Karttunen
    Biophys. J. 88, 414A (2005). (Biophys. Soc. Conference)

  15. Voids in phospholipid/cholesterol bilayers ,
    E. Falck, M. Patra, M. Karttunen, M.T. Hyvönen, and I. Vattulainen
    Biophys. J. 88, 245A (2005). (Biophys. Soc. Conference)

  16. Atomistic simulations of cationic lipid membranes: effect of salt ,
    A. Gurtovenko, M. Miettinen, M. Karttunen, and I. Vattulainen,
    Biophys. J. 88, 420A (2005). (Biophys. Soc. Conference)

2004:

   See also: 2007 | 2006 | 2005 | 2004 | 2003 | 2002 | 2001 | Popular science | Theses | Old | Top

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

  2. 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

  3. Optical nonlinearity enhancement of graded metal-dielectric composite films
    Ji-Ping Huang, L. Dong, and Kin Wah Yu
    Europhys. Lett. 67, 854-858 (2004).

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

  5. Novel Methods in Soft Matter Simulations,
    Mikko Karttunen, Ilpo Vattulainen, and Ari Lukkarinen (Eds.)
    Springer-Verlag, Lecture Notes in Physics series (2004)
    [Contents of the book] [SoftSimu2002]

  6. 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)

  7. 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]

  8. 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

  9. Many-body dipole-induced dipole model for electrorheological fluids
    Ji-Ping Huang and Kin Wah Yu
    Chinese Physics 13, 1065-05 (2004).

  10. 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

  11. 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]

  12. 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]

  13. Dielectric response of graded spherical particles of anisotropic materials
    L. Dong, J.P. Huang, K.W. Yu, and G.Q. Gu
    J. Appl. Phys. 95, 621-624 (2004)
    [online]

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

  15. 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]

  16. Modeling of biologically motivated soft matter systems
    Ilpo Vattulainen and Mikko Karttunen
    to appear in the Handbook of Theoretical and Computational Nanotechnology, edited by M. Rieth and W. Schommers (American Scientific Publishers)
    For a preprint, please email us.

  17. 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)

  18. 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 equilibrium configuration and parameters]
    Selected in July 2004 issue of Molecular Modeling & Computational Chemistry (MMCC)

  19. 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 configuration]

  20. The theory of Turing pattern formation
    Teemu Leppänen
    to appear in Current Topics in Physics (Imperial College Press), 2004.
    [preprint]

2003:

 2007 | 2006 |   See also: 2005 | 2004 | 2003  | 2002 | 2001 | Popular science | Theses | Old | Top

  1. 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]

  2. 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]

  3. Comment on "Microcanonical Mean Field Thermodynamics of Self-Gravitating and Rotating systems"
    Iaroslav Ispolatov and Mikko Karttunen
    submitted
    [Preprint]

  4. 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

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

  6. 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)

  7. 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]

  8. 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]

  9. 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

  10. 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

  11. Decay Rate Distributions of Disordered Slabs and Application to Random Lasers
    M. Patra
    Phys. Rev. E 67, 016603 (2003)
    [Online] [Preprint]

  12. MD simulations of lipid bilayers: Artifacts due to truncating electrostatic interactions
    M. Patra, M. Karttunen, M.T. Hyvönen, E. Falck, P. Lindqvist, and I. Vattulainen
    Eur. Biophys. J. 32, 216 (2003). (conference)

  13. 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]

2002:

 2007 | 2006 |   See also: 2005 | 2004 | 2003 | 2003  | 2001 | Popular science | Theses | Old | Top

  1. 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]

  2. 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]

  3. Theory for the photon statistics of random lasers,
    M. Patra,
    [ Phys. Rev. A, vol. 65, 043809 (2002)]

  4. A hierarchical method for coarse graining molecular systems: From molecular dynamics to mesoscopic simulations,
    Mikko Karttunen, Aatto Laaksonen, Alexander P.Lyubartsev and Ilpo Vattulainen,
    submitted

  5. 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

  6. Computational modeling of DNA-cationic lipid complexation,
    Mikko Karttunen, Antti L. Pakkanen, Paavo K.J. Kinnunen, and Kimmo Kaski,
    Cell. Mol. Biol. Lett., 7, 238 (2002).

  7. Modified EAM potentials for modelling stacking-fault behavior in Cu, Al, Au, and Ni,
    P. Szelestey, M. Patriarca, L. F. Perondi, and K. Kaski,
    accepted for publication in Int. J. Mod. Phys. B

  8. Effects of quenched impurities on diffusion, spreading and ordering of O/W(110),
    P. Nikunen, I. Vattulainen, and T. Ala-Nissila,
    [ J. Chem. Phys., 117, pp. 6757-6765 (2002)]

  9. Dielectrophoresis of charged colloidal suspensions,
    J.P. Huang, Mikko Karttunen, K. W. Yu, and L. Dong,
    accepted for publication in Phys. Rev. E.
    [physics/0211055]

  10. Dielectric response of spherical particles of graded materials,
    K.W. Yu, G.Q. Gu and J.P. Huang,
    [cond-mat/0211532]

2001:

   See also: 2007 | 2006 | 2005 | 2004 | 2003 | 2002 | 2004  | Popular science | Theses | Old | Top

  1. From biomembranes to cationic liposomes. Int'l conference and summer school. Technical Report B26, ISBN 951-22-5429-8, Helsinki University of Technology, Lab. of Computational Engineering, Helsinki/Espoo, August 2001. Mikko Karttunen and Ilpo Vattulainen and Ari Lukkarinen (Eds.).

Popular science, interviews, non peer reviewed articles, etc.

   See also: 2007 | 2006 | 2005 | 2004 | 2003 | 2002 | 2001 | Popular science  | Theses | Old | Top

  1. Applied math rubs up against biology
    Western News, Nov. 16, 2006.

  2. Biologisen fysiikan tutkimus kärkkyy maailman kärkeen
    (Biological physics aiming to the top).
    Lue artikkeli Tekniikka ja Taloudesta, Feb. 26, 2004.

  3. Biologisen fysiikan tutkijat mallintavat soluja tietokoneen avulla.
    interview of Mikko Karttunen and Ilpo Vattulainen in
    Polysteekki 2/2004, pp. 6-8. (in Finnish)

  4. Biologisten systeemien mallinntaminen.
    Modeling biological systems, Mikko Karttunen and Ilpo Vattulainen
    Tietoyhteys 2/2004, pp. 20-22. (in Finnish)

  5. Tiedetorstai: Viinaa solukalvolla,
    TiedeTorstai - tietoa tekniikan tutkimuksesta kerran kuussa
    Booze on cellular membranes - computer simulations of alcohols on cellular membranes, Mikko Karttunen and Ilpo Vattulainen
    TiedeTorstai May 2004. (in Finnish)

  6. Matemaatikko luonnonilmiöiden jäljillä,
    T. Leppänen and K. Kaski, to appear in Arkhimedes 2/2004 (in Finnish), PDF.

  7. Matemaatikko selätti seepran raidat,
    Teemu Leppänen and Kimmo Kaski, Tiede 1/2004 (in Finnish).

  8. Radio interview of Mikko Karttunen and Ilpo Vattulainen,
    in the Finnish Broadcasting Company's (YLE Radio 1) program ``Radiaattori'' May 7 (2003) at 10:03 am - 10.43 am. The program covers topics related to natural sciences and technology, and the interview focused on the interplay of physics and biology

  9. Fysiikka kohtaa biologian -- Biomateriaalien teoria ja mallinnus,
    Ilpo Vattulainen & Mikko Karttunen, Tieteen Päivät 2003. (Physics meets biology -- a pedestrian approach to theory and modeling of biomaterials, National Science Days, 2003).
    Tieteessä Tapahtuu, 7, 2003
    [PDF file in Finnish here.]

  10. Conference report: SoftSimu2002 - Novel Methods in Soft Matter Simulations,
    Mikko Karttunen, Ilpo Vattulainen, and Ari Lukkarinen,
    [Appl. Rheol. 12 (4), 200-201 (2002).]
    SoftSimu2002 Web site: www.softsimu.org/softsimu2002

Theses

   See also: 2007 | 2006 | 2005 | 2004 | 2003 | 2002 | 2001 | Popular science | Theses  | Old | Top

  1. Lei Dong, Dielectric properties of colloidal suspensions, PhD thesis, 2009

  2. Wei Zhao, Molecular modeling of charged membrane systems PhD thesis, Nov. 2006

  3. Petri Nikunen, Studies of surface diffusion and dissipative particle dynamics, Mar. 2006, PhD thesis.

  4. Markus Miettinen, From molten globule to swollen coil: Simulations of a lone polymer chain in an explicit solvent, MSc thesis, Nov. 2004.

  5. Teemu Leppänen, Computational studies of pattern formation in Turing systems, PhD thesis, Nov. 2004.

  6. Teemu Leppänen, Spatial pattern formation in Turing systems, Dec. 2001, MSc thesis.

A very limited number of selected older articles:

   See also: 2007 | 2006 | 2005 | 2004 | 2003 | 2002 | 2001 | Popular science | Theses | Old | Top

  For more older publications, please contact the individual researchers.

  1. 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

  2. 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] [preprint]
    DPD movies

  3. Density profile evolution and nonequilibrium effects in partial and full spreading measurements of surface diffusion,
    Petri Nikunen, Ilpo Vattulainen, and Tapio Ala-Nissila,
    J. Chem. Phys., 114, pp. 6335-6342 (2001)
    [online]