Publications 2007

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

2. 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.

3. 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]

4. 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]

5. 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]

6. 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
   accepted for publication in J. Structural Biology
   [Online]

7. 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]

8. 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]

9. Long-range interactions & parallel scalability in molecular simulations
   M. Patra, M.T. Hyvonen, E. Falck, M. Sabouri-Ghomi, I. Vattulainen, M. Karttunen
   Computer Physics Comm. 176, 14-22 (2007)
   [Online] [ cond-mat/0410210]

10. Elastic response of a nematic liquid crystal to an immersed nanowire
    C.J. Smith and C. Denniston
    Journal of Applied Physics, 100, 014305 (2007).
    [cond-mat/0610048] [Online]

Publications 2006

1. Elastic response of a nematic liquid crystal to an immersed nanowire
   C.J. Smith and C. Denniston
   Journal of Applied Physics, 100, 014305 (2007).
   [cond-mat/0610048] [Online]

2. General continuum boundary conditions for miscible binary fluids from molecular dynamics simulations
   C. Denniston and M.O. Robbins
   J. Chem. Phys. 125, 214102 (2006).
   [Online]

3. Simulations of collision times in gravity driven granular flow
   J. J. Drozd and C. Denniston
   Europhysics Letters 76, 360 (2006).
   [cond-mat/0609330] [Online]

4. On the orientation of lamellar block copolymer phases under shear
   B. Fraser, C. Denniston, M. Müser
   J. Chem. Phys. 124, 104902 (2006).
   [Online]

5. An Investigation of Uniform Expansions of Large Order Bessel Functions in Gravitational Wave Signals from Pulsars
   F.A. Chishtie, K.M. Rao, I. Kotsireas and S.R. Valluri
   Classical and Quantum Gravity, submitted.
   [Online]

6. The Gravitational Wave Pulsar Signal with Jovian and Lunar Perturbations and Orbital Eccentricity Corrections
   S.R. Valluri, F.A. Chishtie and Adam Vajda
   Classical and Quantum Gravity 23 No 10, 3323-3332 (2006).
   [Online]

7. A study of the gravitational wave pulsar signal with orbital and spindown effects
   S.R. Valluri, K.M. Rao, P. Wiegert, and F.A. Chishtie
   Canadian Journal Physics 84, Number 6-7, 607-630 (2006).
   [Online]

8. Development of an unbiased statistical method for the analysis of unigenic evolution.
   Behrsin, C.D., Brandl, C.J., Litchfield, D.W., Shilton, B.H. and Wahl, L.M.
   BMC Bioinformatics 7, 150 (2006).
   [Online]

9. Improving estimates of the basic reproductive ratio: Using both the mean and the dispersal of transition times.
   Heffernan, J.M. and Wahl, L.M.
   Theoretical Population Biology 70, 135-145 (2006).
   

10. Dynamics of recurrent viral infection.
    Yao, W., Hertel, L. and Wahl, L.M.
    Proceedings of the Royal Society, Biological 273, 2193-2199 (2006).
    

11. Natural variation in HIV infection: Monte Carlo estimates that include CD8 effector cells.
    Heffernan, J.M. and Wahl, L.M.
    Journal of Theoretical Biology 243, 191-204 (2006).
    

12. Functionally important residues in the peptidyl-prolyl isomerase Pin1 revealed by unigenic evolution.
    Behrsin, C.D., Bateman, K.S., Hamilton, K.S., Wahl, L.M., Brandl, C.J., Shilton, B.H. and Litchfield, D.W.
    Journal of Molecular Biology, in press.
    

13. Costs versus Benefits: Best possible and best practical treatment strategies for HIV.
    Krakovska, O. and Wahl, L.M.
    Journal of Mathematical Biology, in press.
    

14. Time course of early response to chemotherapy in non-small cell lung cancer patients with 18-F-FDG-PET/CT.
    Nahmias, C., Hanna, W.T., Wahl, L.M., Long, M.J., Hubner, K.F. and Townsend, D.W.
    Journal of Nuclear Medicine, under review.
    

15. Optimal drug treatment regimens for HIV depend on adherence.
    Krakovska, O. and Wahl, L.M.
    Journal of Theoretical Biology, in revision.
    

16. Drug-sparing regimens for HIV combination therapy: benefits predicted for drug coasting.
    Krakovska, O. and Wahl, L.M.
    Journal of Theoretical Biology, under review.
    

17. Estmating fixation probabilities when generation times are variable: the burst-death model.
    Hubbarde, J.E., Wild, G. and Wahl, L.M.
    Genetics, under review.
    

18. 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, M. Karttunen, I. Vattulainen,
    submitted
    [preprint: contact M. Karttunen]

19. Atomistic Modeling of Friction ,
    N. J. Mosey and M. H. Müser
    Rev. Comp. Chem. (in press) .
    

20. Computer simulations of undercooled fluids and glasses,
    K. Binder, D. Herzbach, J. Horbach, and M. H. Müser
    Lecture Notes in Physics (Springer, in press).

21. Interpretation of experiments on ZDDP anti-wear films through pressure-induced cross-linking,
    N. J. Mosey, T. K. Woo, M. Kasrai, P. R. Norton, G. M. Bancroft, and M. H. Müser
    Tribol. Lett. (in press)
    [preprint]

22. A generalization of the charge equilibration method for non-metallic materials,
    R. A. Nistor, J. G. Polihronov, M. H. Müser, and N. J. Mosey
    J. Chem. Phys (in press)
    [preprint]

23. Practical Green's function approach to the simulation of elastic, semi-infinite solids,
    C. Campana and M. H. Müser
    Phys. Rev. B 74 075420 (2006).
    [preprint]

24. Possible explanation of the lambda-shape anomaly in polymer surface diffusion,
    D. Mukherji and M. H. Müser
    Phys. Rev. E 74 010601 (2006).
    [preprint]

25. Piezoelectric coefficients by molecular dynamics simulations in the constant stress ensemble: A case study of quartz ,
    D. Herzbach and M. H. Müser
    Comput. Phys. Comm. 174 17 (2006).
    [preprint]

26. Reibung ohne Kontakt ,
    M. H. Müser
    Physik Journal 5 (Nr. 7), 21-22 (2006).

27. 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. (in press)
    [preprint: contact M. Karttunen]

28. Molecular dynamics study of Sphingosine/POPC Bilayers: Ordering due to interplay of steric and electrostatic effects
    M. Patra and M. Karttunen
    submitted
    [preprint: contact M. Karttunen]

29. Novel View of Lipid Diffusion in Membranes: From Jumps to Flows
    E. Falck, T. Rog, M. Karttunen, I. Vattulainen
    submitted
    [preprint: contact M. Karttunen]

30. Transient Ordered Domains in Pure Phospholipid Bilayers
    Teemu Murtola, Tomasz Rog, Emma Falck, Mikko Karttunen, Ilpo Vattulainen
    Phys. Rev. Lett. (in press)
    [preprint: contact M. Karttunen]

31. Role of phosphatidylglycerols in the stability of bacterial membranes ,
    Wei Zhao, Tomasz Rog, Andrey A. Gurtovenko, I. Vattulainen, Mikko Karttunen
    submitted
    [Movies] [POPG parameters and configurations] [preprint: contact M. Karttunen]

32. Elastic properties, lateral heterogeneity and lateral pressure profiles of raft membranes through atom-scale simulations
    P.S. Niemela, S. Ollila, M.T. Hyvonen, Mikko Karttunen, I. Vattulainen
    submitted
    [preprint: contact M. Karttunen]

33. Enhanced dielectrophoresis of nanocolloids by dimer formation
    Emppu Salonen, Emma Terama, Ilpo Vattulainen, Mikko Karttunen
    submitted
    [preprint: contact M. Karttunen]

34. 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. (in press)
    [Online]

35. Strain hardening in dense actin networks
    Jan A. Åström, P.B. Sunil Kumar, Ilpo Vattulainen, Mikko Karttunen
    submitted
    [preprint: contact M. Karttunen]

36. Sterol tilt -- major determinant of sterol ordering capability in lipid membranes
    J. Aittoniemi, T. Rog, P. Niemela, M. Pasenkiewicz-Gierula, I. Vattulainen, Mikko Karttunen
    J. Phys. Chem. B. Lett. (in press)

37. Reptational dynamics in dissipative particle simulations of polymer melts,
    P. Nikunen, I. Vattulainen, M. Karttunen,
    submitted.
    [preprint]

38. 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. in press
    [Online] [Downloadable POPG & POPC configurations and parameters] [Movies]

39. 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]

40. 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]

41. 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]

42. 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]
    

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

44. 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

45. 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]

46. 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]