Biophysical Journal

Research outputs

  1. 2020
  2. Published

    Computing Atomic Force Microscopy Images of Chromosomes using Polymer Simulation

    Sumikama, T., Foster, A. S. & Fukuma, T., 7 Feb 2020, In : Biophysical Journal. 118, 3, p. 619A-619A 1 p.

    Research output: Contribution to journalMeeting AbstractScientificpeer-review

  3. 2018
  4. Published

    Quantifying Nuclear Remodeling in Heart Failure

    Bailey, L., Smyl, D., Bossuyt, S. & Bossuyt, J., 2 Feb 2018, In : Biophysical Journal. 114, 3, p. 499A-499A 1 p.

    Research output: Contribution to journalMeeting AbstractScientificpeer-review

  5. 2016
  6. Published

    Oxidized Lipids in Model Membranes: Atomistic Details from Solid-State NMR Experiments and MD Simulations

    Ferreira, T. M., Baerenwald, R., Sood, R., Volinsky, R., Drescher, S., Karlström, G., Topgaard, D., Kinnunen, P., Saalwächter, K. & Ollila, S., 16 Feb 2016, In : Biophysical Journal. 110, 3, Supplement 1, p. 584A 1 p.

    Research output: Contribution to journalMeeting AbstractScientificpeer-review

  7. 2014
  8. Published

    Stable polyglutamine dimers can contain β-hairpins with interdigitated side chains - But not α-helices, β-nanotubes, β-pseudohelices, or steric zippers

    Miettinen, M. S., Monticelli, L., Nedumpully-Govindan, P., Knecht, V. & Ignatova, Z., 15 Apr 2014, In : Biophysical Journal. 106, 8, p. 1721-1728 8 p.

    Research output: Contribution to journalArticleScientificpeer-review

  9. Published

    Lipid Bilayer Structure and Dynamics Studied with Molecular Dynamics Simulations and NMR Measurements

    Ferreira, T., Topgaard, D. & Ollila, S. O. H., 28 Jan 2014, In : Biophysical Journal. 106, 2, p. 41A-41A 1 p.

    Research output: Contribution to journalMeeting AbstractScientificpeer-review

  10. Published

    Polarized THG Microscopy Identifies Compositionally Different Lipid Droplets in Mammalian Cells

    Bautista, G., Pfisterer, S. G., Huttunen, M. J., Kanerva, K., Ikonen, E. & Kauranen, M., 2014, In : Biophysical Journal. 107, p. 2230-2236

    Research output: Contribution to journalArticleScientificpeer-review

  11. 2013
  12. Published

    Impact of Oxidized Phospholipids on Membrane Organization

    Wallgren, M., Quoc, D. P., Lidman, M., Kinnunen, P. K. J., Hof, M. & Grobner, G., 2013, In : Biophysical Journal. 104, 2, p. 249

    Research output: Contribution to journalArticleScientificpeer-review

  13. 2012
  14. Published

    Interfacial tension and surface pressure of high density lipoprotein, low density lipoprotein, and related lipid droplets

    Ollila, O. H. S., Lamberg, A., Lehtivaara, M., Koivuniemi, A. & Vattulainen, I., 19 Sep 2012, In : Biophysical Journal. 103, 6, p. 1236-1244 9 p.

    Research output: Contribution to journalArticleScientificpeer-review

  15. Published

    Oxidized Phosphatidylcholines Promote Phase Separation of Cholesterol-Sphingomyelin Domains

    Volinsky, R., Paananen, R. & Kinnunen, P. K. J., 2012, In : Biophysical Journal. 103, 2, p. 247-254

    Research output: Contribution to journalArticleScientificpeer-review

  16. Published

    The Conformational Ensembles of a-Synuclein and Tau: Combining Single-Molecule FRET and Simulations

    Nath, A., Sammalkorpi, M., DeWitt, D. C., Trexler, A. J., Elbaum-Garfinkle, S., O'Hern, C. S. & Rhoades, E., 2012, In : Biophysical Journal. 103, 9, p. 1940-1947

    Research output: Contribution to journalArticleScientificpeer-review

  17. 2011
  18. Published

    Limitations of Equivalent Circuit Models in Data-Driven Simulation of the Neuron-Electrode Interface

    Thakore, V., Molnar, P. & Hickman, J. J., 2 Feb 2011, In : Biophysical Journal. 100, 3, p. 621-621 1 p.

    Research output: Contribution to journalMeeting AbstractScientificpeer-review

  19. Published

    Single Molecule DNA Interactions of the Nucleic Acid Chaperone Protein from the Line-1 Retrotransposon

    Evans, J., 2 Feb 2011, In : Biophysical Journal. 100, 3, p. 232a 1 p., 10.1016/j.bpj.2010.12.1480.

    Research output: Contribution to journalArticleScientificpeer-review

  20. Published

    Oxidized Phosphatidylcholines Facilitate Phospholipid Flip-Flop in Liposomes

    Volinsky, R., Cwiklik, L., Jurkiewicz, P., Hof, M., Jungwirth, P. & Kinnunen, P. K. J., 2011, In : Biophysical Journal. 101, 6, p. 1376-1384

    Research output: Contribution to journalArticleScientificpeer-review

  21. Published

    Protein shape change has a major effect on the gating energy of a mechanosensitive channel

    Ollila, O. H. S., Louhivuori, M., Marrink, S. J. & Vattulainen, I., 2011, In : Biophysical Journal. 100, 7, p. 1651-1659

    Research output: Contribution to journalArticleScientificpeer-review

  22. 2010
  23. Published

    Revealing the Microstructural Changes in Tissues In-Situ with Positron Annihilation Spectroscopy

    Sane, P., Tuomisto, F., Vattulainen, I. & Holopainen, J., Jan 2010, In : Biophysical Journal. 98, 3, p. 663a-663a 1 p.

    Research output: Contribution to journalArticleScientificpeer-review

  24. Published

    Effect of sphingomyelin head group size on molecular properties and interactions with cholesterol

    Björkbom, A., Rog, T., Kaszuba, K., Kurita, M., Yamaguchi, S., Lönnfors, M., Nyholm, T. K. M., Vattulainen, I., Katsumura, S. & Slotte, J. P., 2010, In : Biophysical Journal. 99, p. 3300-3308

    Research output: Contribution to journalArticleScientificpeer-review

  25. Published

    Lateral Pressure Profile and Curvature Frustration in Mechanosensitive Channel Gating

    Ollila, S. O. H., Louhivuori, M., Marrink, S-J. & Vattulainen, I., 2010, In : Biophysical Journal. 98, 3, p. 20

    Research output: Contribution to journalArticleScientificpeer-review

  26. Published

    Molecular Organization of the Tear Film Lipid Layer

    Rantamäki, A., Telenius, J., Koivuniemi, A., Kulovesi, P., Brezesinski, G., Viitala, T., Puukilainen, E., Ritala, M., Wiedmer, S. K., Vattulainen, I. & Holopainen, J. M., 2010, In : Biophysical Journal. 98, p. 488

    Research output: Contribution to journalArticleScientificpeer-review

  27. Published

    Molecular organization of the tear fluid lipid layer

    Kulovesi, P., Telenius, J., Koivuniemi, A., Brezesinski, G., Rantamaki, A., Viitala, T., Puukilainen, E., Ritala, M., Wiedmer, S. K., Vattulainen, I. & Holopainen, J. M., 2010, In : Biophysical Journal. 99, p. 2559-2567

    Research output: Contribution to journalArticleScientificpeer-review

  28. Published

    Specific Spatial and Orientational Order in Phospholipid Membranes Induced by Cholesterol

    Martinez-Seara, H., Rog, T., Karttunen, M., Reigada, R. & Vattulainen, I., 2010, In : Biophysical Journal. 98, p. 668

    Research output: Contribution to journalArticleScientificpeer-review

  29. 2009
  30. Published

    A Comparison Of Ceramide And Ceramide-1-phosphate Miscibility In Phosphatidylcholine Bilayers

    Morrow, M. R., Helle, A., Perry, J., Vattulainen, I., Wiedmer, S. K. & Holopainen, J. M., 2009, In : Biophysical Journal. 96, p. 162

    Research output: Contribution to journalArticleScientificpeer-review

  31. Published

    Atomistic Simulations of Phosphatidylcholines and Cholesteryl Esters in High Density Lipoprotein-Sized Lipid Droplet and Trilayer: Clues to Cholesteryl Ester Transport and Storage

    Koivuniemi, A., Heikela, M., Kovanen, P., Vattulainen, I. & Hyvonen, M., 2009, In : Biophysical Journal. 96, p. 4099-4108

    Research output: Contribution to journalArticleScientificpeer-review

  32. Published

    Ceramide-1-phosphate, in contrast to ceramide, is not segregated into lateral lipid domains in DPPC bilayers

    Morrow, M. R., Helle, A., Perry, J., Vattulainen, I., Wiedmer, S. K. & Holopainen, J. M., 2009, In : Biophysical Journal. 96, p. 2216-2226

    Research output: Contribution to journalArticleScientificpeer-review

  33. Published

    Interaction of Fullerene with Model Cell Membranes: A Computer Simulation Study

    Monticelli, L., Salonen, E., Ke, P-C. & Vattulainen, I., 2009, In : Biophysical Journal. 96, p. 365

    Research output: Contribution to journalArticleScientificpeer-review

  34. Published

    Probing The Microstructure Of Biomaterials With Positrons

    Sane, P., Tuomisto, F., Vattulainen, I., Salonen, E. & Holopainen, J. M., 2009, In : Biophysical Journal. 96, p. 356

    Research output: Contribution to journalArticleScientificpeer-review

  35. 2008
  36. Published

    Interactions of hydrophobin proteins in solution studied by small-angle X-ray scattering

    Kisko, K., Szilvay, G. R., Vainio, U., Linder, M. B. & Serimaa, R., 1 Jan 2008, In : Biophysical Journal. 94, 1, p. 198-206 9 p.

    Research output: Contribution to journalArticleScientificpeer-review

  37. Published

    Dynamics and Lateral Pressure Profiles of Lipid Rafts

    Vattulainen, I., 2008, In : Biophysical Journal. 94

    Research output: Contribution to journalArticleScientificpeer-review

  38. Published

    From Discoidal to Spheroidal HDL particles through Coarse Grained and All Atom Molecular Dynamics Simulations

    Catte, A., Vuorela, T., Niemelä, P., Murtola, T., Segrest, J., Marrink, S. J., Karttunen, M. & Vattulainen, I., 2008, In : Biophysical Journal. 94

    Research output: Contribution to journalArticleScientificpeer-review

  39. Published

    Interplay of Unsaturated Phospholipids and Cholesterol in Membranes: Effect of the Double Bond Position

    Martinez-Seara, H., Rog, T., Pasenkiewicz-Gierula, M., Vattulainen, ILPO., Karttunen, M. & Reigada, R., 2008, In : Biophysical Journal. 95, p. 3295-3305

    Research output: Contribution to journalArticleScientificpeer-review

  40. Published

    Structure of spheroidal HDL particles revealed by combined atomistic and coarse grained simulations

    Catte, A., Patterson, J. C., Bashtovyy, D., Jones, M. K., Gu, F., Li, L., Rampioni, A., Sengupta, D., Vuorela, T., Niemelä, P., Karttunen, M., Marrink, S. J., Vattulainen, I. & Segrest, J. P., 2008, In : Biophysical Journal. 94, p. 2306-2319

    Research output: Contribution to journalArticleScientificpeer-review

  41. 2007
  42. Published

    Atomic-scale structure and electrostatics of anionic POPG lipid bilayers with Na+ counterions

    Wei, Z., Rog, T., Gurtovenko, A. A., Vattulainen, I. & Karttunen, M., 2007, In : Biophysical Journal. 92, p. 1114-1124

    Research output: Contribution to journalArticleScientificpeer-review

  43. Published

    Effect of farnesol on phospholipid membranes

    Salonen, E., Rowat, A. C., Pencer, J. & Vattulainen, I., 2007, In : Biophysical Journal. Suppl. S, p. 547

    Research output: Contribution to journalArticleScientificpeer-review

  44. Published

    Influence of free pyrene probes on gel and fluid membranes through atomistic simulations

    Curdova, J., Capkova, P., Plasek, J., Repakova, J. & Vattulainen, I., 2007, In : Biophysical Journal. Suppl. S, p. 577

    Research output: Contribution to journalArticleScientificpeer-review

  45. Published

    Insight into the Putative Specific Interactions between Cholesterol, Sphingomyelin and Palmitoyl-Oleoyl Phosphatidylcholine

    Aittoniemi, J., Niemelä, P. S., Hyvönen, M. T., Karttunen, M. & Vattulainen, I., 2007, In : Biophysical Journal. 92, p. 1125-1137

    Research output: Contribution to journalArticleScientificpeer-review

  46. Published

    Ion Leakage Through Transient Water Pores In Protein-Free Lipid Membranes Driven by Transmembrane Ionic Charge Imbalance

    Gurtovenko, A. A. & Vattulainen, I., 2007, In : Biophysical Journal. 92, p. 1878-1890

    Research output: Contribution to journalArticleScientificpeer-review

  47. Published

    Lateral pressure profiles of lipid membranes - Dependence on lipid composition

    Ollila, S., Niemela, P. S., Rog, T., Hyvonen, M. T., Karttunen, M. & Vattulainen, I., 2007, In : Biophysical Journal. Suppl. S, p. 234

    Research output: Contribution to journalArticleScientificpeer-review

  48. Published

    Modeling a spin labeled fusion peptide in a membrane: Implications for the interpretation of EPR experiments

    Sammalkorpi, M. & Lazaridis, T., 2007, In : Biophysical Journal. 92, p. 10

    Research output: Contribution to journalArticleScientificpeer-review

  49. Published

    Preliminary models of spheroidal HDL particles through molecular dynamics

    Catte, A., Patterson, J. C., Bashtovyy, D., Jones, M. K., Gu, F. F., Li, L., Rampioni, A., Sengupta, D., Niemela, P., Vattulainen, I., Marrink, S. J. & Segrest, J. P., 2007, In : Biophysical Journal. Suppl. S, p. 539

    Research output: Contribution to journalArticleScientificpeer-review

  50. Published

    Towards more systematic selection of coarse-grained degrees of freedom

    Murtola, T., Kupiainen, M., Falck, E. & Vattulainen, I., 2007, In : Biophysical Journal. Suppl. S, p. 153

    Research output: Contribution to journalArticleScientificpeer-review

  51. Published

    What happens if cholesterol is made smoother: Importance of methyl substituents in cholesterol ring structure on phosphatidylcholine-sterol interaction

    Rog, T., Pasenkiewicz-Gierula, M., Vattulainen, I. & Karttunen, M., 2007, In : Biophysical Journal. 92, p. 3346-3357

    Research output: Contribution to journalArticleScientificpeer-review

  52. 2006
  53. Published

    Atomistic simulation studies of cholesteryl oleates in the interior of lipoprotein particles

    Heikelä, M., Vattulainen, I. & Hyvönen, M. T., 2006, In : Biophysical Journal. 90, p. 2247-2257

    Research output: Contribution to journalArticleScientificpeer-review

  54. Published

    Cholesterol-sphingomieline interactions: a molecular dynamics simulation study

    Róg, T. & Pasenkiewicz-Gierula, M., 2006, In : Biophysical Journal. 91, p. 3756-3767

    Research output: Contribution to journalArticleScientificpeer-review

  55. Published

    Diffusion mechanisms of lipids in bilayers

    Falck, E., Rog, T., Karttunen, M. & Vattulainen, I., 2006, In : Biophysical Journal. 90, p. 367

    Research output: Contribution to journalArticleScientificpeer-review

  56. Published

    Dynamics, kinetics and partitioning of alcohols in lipid membranes

    Terama, E. M., Patra, M., Rowat, A., Trandum, C., Westh, P., Salonen, E., Karttunen, M. & Vattulainen, I., 2006, In : Biophysical Journal. 90, p. 508

    Research output: Contribution to journalArticleScientificpeer-review

  57. Published

    Influence of chain length and unsaturation on sphingomyelin bilayers

    Niemelä, P., Hyvönen, M. T. & Vattulainen, I., 2006, In : Biophysical Journal. 90, p. 851-863

    Research output: Contribution to journalArticleScientificpeer-review

  58. Published

    Interaction of fusidic acid with lipid membranes: Implications to the mechanism of antibiotic activity

    Falck, E., Hautala, J. T., Karttunen, M., Kinnunen, P. K. J., Patra, M., Saaren-Seppälä, H., Vattulainen, I., Wiedmer, S. K. & Holopainen, J. M., 2006, In : Biophysical Journal. 91, p. 1787-1799

    Research output: Contribution to journalArticleScientificpeer-review

  59. Published

    Molecular dynamics studies of spontaneous pore formation and ion transport through lipid membranes due to cationic electrochemical gradient

    Gurtovenko, A. A. & Vattulainen, I., 2006, In : Biophysical Journal. 90, p. 405

    Research output: Contribution to journalArticleScientificpeer-review

  60. Published

    Specific interactions between cholesterol, sphingomyelin and POPC

    Aittoniemi, J., Niemela, P. S., Hyvonen, M. T., Karttunen, M. & Vattulainen, I., 2006, In : Biophysical Journal. 90, p. 371

    Research output: Contribution to journalArticleScientificpeer-review

  61. Published

    Structure and dynamics of dioxygen bound to cobalt and iron heme

    Degtyarenko, I., Nieminen, R. M. & Rovira, C., 2006, In : Biophysical Journal. 91, 6, p. 2024-2034

    Research output: Contribution to journalArticleScientificpeer-review

  62. Published

    Systematic coarse-graining on multicomponent lipid bilayers

    Murtola, T., Falck, E., Rog, T., Karttunen, M. & Vattulainen, I., 2006, In : Biophysical Journal. 90, p. 289

    Research output: Contribution to journalArticleScientificpeer-review

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