Recent articles have appeared in journals such as Chemical Reviews, Nature clones, PLoS journals, the many journals by the ACS, and Biophysical Journal. The list of our publications is highlighted below.
Many of our articles and in particular the recent ones have been published as Gold Open Access. Those articles for which this has not been possible, have been published as Green Open Access: please see the Open Access repository of the University of Helsinki (https://helda.helsinki.fi/handle/10138/5). If you still cannot find our article as Open Access, please contact the PI (corresponding author) of the author, or Ilpo Vattulainen.
Abraham, B.G., Haikarainen, T., Vuorio, T., Girych, M., Virtanen, A.T., Kurttila, A., Karathanasis, Ch., Heilemann, M., Sharma, V., Vattulainen, I., and Silvennoinen, O. Molecular basis of JAK2 activation in erythropoietin receptor and pathogenic JAK2 signaling. Science Advances 10, eadl2097 (2024). DOI: https://doi.org/10.1126/sciadv.adl2097
Enkavi, G., Girych, M., Moliner, R., Vattulainen, I., and Castrén, E., TrkB transmembrane domain: bridging structural understanding with therapeutic strategy. Trends in Biochemical Sciences (2024). DOI: https://doi.org/10.1016/j.tibs.2024.02.001
Chavda, D., Dutta, D., Patel, K.N., Rathod, A.K., Kulig, W., and Manna, M. Revealing the key structural features promoting the helical conformation in algal polysaccharide carrageenan in solution. Carbohydrate Polymers 331, (2024) 121901. DOI: https://doi.org/10.1016/j.carbpol.2024.121901
Martin, A., Tempra, C., Yu, Y., Liekkinen, J., Thakker, R., Lee, H., de Santos Moreno, B., Vattulainen, I., Rossios, Ch., Javanainen, M., and Bernardino de la Serna, J. Exposure to aldehyde cherry e‑liquid flavoring and its vaping byproduct disrupt pulmonary surfactant biophysical function. Environmental Science and Technology 58, (2024) 1495–1508. DOI: https://doi.org/10.1021/acs.est.3c07874
Żak, A., Korshunova, K., Rajtar, N., Kulig, W., and Kepczynski, M. Deciphering lipid arrangement in phosphatidylserine/phosphatidylcholine mixed membranes: Simulations and experiments. Langmuir 39 (2023)18995–19007. DOI: https://doi.org/10.1021/acs.langmuir.3c03061
Goellner, S., Enkavi, G., Prasad, V., Denolly, S., Eu, S., Mizzon, G., Witte, L., Kulig, W., Uckeley, Z.M., Lavacca, T.M., Haselmann, U., Lozach, P.-Y., Brügger, B., Vattulainen, I., and Bartenschlager, R. Zika virus prM protein contains cholesterol binding motifs required for virus entry and assembly. Nature Communications 14, 7344 (2023). DOI: https://doi.org/10.1038/s41467-023-42985-x
McDowell, M.A., Heimes, M., Enkavi, G., Farkas, Á., Saar, D., Wild, K., Schwappach, B., Vattulainen, I., and Sinning, I. The GET insertase exhibits conformational plasticity and induces membrane thinning. Nature Communications 14, 7355 (2023). DOI: https://doi.org/10.1038/s41467-023-42867-2
Chytrosz-Wrobel, P., Golda-Cepa, M., Drozdz, K., Rysz, J., Kubisiak, P., Kulig, W., Brzychczy-Wloch, M., Cwiklik, L., and Kotarba, A. In Vitro and In Silico Studies of Functionalized Polyurethane Surfaces toward Understanding Biologically Relevant Interactions. ACS Biomaterials Science and Engineering 9, 6112–6122 (2023). DOI: https://doi.org/10.1021/acsbiomaterials.3c01367
Girych, M., Kulig, W., Enkavi, G., and Vattulainen, I. How Neuromembrane Lipids Modulate Membrane Proteins: Insights from G-Protein-Coupled Receptors (GPCRs) and Receptor Tyrosine Kinases (RTKs). Cold Spring Harbor Perspectives in Biology a041419, (2023). DOI: https://doi.org/10.1101/cshperspect.a041419
Lolicato, F., Steringer, J.P., Saleppico, R., Beyer, D., Fernandez-Sobaberas, J., Unger, S., Klein, S., Riegerová, P., Wegehingel, S., Müller, H.-M., Freund, C., Hof, M., Šachl, R., Chlanda, P., Vattulainen, I., and Nickel, W. Disulfide bridge-dependent dimerization triggers FGF2 membrane translocation into the extracellular space. eLife 12, RP88579 (2023). DOI:https://doi.org/10.7554/eLife.88579.1
Moliner, R., Girych, M., Brunello, C.A., Kovaleva, V., Biojone, C., Enkavi, G., Antenucci, L., Kot, E.F., Goncharuk, S.A., Kaurinkoski, K., Kuutti, M., Fred, S.M., Elsilä, L.V., Sakson, S., Cannarozzo, C., Diniz, C.R.A.F., Seiffert, N., Rubiolo, A., Haapaniemi, H., Meshi, E., Nagaeva, E., Öhman, T., Róg, T., Kankuri, E., Vilar, M., Varjosalo, M., Korpi, E.R., Permi, P., Mineev, K.S., Saarma, M., Vattulainen, I., Casarotto, P.C., and Castrén, E. Psychedelics promote plasticity by directly binding to BDNF receptor TrkB. Nature Neuroscience 26, 1032–1041 (2023). DOI: https://doi.org/10.1038/s41593-023-01316-5
Bruininks, B.M.H., Wassenaar, T.A., and Vattulainen, I. Unbreaking assemblies in molecular simulations with periodic boundaries. Journal of Chemical Information and Modeling (2023). DOI: https://doi.org/10.1021/acs.jcim.2c01574
Fábián, B., Vattulainen, I., and Javanainen, M. Protein crowding and cholesterol increase cell membrane viscosity in a temperature dependent manner. Journal of Chemical Theory and Computation 19, 2630–2643 (2023). DOI: https://doi.org/10.1021/acs.jctc.3c00060
Żak, A., Rajtar, N., Kulig, W., and Kepczynski, M. Miscibility of phosphatidylcholines in bilayers: Effect of acyl chain unsaturation. Membranes 13, 411 (2023). DOI: https://doi.org/10.3390/membranes13040411
Liekkinen, J., Olżyńska, A., Cwiklik, L., de la Serna, J.B., Vattulainen, I., and Javanainen, M. Surfactant proteins SP‑B and SP‑C in pulmonary surfactant monolayers: Physical properties controlled by specific protein−lipid interactions. Langmuir 39, 433–4350 (2023). DOI:https://doi.org/10.1021/acs.langmuir.2c03349
Clubb, J.H.A., Kudling, T.V., Girych, M., Haybout, L., Pakola, S., Hamdan, F., Cervera-Carrascon,V., Hemmes, A., Grönberg-Vähä-Koskela, S., Santos, J.M., Quixabeira, D.C.A., Basnet, S., Heiniö, C., Arias, V., Jirovec, E., Kaptan, S., Havunen, R., Sorsa, S., Erikat, A., Schwartz, J., Anttila, M., Aro, K., Viitala, T., Vattulainen, I., Cerullo, V., Kanerva, A., and Hemminki, A. Development of a Syrian hamster anti-PD-L1 monoclonal antibody enables oncolytic adenoviral immunotherapy modelling in an immunocompetent virus replication permissive setting. Frontiers in Immunology 14, 1060540 (2023). DOI: https://doi.org/10.3389/fimmu.2023.1060540
Dumesnil, C., Vanharanta, L., Prasanna, X., Omrane, M., Carpentier, M., Bhapkar, A., Enkavi, G., Salo, V.T., Vattulainen, I., Ikonen, E., and Thiam, A.R. Cholesterol esters form supercooled lipid droplets whose nucleation is facilitated by triacylglycerols. Nature Communications 14, 915 (2023). DOI: https://doi.org/10.1038/s41467-023-36375-6
Chytrosz-Wrobel, P., Golda-Cepa, M., Kubisiak, P., Kulig, W., Cwiklik, L., and Kotarba, A. Sonochemical Formation of Fluorouracil Nanoparticles: Toward Controlled Drug Delivery from Polymeric Surfaces. ACS Applied Nano Materials 6, 4271–4278 (2023). DOI:https://doi.org/10.1021/acsanm.2c05332
Ragaller, F., Andronico, L., Sykora, J., Kulig, W., Rog, R., Urem, U.B., Abhinav, Danylchuk, D.I., Hof, M., Klymchenko, A., Amaro, M., Vattulainen, I., and Sezgin, E. Dissecting the mechanisms of environment sensitivity of smart probes for quantitative assessment of membrane properties. Open Biology 12, 220175 (2022). DOI: https://doi.org/10.1098/rsob.220175
Lolicato, F., Saleppico, R., Griffo, A., Meyer, A., Scollo, F., Pokrandt, B., Müller, H.-M., Ewers, H., Hähl, H., Fleury, J.-B., Seemann, R., Hof, M., Brügger, B., Jacobs, K., Vattulainen, I., and Nickel, W. Cholesterol promotes clustering of PI(4,5)P2 driving unconventional secretion of FGF2. Journal of Cell Biology 221, e202106123 (2022). DOI: https://doi.org/10.1083/jcb.202106123
Kaptan, S., Girych, M., Enkavi, G., Kulig, W., Sharma, V., Vuorio, J., Róg, T., and Vattulainen I. Maturation of the SARS-CoV-2 virus is regulated by dimerization of its main protease. Computational and Structural Biotechnology Journal 20, 3336–3346 (2022). DOI: https://doi.org/10.1016/j.csbj.2022.06.023
Serdiuk, T., Manna M., Zhang, Ch., Mari, S.A., Kulig, W., Pluhackova, K., Kobilka, B.K., Vattulainen, I., and Müller, D.J. A cholesterol analog stabilizes the human beta2-adrenergic receptor nonlinearly with temperature. Science Signaling 15, eabi7031 (2022). DOI: https://doi.org/10.1126/scisignal.abi7031
Korolainen, H., Lolicato, F., Enkavi, G., Pérez-Gil, J., Kulig, W., and Vattulainen, I. Dimerization of the pulmonary surfactant protein C in a membrane environment. PLoS ONE 17, e0267155 (2022). DOI: https://doi.org/10.1371/journal.pone.0267155
Kaptan, S., and Vattulainen, I. Machine learning in the analysis of biomolecular simulations. Advances in Physics X 7, 2006080 (2022). DOI:https://doi.org/10.1080/23746149.2021.2006080
Oliveira, A.A., Róg, T., da Silva, A.B.F., Amaro, R.E., Johnson, M.S., and Postila, P.A. Examining the effect of charged lipids on mitochondrial outer membrane dynamics using atomistic simulations. Biomolecules 12, 183 (2022). DOI: https://doi.org/10.3390/biom12020183
Róg, T., Girych, M., and Bunker, A. Mechanistic understanding from molecular dynamics in pharmaceutical research 2: Lipid membrane in drug design. Pharmaceuticals 14, 1062 (2021). DOI:https://doi.org/10.3390/ph14101062
Salomaa, S.I, Miihkinen, M., Kremneva, E., Paatero, I., Lilja, J., Jacquemet, G., Vuorio, J., Antenucci, L., Kogan, K., Nia, F.H., Hollos, P., Isomursu, A., Vattulainen, I., Coffey, E.T., Kreienkamp, H.-J., Lappalainen, P., and Ivaska, J. SHANK3 conformation regulates direct actin binding and crosstalk with Rap1 signaling. Current Biology 31, 1–15 (2021). DOI: https://doi.org/10.1016/j.cub.2021.09.022
Mahmoudzadeh, M., Magarkar, A., Koivuniemi, A., Róg, T., and Bunker, A. Mechanistic insight into how PEGylation reduces the efficacy of pH-sensitive liposomes from molecular dynamics simulations. Molecular Pharmaceutics 18, 2612–2621 (2021). DOI: https://doi.org/10.1021/acs.molpharmaceut.1c00122
Chmielińska, A., Stepien, P., Bonarek, P., Girych, M., Enkavi, G., Róg, T., Dziedzicka-Wasylewska, M., and Polit, A. Can di-4-ANEPPDHQ reveal the structural differences between nanodiscs and liposomes? BBA - Biomembranes 1863, 183649 (2021). DOI: https://doi.org/10.1016/j.bbamem.2021.183649
Cannarozzo, C., Fred, S.M., Girych, M., Biojone, C., Enkavi, G., Róg, T., Vattulainen, I., Casarotto, P.C., and Castrén, E. Cholesterol-recognition motifs in the transmembrane domain of the tyrosine kinase receptor family: The case of TRKB. European Journal of Neuroscience 53, 3311-3322 (2021). DOI: https://doi.org/10.1111/ejn.15218
Souza, P.C.T., Alessandri, R., Barnoud, J., Thallmair, S., Faustino, I., Grünewald, F., Patmanidis, I., Abdizadeh, H., Bruininks, B.M.H., Wassenaar, T.A., Kroon, P.C., Melcr, J., Nieto, V., Corradi, V., Khan, H.M., Domański, J., Javanainen, M., Martinez-Seara, H., Reuter, N., Best, R.B., Vattulainen, I., Monticelli, L., Periole, X., Tieleman, D.P., de Vries, A.H., and Marrink, S.J. Martini 3: a general purpose force field for coarse-grained molecular dynamics. Nature Methods 18, 382–388 (2021). DOI: https://doi.org/10.1038/s41592-021-01098-3
Casarotto, P.C., Girych, M., Fred, S.M., Kovaleva, V., Moliner, R., Enkavi, G., Biojone, C., Cannarozzo, C., Sahu, M.P., Kaurinkoski, K., Brunello, C.A., Steinzeig, A., Winkel, F., Patil, S., Vestring, S., Serchov, T., Diniz, C.R.A.F., Laukkanen, L., Cardon, I., Antila, H., Róg, T., Piepponen, T.P., Bramham, C.R., Normann, C., Lauri, S.E., Saarma, M., Vattulainen, I., and Castrén, E. Antidepressant drugs act by directly binding to TRKB neurotrophin receptors. Cell 184, 1299-1313.e19 (2021). DOI: https://doi.org/10.1016/j.cell.2021.01.034
Vuorio, J., Škerlová, J., Fábry, M., Veverka, V., Vattulainen, I., Řezáčová, P., and Martinez-Seara, H. N-Glycosylation can selectively block or foster different receptor–ligand binding modes. Scientific Reports 11, 5239 (2021). DOI: https://doi.org/10.1038/s41598-021-84569-z
Prasanna, X., Salo, V.T., Li, S.Q., Ven, K., Vihinen, H., Jokitalo, E., Vattulainen, I., and Ikonen, E. Seipin traps triacylglycerols to facilitate their nanoscale clustering in the endoplasmic reticulum membrane. PLoS Biology 19, e3000998 (2021). DOI: https://doi.org/10.1371/journal.pbio.3000998
Bunker, A., and Róg, T. Mechanistic understanding from molecular dynamics simulation in pharmaceutical research 1: Drug delivery. Frontiers in Molecular Biosciences 7, 604770 (2020). DOI: https://doi.org/10.3389/fmolb.2020.604770
Lucendo, E., Sancho, M., Lolicato, F., Javanainen, M., Kulig, W., Leiva, D., Duart, G., Andreu-Fernández, V., Mingarro, V., and Orzáez, M. Mcl-1 and Bok transmembrane domains: Unexpected players in the modulation of apoptosis. Proceedings of the National Academy of Sciences 117, 27980-27988 (2020). DOI: https://doi.org/10.1073/pnas.2008885117
Kukkurainen, S., Azizi, L., Zhang, P., Jacquier, M.-C., Baikoghli, M., von Essen, M., Tuukkanen, A., Laitaoja, M., Liu, X., Rahikainen, R., Orłowski, A., Jänis, J., Määttä, J.E.A., Varjosalo, M., Vattulainen, I., Róg, T., Svergun, D., Cheng, H., Wu, J., Hytönen, V.P., and Wehrle-Haller, B. The F1 loop of the talin head domain acts as a gatekeeper inintegrin activation and clustering. Journal of Cell Science 133, jcs239202 (2020). DOI: https://doi.org/10.1242/jcs.239202
Lautala, S., Provenzani, R., Koivuniemi, A., Kulig, W., Talman, V., Róg, T., Tuominen, R.K., Yli-Kauhaluoma, J., and Bunker, A. Rigorous computational study reveals what docking overlooks: Double trouble from membrane association in protein kinase C modulators. Journal of Chemical Information and Modeling, 60, 5624–5633 (2020). DOI: https://doi.org/10.1021/acs.jcim.0c00624
Kasparyan, G., Poojari, Ch., Róg, T., and Hub, J.S. Cooperative effects of an antifungal moiety and DMSO on pore formation over lipid membranes revealed by free energy calculations. Journal of Physical Chemistry B, 124, 8811–8821 (2020). DOI: https://doi.org/10.1021/acs.jpcb.0c03359
Stepien, P., Augustyn, B., Poojari, Ch., Galan, W., Polit, A., Vattulainen, I., Wisnieska-Becker, A., and Rog, T. Complexity of seemingly simple lipid nanodiscs. BBA - Biomembranes, 11, 183420 (2020). DOI: https://doi.org/10.1016/j.bbamem.2020.183420
Olżyńska, A., Kulig, W., Mikkolainen, H., Czerniak, T., Jurkiewicz, P., Cwiklik, L., Rog, T., Hof, M., Jungwirth, P., and Vattulainen, I. Tail-oxidized cholesterol enhances membrane permeability for small solutes. Langmuir, 36, 10438–10447 (2020). DOI: https://doi.org/10.1021/acs.langmuir.0c01590
Lolicato, F., Juhola, H., Zak, A., Postila, P.A., Saukko, A., Rissanen, S., Enkavi, G., Vattulainen, I., Kepczynski, M., and Róg, T. Membrane-dependent binding and entry mechanism of dopamine into its receptor. ACS Chemical Neuroscience, 11, 1914-1924 (2020). DOI: https://doi.org/10.1021/acschemneuro.9b00656
Ruskamo, S., Krokengen, O.C., Kowal, J., Nieminen, T., Lehtimaki, M., Raasakka, A., Dandey, V.P., Vattulainen, I., Stahlberg, H., and Kursula, P. Cryo-EM, X-ray diffraction, and atomistic simulations reveal determinants for the formation of a supramolecular myelin-like proteolipid lattice. Journal of Biological Chemistry, 295, 8692-8705 (2020). DOI: https://doi.org/10.1074/jbc.RA120.013087
Liekkinen, J., Enkavi, G., Javanainen, M., Olmeda, B., Pérez-Gil, J., and Vattulainen, I. Pulmonary surfactant lipid reorganization induced by the adsorption of the oligomeric surfactant protein B complex. Journal of Molecular Biology, 432, 3251-3268 (2020). DOI: https://doi.org/10.1016/j.jmb.2020.02.028
Vanharanta, L., Peränen, J., Pfisterer, S.G., Enkavi, G., Vattulainen, I., and Ikonen, E. High-content imaging and structure-based predictions reveal functional differences between Niemann-Pick C1 variants. Traffic, 21, 386-397 (2020). DOI: https://doi.org/10.1111/tra.12727
Legrand, C., Saleppico, R., Sticht, J., Lolicato, F., Muller, H.M., Wegehingel, S., Dimou, E., Steringer, J.P., Ewers, H., Vattulainen, I., Freund, C., and Nickel, W. The Na,K-ATPase acts upstream of phosphoinositide PI(4,5)P-2 facilitating unconventional secretion of Fibroblast Growth Factor 2. Communications Biology, 3, 141 (2020). DOI: https://doi.org/10.1038/s42003-020-0871-y
Wilmes, S., Hafer, M., Vuorio, J., Tucker, J.A., Winkelmann, H., Lochte, S., Stanly, T.A., Pulgar Prieto, K.D., Poojari, Ch., Sharma, V., Richter, Ch.P., Kurre, R., Hubbard, S.R., Garcia, K.Ch., Moraga, I., Vattulainen, I., Hitchcock, I.S., and Piehler, J. Mechanism of homodimeric cytokine receptor activation and dysregulation by oncogenic mutations. Science, 367, 643-652 (2020). DOI: https://doi.org/10.1126/science.aaw3242
Gutmann, T., Schäfer, I.B., Poojari, Ch., Brankatschk, B., Vattulainen, I., Strauss, M., and Coskun, Ü. Cryo-EM structure of the complete and ligand-saturated insulin receptor ectodomain. Journal of Cell Biology, 219, e201907210 (2020). DOI: https://doi.org/10.1083/jcb.201907210
Postila, P.A., and Róg, T. A perspective: Active role of lipids in neurotransmitter dynamics. Molecular Neurobiology, 57, 910-925 (2020). DOI: https://doi.org/10.1007/s12035-019-01775-7
Chronopoulos, A., Thorpe, S.D., Cortes, E., Lachowski, D., Rice, A.J., Mykuliak, V.V., Róg, T., Lee, D.A., Hytonen, V.P., and del Río Hernández, A.E. Syndecan-4 tunes cell mechanics by activating the kindlin-integrin-RhoA pathway. Nature Materials, 19, 669–678 (2020). DOI: https://doi.org/10.1038/s41563-019-0567-1
Poojari, Ch., Zak, A., Dzieciuch-Rojek, M., Bunker, A., Kepczynski, M., and Róg, T. Cholesterol reduces partitioning of antifungal drug itraconazole into lipid bilayers. Journal of Physical Chemistry B, 124, 2139-2148 (2020). DOI: https://doi.org/10.1021/acs.jpcb.9b11005
Golda-Cepa, M., Riedlová, K., Kulig, W., Cwiklik, L., and Kotarba, A. Functionalization of the parylene C surface enhances the nucleation of calcium phosphate: Combined experimental and molecular dynamics simulations approach. ACS Applied Materials and Interfaces, 12, 12426-12435 (2020). DOI: https://doi.org/10.1021/acsami.9b20877
Kotila, T., Wioland, H., Enkavi, G., Kogan, K., Vattulainen, I., Jégou, A., Romet-Lemonne, G., and Lappalainen, P. Mechanism of synergistic actin filament pointed end depolymerization by cyclase-associated protein and cofilin. Nature Communications, 10, 5320 (2019). DOI: https://doi.org/10.1038/s41467-019-13213-2
Augustyn, B., Stepien, P., Poojari, Ch., Mobarak, E., Polit, P., Wisniewska-Becker, A., and Rog, T. Cholesteryl hemisuccinate is not a good replacement for cholesterol in lipid nanodiscs. The Journal of Physical Chemistry B, 123, 9839-9845 (2019). DOI: https://doi.org/10.1021/acs.jpcb.9b07853
Poojari, Ch., Wilkosz, N., Lira, R.B., Dimova, R., Jurkiewicz, P., Petka, R., Kepczynski, M., and Rog, T. Behavior of the DPH fluorescence probe in membranes perturbed by drugs. Chemistry and Physics of Lipids, 223, 104784 (2019). DOI: https://doi.org/10.1016/j.chemphyslip.2019.104784
Li, S., Prasanna, X., Salo, V.T., Vattulainen, I., and Ikonen, E. An efficient auxin-inducible degron system with low basal degradation in human cells. Nature Methods 16, 866–869 (2019). DOI: http://doi.org/10.1038/s41592-019-0512-x
Paananen, R., Javanainen, M., Holopainen, J., and Vattulainen, I. Crystalline wax esters regulate the evaporation resistance of tear film lipid layers associated with dry eye syndrome. The Journal of Physical Chemistry Letters 10, 3893-3898 (2019). DOI: http://doi.org/10.1021/acs.jpclett.9b01187
Javanainen, M., Enkavi, G., Guixà-Gonzaléz, R., Kulig, W., Martinez-Seara, H., Levental, I., and Vattulainen, I. Reduced level of docosahexaenoic acid shifts GPCR neuroreceptors to less ordered membrane regions. PLOS Computational Biology 15, e1007033 (2019). DOI: http://doi.org/10.1371/journal.pcbi.1007033
Enkavi, G., Javanainen, M., Kulig, W., Róg, T., and Vattulainen, I. Multiscale simulations of biological membranes: The challenge to understand biological phenomena in a living substance. Chemical Reviews 119, 5607-5774 (2019). DOI: http://doi.org/10.1021/acs.chemrev.8b00538
Lolicato, F., Joly, L., Martinez-Seara, H., Fragneto, G., Scoppola, E., Baldelli Bombelli, F., Vattulainen, I., Akola, J., and Maccarini, M. The role of temperature and lipid charge on intake/uptake of cationic gold nanoparticles into lipid bilayers. Small 1805046, (2019). DOI: http://doi.org/10.1002/smll.201805046
Manna, M., Nieminen, T., and Vattulainen, I. Understanding the role of lipids in signaling through atomistic and multiscale simulations of cell membranes. Annual Review of Biophysics 48, 421-439 (2019). DOI: http://doi.org/10.1146/annurev-biophys-052118-115553
Gurtovenko, A., Javanainen, M., Lolicato, F., and Vattulainen, I. The devil is in the details: What do we really track in single-particle tracking experiments of diffusion in biological membranes? The Journal of Physical Chemistry Letters 10, 1005-1011 (2019). DOI: http://doi.org/10.1021/acs.jpclett.9b00065
Kulig, W., Korolainen, H., Zatorska, M., Kwolek, U., Wydro, P., Kepczynski, M., and Róg, T. Complex behavior of phosphatidylcholine–phosphatidic acid bilayers and monolayers: Effect of acyl chain unsaturation. Langmuir 35, 5944-5956 (2019). DOI: http://doi.org/10.1021/acs.langmuir.9b00381 Parameters and configuration files available here.
Vähäheikkilä, M., Peltomaa, T., Rog, T., Vazdar, M., Pöyry, S., and Vattulainen, I. How cardiolipin peroxidation alters the properties of the inner mitochondrial membrane? Chemistry and Physics of Lipids 214, 15 (2018). DOI: http://doi.org/10.1016/j.chemphyslip.2018.04.005 Parameters and configuration files available here.
Filipe, H.A.L., Javanainen, M., Salvador, A., Galvão, A.M., Vattulainen, I., Loura, L.M.S., and Moreno, M.J. Quantitative Assessment of Methods Used To Obtain Rate Constants from Molecular Dynamics Simulations-Translocation of Cholesterol across Lipid Bilayers. Journal of Chemical Theory and Computation 14, 3840-3848 (2018). DOI: http://doi.org/10.1021/acs.jctc.8b00150 Parameters and configuration files available here.
Hakala, M., Kalimeri, M., Enkavi, G., Vattulainen, I., and Lappalainen, P. Molecular mechanism for inhibition of twinfilin by phosphoinositides. Journal of Biological Chemistry 293, 4818-4829 (2018). DOI: http://doi.org/10.1074/jbc.RA117.000484 Parameters and configuration files available here.
Mobarak, E., Javanainen, M., Kulig, W., Honigmann, A., Sezgin, E., Aho, N., Eggeling, Ch., Rog, T., and Vattulainen, I., How to minimize dye-induced perturbations while studying biomembrane structure and dynamics: PEG linkers as a rational alternative. Biochimica et Biophysica Acta (BBA) - Biomembranes 1860, 2436 (2018). DOI: http://doi.org/10.1016/j.bbamem.2018.07.003 Parameters and configuration files available here.
Mobarak, E., Håversen, L., Manna, M., Rutberg, M., Levin, M., Perkins, R., Rog, T., Vattulainen, I., and Borén, J. Glucosylceramide modifies the LPS-induced inflammatory response in macrophages and the orientation of the LPS/TLR4 complex in silico. Scientific Reports 8, 13600 (2018). DOI: http://doi.org/10.1038/s41598-018-31926-0 Parameters and configuration files available here.
Pantsar, T., Rissanen, S., Dauch, D., Laitinen, T., Vattulainen, I., and Poso, A. Assessment of mutation probabilities of KRAS G12 missense mutants and their long-timescale dynamics by atomistic molecular simulations and Markov state modeling. PLOS Computational Biology 14, e1006458 (2018). DOI: http://doi.org/10.1371/journal.pcbi.1006458
Warnau, J., Sharma, V., Gamiz-Hernandez, A.P., Di Luca, A., Haapanen, O., Vattulainen, I., Wikström, M., Hummer, G., and Kaila, V.R.I. Redox-coupled quinone dynamics in the respiratory complex I. Proc Natl Acad Sci USA 115, E8413-E8420 (2018). DOI: http://doi.org/10.1073/pnas.1805468115
Laulumaa, S., Nieminen, T., Raasakka, A., Krokengen, O.C., Safaryan, A., Hallin, E.I., Brysbaert, G., Lensink, M.F., Ruskamo, S., Vattulainen I., and Kursula, P. Structure and dynamics of a human myelin protein P2 portal region mutant indicate opening of the β barrel in fatty acid binding proteins. BMC Structural Biology 18, 8 (2018). DOI: http://dx.doi.org/10.1186/s12900-018-0087-2 Parameters and configuration files available here.
Javanainen, M., Lamberg, A., Cwiklik, L., Vattulainen, I., and Ollila, O.H.S., Atomistic Model for Nearly Quantitative Simulations of Langmuir Monolayers. Langmuir 34, 2565-2572 (2018). DOI: http://dx.doi.org/10.1021/acs.langmuir.7b02855 Parameters and configuration files available here, here, here, here, here, here, here, here, and here.
Zhou, K., Dichlberger, A., Martinez-Seara, H., Nyholm, T.K.M., Li, S., Kim, Y.A., Vattulainen, I., Ikonen, E., and Blom T. Ceramide-Regulated Element in the Late Endosomal Protein LAPTM4B Controls Amino Acid Transporter Interaction. ACS Central Science 4, 548-558 (2018). DOI: http://dx.doi.org/10.1021/acscentsci.7b00582
Owen, M.C., Kulig, W., Poojari, Ch., Rog, T., and Strodel, B. Physiologically-relevant levels of sphingomyelin, but not GM1, induces a β-sheet-rich structure in the amyloid-β(1-42) monomer. Biochimica et Biophysica Acta (BBA) - Biomembranes, 1860, 1709-1720, (2018). DOI: http://dx.doi.org/10.1016/j.bbamem.2018.03.026 Parameters and configuration files available here.
Lajunen, T., Nurmi, R., Wilbie, D., Ruoslahti, T., Johansson, N.G., Korhonen, O., Rog, T., Bunker, A., Ruponen, M., and Urtti, A. The effect of light sensitizer localization on the stability of indocyanine green liposomes. Journal of Controlled Release, 284, 213 (2018). DOI: http://dx.doi.org/10.1016/j.jconrel.2018.06.029 Parameters and configuration files available here.
Magarkar, A., Parkkila, P., Viitala, T., Lajunen, T., Mobarak, E., Licari, G., Cramariuc, O., Vauthey, E., Róg, T., and Bunker A. Membrane bound COMT isoform is an interfacial enzyme: general mechanism and new drug design paradigm. Chemical Communications, 54, 3440-3443 (2018). DOI: http://dx.doi.org/10.1039/C8CC00221E Parameters and configuration files available here.
Owen, M.C., Kulig, W., Rog, T., Vattulainen, I., and Strodel, B. Cholesterol Protects the Oxidized Lipid Bilayer from Water Injury: An All-Atom Molecular Dynamics Study. Journal of Membrane Biology, 251, 521 (2018). DOI: http://dx.doi.org/10.1007/s00232-018-0028-9 Parameters and configuration files available here.
Kotila, T., Kogan, K., Enkavi, G., Guo, S., Vattulainen, I., Goode B. L., and Lappalainen, P. Structural basis of actin monomer recharging by cyclase-associated protein. Nature Communications, 9, 1892 (2018). DOI: http://dx.doi.org/10.1038/s41467-018-04231-7 Parameters and configuration files available here.
Melcr, J., Martinez-Seara, H., Nencini, R., Kolafa, J., Jungwirth, P., and Ollila, O. S. Accurate Binding of Sodium and Calcium to a POPC Bilayer by Effective Inclusion of Electronic Polarization. The Journal of Physical Chemistry B, 122, 4546-4557 (2018). DOI: http://dx.doi.org/10.1021/acs.jpcb.7b12510
Juhola, H., Postila, P. A., Rissanen, S., Lolicato, F., Vattulainen, I., and Róg, T. Negatively Charged Gangliosides Promote Membrane Association of Amphipathic Neurotransmitters. Neuroscience 384, 214–223 (2018). DOI: http://dx.doi.org/10.1016/j.neuroscience.2018.05.035 Parameters and configuration files available here.
Viennet, T., Wördehoff, M. M., Uluca, B., Poojari, Ch., Shaykhalishahi, H., Willbold, D., Strodel, B., Heise, H., Buell, A. K., Hoyer, W. and Etzkorn, M. Structural insights from lipid-bilayer nanodiscs link α-Synuclein membrane-binding modes to amyloid fibril formation. Communications Biology 1, 44 (2018). DOI: http://dx.doi.org/10.1038/s42003-018-0049-z Parameters and configuration files available here.
Kulig, W., Mikkolainen, H., Olzynska, A., Jurkiewicz, P., Cwiklik, L., Hof, M., Vattulainen, I., Jungwirth, P. and Rog, T. Bobbing of oxysterols: Molecular mechanism for translocation of tail-oxidized sterols through biological membranes. The Journal of Physical Chemistry Letters 9, 1118–1123 (2018). DOI: http://dx.doi.org/10.1021/acs.jpclett.8b00211 Parameters and configuration files available here.
Riedlová K., Nekardová M., Kačer P., Syslová K., Vazdar M., Jungwirth P., Kudová E. and Cwiklik L. Distributions of therapeutically promising neurosteroids in cellular membranes. Chemistry and physics of lipids. Chemistry and Physics of Lipids, 203, 78-86 (2017). DOI: http://dx.doi.org/10.1016/j.chemphyslip.2016.12.004
Magarkar, A., Jurkiewicz, P., Allolio, C., Hof, M., and Jungwirth, P. Increased Binding of Calcium Ions at Positively Curved Phospholipid Membranes. The Journal of Physical Chemistry Letters, 8, 518-523 (2017). DOI: http://dx.doi.org/10.1021/acs.jpclett.6b02818
Grau, B., Javanainen, M., Garcia-Murria, M. J., Kulig, W., Vattulainen, I., Mingarro, I. and Martinez-Gil, L. The role of hydrophobic matching on transmembrane helix packing in cells. Cell Stress 1, 90–106 (2017). DOI: http://dx.doi.org/10.15698/cst2017.11.111
Javanainen, M., Martinez-Seara, H. and Vattulainen, I. Excessive aggregation of membrane proteins in the Martini model. PLOS ONE 12, e0187936 (2017). DOI: http://dx.doi.org/10.1371/journal.pone.0187936
Senju, Y., Kalimeri, M., Koskela, E. V., Somerharju, P., Zhao, H., Vattulainen, I. and Lappalainen, P. Mechanistic principles underlying regulation of the actin cytoskeleton by phosphoinositides. Proceedings of the National Academy of Sciences 114, E8977–E8986 (2017). DOI: http://dx.doi.org/10.1073/pnas.1705032114
Enkavi, G., Mikkolainen, H., Gungor, B., Ikonen, E. and Vattulainen, I. Concerted regulation of NPC2 binding to endosomal/lysosomal membranes by bis(monoacylglycero)phosphate and sphingomyelin. PLOS Computational Biology 13, e1005831 (2017). DOI: http://dx.doi.org/10.1371/journal.pcbi.1005831
Danne, R., Poojari, C., Martinez-Seara, H., Rissanen, S., Lolicato, F., Rog, T. and Vattulainen, I. doGlycans – Tools for preparing carbohydrate structures for atomistic simulations of glycoproteins, glycolipids, and carbohydrate polymers for GROMACS. Journal of Chemical Information and Modeling 57, 2401–2406 (2017). DOI: http://dx.doi.org/10.1021/acs.jcim.7b00237
Javanainen, M., Martinez-Seara, H., Metzler, R. and Vattulainen, I. Diffusion of integral membrane proteins in protein-rich membranes. The Journal of Physical Chemistry Letters 8, 4308–4313 (2017). DOI: http://dx.doi.org/10.1021/acs.jpclett.7b01758
Grabon, A., Orlowski, A., Tripathi, A., Vuorio, J., Javanainen, M., Rog, T., Lonnfors, M., McDermott, M. I., Siebert, G., Somerharju, P., Vattulainen, I. and Bankaitis, V. A. Dynamics and energetics of the mammalian phosphatidylinositol transfer protein phospholipid exchange cycle. Journal of Biological Chemistry 292, 14438–14455 (2017). DOI: http://dx.doi.org/10.1074/jbc.M117.791467
Kalli, A. C., Rog, T., Vattulainen, I., Campbell, I. D. and Sansom, M. S. P. The integrin receptor in biologically relevant bilayers: Insights from molecular dynamics simulations. The Journal of Membrane Biology 250, 337–351 (2017). DOI: http://dx.doi.org/10.1007/s00232-016-9908-z
Ruskamo, S., Nieminen, T., Kristiansen, C. K., Vatne, G. H., Baumann, A., Hallin, E. I., Raasakka, A., Joensuu, P., Bergmann, U., Vattulainen, I. and Kursula, P. Molecular mechanisms of Charcot-Marie-Tooth neuropathy linked to mutations in human myelin protein P2. Scientific Reports 7, 6510 (2017). DOI: http://dx.doi.org/10.1038/s41598-017-06781-0
Steringer, J. P., Lange, S., Cujova, S., Sachl, R., Poojari, Ch., Lolicato, F., Beutel, O., Muller, H.-M., Unger, S., Coskun, U., Honigmann, A., Vattulainen, I., Hof, M., Freund, Ch., and Nickel, W. Key steps in unconventional secretion of fibroblast growth factor 2 reconstituted with purified components. eLife 6 e28985 (2017). DOI: http://dx.doi.org/10.7554/eLife.28985
Vuorio, J., Vattulainen, I. and Martinez-Seara, H. Atomistic fingerprint of hyaluronan-CD44 binding. PLOS Computational Biology 13, e1005663 (2017). DOI: http://dx.doi.org/10.1371/journal.pcbi.1005663
Rissanen, S., Grzybek, M., Orlowski, A., Rog, T., Cramariuc, O., Levental, I., Eggeling, C., Sezgin, E. and Vattulainen, I. Phase partitioning of GM1 and its bodipy-labeled analog determine their different binding to cholera toxin. Frontiers in Physiology 8, 252 (2017). DOI: http://dx.doi.org/10.3389/fphys.2017.00252
Mokkila, S., Postila, P. A., Rissanen, S., Juhola, H., Vattulainen, I. and Rog, T. Calcium assists dopamine release by preventing aggregation on the inner leaflet of presynaptic vesicles. ACS Chemical Neuroscience 8, 1242–1250 (2017). DOI: http://dx.doi.org/10.1021/acschemneuro.6b00395
Manna, M., Javanainen, M., Monne, H. M.-S., Gabius, H.-J., Rog, T. and Vattulainen, I. Long-chain GM1 gangliosides alter transmembrane domain registration through interdigitation. Biochimica et Biophysica Acta (BBA) - Biomembranes 1859, 870–878 (2017). DOI: http://dx.doi.org/10.1016/j.bbamem.2017.01.033
Javanainen, M., Martinez-Seara, H. and Vattulainen, I. Nanoscale membrane domain formation driven by cholesterol. Scientific Reports 7, 1143 (2017). DOI: http://dx.doi.org/10.1038/s41598-017-01247-9
Dzieciuch-Rojek, M., Poojari, C., Bednar, J., Bunker, A., Kozik, B., Nowakowska, M., Vattulainen, I., Wydro, P., Kepczynski, M. and Rog, T. Effects of membrane PEGylation on entry and location of antifungal drug itraconazole and their pharmacological implications. Molecular Pharmaceutics 14, 1057–1070 (2017). DOI: http://dx.doi.org/10.1021/acs.molpharmaceut.6b00969
Bilkova, E., Pleskot, R., Rissanen, S., Sun, S., Czogalla, A., Cwiklik, L., Rog, T., Vattulainen, I., Cremer, P. S., Jungwirth, P. and Coskun, U. Calcium directly regulates phosphatidylinositol 4,5-bisphosphate headgroup conformation and recognition. Journal of the American Chemical Society 139, 4019–4024 (2017). DOI: http://dx.doi.org/10.1021/jacs.6b11760
Euro, L., Haapanen, O., Rog, T., Vattulainen, I., Suomalainen, A. and Sharma, V. Atomistic molecular dynamics simulations of mitochondrial DNA polymerase γ: Novel mechanisms of function and pathogenesis. Biochemistry 56, 1227–1238 (2017). DOI: http://dx.doi.org/10.1021/acs.biochem.6b00934
Polley, A., Orlowski, A., Danne, R., Gurtovenko, A. A., Bernardino de la Serna, J., Eggeling, C., Davis, S. J., Rog, T. and Vattulainen, I. Glycosylation and lipids working in concert direct CD2 ectodomain orientation and presentation. The Journal of Physical Chemistry Letters 8, 1060–1066 (2017). DOI: http://dx.doi.org/10.1021/acs.jpclett.6b02824
Javanainen, M., Enkavi, G., Guixa-Gonzalez, R., Kulig, W., Martinez-Seara, H. and Vattulainen, I. The effect of membrane polyunsaturated fatty acids on receptor partitioning to ordered domains. Biophysical Journal 112, 230a–231a (2017). DOI: http://dx.doi.org/10.1016/j.bpj.2016.11.1266
Kulig, W. T., Mikkolainen, H., Olzynska, A., Jurkiewicz, P., Cwiklik, L., Rog, T., Hof, M., Vattulainen, I. and Jungwirth, P. Oxidation of cholesterol changes the permeability of lipid membranes. Biophysical Journal 112, 377a (2017). DOI: http://dx.doi.org/10.1016/j.bpj.2016.11.2047
Juhola, H., Lolicato, F., Postila, P., Vattulainen, I. and Rog, T. Lipids, neurotransmitters and their receptors. Biophysical Journal 112, 392a (2017). DOI: http://dx.doi.org/10.1016/j.bpj.2016.11.2130
Rissanen, S., Salmela, L., Vattulainen, I. and Rog, T. PI(4,5)P2 binds to phospholipase C Delta 1 in a cholesterol concentration dependent manner: Perspective on implications to PI(4,5)P2-binding proteins. Biophysical Journal 112, 137a–138a (2017). DOI: http://dx.doi.org/10.1016/j.bpj.2016.11.762
Poojari, C. S., Roodhuizen, J., Lolicato, F., Rog, T. and Vattulainen, I. Molecular basis of GLUT4 in glucose transport: Atomistic molecular dynamics study. Biophysical Journal 112, 139a (2017). DOI: http://dx.doi.org/10.1016/j.bpj.2016.11.768
Javanainen, M., Vattulainen, I. and Monticelli, L. On atomistic models for molecular oxygen. The Journal of Physical Chemistry B 121, 518–528 (2017). DOI: http://dx.doi.org/10.1021/acs.jpcb.6b11183
Wilkosz, N., Rissanen, S., Cyza, M., Szybka, R., Nowakowska, M., Bunker, A., Rog, T. and Kepczynski, M. Effect of piroxicam on lipid membranes: Drug encapsulation and gastric toxicity aspects. European Journal of Pharmaceutical Sciences 100, 116–125 (2017). DOI: http://dx.doi.org/10.1016/j.ejps.2017.01.007
Magarkar, A., Rog, T. and Bunker, A. A computational study suggests that replacing PEG with PMOZ may increase exposure of hydrophobic targeting moiety. European Journal of Pharmaceutical Sciences 103, 128–135 (2017). DOI: http://dx.doi.org/10.1016/j.ejps.2017.03.008
Magarkar, A., Jurkiewicz, P., Allolio, C., Hof, M. and Jungwirth, P. Increased binding of calcium ions at positively curved phospholipid membranes. The Journal of Physical Chemistry Letters 8, 518–523 (2017). DOI: http://dx.doi.org/10.1021/acs.jpclett.6b02818
Riedlova, K., Nekardova, M., Kacer, P., Syslova, K., Vazdar, M., Jungwirth, P., Kudova, E. and Cwiklik, L. Distributions of therapeutically promising neurosteroids in cellular membranes. Chemistry and Physics of Lipids 203, 78–86 (2017). DOI: http://dx.doi.org/10.1016/j.chemphyslip.2016.12.004
Rahaman, O., Kalimeri, M., Katava, M., Paciaroni, A. and Sterpone, F. Configurational disorder of water hydrogen-bond network at the protein dynamical transition. The Journal of Physical Chemistry B 121, 6792–6798 (2017). DOI: http://dx.doi.org/10.1021/acs.jpcb.7b03888
Sciacca, M. F. M., Romanucci, V., Zarrelli, A., Monaco, I., Lolicato, F., Spinella, N., Galati, C., Grasso, G., DUrso, L., Romeo, M., Diomede, L., Salmona, M., Bongiorno, C., Di Fabio, G., La Rosa, C., and Milardi, D. Inhibition of Aβ amyloid growth and toxicity by silybins: The crucial role of stereochemistry. ACS Chemical Neuroscience 8, 1767–1778 (2017). DOI: http://dx.doi.org/10.1021/acschemneuro.7b00110
Chatzigeorgiou, M., Constantoudis, V., Diakonos, F., Karamanos, K., Papadimitriou, C., Kalimeri, M. and Papageorgiou, H. Multifractal correlations in natural language written texts: Effects of language family and long word statistics. Physica A: Statistical Mechanics and its Applications 469, 173–182 (2017). DOI: http://dx.doi.org/10.1016/j.physa.2016.11.028
Haapanen, O. and Sharma, V. Role of water and protein dynamics in proton pumping by respiratory complex I. Scientific Reports 7, 7747 (2017). DOI: http://dx.doi.org/10.1038/s41598-017-07930-1
Guixa-Gonzalez, R., Albasanz, J. L., Rodriguez-Espigares, I., Pastor, M., Sanz, F., Marti-Solano, M., Manna, M., Martinez-Seara, H., Hildebrand, P. W., Martin, M. and Selent, J. Membrane cholesterol access into a G-protein-coupled receptor. Nature Communications 8, 14505 (2017). DOI: http://dx.doi.org/10.1038/ncomms14505
Javanainen, M., Melcrova, A., Magarkar, A., Jurkiewicz, P., Hof, M., Jungwirth, P. and Martinez-Seara, H. Two cations, two mechanisms: Interactions of sodium and calcium with zwitterionic lipid membranes. Chem. Commun. 53, 5380-5383 (2017). DOI: http://dx.doi.org/10.1039/C7CC02208E
Golda-Cepa, M., Kulig, W., Cwiklik, L. and Kotarba, A. Molecular dynamics insights into water–parylene C interface: Relevance of oxygen plasma treatment for biocompatibility. ACS Applied Materials and Interfaces 9, 16685–16693 (2017). DOI: http://dx.doi.org/10.1021/acsami.7b03265
Timr, S., Pleskot, R., Kadlec, J., Kohagen, M., Magarkar, A. and Jungwirth, P. Membrane binding of recoverin: From mechanistic understanding to biological functionality. ACS Central Science 3, 868–874 (2017). DOI: http://dx.doi.org/10.1021/acscentsci.7b00210
Wnetrzak, A., Makyla-Juzak, K., Filiczkowska, A., Kulig, W. and Dynarowicz-atka, P. Oxysterols versus cholesterol in model neuronal membrane. I. The case of 7-ketocholesterol. The Langmuir monolayer study. The Journal of Membrane Biology 250, 553–564 (2017). DOI: http://dx.doi.org/10.1007/s00232-017-9984-8
Manna, M., Niemela, M., Tynkkynen, J., Javanainen, M., Kulig, W., Muller, D. J., Rog, T. and Vattulainen, I. Mechanism of allosteric regulation of β2-adrenergic receptor by cholesterol. eLife 5 18432 (2016). DOI: http://dx.doi.org/10.7554/eLife.18432
Falkovich, S. G., Martinez-Seara, H., Nesterenko, A. M., Vattulainen, I. and Gurtovenko, A. A. What Can We Learn about Cholesterols Transmembrane Distribution Based on Cholesterol-Induced Changes in Membrane Dipole Potential? The Journal of Physical Chemistry Letters 7, 4585–4590 (2016). DOI: http://dx.doi.org/10.1021/acs.jpclett.6b02123
Vattulainen, I. and Rog, T. Lipid membranes: Theory and simulations bridged to experiments. Biochimica et Biophysica Acta (BBA) - Biomembranes 1858, 2251–2253 (2016). DOI: https://dx.doi.org/10.1016/j.bbamem.2016.06.007
Poyry, S. and Vattulainen, I. Role of charged lipids in membrane structures - Insight given by simulations. Biochimica et Biophysica Acta (BBA) - Biomembranes 1858, 2322–2333 (2016). DOI: https://dx.doi.org/10.1016/j.bbamem.2016.03.016
Postila, P. A., Kaszuba, K., Kuleta, P., Vattulainen, I., Sarewicz, M., Osyczka, A. and Rog, T. Atomistic determinants of co-enzyme Q reduction at the Qi-site of the cytochrome bc1 complex. Scientific Reports 6, 33607 (2016). DOI: https://dx.doi.org/10.1038/srep33607
Kulig,W., Cwiklik, L., Jurkiewicz, P., Rog, T. and Vattulainen, I. Cholesterol oxidation products and their biological importance. Chemistry and Physics of Lipids 199, 144–160 (2016). DOI: https://dx.doi.org/10.1016/j.chemphyslip.2016.03.001
Kaurola, P., Sharma, V., Vonk, A., Vattulainen, I. and Rog, T. Distribution and dynamics of quinones in the lipid bilayer mimicking the inner membrane of mitochondria. Biochimica et Biophysica Acta (BBA) - Biomembranes 1858, 2116–2122 (2016). DOI: https://dx.doi.org/10.1016/j.bbamem.2016.06.016
Jeon, J.-H., Javanainen, M., Martinez-Seara, H., Metzler, R. and Vattulainen, I. Protein Crowding in Lipid Bilayers Gives Rise to Non-Gaussian Anomalous Lateral Diffusion of Phospholipids and Proteins. Physical Review X 6, 021006 (2016). DOI: https://dx.doi.org/10.1103/PhysRevX.6.021006
Manna, M., Kulig, W., Javanainen, M., Tynkkynen, J., Hensen, U., Muller, D. J., Rog, T. and Vattulainen, I. Protocol to Avoid Possible Artifacts in Atomistic Simulation of GPCR Proteins whose Crystal Structure is Heavily Engineered. Biophysical Journal 110, 59a (2016). DOI: https://dx.doi.org/10.1016/j.bpj.2015.11.386
Kulig, W., Olzynska, A., Jurkiewicz, P., Kantola, A. M., Komulainen, S., Manna, M., Pourmousa, M., Vazdar, M., Cwiklik, L., Rog, T., Khelashvili, G., Harries, D., Telkki, V.-V., Hof, M., Vattulainen, I. and Jungwirth, P. Oxidation of Cholesterol Changes the Physical Properties of Lipid Membranes. Biophysical Journal 110, 84a (2016). DOI: https://dx.doi.org/10.1016/j.bpj.2015.11.512
Kaszuba, K., Grzybek, M., Orlowski, A., Danne, R., Rog, T., Simons, K., Coskun, U. and Vattulainen, I. Glycosylation affects the conformational behavior of EGFR. Biophysical Journal 110, 89a (2016). DOI: https://dx.doi.org/10.1016/j.bpj.2015.11.539
Rog, T., Orlowski, A., Manna, M., Llorente, A., Skotland, T., Sylvanne, T., Kauhanen, D., Ekroos, K., Sandvig, K. and Vattulainen, I. Cholesterol Modulated Interdigitation of Long-Chain Sphingomyelin and Glycolipids. Biophysical Journal 110, 578a–579a (2016). DOI: https://dx.doi.org/10.1016/j.bpj.2015.11.3094
Rog, T., Orlowski, A., Llorente, A., Skotland, T., Sylvanne, T., Kauhanen, D., Ekroos, K., Sandvig, K. and Vattulainen, I. Interdigitation of long-chain sphingomyelin induces coupling of membrane leaflets in a cholesterol dependent manner. Biochimica et Biophysica Acta (BBA) - Biomembranes 1858, 281–288 (2016). DOI: https://dx.doi.org/10.1016/j.bbamem.2015.12.003
Postila, P. A., Vattulainen, I. and Rog, T. Selective effect of cell membrane on synaptic neurotransmission. Scientific Reports 6, 19345 (2016). DOI: https://dx.doi.org/10.1038/srep19345
Kuleta, P., Sarewicz, M., Postila, P., Rog, T. and Osyczka, A. Identifying involvement of Lys251/Asp252 pair in electron transfer and associated proton transfer at the quinone reduction site of Rhodobacter capsulatus cytochrome bc1. Biochimica et Biophysica Acta (BBA) - Bioenergetics 1857, 1661–1668 (2016). DOI: https://dx.doi.org/10.1016/j.bbabio.2016.07.003
Kepczynski, M. and Rog, T. Functionalized lipids and surfactants for specific applications. Biochimica et Biophysica Acta (BBA) - Biomembranes 1858, 2362–2379 (2016). DOI: https://dx.doi.org/10.1016/j.bbamem.2016.02.038
Lajunen, T., Kontturi, L.-S., Viitala, L., Manna, M., Cramariuc, O.,Rog, T., Bunker, A., Laaksonen, T., Viitala, T., Murtomaki, L. and Urtti, A. Indocyanine Green-Loaded Liposomes for Light-Triggered Drug Release. Molecular Pharmaceutics 13, 2095–2107 (2016). DOI: https://dx.doi.org/10.1021/acs.molpharmaceut.6b00207
Rog, T., Orlowski, A., Llorente, A., Skotland, T., Sylvanne, T., Kauhanen, D., Ekroos, K., Sandvig, K. and Vattulainen, I. Data including GROMACS input files for atomistic molecular dynamics simulations of mixed, asymmetric bilayers including molecular topologies, equilibrated structures, and force field for lipids compatible with OPLS-AA parameters. Data in Brief 7, 1171–1174 (2016). DOI: https://dx.doi.org/10.1016/j.dib.2016.03.067
Rog, T. and Koivuniemi, A. The biophysical properties of ethanolamine plasmalogens revealed by atomistic molecular dynamics simulations. Biochimica et Biophysica Acta (BBA) - Biomembranes 1858, 97–103 (2016). DOI: https://dx.doi.org/10.1016/j.bbamem.2015.10.023
Pathak, P. et al. Design of cholesterol arabinogalactan anchored liposomes for asialoglycoprotein receptor mediated targeting to hepatocellular carcinoma: In silico modeling, in vitro and in vivo evaluation. International Journal of Pharmaceutics 509, 149–158 (2016). DOI: https://dx.doi.org/10.1016/j.ijpharm.2016.05.041
Kulig, W., Pasenkiewicz-Gierula, M. and Rog, T. Cis and trans unsaturated phosphatidylcholine bilayers: A molecular dynamics simulation study. Chemistry and Physics of Lipids 195, 12–20 (2016). DOI: 10.1016/j.chemphyslip.2015.07.002
Dhawan, V., Magarkar, A., Joshi, G., Makhija, D., Jain, A., Shah, J., Reddy, B. V. V., Krishnapriya, M., Rog, T., Bunker, A., Jagtap, A. and Nagarsenker, M. Stearylated cycloarginine nanosystems for intracellular delivery - simulations, formulation and proof of concept. RSC Adv. 6, 113538–113550 (2016). DOI: http://dx.doi.org/10.1039/c6ra16432c
Sciacca, M., Lolicato, F., DiMauro, G., Milardi, D., DUrso, L., Satriano, C., Ramamoorthy, A. and LaRosa, C. The Role of Cholesterol in Driving IAPP-Membrane Interactions. Biophysical Journal 111, 140–151 (2016). DOI: https://dx.doi.org/10.1016/j.bpj.2016.05.050
La Rosa, C., Scalisi, S., Lolicato, F., Pannuzzo, M. and Raudino, A. Lipid-assisted protein transport: A diffusion-reaction model supported by kinetic experiments and molecular dynamics simulations. The Journal of Chemical Physics 144, 184901 (2016). DOI: https://dx.doi.org/10.1063/1.4948323
Katava, M., Kalimeri, M., Stirnemann, G. and Sterpone, F. Stability and Function at High Temperature. What Makes a Thermophilic GTPase Different from Its Mesophilic Homologue. The Journal of Physical Chemistry B 120, 2721–2730 (2016). DOI: https://dx.doi.org/10.1021/acs.jpcb.6b00306
Guixa-Gonzalez, R., Javanainen, M., Gomez-Soler, M., Cordobilla, B., Domingo, J. C., Sanz, F., Pastor, M., Ciruela, F., Martinez-Seara, H. and Selent, J. Membrane omega-3 fatty acids modulate the oligomerisation kinetics of adenosine A2A and dopamine D2 receptors. Scientific Reports 6, 19839 (2016). DOI: https://dx.doi.org/10.1038/srep19839
Javanainen, M. and Martinez-Seara, H. Efficient preparation and analysis of membrane and membrane protein systems. Biochimica et Biophysica Acta (BBA) - Biomembranes 1858, 2468-2482 (2016). DOI: https://dx.doi.org/10.1016/j.bbamem.2016.02.036
Kovacic, F., Mandrysch, A., Poojari, C., Strodel, B. and Jaeger, K.-E. Structural features determining thermal adaptation of esterases. Protein Engineering Design and Selection 29, 65–76 (2016). DOI: https://dx.doi.org/10.1093/protein/gzv061
Sharma, V. and Wikstrom, M. The role of the K-channel and the active-site tyrosine in the catalytic mechanism of cytochrome c oxidase. Biochimica et Biophysica Acta (BBA) - Bioenergetics 1857, 1111-1115 (2016). DOI: https://dx.doi.org/10.1016/j.bbabio.2016.02.008
Sharma, V., Warnau, J., Gamiz-Hernandez, A. P., Haapanen, O., di Luca, A., Vattulainen, I., Wikstrom, M., Hummer, G. and Kaila, V. R. Computational investigation of the redox-coupled proton pumping in respiratory complex I. Biochimica et Biophysica Acta (BBA) - Bioenergetics 1857, e44 (2016). DOI: https://dx.doi.org/10.1016/j.bbabio.2016.04.316
Kaila, V. R., di Luca, A., Gamiz-Hernandez, A. P., Jussupow, A., Johansson, M. P., Sharma, V., Wikstrom, M. and Hummer, G. Towards a mechanistic model for redox-driven proton pumping in respiratory complex I. Biochimica et Biophysica Acta (BBA) - Bioenergetics 1857, e40 (2016). DOI: https://dx.doi.org/10.1016/j.bbabio.2016.04.304
Sharma, V. and Wikstrom, M. The role of the K-channel and the active-site tyrosine in the catalytic mechanism of cytochrome c oxidase. Biochimica et Biophysica Acta (BBA) - Bioenergetics 1857, e2 (2016). DOI: https://dx.doi.org/10.1016/j.bbabio.2016.04.014
Kastinen, T., Niskanen, M., Risko, C., Cramariuc, O. and Hukka, T. I. On describing the optoelectronic characteristics of poly(benzodithiophene-co-quinoxaline)fullerene complexes: the influence of optimally tuned density functionals. Phys. Chem. Chem. Phys. 18, 27654–27670 (2016). DOI: https://dx.doi.org/10.1039/C6CP04567G
Kastinen, T., Niskanen, M., Risko, C., Cramariuc, O. and Hukka, T. I. Intrinsic Properties of Two Benzodithiophene-Based Donor Acceptor Copolymers Used in Organic Solar Cells: A Quantum-Chemical Approach. The Journal of Physical Chemistry A 120, 1051–1064 (2016). DOI: https://dx.doi.org/10.1021/acs.jpca.5b08465
Grosu, M. C., Lupu, I. G., Cramariuc, O. and Hristian, L. Magnetic cotton yarns optimization of magnetic properties. The Journal of The Textile Institute 107, 757–765 (2016). DOI: https://dx.doi.org/10.1080/00405000.2015.1061761
Paajanen, A., Sonavane, Y., Ignasiak, D., Ketoja, J. A., Maloney, T. and Paavilainen, S. Atomistic molecular dynamics simulations on the interaction of tempo-oxidized cellulose nanofibrils in water. Cellulose 23, 3449–3462 (2016). DOI: https://dx.doi.org/10.1007/s10570-016-1076-X
Metzler, R., Jeon, J.-H. and Cherstvy, A. Non-Brownian diffusion in lipid membranes: Experiments and simulations. Biochimica et Biophysica Acta (BBA) - Biomembranes 1858, 2451–2467 (2016). DOI: https://dx.doi.org/10.1016/j.bbamem.2016.01.022
Palyulin, V. V., Chechkin, A. V., Klages, R. and Metzler, R. Search reliability and search efficiency of combined Levy-Brownian motion: long relocations mingled with thorough local exploration. Journal of Physics A: Mathematical and Theoretical 49, 394002 (2016). DOI: https://dx.doi.org/10.1088/1751-8113/49/39/394002
Godec, A. and Metzler, R. First passage time distribution in heterogeneity controlled kinetics: going beyond the mean first passage time. Scientific Reports 6, 20349 (2016). DOI: https://dx.doi.org/10.1038/srep20349
Ghosh, S. K., Cherstvy, A. G., Grebenkov, D. S. and Metzler, R. Anomalous, non-Gaussian tracer diffusion in crowded two-dimensional environments. New Journal of Physics 18, 013027 (2016). DOI: https://dx.doi.org/10.1088/1367-2630/18/1/013027
Sandev, T., Iomin, A., Kantz, H., Metzler, R. and Chechkin, A. Comb Model with Slow and Ultraslow Diffusion. Mathematical Modelling of Natural Phenomena 11, 18–33 (2016). DOI: https://dx.doi.org/10.1051/mmnp/201611302
Robison, A. D., Sun, S., Poyton, M. F., Johnson, G. A., Pellois, J.-P., Jungwirth, P., Vazdar, M. and Cremer, P. S. Polyarginine Interacts More Strongly and Cooperatively than Polylysine with Phospholipid Bilayers. The Journal of Physical Chemistry B 120, 9287–9296 (2016). DOI: https://dx.doi.org/10.1021/acs.jpcb.6b05604
Melcr, J., Bonhenry, D., Timr, S. and Jungwirth, P. Transmembrane Potential Modeling: Comparison between Methods of Constant Electric Field and Ion Imbalance. Journal of Chemical Theory and Computation 12, 2418–2425 (2016). DOI: https://dx.doi.org/10.1021/acs.jctc.5b01202
Allolio, C., Baxova, K., Vazdar, M. and Jungwirth, P. Guanidinium pairing facilitates membrane translocation. The Journal of Physical Chemistry B 120, 143–153 (2016). DOI: https://dx.doi.org/10.1021/acs.jpcb.5b10404
De Franceschi, N., Peuhu, E., Parsons, M., Rissanen, S., Vattulainen, I., Salmi, M., Ivaska, J., Pouwels, J. and Gullberg, D. Mutually Exclusive Roles of SHARPIN in Integrin Inactivation and NF-KB Signaling. PLOS ONE 10, e0143423 (2015). DOI: http://dx.doi.org/10.1371/journal.pone.0143423
Raghupathy, R., Anilkumar, A. A., Polley, A., Singh, P. P., Yadav, M., Johnson, Ch., Suryawanshi, S., Saikam, V., Sawant, S. D., Panda, A., Guo, Z., Vishwakarma, R., A., Rao, M. and Mayor, S. Transbilayer Lipid Interactions Mediate Nanoclustering of Lipid-Anchored Proteins. Cell 161, 581-594 (2015). DOI: http://dx.doi.org/10.1016/j.cell.2015.03.048
Karilainen, T., Cramariuc, O., Kuisma, M., Tappura, K. and Hukka, T. I. van der Waals interactions are critical in Car-Parrinello molecular dynamics simulations of porphyrin-fullerene dyads. Journal of Computational Chemistry 36, 612-621 (2015). DOI: http://dx.doi.org/10.1002/jcc.23834
Orlowski, A., Rog, T., Paavilainen, S., Manna, M., Heiskanen, I., Backfolk, K., Timonen, J. and Vattulainen, I. How endoglucanase enzymes act on cellulose nanofibrils: role of amorphous regions revealed by atomistic simulations. Cellulose 22, 2911-2925 (2015). DOI: http://dx.doi.org/10.1007/s10570-015-0705-0
Orlowski, A., Kukkurainen, S., Poyry, A., Rissanen, S., Vattulainen, I., Hytonen, V. P. and Rog, T. PIP2 and Talin Join Forces to Activate Integrin. The Journal of Physical Chemistry B 119, 12381-12389 (2015). DOI: http://dx.doi.org/10.1021/acs.jpcb.5b06457
Sharma, V., Belevich, G., Gamiz-Hernandez, A. P., Rog, T., Vattulainen, I., Verkhovskaya, M. L., Wikstrom, M., Hummer, G. and Kaila, V. R. I. Redox-induced activation of the proton pump in the respiratory complex I. Proceedings of the National Academy of Sciences 112, 11571-11576 (2015). DOI: http://dx.doi.org/10.1073/pnas.1503761112
Sharma, V., Ala-Vannesluoma, P., Vattulainen, I., Wikstrom, M. and Rog, T. Role of subunit III and its lipids in the molecular mechanism of cytochrome c oxidase. Biochimica et Biophysica Acta (BBA) - Bioenergetics 1847, 690-697 (2015). DOI: http://dx.doi.org/10.1016/j.bbabio.2015.04.007
Koivuniemi, A. and Vattulainen, I. Biogenesis of Nascent High Density Lipoprotein Particles. Structure 23, 1153-1154 (2015). DOI: http://dx.doi.org/10.1016/j.str.2015.06.006
Kaszuba, K., Grzybek, M., Simon, K., Vattulainen, I. and Coskun, U. N-Glycosylation as determinant of Epidermal Growth Factor Receptor conformation in membranes. FEBS JOURNAL 282, 225 (2015). 40th Congress of the Federation-of-European-Biochemical-Societies (FEBS)-The Biochemical Basis of Life, Berlin, GERMANY, JUL 04-09, 2015. DOI: http://onlinelibrary.wiley.com/doi/10.1111/febs.13339/epdf
Manna, M., Kulig, W., Javanainen, M., Tynkkynen, J., Hensen, U., Muller, D. J., Rog, T. and Vattulainen, I. How To Minimize Artifacts in Atomistic Simulations of Membrane Proteins, Whose Crystal Structure Is Heavily Engineered: β(2)-Adrenergic Receptor in the Spotlight. Journal of Chemical Theory and Computation 11, 3432-3445 (2015). DOI: http://dx.doi.org/10.1021/acs.jctc.5b00070
Kulig, W., Olzynska, A., Jurkiewicz, P., Kantola, A. M., Komulainen, S., Manna, M., Pourmousa, M., Vazdar, M., Cwiklik, L., Rog, T., Khelashvili, G., Harries, D., Telkki, V.-V., Hof, M., Vattulainen, I. and Jungwirth, P. Cholesterol under oxidative stress how lipid membranes sense oxidation as cholesterol is being replaced by oxysterols. Free Radical Biology and Medicine 84 30-41 (2015). DOI: http://dx.doi.org/10.1016/j.freeradbiomed.2015.03.006
Laulumaa, S., Nieminen, T., Lehtimaki, M., Aggarwal, S., Simons, M., Koza, M. M., Vattulainen, I., Kursula, P. and Natali, F. Dynamics of the Peripheral Membrane Protein P2 from Human Myelin Measured by Neutron Scattering - A Comparison between Wild-Type Protein and a Hinge Mutant. PLOS ONE 10, e0128954 (2015). DOI: http://dx.doi.org/10.1371/journal.pone.0128954
Dzieciuch, M., Rissanen, S., Szydlowska, N., Bunker, A., Kumorek, M., Jamroz, D., Vattulainen, I., Nowakowska, M., Rog, T. and Kepczynski, M. PEGylated Liposomes as Carriers of Hydrophobic Porphyrins. The Journal of Physical Chemistry B 119, 6646-6657 (2015). DOI: http://dx.doi.org/10.1021/acs.jpcb.5b01351
Nguyen, S. D., Javanainen, M., Rissanen, S., Zhao, H., Huusko, J., Kivela, A. M., Yla-Herttuala, S., Navab, M., Fogelman, A. M., Vattulainen, I., Kovanen, P. T. and Oorni, K. Apolipoprotein A-I mimetic peptide 4F blocks sphingomyelinase-induced LDL aggregation. Journal of Lipid Research 56, 1206-1221 (2015). DOI: http://dx.doi.org/10.1194/jlr.M059485
Ghosh, R., de Campos, M. K. F., Huang, J., Huh, S. K., Orlowski, A., Yang, Y., Tripathi, A., Nile, A., Lee, H.-C., Dynowski, M., Schafer, H., Rog, T., Lete, M. G., Ahyayauch, H., Alonso, A., Vattulainen, I., Igumenova, T. I., Schaaf, G. and Bankaitis, V. A. Sec14-nodulin proteins and the patterning of phosphoinositide landmarks for developmental control of membrane morphogenesis. Molecular Biology of the Cell 26, 1764-1781 (2015). DOI: http://dx.doi.org/10.1091/mbc.E14-10-1475
Kaszuba, K., Grzybek, M., Orlowski, A., Danne, R., Rog, T., Simons, K., Coskun, U. and Vattulainen, I. N-Glycosylation as determinant of epidermal growth factor receptor conformation in membranes. Proceedings of the National Academy of Sciences 112, 4334-4339 (2015). DOI: http://dx.doi.org/10.1073/pnas.1503262112
Karilainen, T., Timr, S., Vattulainen, I. and Jungwirth, P. Oxidation of Cholesterol Does Not Alter Significantly Its Uptake into High-Density Lipoprotein Particles. The Journal of Physical Chemistry B 119, 4594–4600 (2015). DOI: http://dx.doi.org/10.1021/acs.jpcb.5b00240
Sharma, V., Enkavi, G., Vattulainen, I., Rog, T. and Wikstrom, M. Proton-coupled electron transfer and the role of water molecules in proton pumping by cytochrome. Proceedings of the National Academy of Sciences 112, 2040-2045 (2015). DOI: http://dx.doi.org/10.1073/pnas.1409543112
Kulig, W., Jurkiewicz, P., Olzynska, A., Tynkkynen, J., Javanainen, M., Manna, M., Rog, T., Hof, M., Vattulainen, I. and Jungwirth, P. Experimental determination and computational interpretation of biophysical properties of lipid bilayers enriched by cholesteryl hemisuccinate. Biochimica et Biophysica Acta (BBA) - Biomembranes 1848, 422-432 (2015). DOI: http://dx.doi.org/10.1016/j.bbamem.2014.10.032
Rog, T., Poyry, S. and Vattulainen, I. Building Synthetic Sterols Computationally Unlocking the Secrets of Evolution? Frontiers in Bioengineering and Biotechnology 3, 121 (2015). DOI: http://dx.doi.org/10.3389/fbioe.2015.00121
Wikstrom, M., Sharma, V., Kaila, V. R. I., Hosler, J. P. and Hummer, G. New Perspectives on Proton Pumping in Cellular Respiration. Chemical Reviews 115, 2196–2221 (2015). DOI: http://dx.doi.org/10.1021/CR500448T
Lolicato, F., Raudino, A., Milardi, D. and La Rosa, C. Resveratrol interferes with the aggregation of membrane-bound human-IAPP: A molecular dynamics study. European Journal of Medicinal Chemistry 92, 876-881 (2015). DOI: http://dx.doi.org/10.1016/j.ejmech.2015.01.047
Schuler, B., Persson, M., Paavilainen, S., Pavlicek, N., Gross, L., Meyer, G. and Repp, J. Effect of electron-phonon interaction on the formation of one-dimensional electronic states in coupled Cl vacancies. Physical Review B 91, 235443 (2015). DOI: http://dx.doi.org/10.1103/PhysRevB.91.235443
Manea, L. R., Cramariuc, B., Popescu, V., Cramariuc, R., Sandu, I. and Cramariuc, O. Equipment for Obtaining Polimeric Nanofibres by Electrospinning Technology II. The obtaining of polimeric nanofibers. MATERIALE PLASTICE 52, 180-185 (2015). DOI: http://www.revmaterialeplastice.ro/pdf/MANEA%20L.pdf%202%2015.pdf
Kwolek, U., Kulig, W., Wydro, P., Nowakowska, M., Rog, T. and Kepczynski, M. Effect of Phosphatidic Acid on Biomembrane: Experimental and Molecular Dynamics Simulations Study. The Journal of Physical Chemistry B 119, 10042–10051 (2015). DOI: http://dx.doi.org/10.1021/acs.jpcb.5b03604
Kulig, W., Pasenkiewicz-Gierula, M. and Rog, T. Topologies, structures and parameter files for lipid simulations in GROMACS with the OPLS-aa force field: DPPC, POPC, DOPC, PEPC, and cholesterol. Data in Brief 5, 333–336 (2015). DOI: http://dx.doi.org/10.1016/j.dib.2015.09.013
Fuchs, P. F. J., Javanainen, M., Lamberg, A., Miettinen, M. S., Monticelli, L., Maatta, J., Ollila, O. H. S., Retegan, M. and Santuz, H. Open Collaboration that uses NMR Data to Judge the Correctness of Phospholipid Glycerol and Head Group Structures in Molecular Dynamics Simulations. Biophysical Journal 108, 411A (2015). 59th Annual Meeting of the Biophysical-Society, Baltimore, MD, FEB 07-11, 2015.DOI: http://dx.doi.org/10.1016/j.bpj.2014.11.2255
Basu, I., Manna, M. and Mukhopadhyay, C. Insights into the behavioral difference of water in the presence of GM1. FEBS Letters 589, 3887–3892 (2015). DOI: http://dx.doi.org/10.1016/j.febslet.2015.11.014
Botan, A., Favela-Rosales, F., Fuchs, P. F. J., Javanainen, M., Kanduc, M., Kulig, W., Lamberg, A., Loison, C., Lyubartsev, A., Miettinen, M. S., Monticelli, L., Maatta, J., Ollila, O. H. S., Retegan, M., Rog, T., Santuz, H., and Tynkkynen, J. Toward Atomistic Resolution Structure of Phosphatidylcholine Headgroup and Glycerol Backbone at Different Ambient Conditions. The Journal of Physical Chemistry B 119, 15075–15088 (2015). DOI: http://dx.doi.org/10.1021/acs.jpcb.5b04878
Sandev, T., Chechkin, A. V., Korabel, N., Kantz, H., Sokolov, I. M. and Metzler, R. Distributed-order diffusion equations and multifractality: Models and solutions. Physical Review E 92, 042117 (2015). DOI: http://dx.doi.org/10.1103/PhysRevE.92.042117
Safdari, H., Cherstvy, A. G., Chechkin, A. V., Thiel, F., Sokolov, I. M. and Metzler, R. Quantifying the non-ergodicity of scaled Brownian motion. Journal of Physics A: Mathematical and Theoretical 48, 375002 (2015). DOI: http://dx.doi.org/10.1088/1751-8113/48/37/375002
Sandev, T., Chechkin, A., Kantz, H. and Metzler, R. Diffusion and Fokker-Planck-Smoluchowski Equations with Generalized Memory Kernel. Fractional Calculus and Applied Analysis 18 1006-1038 (2015). DOI: http://dx.doi.org/10.1515/fca-2015-0059
Krusemann, H., Godec, A. and Metzler, R. Ageing first passage time density in continuous time random walks and quenched energy landscapes. Journal of Physics A: Mathematical and Theoretical 48, 285001 (2015). DOI: http://dx.doi.org/10.1088/1751-8113/48/28/285001
Bauer, M., Rasmussen, E. S., Lomholt, M. A. and Metzler, R. Real sequence effects on the search dynamics of transcription factors on DNA. Scientific Reports 5, 10072 (2015). DOI: http://dx.doi.org/10.1038/srep10072
Godec, A. and Metzler, R. Signal focusing through active transport. Physical Review E 92, 010701 (2015). DOI: http://dx.doi.org/10.1103/PhysRevE.92.010701
Reverey, J. F., Jeon, J.-H., Bao, H., Leippe, M., Metzler, R. and Selhuber-Unkel, C. Superdiffusion dominates intracellular particle motion in the supercrowded cytoplasm of pathogenic Acanthamoeba castellanii. Scientific Reports 5, 11690 (2015). DOI: http://dx.doi.org/10.1038/srep11690
Bodrova, A. S., Chechkin, A. V., Cherstvy, A. G. and Metzler, R. Ultraslow scaled Brownian motion. New Journal of Physics 17, 063038 (2015). DOI: http://dx.doi.org/10.1088/1367-2630/17/6/063038
Godec, A. and Metzler, R. Optimization and universality of Brownian search in a basic model of quenched heterogeneous media. Physical Review E 91, 052134 (2015). DOI: http://dx.doi.org/10.1103/PhysRevE.91.052134
Cherstvy, A. G. and Metzler, R. Ergodicity breaking, ageing, and confinement in generalized diffusion processes with position and time dependent diffusivity. Journal of Statistical Mechanics: Theory and Experiment 2015, P05010 (2015). DOI: http://dx.doi.org/10.1088/1742-5468/2015/05/P05010
Cherstvy, A. G. and Metzler, R. Ergodicity breaking and particle spreading in noisy heterogeneous diffusion processes. The Journal of Chemical Physics 142, 144105 (2015). DOI: http://dx.doi.org/10.1063/1.4917077
Safdari, H., Chechkin, A. V., Jafari, G. R. and Metzler, R. Aging scaled Brownian motion. Physical Review E 91, 042107 (2015). DOI: http://dx.doi.org/10.1103/PhysRevE.91.042107
Blavatska, V. and Metzler, R. Conformational properties of complex polymers: rosette versus star-like structures. Journal of Physics A: Mathematical and Theoretical 48, 135001 (2015). DOI: http://dx.doi.org/10.1088/1751-8113/48/13/135001
Shin, J., Cherstvy, A. G. and Metzler, R. Polymer Looping Is Controlled by Macromolecular Crowding, Spatial Confinement, and Chain Stiffness. ACS Macro Letters 4, 202-206 (2015). DOI: http://dx.doi.org/10.1021/mz500709w
Bodrova, A., Chechkin, A. V., Cherstvy, A. G. and Metzler, R. Quantifying non-ergodic dynamics of force-free granular gases. Phys. Chem. Chem. Phys. 17, 21791–21798 (2015). DOI: http://dx.doi.org/10.1039/C5CP02824H
de Carvalho, S. J., Metzler, R. and Cherstvy, A. G. Inverted critical adsorption of polyelectrolytes in confinement. Soft Matter 11, 4430-4443 (2015). DOI: http://dx.doi.org/10.1039/c5sm00635j
Shin, J., Cherstvy, A. G. and Metzler, R. Kinetics of polymer looping with macromolecular crowding: effects of volume fraction and crowder size. Soft Matter 11, 472-488 (2015). DOI: http://dx.doi.org/10.1039/c4sm02007c
Ghosh, S. K., Cherstvy, A. G. and Metzler, R. Non-universal tracer diffusion in crowded media of non-inert obstacles. Phys. Chem. Chem. Phys. 17, 1847-1858 (2015). DOI: http://dx.doi.org/10.1039/c4cp03599b
Timr, S., Brabec, J., Bondar, A., Ryba, T., Zelezny, M., Lazar, J. and Jungwirth, P. Nonlinear Optical Properties of Fluorescent Dyes Allow for Accurate Determination of Their Molecular Orientations in Phospholipid Membranes. The Journal of Physical Chemistry B 119, 9706–9716 (2015). DOI: http://dx.doi.org/10.1021/acs.jpcb.5b05123
Pleskot, R., Cwiklik, L., Jungwirth, P., Zasky, V. and Potocky, M. Membrane targeting of the yeast exocyst complex. Biochimica et Biophysica Acta (BBA) - Biomembranes 1848, 1481-1489 (2015). DOI: http://dx.doi.org/10.1016/j.bbamem.2015.03.026
Constantoudis, V., Kalimeri, M., Diakonos, F., Karamanos, K., Papadimitriou, C., Chatzigeorgiou, M. and Papageorgiou, H. Long-range correlations and burstiness in written texts: Universal and language-specific aspects. International Journal of Modern Physics B 30, 1541005 (2015). DOI: http://dx.doi.org/10.1142/S0217979215410052
Lehto, M., Karilainen, T., Rog, T., Cramariuc, O., Vanhala, E., Tornaeus, J., Taberman, H., Janis, J., Alenius, H., Vattulainen, I. and Laine, O. Co-Exposure with Fullerene May Strengthen Health Effects of Organic Industrial Chemicals. PLoS ONE 9, e114490 (2014). DOI: http://dx.doi.org/10.1371/journal.pone.0114490
Aijanen, T., Koivuniemi, A., Javanainen, M., Rissanen, S., Rog, T. and Vattulainen, I. How Anacetrapib Inhibits the Activity of the Cholesteryl Ester Transfer Protein? Perspective through Atomistic Simulations. PLoS Computational Biology 10, e1003987 (2014). DOI: http://dx.doi.org/10.1371/journal.pcbi.1003987
Sharma, V., Wikstrom, M., Vattulainen, I. and Rog, T. Molecular nature of the conformational and electrostatic coupling in the proton pumping mechanism of complex I. Biochimica et Biophysica Acta (BBA) - Bioenergetics 1837, e40 (2014). DOI: http://dx.doi.org/10.1016/j.bbabio.2014.05.048
Rog, T. and Vattulainen, I. Cholesterol, sphingolipids, and glycolipids: What do we know about their role in raft-like membranes? Chemistry and Physics of Lipids 184, 82-104 (2014). DOI: http://dx.doi.org/10.1016/j.chemphyslip.2014.10.004
Heikkila, E., Martinez-Seara, H., Gurtovenko, A. A., Vattulainen, I. and Akola, J. Atomistic simulations of anionic Au144(SR)60 nanoparticles interacting with asymmetric model lipid membranes. Biochimica et Biophysica Acta (BBA) - Biomembranes 1838, 2852-2860 (2014). DOI: http://dx.doi.org/10.1016/j.bbamem.2014.07.027
Neuvonen, M., Manna, M., Mokkila, S., Javanainen, M., Rog, T., Liu, Z., Bittman, R., Vattulainen, I. and Ikonen, E. Enzymatic Oxidation of Cholesterol: Properties and Functional Effects of Cholestenone in Cell Membranes. PLoS ONE 9, e103743 (2014). DOI: http://dx.doi.org/10.1371/journal.pone.0103743
Manna, M., Rog, T. and Vattulainen, I. The challenges of understanding glycolipid functions: An open outlook based on molecular simulations. Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids 1841, 1130-1145 (2014). DOI: http://dx.doi.org/10.1016/j.bbalip.2013.12.016
Pourmousa, M., Rog, T., Mikkeli, R., Vattulainen, l., Solanko, L. M., Wustner, D., List, N. H., Kongsted, J., and Karttunen, M. Dehydroergosterol as an Analogue for Cholesterol: Why It Mimics Cholesterol So Well or Does It? The Journal of Physical Chemistry B 118, 7345-7357 (2014). DOI: http://dx.doi.org/10.1021/jp406883k
Heikkila, E., Martinez-Seara, H., Gurtovenko, A. A., Javanainen, M.,Hakkinen, H., Vattulainen, I., and Akola, J. Cationic Au Nanoparticle Binding with Plasma Membrane-like Lipid Bilayers: Potential Mechanism for Spontaneous Permeation to Cells Revealed by Atomistic Simulations. The Journal of Physical Chemistry C 118, 11131-11141 (2014). DOI: http://dx.doi.org/10.1021/jp5024026
Maciejewski, A., Pasenkiewicz-Gierula, M., Cramariuc, O., Vattulainen, I., and Rog, T. Refined OPLS All-Atom Force Field for Saturated Phosphatidylcholine Bilayers at Full Hydration. The Journal of Physical Chemistry B 118, 4571-4581 (2014). DOI: http://dx.doi.org/10.1021/jp5016627
Franova, M. D., Vattulainen, I., and Ollila, O. H. S. Can pyrene probes be used to measure lateral pressure profiles of lipid membranes? Perspective through atomistic simulations. Biochimica et Biophysica Acta (BBA) - Biomembranes 1838, 1406-1411 (2014). DOI: http://dx.doi.org/10.1016/j.bbamem.2014.01.030
Filipe, H. A. L., Moreno, M. J., Rog, T., Vattulainen, I., and Loura, L. M. S. How To Tackle the Issues in Free Energy Simulations of Long Amphiphiles Interacting with Lipid Membranes: Convergence and Local Membrane Deformations. The Journal of Physical Chemistry B 118, 3572-3581 (2014). DOI: http://dx.doi.org/10.1021/jp501622d
Kulig, W., Tynkkynen, J., Javanainen, M., Manna, M., Rog, T., Vattulainen, I., and Jungwirth, P. How well does cholesteryl hemisuccinate mimic cholesterol in saturated phospholipid bilayers? Journal of Molecular Modeling 20, 2121 (2014). DOI: http://dx.doi.org/10.1007/s00894-014-2121-z
Poyry, S., Cramariuc, O., Postila, P., Kaszuba, K., Sarewicz, M., Osyczka, A., Rog, T. and Vattulainen, I. Clarifying the Roles of Cardiolipin. Biophysical Journal 106, 513a-514a (2014). DOI: http://dx.doi.org/10.1016/j.bpj.2013.11.2870
Guixa-Gonzalez, R., Javanainen, M., Martinez-Seara, H., Gomez-Soler, M., Carles Domingo, J., Vattulainen, I., Ciruela, F. and Selent, J. Cell Membrane Composition Affects GPCR Aggregation. Biophysical Journal 106, 517a-518a (2014). DOI: http://dx.doi.org/10.1016/j.bpj.2013.11.2890
Postila, P. A., Cramariuc, O., Poyry, S., Kaszuba, K., Vattulainen, I., Sarewicz, M., Osyczka, A. and Rog, T. Bridging a Gap Between Cytochrome Bc1 Cmplex Structure and Function. Biophysical Journal 106, 586a-587a (2014). DOI: http://dx.doi.org/10.1016/j.bpj.2013.11.3250
Manna, M., Mokkila, S., Javanainen, M., Rog, T., Neuvonen, M., Ikonen, E., and Vattulainen, I. What Happens for Sterol Dynamics When Cholesterol is Enzymatically Oxidized? Biophysical Journal 106, 704a (2014). DOI: http://dx.doi.org/10.1016/j.bpj.2013.11.3895
Nieminen, T., Javanainen, M., Danne, R., Rog, T., Gurtovenko, A. A. and Vattulainen, I. Flip-Flops of Lipids in the Absence of ATP: Role of Membrane Proteins. Biophysical Journal 106, 705a (2014). DOI: http://dx.doi.org/10.1016/j.bpj.2013.11.3903
Javanainen, M., Martinez-Seara, H. and Vattulainen, I. Characterisation of Coexisting Liquid Phases in Mixtures of Dipalmitoylphosphatidylcholine and Cholesterol. Biophysical Journal 106, 709a-710a (2014). DOI: http://dx.doi.org/10.1016/j.bpj.2013.11.3914
Rissanen, S., Kumorek, M., Martinez-Seara, H., Li, Y.-C., Jamroz, D., Bunker, A., Nowakowska, M., Vattulainen, I., Kepczynski, M., and Rog, T. Effect of PEGylation on Drug Entry into Lipid Bilayer. The Journal of Physical Chemistry B 118, 144-151 (2014). DOI: http://dx.doi.org/10.1021/jp4105745
Franova, M. D., Repakova, J., Holopainen, J. M., and Vattulainen, I. How to link pyrene to its host lipid to minimize the extent of membrane perturbations and to optimize pyrene dimer formation. Chemistry and Physics of Lipids 177, 19-25 (2014). DOI: http://dx.doi.org/10.1016/j.chemphyslip.2013.10.004
Koivuniemi, A., and Vattulainen, I. Modeling of Lipid Membranes and Lipoproteins. In Oresic, M., and Vidal-Puig, A. (eds.) A Systems Biology Approach to Study Metabolic Syndrome, 299-318 (Springer International Publishing, 2014). DOI: http://www.springer.com/us/book/9783319010076 10.1007/978-3-319-01008-3
Metzler, R., Jeon, J.-H., Cherstvy, A. G. and Barkai, E. Anomalous diffusion models and their properties: non-stationarity, non-ergodicity, and ageing at the centenary of single particle tracking. Phys. Chem. Chem. Phys. 16, 24128-24164 (2014). DOI: http://dx.doi.org/10.1039/c4cp03465a
Godec, A., Bauer, M. and Metzler, R. Collective dynamics effect transient subdiffusion of inert tracers in flexible gel networks. New Journal of Physics 16, 092002 (2014). DOI: http://dx.doi.org/10.1088/1367-2630/16/9/092002
Ghosh, S. K., Cherstvy, A. G. and Metzler, R. Deformation propagation in responsive polymer network films. The Journal of Chemical Physics 141, 074903 (2014). DOI: http://dx.doi.org/10.1063/1.4893056
Goychuk, I., Kharchenko, V. O. and Metzler, R. Molecular motors pulling cargos in the viscoelastic cytosol: how power strokes beat subdiffusion. Physical Chemistry Chemical Physics 16, 16524 (2014). DOI: http://dx.doi.org/10.1039/C4CP01234H
Cherstvy, A. G. and Metzler, R. Nonergodicity, fluctuations, and criticality in heterogeneous diffusion processes. Physical Review E 90, 012134 (2014). DOI: http://dx.doi.org/10.1103/PhysRevE.90.012134
Shin, J., Cherstvy, A. G. and Metzler, R. Mixing and segregation of ring polymers: spatial confinement and molecular crowding effects. New Journal of Physics 16, 053047 (2014). DOI: http://dx.doi.org/10.1088/1367-2630/16/5/053047
Krusemann, H., Godec, A. and Metzler, R. First-passage statistics for aging diffusion in systems with annealed and quenched disorder. Physical Review E 89, 040101 (2014). DOI: http://dx.doi.org/10.1103/PhysRevE.89.040101
Talukder, S., Sen, S., Chakraborti, P., Metzler, R., Banik, S. K., and Chaudhury, P. Publisher's Note: Breathing dynamics based parameter sensitivity analysis of hetero-polymeric DNA [J. Chem. Phys. 140, 125101 (2014)]. The Journal of Chemical Physics 140, 149901 (2014). DOI: http://dx.doi.org/10.1063/1.4871297
Shin, J., Cherstvy, A. G., and Metzler, R. Sensing Viruses by Mechanical Tension of DNA in Responsive Hydrogels. Physical Review X 4, 021002 (2014). DOI: http://dx.doi.org/10.1103/PhysRevX.4.021002
Talukder, S., Sen, S., Chakraborti, P., Metzler, R., Banik, S. K., and Chaudhury, P. Breathing dynamics based parameter sensitivity analysis of hetero-polymeric DNA. The Journal of Chemical Physics 140, 125101 (2014). DOI: http://dx.doi.org/10.1063/1.4869112
Goychuk, I., Kharchenko, V. O., and Metzler, R. How Molecular Motors Work in the Crowded Environment of Living Cells: Coexistence and Efficiency of Normal and Anomalous Transport. PLoS ONE 9, e91700 (2014). DOI: http://dx.doi.org/10.1371/journal.pone.0091700
Schulz, J. H., Barkai, E., and Metzler, R. Aging Renewal Theory and Application to Random Walks. Physical Review X 4, 011028 (2014). DOI: http://dx.doi.org/10.1103/PhysRevX.4.011028
Palyulin, V. V., Chechkin, A. V., and Metzler, R. Levy flights do not always optimize random blind search for sparse targets. Proceedings of the National Academy of Sciences 111, 2931-2936 (2014). DOI: http://dx.doi.org/10.1073/pnas.1320424111
Sandev, T., Metzler, R., and Tomovski, Z. Correlation functions for the fractional generalized langevin equation in the presence of internal and external noise. Journal of Mathematical Physics 55, 023301 (2014). DOI: http://dx.doi.org/10.1063/1.4863478
Palyulin, V. V., and Metzler, R. Speeding up the first-passage for subdiffusion by introducing a finite potential barrier. Journal of Physics A: Mathematical and Theoretical 47, 032002 (2014). DOI: http://dx.doi.org/10.1088/1751-8113/47/3/032002
Nezhadhaghighi, M. G., Chechkin, A., and Metzler, R. Numerical approach to unbiased and driven generalized elastic model. The Journal of Chemical Physics 140, 024106 (2014). DOI: http://dx.doi.org/10.1063/1.4858425
Jeon, J.-H., Chechkin, A. V. and Metzler, R. Scaled Brownian motion: a paradoxical process with a time dependent diffusivity for the description of anomalous diffusion. Physical Chemistry Chemical Physics 16, 15811 (2014). DOI: http://dx.doi.org/10.1039/C4CP02019G
Palyulin, V. V., Ala-Nissila, T. and Metzler, R. Polymer translocation: the first two decades and the recent diversification. Soft Matter 10, 9016-9037 (2014). DOI: http://dx.doi.org/10.1039/c4sm01819b
de Carvalho, S. J., Metzler, R. and Cherstvy, A. G. Critical adsorption of polyelectrolytes onto charged Janus nanospheres. Physical Chemistry Chemical Physics 16, 15539 (2014). DOI: http://dx.doi.org/10.1039/C4CP02207F
Bauer, M., Godec, A., and Metzler, R. Diffusion of finite-size particles in two-dimensional channels with random wall configurations. Physical Chemistry Chemical Physics 16, 6118 (2014). DOI: http://dx.doi.org/10.1039/C3CP55160A
Cherstvy, A. G., Chechkin, A. V., and Metzler, R. Particle invasion, survival, and non-ergodicity in 2D diffusion processes with space-dependent diffusivity. Soft Matter 10, 1591 (2014). DOI: http://dx.doi.org/10.1039/c3sm52846d
Stetter, F. W., Cwiklik, L., Jungwirth, P. and Hugel, T. Single Lipid Extraction: The Anchoring Strength of Cholesterol in Liquid-Ordered and Liquid-Disordered Phases. Biophysical Journal 107, 1167-1175 (2014). DOI: http://dx.doi.org/10.1016/j.bpj.2014.07.018
Timr, S., Bondar, A., Cwiklik, L., Stefl, M., Hof, M., Vazdar, M., Lazar, J., and Jungwirth, P. Accurate Determination of the Orientational Distribution of a Fluorescent Molecule in a Phospholipid Membrane. The Journal of Physical Chemistry B 118, 855-863 (2014). DOI: http://dx.doi.org/10.1021/jp4067026
Polishchuk, A., Emelina, T., Karaseva, E., Cramariuc, O., Chukharev, V., and Karasev, V. Photochemical Behavior and Photolysis of Protonated Forms of Levofloxacin. Photochemistry and Photobiology 90, 79-84 (2014). DOI: http://dx.doi.org/10.1111/php.12152
Wizert, A., Iskander, D. R., and Cwiklik, L. Organization of Lipids in the Tear Film: A Molecular-Level View. PLoS ONE 9, e92461 (2014). DOI: http://dx.doi.org/10.1371/journal.pone.0092461
Guixa-Gonzalez, R., Rodriguez-Espigares, I., Ramirez-Anguita, J. M., Carrio-Gaspar, P., Martinez-Seara, H., Giorgino, T., and Selent, J. MEMBPLUGIN: studying membrane complexity in VMD. Bioinformatics 30, 1478-1480 (2014). DOI: http://dx.doi.org/10.1093/bioinformatics/btu037
Magarkar, A., Rog, T. and Bunker, A. Molecular Dynamics Simulation of Inverse-Phosphocholine Lipids. The Journal of Physical Chemistry C 118, 19444-19449 (2014). DOI: http://dx.doi.org/10.1021/jp505633y
Magarkar, A., Rog, T. and Bunker, A. Molecular Dynamics Simulation of PEGylated Membranes with Cholesterol: Building Toward the DOXIL Formulation. The Journal of Physical Chemistry C 118, 15541-15549 (2014). DOI: http://dx.doi.org/10.1021/jp504962m
Magarkar, A., Dhawan, V., Kallinteri, P., Viitala, T., Elmowafy, M., Rog, T., and Bunker, A. Cholesterol level affects surface charge of lipid membranes in saline solution. Scientific Reports 4, 5005 (2014). DOI: http://dx.doi.org/10.1038/srep05005
Javanainen, M. Universal Method for Embedding Proteins into Complex Lipid Bilayers for Molecular Dynamics Simulations. Journal of Chemical Theory and Computation 10, 2577-2582 (2014). DOI: http://dx.doi.org/10.1021/ct500046e
Sharma, V. and Wikstrom, M. A structural and functional perspective on the evolution of the hemecopper oxidases. FEBS Letters 588, 3787-3792 (2014). DOI: http://dx.doi.org/10.1016/j.febslet.2014.09.020
Llorente, A., Skotland, T., Sylvanne, T., Kauhanen, D., Rog, T., Orlowski, A., Vattulainen, I., Ekroos, K., and Sandvig, K. Molecular lipidomics of exosomes released by PC-3 prostate cancer cells. Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids 1831, 1302-1309 (2013). DOI: http://dx.doi.org/10.1016/j.bbalip.2013.04.011
Kaszuba, K., Postila, P. A., Cramariuc, O., Sarewicz, M., Osyczka, A., Vattulainen, I., and Rog, T. Parameterization of the prosthetic redox centers of the bacterial cytochrome bc1 complex for atomistic molecular dynamics simulations. Theoretical Chemistry Accounts 132, 1370 (2013). DOI: http://dx.doi.org/10.1007/s00214-013-1370-8
Postila, P. A., Kaszuba, K., Sarewicz, M., Osyczka, A., Vattulainen, I., and Rog, T. Key role of water in proton transfer at the Q0-site of the cytochrome bc1 complex predicted by atomistic molecular dynamics simulations. Biochimica et Biophysica Acta (BBA) - Bioenergetics 1827, 761-768 (2013). DOI: http://dx.doi.org/10.1016/j.bbabio.2013.02.005
Poyry, S., Cramariuc, O., Postila, P. A., Kaszuba, K., Sarewicz, M., Osyczka, A., Vattulainen, I., and Rog, T. Atomistic simulations indicate cardiolipin to have an integral role in the structure of the cytochrome bc1 complex. Biochimica et Biophysica Acta (BBA) - Bioenergetics 1827, 769-778 (2013). DOI: http://dx.doi.org/10.1016/j.bbabio.2013.03.005
Kaszuba, K., Karttunen, M., Vattulainen, I., and Rog, T. Water Matters: Role of Water in the Binding Selectivity of β-Blockers to Human β-Adrenergic Receptors. Biophysical Journal 104, 405a (2013). DOI: http://dx.doi.org/10.1016/j.bpj.2012.11.2259
Poyry, S., Postila, P. A., Cramariuc, O., Kaszuba, K., Vattulainen, I., Sarewicz, M., Osyczka, A., and Rog, T. Atomistic Simulations Indicate Cardiolipin to have an Integral Role in the Structure of the Cytochrome bc1 Complex. Biophysical Journal 104, 431a (2013). DOI: http://dx.doi.org/10.1016/j.bpj.2012.11.2399
Kalli, A. C., Rog, T., Vattulainen, I., and Sansom, M. S. Computational Studies of the Integrin Receptor in Complex Biologically Relevant Lipid Bilayers. Biophysical Journal 104, 432a (2013). DOI: http://dx.doi.org/10.1016/j.bpj.2012.11.2403
Postila, P. A., Kaszuba, K., Sarewicz, M., Osyczka, A., Vattulainen, I., and Rog, T. Substrate Binding at the QO-Site of the Bacterial Cytochrome bc1 Complex Predicted by Atomistic Molecular Dynamics Simulations. Biophysical Journal 104, 490a (2013). DOI: http://dx.doi.org/10.1016/j.bpj.2012.11.2702
Orlowski, A., Grzybek, M., Bunker, A., Pasenkiewicz-Gierula, M., Vattulainen, I., Mannisto, P. T., and Rog, T. The Interactions of Dopamine and L-Dopa with Lipid Headgroup and its Implication for Neurotransmitters Metabolism. Biophysical Journal 104, 498a (2013). DOI: http://dx.doi.org/10.1016/j.bpj.2012.11.2748
Heikkila, E., Gurtovenko, A., Martinez-Seara, H., Hkkinen, H., Vattulainen, I., and Akola, J. Atomistic Simulations of Functional Gold Nanoparticles Au144(Sr)60 Interacting with Membranes. Biophysical Journal 104, 664a (2013). DOI: http://dx.doi.org/10.1021/jp301094m
Martinez-Seara Monne, H., Danne, R., Rog, T., Vattulainen, I., and Gurtovenko, A. Structure of Glycocalyx. Biophysical Journal 104, 251a (2013). DOI: http://dx.doi.org/10.1016/j.bpj.2012.11.1412
Kursawe, J., Schulz, J., and Metzler, R. Transient aging in fractional brownian and langevin-equation motion. Physical Review E 88, 062124 (2013). DOI: http://dx.doi.org/10.1103/PhysRevE.88.062124
Schulz, J. H. P., Chechkin, A. V., and Metzler, R. Correlated continuous time random walks: combining scale-invariance with long-range memory for spatial and temporal dynamics. Journal of Physics A: Mathematical and Theoretical 46, 475001 (2013). DOI: http://dx.doi.org/10.1088/1751-8113/46/47/475001
Talkuder, S., Sen, S., Metzler, R., Banik, S., and Chaudhury, P. Stochastic optimization-based study of dimerization kinetics. Journal of Chemical Sciences 125, 1619-1627 (2013). DOI: http://dx.doi.org/10.1007/s12039-013-0502-y
Maity, A. K., Bandyopadhyay, A., Chattopadhyay, S., Chaudhuri, J. R., Metzler, R., Chaudhury, P., and Banik, S. K. Quantification of noise in bifunctionality-induced post-translational modification. Physical Review E 88, 032716 (2013). DOI: http://dx.doi.org/10.1103/PhysRevE.88.032716
Jeon, J.-H., Barkai, E., and Metzler, R. Noisy continuous time random walks. The Journal of Chemical Physics 139, 121916 (2013). DOI: http://dx.doi.org/10.1063/1.4816635
Cherstvy, A. G., Chechkin, A. V., and Metzler, R. Anomalous diffusion and ergodicity breaking in heterogeneous diffusion processes. New Journal of Physics 15, 083039 (2013). DOI: http://dx.doi.org/10.1088/1367-2630/15/8/083039
Godec, A., and Metzler, R. Linear response, fluctuation-dissipation, and finite-system-size effects in superdiffusion. Physical Review E 88, 012116 (2013). DOI: http://dx.doi.org/10.1103/PhysRevE.88.012116
Barkai, E., Garini, Y., and Metzler, R. Electrostatic effects in living cells. Physics Today 66, 11 (2013). DOI: http://dx.doi.org/10.1063/PT.3.2029
Lomholt, M. A., Lizana, L., Metzler, R., and Ambjornsson, T. Microscopic Origin of the Logarithmic Time Evolution of Aging Processes in Complex Systems. Physical Review Letters 110, 208301 (2013). DOI: http://dx.doi.org/10.1103/PhysRevLett.110.208301
Pulkkinen, O., and Metzler, R. Distance Matters: The Impact of Gene Proximity in Bacterial Gene Regulation. Physical Review Letters 110, 198101 (2013). DOI: http://dx.doi.org/10.1103/PhysRevLett.110.198101
Vahabi, M., Schulz, J. H. P., Shokri, B., and Metzler, R. Area coverage of radial levy flights with periodic boundary conditions. Physical Review E 87, 042136 (2013). DOI: http://dx.doi.org/10.1103/PhysRevE.87.042136
Jeon, J.-H., Leijnse, N., Oddershede, L. B., and Metzler, R. Anomalous diffusion and power-law relaxation of the time averaged mean squared displacement in worm-like micellar solutions. New Journal of Physics 15, 045011 (2013). DOI: http://dx.doi.org/10.1088/1367-2630/15/4/045011
Eliazar, I., and Metzler, R. Anomalous statistics of random relaxations in random environments. Physical Review E 87, 022141 (2013). DOI: http://dx.doi.org/10.1103/PhysRevE.87.022141
Bauer, M., Metzler, R., and Levy, Y. K. In Vivo Facilitated Diffusion Model. PLoS ONE 8, e53956 (2013). DOI: http://dx.doi.org/10.1371/journal.pone.0053956
Godec, A., and Metzler, R. Finite-Time Effects and Ultraweak Ergodicity Breaking in Superdiffusive Dynamics. Physical Review Letters 110, 020603 (2013). DOI: http://dx.doi.org/10.1103/PhysRevLett.110.020603
Schulz, J. H. P., Barkai, E., and Metzler, R. Aging Effects and Population Splitting in Single-Particle Trajectory Averages. Physical Review Letters 110, 020602 (2013). DOI: http://dx.doi.org/10.1103/PhysRevLett.110.020602
Cherstvy, A. G., and Metzler, R. Population splitting, trapping, and non-ergodicity in heterogeneous diffusion processes. Physical Chemistry Chemical Physics 15, 20220 (2013). DOI: http://dx.doi.org/10.1039/C3CP53056F
Chechkin, A. V., Zaid, I. M., Lomholt, M. A., Sokolov, I. M., Metzler, R., Nepomnyashchy, A., and Volpert, V. Bulk-mediated Surface Diffusionon a Cylinder in the Fast Exchange Limit. Mathematical Modelling of Natural Phenomena 8, 114-126 (2013). DOI: http://dx.doi.org/10.1051/mmnp/20138208
Vazdar, M., Wernersson, E., Khabiri, M., Cwiklik, L., Jurkiewicz, P., Hof, M., Mann, E., Kolusheva, S., Jelinek, R., and Jungwirth, P. Aggregation of Oligoarginines at Phospholipid Membranes: Molecular Dynamics Simulations, Time-Dependent Fluorescence Shift, and Biomimetic Colorimetric Assays. The Journal of Physical Chemistry B 117, 11530-11540 (2013). DOI: http://dx.doi.org/10.1021/jp405451e
Lupu, I. G., Cramariuc, O., Hogas, H. I., and Hristian, L. Parameters optimization for the production of needle-punched nonwoven agrotextiles. Journal of the Textile Institute 104, 1125-1131 (2013). DOI: http://dx.doi.org/10.1080/00405000.2013.777581
Cramariuc, B., Cramariuc, R., Scarlet, R., Manea, L. R., Lupu, I. G., and Cramariuc, O. Fiber diameter in electrospinning process. Journal of Electrostatics 71, 189-198 (2013). DOI: http://dx.doi.org/10.1016/j.elstat.2012.12.018
Cramariuc, O., Aittala, P. J., and Hukka, T. I. Molecular dipole effects on tuning electron transfer in a porphinequinone complex: a DFT and TDDFT study. Journal of Molecular Modeling 19, 697-704 (2013). DOI: http://dx.doi.org/10.1007/s00894-012-1595-9
Niskanen, M., Kuisma, M., Cramariuc, O., Golovanov, V., Hukka, T. I., Tkachenko, N., and Rantala, T. T. Porphyrin adsorbed on the (1010) surface of the wurtzite structure of ZnO conformation induced effects on the electron transfer characteristics. Physical Chemistry Chemical Physics 15, 17408 (2013). DOI: http://dx.doi.org/10.1039/c3cp51685g
Manna, M., and Mukhopadhyay, C., Binding, Conformational Transition and Dimerization of Amyloid-β; Peptide on GM1-Containing Ternary Membrane: Insights from Molecular Dynamics Simulation. PLoS ONE 8, e71308 (2013). DOI: http://dx.doi.org/10.1371/journal.pone.0071308
Knuuti, J., Belevich, G., Sharma, V., Bloch, D. A., and Verkhovskaya, M. A single amino acid residue controls ROS production in the respiratory Complex I from Escherichia coli. Molecular Microbiology 90, 1190-1200 (2013). DOI: http://dx.doi.org/10.1111/mmi.12424
Sharma, V., Karlin, K. D., and Wikstrom, M. Computational study of the activated O-H state in the catalytic mechanism of cytochrome c oxidase. Proceedings of the National Academy of Sciences 110, 16844-16849 (2013). DOI: http://dx.doi.org/10.1073/pnas.1220379110
Javanainen, M., Hammaren, H., Monticelli, L., Jeon, J.-H., Miettinen, M. S., Martinez-Seara, H., Metzler, R., and Vattulainen, I. Anomalous and normal diffusion of lipids and proteins in crowded membranes. Faraday Discussions vol. 161, 397 (2012). DOI: http://dx.doi.org/10.1039/C2FD20085F
Heikkila, E., Gurtovenko, A. A., Martinez-Seara, H., Hakkinen, H., Vattulainen, I., and Akola, J. Atomistic simulations of functional Au144SR60 gold nanoparticles in aqueous environment. The Journal of Physical Chemistry C vol. 116, 9805 (2012). DOI: http://dx.doi.org/10.1021/jp301094m
Stepniewski, M., Kepczynski, M., Jamroz, D., Nowakowska, M., Rissanen, S., Vattulainen, I., and Rog, T. Interaction of hematoporphyrin with lipid membranes. The Journal of Physical Chemistry B vol. 116, 4889 (2012). DOI: http://dx.doi.org/10.1021/jp300899b
Koivuniemi, A., Vuorela, T., Kovanen, P. T., Vattulainen, I., and Hyvonen, M. Lipid exchange mechanism of the cholesteryl ester transfer protein clarified by atomistic and coarse-grained simulations. PLoS Computational Biology 8, e1002299 (2012). DOI: http://dx.doi.org/10.1371/journal.pcbi.1002299
Koivuniemi, A., and Vattulainen, I. High density lipoproteins: Revealing their structural and dynamical properties through molecular simulations. Soft Matter 8, 1262-1267 (2012). DOI: http://dx.doi.org/10.1039/C1SM06742G
Zhao, W., Gurtovenko, A. A., Vattulainen, I., and Karttunen, M. Cationic DMPC and DOTAP lipid bilayers: Atomistic insight for structure and dynamics. The Journal of Physical Chemistry B 116, 269-276 (2012). DOI: http://dx.doi.org/10.1021/jp210619q
Subrizi, A., Tuominen, E., Bunker, A., Rog, T., Antopolsky, M., and Urtti, A. TAT(48-60) peptide amino acid sequence is not unique in its cell penetrating properties and cell-surface glycosaminoglycans inhibit its cellular uptake. Journal of Controlled Release vol. 158, 277 (2012). DOI: http://dx.doi.org/10.1016/j.jconrel.2011.11.007
St-Pierre, J.-F., Bunker, A., Rog, T., Karttunen, M., and Mousseau, N. Molecular dynamics simulations of the bacterial ABC Transporter SAV1866 in the closed form. The Journal of Physical Chemistry B vol. 116, 2934 (2012). DOI: http://dx.doi.org/10.1021/jp209126c
Tomovski, Z., Sandev, T., Metzler, R., and Duddeldam, J. Generalized space-time fractional diffusion equation with composite fractional time derivative. Physica A vol. 391, 2527 (2012). DOI: http://dx.doi.org/10.1016/j.physa.2011.12.035
Jeon, J.-H., and Metzler, R. Inequivalence of time and ensemble averages in ergodic systems: Exponential versus power-law relaxation in confinement. Physical Review E vol. 85, 021147 (2012). DOI: http://dx.doi.org/10.1103/PhysRevE.85.021147
Palyulin, V. V., and Metzler, R. How a finite potential barrier decreases the mean first-passage time. Journal of Statistical Mechanics - Theory and Experiment, L03001 (2012). DOI: http://dx.doi.org/10.1088/1742-5468/2012/03/L03001
Sereshki, L. E., Lomholt, M. A., and Metzler, R. A solution to the subdiffusion-efficiency paradox: Inactive states enhance reaction efficiency at subdiffusion conditions in living cells. EPL vol. 97, 20008 (2012). DOI: http://dx.doi.org/10.1209/0295-5075/97/20008
Martinez-Seara, H., and Rog, T. Molecular dynamics simulation of a lipid bilayer: Simple recipe of how to do it. In: Biomolecular simulations: methods and protocols, edited by L. Monticelli and E. Salonen. Methods in Molecular Biology (Humana Press, Springer 2011), Ch. 15; ISBN 978-1-62703-016-8. DOI: http://dx.doi.org/10.1007/978-1-62703-017-5_15
Kulovesi, P., Telenius, J., Koivuniemi, K., Brezesinski, G., Vattulainen, I., and Holopainen, J. M. The impact of lipid composition on the stability of the tear fluid lipid layer. Soft Matter vol. 8, 5826 (2012). DOI: http://dx.doi.org/10.1039/C2SM25210D
Khandelia, H., and Vattulainen, I. Organization, aggregation, and lipid self-assembly. In: Encyclopedia of Biophysics (Springer, 2012), edited by G. C. K. Roberts. DOI: http://dx.doi.org/10.1007/978-3-642-16712-6_541
Kaszuba, K., Rog, T., Danne, R., Canning, P., Fulop, V., St. Pierre, J.-F., Garcıa-Horsman, A., Mannisto, P. T., Karttunen, M., Hokkanen, J., and Bunker A. Molecular dynamics, crystallography and mutagenesis studies on the substrate gating mechanism of prolyl oligopeptidase. Biochimie 94, 1398 (2012). DOI: http://dx.doi.org/10.1016/j.biochi.2012.03.012
Lehtinen, J., Magarkar, A., Stepniewski, M., Hakola, S., Bergman, M., Rog, T., Yliperttula, M., Urtti, A., and Bunker, A. Analysis of cause of failure of new targeting peptide in PEGylated liposome: Molecular modeling as rational design for nanomedicine. Eur J Pharma Sci 46, vol. 121 (2012). DOI: http://dx.doi.org/10.1016/j.ejps.2012.02.009
Orlowski, A., Bunker, A., Pasenkiewicz-Gierula, M., Vattulainen, I., Mannisto, P. T., and Rog, T. Strong preferences of dopamine and L-dopa towards lipid head group: Importance of phosphatidylserine and its implication for neurotransmitters metabolism. Journal of Neurochemistry vol. 122, 681 (2012). DOI: http://dx.doi.org/10.1111/j.1471-4159.2012.07813.x
Cramariuc, O., Rog, T., Javanainen, M., Monticelli, L., Polishchuk, A., and Vattulainen, I. Mechanism for translocation of fluoroquinolones across lipid membranes. BBA Biomembranes vol. 1818, 2563 (2012). DOI: http://dx.doi.org/10.1016/j.bbamem.2012.05.027
Kaszuba, K., Postila, P. A., Cramariuc, O., Sarewicz, M., Osyczka, A., Vattulainen, I., and Rog, T. Parameterization of the prosthetic redox centers of the bacterial cytochrome bc1 complex for atomistic molecular dynamics simulations . Submitted (2012). DOI: http://dx.doi.org/10.1007/s00214-013-1370-8
Tomilov, A., Videcoq, A., Chartier, T., Ala- Nissila, T., and Vattulainen, I. Tracer diffusion of colloids under both dilute and crowded conditions elucidated by hydrodynamic simulations. Journal of Chemical Physics vol. 137, 014503 (2012). DOI: http://dx.doi.org/10.1063/1.4731661
Monticelli, L., Barnoud, J., Orlowski, A., and Vattulainen, I. Interaction of C70 fulerene with the Kv1.2 potassium channel. PCCP vol. 14, 12526 (2012). DOI: http://dx.doi.org/10.1039/C2CP41117B
Ollila, O. H. S., Lamberg, A., Lehtivaara, M., Koivuniemi, A., and Vattulainen, I. Interfacial tension and surface pressure of high density lipoprotein, low density lipoprotein, and related lipid droplets. Biophys J vol. 103, 1236 (2012). DOI: http://dx.doi.org/10.1016/j.bpj.2012.08.023
Paavilainen, S., McWhirter, J. L., Rog, T., Vattulainen, I., and Ketoja, J. Mechanical properties of cellulose nanofibrils determined through atomistic molecular dynamics simulations. Nordic Paper Research vol. 27, 282 (2012). DOI: http://dx.doi.org/10.3183/NPPRJ-2012-27-02-p282-286
Rantamaki, A. H., Javanainen, M., Vattulainen, I., and Holopainen, J. M. Do lipids retard the evaporation of the tear fluid? Inv Opth Vis Sci vol. 53, 6442 (2012). DOI: http://dx.doi.org/10.1167/iovs.12-10487
Cramariuc, O., Rog, T., Vattulainen, I. Drug-lipid membrane interaction mechanisms revealed through molecular simulations. Current Physical Chemistry vol. 2, 379-400 (2012). DOI: http://dx.doi.org/10.2174/1877946811202040379
Telenius, J., Koivuniemi, A., Kulovesi, P., Holopainen, J. M., Vattulainen, I. Role of neutral lipids in tear fluid lipid layer: Coarse-grained simulation study. Langmuir vol. 28, 17092 (2012). DOI: http://dx.doi.org/10.1021/la304366d
Li, Y. C., Rissanen, S., Stepniewski, M., Cramariuc, O., Rog, T., Mirza, S., Xhaard, H., Wytrwal, M., Kepczynski, M., and Bunker, A. Study of interaction between PEG carrier and three relevant drug molecules: piroxicam, paclitaxel, and hematoporphyrin. The Journal of Physical Chemistry B vol. 116, 7334 (2012). DOI: http://dx.doi.org/10.1021/jp300301z
Magarkar, A., Karakas, E., Stepniewski, M., Rog, T., Bunker A. Molecular dynamics simulation of PEGylated bilayer interacting with salt ions: A model of the liposome surface in bloodstream. J Phys Chem B vol. 116, 4212 (2012). DOI: http://dx.doi.org/10.1021/jp300184z
Polischuk A. V., et al. Photolysis and quantum-chemical calculations of the nalidixic acid radical states. Russian J Gen Chem vol. 82, 323 (2012). DOI: http://dx.doi.org/10.1134/S1070363212020247
Scarlet, R., Manea, L. R., Sandu I., Martinova, L.,Cramariuc, O., and Sandu I. G. Study on the solubility of polyetherimide for nanostructural electrospinning. Revista de Chimie vol. 63, 688 (2012). DOI: http://www.revistadechimie.ro/pdf/SCARLET%20R%207%2012.pdf
Metzler, R., Jeon, J. H. The role of ergodicity in anomalous stochastic processes: Analysis of single-particle trajectories. Physica Scripta vol. 86, 058510 (2012). DOI: http://dx.doi.org/10.1088/0031-8949/86/05/058510
Jeon, J. H., Monne, H. M. S., Javanainen, M., Metzler, R. Anomalous diffusion of phospholipids and cholesterols in a lipid bilayer and its origins Physical Review Letters vol. 109, 188103 (2012). DOI: http://dx.doi.org/10.1103/PhysRevLett.109.188103
Chechkin, A. V., Zaid, I. M., Lomholt, M. A., Sokolov, I. M., Metzler, R. Bulk-mediated diffusion on a planar surface. Phys Rev E vol. 86, 041101 (2012). DOI: http://dx.doi.org/10.1103/PhysRevE.86.041101
Mattos, T. G., Meija-Monasterio, C., Metzler, R., Oshanin, G. First-passages in bounded domains: When is the mean first passage time meaningful? Phys Rev E vol. 86, 031143 (2012). DOI: http://dx.doi.org/10.1103/PhysRevE.86.031143
Sandev, T., Metzler, R., Tomovski, Z. Velocity and displacement correlation functions for fractional generalized Langevin equations. Fractional Calculus and Applied Analysis vol. 15, 426 (2012). DOI: http://dx.doi.org/10.2478/s13540-012-0031-2
Barkai, E., Garini, Y., Metzler, R. Strange kinetics of single molecules in living cells. Physics Today vol. 65, 29 (2012). DOI: http://dx.doi.org/10.1063/PT.3.1677
Bauer, M., Metzler, R. Generalized facilitated diffusion model for DNA-binding proteins with search and recognition states. Biophys J vol. 102, 2321 (2012). DOI: http://dx.doi.org/10.1016/j.bpj.2012.04.008
Magdziarz, M., Metzler, R., Szczotka, W., Zebrowski, P. Correlated continuous-time random walks in external force fields. Phys Rev E vol. 85, 051103 (2012). DOI: http://dx.doi.org/10.1103/PhysRevE.85.051103
Magdziarz, M., Metzler, R., Szczotka, W., Zebrowski, P. Correlated continuous-time random walks scaling limits and Langevin picture. J Stat Mech Th Exp no. P04010 (2012). DOI: http://dx.doi.org/10.1088/1742-5468/2012/04/P04010
Lejinse, N., Jeon, J. H., Loft, S., Metzler, R., Oddershede, L. B. Diffusion inside living human cells. Eur Phys J vol. 204, 75 (2012). DOI: http://dx.doi.org/10.1140/epjst/e2012-01553-y
Adamcik, J., Jeon, J. H., Karczewski, K. J., Metzler, R., Dietler, G. Quantifying supercoiling-induced denaturation bubbles in DNA Soft Matter vol. 8, 8651 (2012). DOI: http://dx.doi.org/10.1039/C2SM26089A
Lingwood, D., Binnington, B., Rog, T., Vattulainen, I., Grzybek, M., Coskun, U., Lingwood, C. A., and Simons, K. Cholesterol modulates glycolipid conformation and receptor activity. Nature Chemical Biology 7, 260-262 (2011). DOI: https://dx.doi.org/10.1038/nchembio.551
Koivuniemi, A., Vuorela, T., Kovanen, P. T., Hyvonen, M., and Vattulainen, I. Trafficking of lipids between high density lipoprotein and cholesteryl ester transfer protein. European Biophysics Journal with Biophysics Letters 40, S120 (2011). DOI: https://dx.doi.org/10.1007/s00249-011-0734-z
Orlowski, A., St-Pierre, J.-F., Magarkar, A., Bunker, A., Pasenkiewicz-Gierula, M., Vattulainen, I., and Rog, T. Properties of the membrane binding component of catechol-O-methyltransferase revealed by atomistic molecular dynamics simulations. The Journal of Physical Chemistry B 115, 13541-13550 (2011). DOI: https://dx.doi.org/10.1021/JP207177P
Hall. A., Rog, T., and Vattulainen, I. Effect of galactosylceramide on dynamics of cholesterol-rich lipid membranes. The Journal of Physical Chemistry B 115, 14424-14434 (2011). DOI: https://dx.doi.org/10.1021/jp203234n
Yetukuri, L., Huopaniemi, I., Koivuniemi, A., Maranghi, M., Hiukka, A., Nygren, H., Kaski, S., Taskinen, M.-R., Vattulainen, I., Jauhiainen, M., and Oresic, O. High density lipoprotein structural changes and drug response in lipidomic profiles following the long-term fenofibrate therapy in the FIELD substudy. PLoS One 6, e23589 (2011). DOI: https://dx.doi.org/10.1371/journal.pone.0023589
Kaiser, H. J., Orlowski, A., Rog, T., Chai, W., Feizi, T., Lingwood, D., Vattulainen, I., and Simons, K. Lateral sorting in model membranes by cholesterol-mediated hydrophobic matching. Proceedings of the National Academy of Science USA 108, 16628-16633 (2011). DOI: https://dx.doi.org/10.1073/pnas.1103742108
Murtola, T., Vuorela, T., Hyvonen, M. T., Marrink, S. J., Karttunen, M., and Vattulainen, I. Low-density lipoprotein: Structure, dynamics and lipid - apoB-100 interactions. Soft Matter 7, 8135-8141 (2011). DOI: https://dx.doi.org/10.1039/C1SM05367A
Pietilainen, K., Rog, T., Seppanen-Laakso, T., Virtue, S., Gopalacharyulu, P., Tang, J., Rodriguez-Cuenca, S., Maciejewski, A., Naukkarinen, J., Ruskeepaa, A.-L., Niemela, P., Yetukuri, L., Tan, C. Y., Velagapudi, V., Castillo, S., Nygren, H., Hyotylainen, T., Rissanen, A., Kaprio, J., Yki-Jarvinen, H., Vattulainen, I., Vidal-Plug, A., and Oresic, M. Association of lipidome remodelling in the adipocyte membrane with acquired obesity in humans. PLoS Biology 9, e1000623 (2011). DOI: https://dx.doi.org/10.1371/journal.pbio.1000623
Vattulainen, I., and Rog, T. Lipid simulations - Perspectives to lipids in action. Cold Spring Harbor Series in Biology 3, a004655 (2011). DOI: https://dx.doi.org/10.1101/cshperspect.a004655
Paavilainen, S., Rog, T., and Vattulainen, I. Analysis of twisting of cellulose nanofibrils in atomistic molecular dynamics simulations. J. Phys. Chem. B 115, 3747-3755 (2011). DOI: https://dx.doi.org/10.1021/jp111459b
Kalikka, J. and Akola, J. Steered molecular dynamics simulations of ligand-receptor interaction in lipocalins, European Biophysics Journal with Biophysics Letters 40, 181-194 (2011). DOI: https://dx.doi.org/10.1007/s00249-010-0638-3
Ollila, O. H. S., Louhivuori, M., Marrink, S. J., and Vattulainen, I. Protein shape change has a major effect on the gating energy of a mechanosensitive channel, Biophys. J. 100, 1651-1659 (2011). DOI: https://dx.doi.org/10.1016/j.bpj.2011.02.027
Rossi, G., Ioannis, G., Monticelli, L., Rostedt, N. K. J., Puisto, S. R., Lowe, C., Taylor, A. C., Vattulainen, I., and Ala-Nissila, T. A MARTINI coarse-grained model of a thermoset polyester coating, Macromolecules 44, 6198-6208 (2011). DOI: https://dx.doi.org/10.1021/ma200788a
Rossi, G., Monticelli, L., Puisto, S. R., Vattulainen, I., and Ala-Nissila, T. Coarse-graining polymers with the MARTINI force field: Polysterene as a benchmark case, Soft Matter 7, 698-708 (2011). DOI: https://dx.doi.org/10.1039/C0SM00481B
Bjorkbom, A., Rog, T., Kankaanpaa, P., Lindroos, D., Kaszuba, K., Kurita, M., Yamaguchi, S., Yamamoto, T., Jaikishan, S., Paavolainen, L., Paivarinne, J., Nyholm, T. K. M., Katsumura, S., Vattulainen, I., and Slotte, J. P. N- and O-methylation of sphingomyelin markedly affects its membrane properties and interactions with cholesterol. Biochimica et Biophysica Acta – Biomembranes 1808, 1179-1186 (2011). DOI: https://dx.doi.org/10.1016/j.bbamem.2011.01.009
Rantamaki, A., Telenius, J., Koivuniemi, A., Vattulainen, I., and Holopainen, J. M. Lessons from the biophysics of interfaces: Lung surfactant and tear fluid. Progress in Retinal and Eye Research 30, 204-215 (2011). DOI: https://dx.doi.org/10.1016/j.preteyeres.2011.02.002
Stepniewski, M., Pasenkiewicz-Gierula, M., Rog, T., Danne, R., Orlowski, A., Karttunen, M., Urtti, A., Yliperttula, A., Vuorimaa, E., and Bunker, A. A study of PEGylated lipid membrane structure in physiological conditions using all atom molecular dynamics simulation and Langmuir monolayer studies. Langmuir 27, 7788-7798 (2011). DOI: https://dx.doi.org/10.1021/la200003n
St. Pierre, J.-F., Mousseau, N., Rog, T., Karttunen, M., and Bunker, A. Use of umbrella sampling to calculate the entrance/exit pathway for Z-pro-prolinal inhibitor in Prolyl Oligopeptidase. J Comput. Theor. Chem. 7, 1583-1594 (2011). DOI: https://dx.doi.org/10.1021/ct1007058
Abdolvahab, R. H., Ejtehadi, M. R., and Metzler, R. Sequence-dependence of the binding energy in chaperone-driven polymer translocation through a nanopore. Phys. Rev. E 83, 011902 (2011). DOI: https://dx.doi.org/10.1103/PhysRevE.83.011902
Burov, S., Jeon, J.-H., Metzler, R., and Barkai, E. Single particle tracking in systems showing anomalous diffusion: the role of weak ergodicity breaking. Phys. Chem. Chem. Phys. 13, 1800 (2011). DOI: https://dx.doi.org/10.1039/C0CP01879A
Jeon, J.-H., Tejedor, V., Burov, S., Barkai, E., Selhuber-Unkel, C., Berg-Sorensen, K., Oddershede, L., and Metzler, R. In vivo anomalous diffusion and weak ergodicity breaking of lipid granules. Phys. Rev. Lett. 106, 048103 (2011). DOI: https://dx.doi.org/10.1103/PhysRevLett.106.048103
Luo, K., and Metzler, R. The chain sucker: translocation dynamics of a polymer chain into a long narrow channel driven by longitudinal flow. J. Chem. Phys 134, 135102 (2011). DOI: https://dx.doi.org/10.1063/1.3575239
Jeon, J.-H., Chechkin, A. V., and Metzler, R. First passage behavior of fractional Brownian motion in two-dimensional wedge domains. Europhys. Lett. 94, 20008 (2011). DOI: https://dx.doi.org/10.1209/0295-5075/94/20008
Sandev, T., Metzler, R., and Tomovski, Z. Fractional diffusion equation with a generalized Riemann-Liouville time fractional derivative. J. Phys. A. 44, 255203 (2011). DOI: https://dx.doi.org/10.1088/1751-8113/44/25/255203
Tejedor, V., Benichou, O., Metzler, R., and Voituriez, R. Residual mean first-passage time for jump processes: theory and applications to Levy flights and fractional Brownian motion. J. Phys. A 44, 255003 (2011). DOI: https://dx.doi.org/10.1088/1751-8113/44/25/255003
Chechkin, A. V., Zaid, I. M., Lomholt, M. A., Sokolov, I. M., and Metzler, R. Effective surface motion on a reactive cylinder of particles that perform intermittent bulk diffusion. J. Chem. Phys. 134, 204116 (2011). DOI: https://dx.doi.org/10.1063/1.3593198
Tejedor, V., Schad, M., Benichou, O., Voituriez, R., and Metzler, R. Encounter distribution of two random walkers on a finite one-dimensional interval. J. Phys. A 44, 395005 (2011). DOI: https://dx.doi.org/10.1088/1751-8113/44/39/395005
Abdolvahab, R. H., Metzler, R. and Ejtehadi, M. R. First passage time distribution of chaperone driven polymer translocation through a nanopore: Homopolymer and heteropolymer cases. Journal of Chemical Physics 135, 245102 (2011). DOI: https://dx.doi.org/10.1063/1.3669427
Talukder, S., Chaudhury, S., Metzler, R., and Banik, S. K. Determining the DNA stability parameters for the breathing dynamics of heterogeneous DNA by stochastic optimization. J. Chem. Phys. 135, 165103(2011). DOI: https://dx.doi.org/10.1063/1.3654958
Niinivehmas, S. P., Virtanen, S. I., Lehtonen, J. V., Postila, P. A., Pentikainen, O. T. Comparison of virtual high-throughput screening methods for the identification of phosphodiesterase-5 inhibitors. J. Chem. Inf. Model. 51, 1353-1363 (2011). DOI: https://dx.doi.org/10.1021/ci1004527
Metzler, R. and Jae-Hyung, J. Anomalous Diffusion and Fractional Transport Equations. In: Fractional Dynamics, edited by Klafter, J., Lim, S.C. and Metzler, R. (World Scientific, Singapore, 2011) pp. 3-32. DOI: https://dx.doi.org/10.1142/9789814340595_0001
Javanainen, M., Monticelli, L., de la Serna, J. B. and Vattulainen, I. Free Volume Theory Applied to Lateral Diffusion in Langmuir Monolayers: Atomistic Simulations for a Protein-Free Model of Lung Surfactant. Langmuir 26, 15436–15444 (2010). DOI: http://dx.doi.org/10.1021/la102454m
Vuorela, T., Catte, A., Niemela, P. S., Hall, A., Hyvonen, M. T., Marrink, S.-J., Karttunen, M. and Vattulainen, I. Role of Lipids in Spheroidal High Density Lipoproteins. PLoS Computational Biology 6, e1000964 (2010). DOI: http://dx.doi.org/10.1371/journal.pcbi.1000964
Kohara, S., Ohno, H., Takata, M., Usuki, T., Morita, H., Suzuya, K., Akola, J. and Pusztai, L. Lead silicate glasses: Binary network-former glasses with large amounts of free volume. Physical Review B 82, 134209 (2010). DOI: http://dx.doi.org/10.1103/PhysRevB.82.134209
Akola, J., Kacprzak, K. A., Lopez-Acevedo, O., Walter, M., Gronbeck, H. and Hakkinen, H. Thiolate-Protected Au25 Superatoms as Building Blocks: Dimers and Crystals. The Journal of Physical Chemistry C 114, 15986–15994 (2010). DOI: http://dx.doi.org/10.1021/jp1015438
Jiang, D.-e., Walter, M. and Akola, J. On the Structure of a Thiolated Gold Cluster: Au44(SR)282-. The Journal of Physical Chemistry C 114, 15883–15889 (2010). DOI: http://dx.doi.org/10.1021/jp9097342
Bjorkbom, A., Rog, T., Kaszuba, K., Kurita, M., Yamaguchi, S., Lonnfors, M., Nyholm, T. K., Vattulainen, I., Katsumura, S. and Slotte, J. P. Effect of Sphingomyelin Headgroup Size on Molecular Properties and Interactions with Cholesterol. Biophysical Journal 99, 3300–3308 (2010). DOI: http://dx.doi.org/10.1016/j.bpj.2010.09.049
Dias, C. L., Ala-Nissila, T., Wong-ekkabut, J., Vattulainen, I., Grant, M. and Karttunen, M. Reply to the comment by Graziano on "The hydrophobic effect and its role in cold denaturation". Cryobiology 60, 356–357 (2010). DOI: http://dx.doi.org/10.1016/j.cryobiol.2010.03.006
Niemela, P. S., Miettinen, M. S., Monticelli, L., Hammaren, H., Bjelkmar, P., Murtola, T., Lindahl, E. and Vattulainen, I. Membrane ProteinsDiffuse as Dynamic Complexes with Lipids. Journal of the American Chemical Society 132, 7574–7575 (2010). DOI: http://dx.doi.org/10.1021/ja101481b
Hall, A., Rog, T., Karttunen, M. and Vattulainen, I. Role of Glycolipids in Lipid Rafts: A View through Atomistic Molecular Dynamics Simulations with Galactosylceramide. The Journal of Physical Chemistry B 114, 7797–7807 (2010). DOI: http://dx.doi.org/10.1021/JP912175D
Kulovesi, P., Telenius, J., Koivuniemi, A., Brezesinski, G., Rantamaki, A., Viitala, T., Puukilainen, E., Ritala, M., Wiedmer, S. K., Vattulainen, I. and Holopainen, J. M. Molecular Organization of the Tear Fluid Lipid Layer. Biophysical Journal 99, 2559–2567 (2010). DOI: http://dx.doi.org/10.1016/j.bpj.2010.08.001
Lahdesmaki, K., Ollila, O. S., Koivuniemi, A., Kovanen, P. T. and Hyvonen, M. T. Membrane simulations mimicking acidic pH reveal increased thickness and negative curvature in a bilayer consisting of lysophosphatidylcholines and free fatty acids. Biochimica et Biophysica Acta (BBA) - Biomembranes 1798, 938–946 (2010). DOI: http://dx.doi.org/10.1016/j.bbamem.2010.01.020
Akola, J. and Jones, R. O. Comment on "Formation of Large Voids in the Amorphous Phase-Change Memory Ge2Sb2Te5 Alloy." Physical Review Letters 104, 019603 (2010). DOI: http://dx.doi.org/10.1103/PhysRevLett.104.019603
Lopez-Acevedo, O., Kacprzak, K. A., Akola, J. and Hakkinen, H. Quantum size effects in ambient CO oxidation catalysed by ligand-protected gold clusters. Nature Chemistry 2, 329–334 (2010). DOI: http://dx.doi.org/10.1038/NCHEM.589
Gurtovenko, A. A., Anwar, J. and Vattulainen, I. Defect-Mediated Trafficking across Cell Membranes: Insights from in Silico Modeling. Chemical Reviews 110, 6077–6103 (2010). DOI: http://dx.doi.org/10.1021/cr1000783
Martinez-Seara, H., Rog, T., Karttunen, M., Reigada, R. and Vattulainen, I. Specific Spatial and Orientational Order in Phospholipid Membranes Induced by Cholesterol. Biophysical Journal 98, 668a (2010). DOI: http://dx.doi.org/10.1016/j.bpj.2009.12.3669
Sane, P., Tuomisto, F., Vattulainen, I. and Holopainen, J. Revealing the Microstructural Changes in Tissues In-Situ with Positron Annihilation Spectroscopy. Biophysical Journal 98, 663a (2010). DOI: http://dx.doi.org/10.1016/j.bpj.2009.12.4248
Rantamaki, A., Telenius, J., Koivuniemi, A., Kulovesi, P., Brezesinski, G., Viitala, T., Puukilainen, E., Ritala, M., Wiedmer, S., Vattulainen, I. and Holopainen, J. Molecular Organization of the Tear Film Lipid Layer. Biophysical Journal 98, 488a (2010). DOI: http://dx.doi.org/10.1016/j.bpj.2009.12.2658
Ollila, S. O., Louhivuori, M., Marrink, S.-J. and Vattulainen, I. Lateral Pressure Profile and Curvature Frustration in Mechanosensitive Channel Gating. Biophysical Journal 98, 20a (2010). DOI: http://dx.doi.org/10.1016/j.bpj.2009.12.121
Sane, P., Tuomisto, F., Wiedmer, S. K., Nyman, T., Vattulainen, I. and Holopainen, J. M. Temperature-induced structural transition in-situ in porcine lens – Changes observed in void size distribution. Biochimica et Biophysica Acta (BBA) - Biomembranes 1798, 958–965 (2010). DOI: http://dx.doi.org/10.1016/j.bbamem.2010.01.011
Yetukuri, L., Soderlund, S., Koivuniemi, A., Seppanen-Laakso, T., Niemela, P. S., Hyvonen, M., Taskinen, M.-R., Vattulainen, I., Jauhiainen, M. and Oresic, M. Composition and lipid spatial distribution of HDL particles in subjects with low and high HDL-cholesterol. The Journal of Lipid Research 51, 2341–2351 (2010). DOI: http://dx.doi.org/10.1194/jlr.M006494
Kaszuba, K., Rog, T., Bryl, K., Vattulainen, I. and Karttunen, M. Molecular Dynamics Simulations Reveal Fundamental Role of Water As Factor Determining Affinity of Binding of β-Blocker Nebivolol to β2-Adrenergic Receptor. The Journal of Physical Chemistry B 114, 8374–8386 (2010). DOI: http://dx.doi.org/10.1021/jp909971f
Franova, M., Repakova, J., Capkova, P., Holopainen, J. M. and Vattulainen, I. Effects of DPH on DPPC-Cholesterol Membranes with Varying Concentrations of Cholesterol: From Local Perturbations to Limitations in Fluorescence Anisotropy Experiments. The Journal of Physical Chemistry B 114, 2704–2711 (2010). DOI: http://dx.doi.org/10.1021/JP908533X
Martinez-Seara, H., Rog, T., Karttunen, M., Vattulainen, I. and Reigada, R. Cholesterol Induces Specific Spatial and Orientational Order in Cholesterol/Phospholipid Membranes. PLoS ONE 5, e11162 (2010). DOI: http://dx.doi.org/10.1371/journal.pone.0011162
Dias, C. L., Ala-Nissila, T., Wong-ekkabut, J., Vattulainen, I., Grant, M. and Karttunen, M. The hydrophobic effect and its role in cold denaturation. Cryobiology 60, 91–99 (2010). DOI: http://dx.doi.org/10.1016/j.cryobiol.2009.07.005
Apajalahti, T., Niemela, P., Govindan, P. N., Miettinen, M. S., Salonen, E., Marrink, S.-J. and Vattulainen, I. Concerted diffusion of lipids in raft-like membranes. Faraday Discuss. 144, 411–430 (2010). DOI: http://dx.doi.org/10.1039/b901487j
Ollila, O. H. S. and Vattulainen, I. Chapter 2: Lateral Pressure Profiles in Lipid Membranes: Dependence on Molecular Composition. In Molecular Simulations and Biomembranes: From Biophysicsto Function, 26–55 (The Royal Society of Chemistry, 2010). DOI: http://dx.doi.org/10.1039/9781849732154-00026
Monticelli, L., Salonen, E., Ke, P. C. and Vattulainen, I. Interaction of Fullerene with Model Cell Membranes: a Computer Simulation Study. Biophysical Journal 96, 365a–366a (2009). DOI: http://dx.doi.org/10.1016/j.bpj.2008.12.1968
Sane, P., Tuomisto, F., Vattulainen, I., Salonen, E. and Holopainen, J. Probing the Microstructure Of Biomaterials With Positrons. Biophysical Journal 96, 356a (2009). DOI: http://dx.doi.org/10.1016/j.bpj.2008.12.1793
Morrow, M. R., Helle, A., Perry, J., Vattulainen, I., Wiedmer, S. K. and Holopainen, J. M. A Comparison Of Ceramide And Ceramide-1-phosphate Miscibility In Phosphatidylcholine Bilayers. Biophysical Journal 96, 162a–163a (2009). DOI: http://dx.doi.org/10.1016/j.bpj.2008.12.746
Kacprzak, K. A., Lehtovaara, L., Akola, J., Lopez-Acevedo, O. and Hakkinen, H. A density functional investigation of thiolate-protected bimetal PdAu24(SR)18z clusters: doping the superatom complex. Physical Chemistry Chemical Physics 11, 7123 (2009). DOI: http://dx.doi.org/10.1039/B904491D
Kacprzak, K. A., Akola, J. and Hakkinen, H. First-principles simulations of hydrogen peroxide formation catalyzed by small neutral gold clusters. Physical Chemistry Chemical Physics 11, 6359 (2009). DOI: http://dx.doi.org/10.1039/B822765A
Akola, J. and Jones, R. O. Structure of liquid phase change material AgInSbTe from density functional/molecular dynamics simulations. Applied Physics Letters 94, 251905 (2009). DOI: http://dx.doi.org/10.1063/1.3157166
Akola, J. and Jones, R. O. Structure of amorphous Ge8Sb2Te11: GeTeSb2Te3 alloys and optical storage. Physical Review B 79, 134118 (2009). DOI: http://dx.doi.org/10.1103/PhysRevB.79.134118
Yin, F., Akola, J., Koskinen, P., Manninen, M. and Palmer, R. E. Bright Beaches of Nanoscale Potassium Islands on Graphite in STM Imaging. Physical Review Letters 102, 106102 (2009). DOI: http://dx.doi.org/10.1103/PhysRevLett.102.106102
Pakkanen, K., Salonen, E., Mkel, A. R., Oker-Blom, C., Vattulainen, I. and Vuento, M. Desipramine induces disorder in cholesterol-rich membranes: implications for viral trafficking. Physical Biology 6, 046004 (2009). DOI: http://dx.doi.org/10.1088/1478-3975/6/4/046004
Poyry, S., Rog, T., Karttunen, M. and Vattulainen, I. Mitochondrial Membranes with Mono- and Divalent Salt: Changes Induced by Salt Ions on Structure and Dynamics. The Journal of Physical Chemistry B 113, 15513–15521 (2009). DOI: http://dx.doi.org/10.1021/jp905915m
Monticelli, L., Salonen, E., Ke, P. C. and Vattulainen, I. Effects of carbon nanoparticles on lipid membranes: a molecular simulation perspective. Soft Matter 5, 4433 (2009). DOI: http://dx.doi.org/10.1039/b912310e
Gurtovenko, A. A. and Vattulainen, I. Biomembrane Frontiers: Nanostructures, Models, and the Design of Life, chap. Collective Dynamics in Lipid Membranes: From Pore Formation to Flip-Flops, 121–139 (Humana Press, Totowa, NJ, 2009). DOI: http://dx.doi.org/10.1007/978-1-60761-314-5_5
Gurtovenko, A. A. and Vattulainen, I. Intrinsic Potential of Cell Membranes: Opposite Effects of Lipid Transmembrane Asymmetry and Asymmetric Salt Ion Distribution. The Journal of Physical Chemistry B 113, 7194–7198 (2009). DOI: http://dx.doi.org/10.1021/jp902794q
Murtola, T., Karttunen, M. and Vattulainen, I. Systematic coarse graining from structure using internal states: Application to phospholipid/cholesterol bilayer. The Journal of Chemical Physics 131, 055101 (2009). DOI: http://dx.doi.org/10.1063/1.3167405
Gurtovenko, A. A. and Vattulainen, I. Calculation of the electrostatic potential of lipid bilayers from molecular dynamics simulations: Methodological issues. The Journal of Chemical Physics 130, 215107 (2009). DOI: http://dx.doi.org/10.1063/1.3148885
Miettinen, M. S., Gurtovenko, A. A., Vattulainen, I. and Karttunen, M. Ion Dynamics in Cationic Lipid Bilayer Systems in Saline Solutions. The Journal of Physical Chemistry B 113, 9226–9234 (2009). DOI: http://dx.doi.org/10.1021/jp810233q
Martinez-Seara, H., Rog, T., Karttunen, M., Vattulainen, I. and Reigada, R. Why is the sn-2 chain of monounsaturated glycerophospholipids usually unsaturated whereas the sn-1 chain is saturated? Studies of 1-stearoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine (SOPC) and 1-oleoyl-2-stearoyl-sn-glycero-3-phosphatidylcholine (OSPC) membranes with and without cholesterol. The Journal of Physical Chemistry B 113, 8347–8356 (2009). DOI: http://dx.doi.org/10.1021/jp902131b
Telenius, J., Vattulainen, I. and Monticelli, L. Lipidomics: Volume 2: Methods and Protocols, chap. Visualization of Complex Processes in Lipid Systems Using Computer Simulations and Molecular Graphics, 317–338 (Humana Press, Totowa, NJ, 2010). DOI: http://dx.doi.org/10.1007/978-1-60761-325-1_18
Koivuniemi, A., Heikela, M., Kovanen, P. T., Vattulainen, I. and Hyvonen, M. T. Atomistic Simulations of Phosphatidylcholines and Cholesteryl Esters in High-Density Lipoprotein-Sized Lipid Droplet and Trilayer: Clues to Cholesteryl Ester Transport and Storage. Biophysical Journal 96, 4099–4108 (2009). DOI: http://dx.doi.org/10.1016/j.bpj.2009.01.058
Sane, P., Salonen, E., Falck, E., Repakova, J., Tuomisto, F., Holopainen, J. M. and Vattulainen, I. Probing Biomembranes with Positrons. The Journal of Physical Chemistry B 113, 1810–1812 (2009). DOI: http://dx.doi.org/10.1021/jp809308j
Rog, T., Pasenkiewicz-Gierula, M., Vattulainen, I. and Karttunen, M. Ordering effects of cholesterol and its analogues. Biochimica et Biophysica Acta (BBA) - Biomembranes 1788, 97–121 (2009). DOI: http://dx.doi.org/10.1016/j.bbamem.2008.08.022
Murtola, T., Bunker, A., Vattulainen, I., Deserno, M. and Karttunen, M. Multiscale modeling of emergent materials: biological and soft matter. Physical Chemistry Chemical Physics 11, 1869 (2009). DOI: http://dx.doi.org/10.1039/B818051B
Bjelkmar, P., Niemela, P. S., Vattulainen, I., Lindahl, E. and Roux, B. Conformational Changes and Slow Dynamics through Microsecond Polarized Atomistic Molecular Simulation of an Integral Kv1.2 Ion Channel. PLoS Computational Biology 5, e1000289 (2009). DOI: http://dx.doi.org/10.1371/journal.pcbi.1000289
Rog, T., Martinez-Seara, H., Munck, N., Oresic, M., Karttunen, M. and Vattulainen, I. Role of Cardiolipins in the Inner Mitochondrial Membrane: Insight Gained through Atom-Scale Simulations. The Journal of Physical Chemistry B 113, 3413–3422 (2009). DOI: http://dx.doi.org/10.1021/jp8077369
Ollila, O. H. S., Risselada, H. J., Louhivuori, M., Lindahl, E., Vattulainen, I. and Marrink, S. J. 3D Pressure Field in Lipid Membranes and Membrane-Protein Complexes. Physical Review Letters 102, 078101 (2009). DOI: http://dx.doi.org/10.1103/PhysRevLett.102.078101
Karttunen, M., Haataja, M. P., Saily, M., Vattulainen, I. and Holopainen, J. M. Lipid Domain Morphologies in Phosphatidylcholine-Ceramide Monolayers. Langmuir 25, 4595–4600 (2009). DOI: http://dx.doi.org/10.1021/la803377s
Niemela, P. S., Hyvonen, M. T. and Vattulainen, I. Atom-scale molecular interactions in lipid raft mixtures. Biochimica et Biophysica Acta (BBA) - Biomembranes 1788, 122–135 (2009). DOI: http://dx.doi.org/10.1016/j.bbamem.2008.08.018
Morrow, M. R., Helle, A., Perry, J., Vattulainen, I., Wiedmer, S. K. and Holopainen, J. M. Ceramide-1-Phosphate, in Contrast to Ceramide, Is Not Segregated into Lateral Lipid Domains in Phosphatidylcholine Bilayers. Biophysical Journal 96, 2216–2226 (2009). DOI: http://dx.doi.org/10.1016/j.bpj.2008.11.060
Xing, C., Ollila, O. H. S., Vattulainen, I. and Faller, R. Asymmetric nature of lateral pressure profiles in supported lipid membranes and its implications for membrane protein functions. Soft Matter 5, 3258 (2009). DOI: http://dx.doi.org/10.1039/b901664c
Martinez-Seara, H., Rog, T., Karttunen, M., Reigada, R. and Vattulainen, I. Influence of cis double-bond parametrization on lipid membrane properties: How seemingly insignificant details in force-field change even qualitative trends. The Journal of Chemical Physics 129, 105103 (2008). DOI: http://dx.doi.org/10.1063/1.2976443
Karttunen, M., Rottler, J., Vattulainen, I. and Sagui, C. Chapter 2 electrostatics in biomolecular simulations: Where are we now and where are we heading? In Feller, S. E. (ed.) Computational Modeling of Membrane Bilayers, vol. 60 of Current Topics in Membranes, 49 – 89 (Academic Press, 200). DOI: http://www.sciencedirect.com/science/article/pii/S1063582308000021
Rog, T., Vattulainen, I., Jansen, M., Ikonen, E. and Karttunen, M. Comparison of cholesterol and its direct precursors along the biosynthetic pathway: Effects of cholesterol, desmosterol and 7-dehydrocholesterol on saturated and unsaturated lipid bilayers. The Journal of Chemical Physics 129, 154508 (2008). DOI: http://dx.doi.org/10.1063/1.2996296
Holtta-Vuori, M., Uronen, R.-L., Repakova, J., Salonen, E., Vattulainen, I., Panula, P., Li, Z., Bittman, R. and Ikonen, E. BODIPY-Cholesterol: A New Tool to Visualize Sterol Trafficking in Living Cells and Organisms. Traffic 9, 1839–1849 (2008). DOI: http://dx.doi.org/10.1111/j.1600-0854.2008.00801.x
Wong-Ekkabut, J., Baoukina, S., Triampo, W., Tang, I.-M., Tieleman, D. P. and Monticelli, L. Computer simulation study of fullerene translocation through lipid membranes. Nature Nanotechnology 3, 363–368 (2008). DOI: http://dx.doi.org/10.1038/nnano.2008.130
Hall, A., Repakova, J. and Vattulainen, I. Modeling of the Triglyceride-Rich Core in Lipoprotein Particles. The Journal of Physical Chemistry B 112, 13772–13782 (2008). DOI: http://dx.doi.org/10.1021/jp803950w
Poyry, S., Rog, T., Karttunen, M. and Vattulainen, I. Significance of Cholesterol Methyl Groups. The Journal of Physical Chemistry B 112, 2922–2929 (2008). DOI: http://dx.doi.org/10.1021/jp7100495
Catte, A., Patterson, J. C., Bashtovyy, D., Jones, M. K., Gu, F., Li, L., Rampioni, A., Sengupta, D., Vuorela, T., Niemela, P., Karttunen, M., Marrink, S. J., Vattulainen, I., and Segrest, J. P. Structure of Spheroidal HDL Particles Revealed by Combined Atomistic and Coarse-Grained Simulations. Biophysical Journal 94, 2306–2319 (2008). DOI: http://dx.doi.org/10.1529/biophysj.107.115857
Martinez-Seara, H., Rog, T., Pasenkiewicz-Gierula, M., Vattulainen, I., Karttunen, M. and Reigada, R. Interplay of Unsaturated Phospholipids and Cholesterol in Membranes: Effect of the Double-Bond Position. Biophysical Journal 95, 3295–3305 (2008). DOI: http://dx.doi.org/10.1529/biophysj.108.138123
Lyulin, S. V., Vattulainen, I. and Gurtovenko, A. A. Complexes Comprised of Charged Dendrimers, Linear Polyelectrolytes, and Counterions: Insight through Coarse-Grained Molecular Dynamics Simulations. Macromolecules 41, 4961–4968 (2008). DOI: http://dx.doi.org/10.1021/MA800736P
Murtola, T., Vattulainen, I. and Karttunen, M. Systematic approach to coarse-graining of molecular descriptions and interactions with applications to lipid membranes. In Voth, G. (ed.) Coarse-Graining of Condensed Phase and Biomolecular Systems, 83–106 (CRC Press, 2008). DOI: http://dx.doi.org/10.1201/9781420059564.ch7
Falck, E., Rog, T., Karttunen, M. and Vattulainen, I. Lateral Diffusion in Lipid Membranes through Collective Flows. Journal of the American Chemical Society 130, 44–45 (2008). DOI: http://dx.doi.org/10.1021/ja7103558
Punkkinen, O., Naji, A., Podgornik, R., Vattulainen, I. and Hansen, P.-L. Ionic cloud distribution close to a charged surface in the presence of salt. EPL (Europhysics Letters) 82, 48001 (2008). DOI: http://dx.doi.org/10.1209/0295-5075/82/48001
Salonen, E., Lin, S., Reid, M. L., Allegood, M., Wang, X., Rao, A. M., Vattulainen, I. and Ke, P. C. Real-Time Translocation of Fullerene Reveals Cell Contraction. Small 4, 1986–1992 (2008). DOI: http://dx.doi.org/10.1002/smll.200701279
Gurtovenko, A. A. and Vattulainen, I. Membrane Potential and Electrostatics of Phospholipid Bilayers with Asymmetric Transmembrane Distribution of Anionic Lipids. The Journal of Physical Chemistry B 112, 4629–4634 (2008). DOI: http://dx.doi.org/10.1021/jp8001993
Vattulainen, I. Lipids: Organization and aggregation. In Begley, T. P. (ed.) Wiley Encyclopedia of Chemical Biology (John Wiley and Sons, Inc., 2007). DOI: http://dx.doi.org/10.1002/9780470048672.wecb664
Gurtovenko, A. A. and Vattulainen, I. Effect of NaCl and KCl on Phosphatidylcholine and Phosphatidylethanolamine Lipid Membranes: Insight from Atomic-Scale Simulations for Understanding Salt-Induced Effects in the Plasma Membrane. The Journal of Physical Chemistry B 112, 1953–1962 (2008). DOI: http://dx.doi.org/10.1021/jp0750708
Rog, T., Stimson, L. M., Pasenkiewicz-Gierula, M., Vattulainen, I. and Karttunen, M. Replacing the Cholesterol Hydroxyl Group with the Ketone Group Facilitates Sterol Flip-Flop and Promotes Membrane Fluidity. The Journal of Physical Chemistry B 112, 1946–1952 (2008). DOI: http://dx.doi.org/10.1021/JP075078H
Terama, E., Ollila, O. H. S., Salonen, E., Rowat, A. C., Trandum, C., Westh, P., Patra, M., Karttunen, M. and Vattulainen, I. Influence of Ethanol on Lipid Membranes: From Lateral Pressure Profiles to Dynamics and Partitioning. The Journal of Physical Chemistry B 112, 4131–4139 (2008). DOI: http://dx.doi.org/10.1021/jp0750811
Dias, C. L., Ala-Nissila, T., Karttunen, M., Vattulainen, I. and Grant, M. Microscopic Mechanism for Cold Denaturation. Physical Review Letters 100, 118101 (2008). DOI: http://dx.doi.org/10.1103/PhysRevLett.100.118101
Murtola, T., Vattulainen, I. and Falck, E. Insights into activation and RNA binding of trp RNA-binding attenuation protein (TRAP) through all-atom simulations. Proteins: Structure, Function, and Bioinformatics 71, 1995–2011 (2008). DOI: http://dx.doi.org/10.1002/prot.21878
Zhao, W., Rog, T., Gurtovenko, A. A., Vattulainen, I. and Karttunen, M. Role of phosphatidylglycerols in the stability of bacterial membranes. Biochimie 90, 930–938 (2008). DOI: http://dx.doi.org/10.1016/j.biochi.2008.02.025
Astrom, J. A., Kumar, P. B. S., Vattulainen, I. and Karttunen, M. Strain hardening, avalanches, and strain softening in dense cross-linked actin networks. Physical Review E 77, 051913 (2008). DOI: http://dx.doi.org/10.1103/PhysRevE.77.051913
Hall, A., Repakova, J. and Vattulainen, I. Molecular dynamics simulations of neutral lipids found in lipoproteins. Chemistry and Physics of Lipids 149, S78 (2007). DOI: http://dx.doi.org/10.1016/j.chemphyslip.2007.06.180
Salonen, E., Heikkila, K. and Vattulainen, I. Transport and effects of chlorpromazine on POPC and POPS lipid bilayers. Chemistry and Physics of Lipids 149, S42 (2007). DOI: http://dx.doi.org/10.1016/j.chemphyslip.2007.06.095
Rog, T., Stimson, L. M., Pasenkiewicz-Gierula, M., Vattulainen, I. and Karttunen, M. Effect of replacement of cholesterol hydroxyl group by ketone group. Chemistry and Physics of Lipids 149, S41–S42 (2007). DOI: http://dx.doi.org/10.1016/j.chemphyslip.2007.06.094
Poyry, S., Rog, T., Karttunen, M. and Vattulainen, I. Cholesterol methyl groupsmolecular fossils? Chemistry and Physics of Lipids 149, S41 (2007). DOI: http://dx.doi.org/10.1016/j.chemphyslip.2007.06.092
Ollila, S., Niemela, P., Rog, T., Hyvonen, M. T., Karttunen, M. and Vattulainen, I. Differences between lateral pressure profiles of one-component and many-component lipid membranes. Chemistry and Physics of Lipids 149, S15–S16 (2007). DOI: http://dx.doi.org/10.1016/j.chemphyslip.2007.06.033
Murtola, T., Rog, T., Falck, E., Karttunen, M. and Vattulainen, I. Multiscale simulations of domain formation in single-component phospholipid bilayers. Chemistry and Physics of Lipids 149, S15 (2007). DOI: http://dx.doi.org/10.1016/j.chemphyslip.2007.06.032
Warrier, M., Schneider, R., Salonen, E. and Nordlund, K. Effect of the porous structure of graphite on atomic hydrogen diffusion and inventory. Nuclear Fusion 47, 1656–1663 (2007). DOI: http://dx.doi.org/10.1088/0029-5515/47/12/003
Martinez-Seara, H., Rog, T., Pasenkiewicz-Gierula, M., Vattulainen, I., Karttunen, M. and Reigada, R. Effect of Double Bond Position on Lipid Bilayer Properties: Insight through Atomistic Simulations. The Journal of Physical Chemistry B 111, 11162–11168 (2007). DOI: http://dx.doi.org/10.1021/JP071894D
Gurtovenko, A. A. and Vattulainen, I. Molecular Mechanism for Lipid Flip-Flops. The Journal of Physical Chemistry B 111, 13554–13559 (2007). DOI: http://dx.doi.org/10.1021/jp077094k
Rog, T., Vattulainen, I., Bunker, A. and Karttunen, M. Glycolipid Membranes through Atomistic Simulations: Effect of Glucose and Galactose Head Groups on Lipid Bilayer Properties. The Journal of Physical Chemistry B 111, 10146–10154 (2007). DOI: http://dx.doi.org/10.1021/jp0730895
Gurtovenko, A. A. and Vattulainen, I. Lipid Transmembrane Asymmetry and Intrinsic Membrane Potential: Two Sides of the Same Coin. Journal of the American Chemical Society 129, 5358–5359 (2007). DOI: http://dx.doi.org/10.1021/ja070949m
Salonen, E., Terama, E., Vattulainen, I. and Karttunen, M. Enhanced dielectrophoresis of nanocolloids by dimer formation. Europhysics Letters (EPL) 78, 48004 (2007). DOI: http://dx.doi.org/10.1209/0295-5075/78/48004
Murtola, T., Falck, E., Karttunen, M. and Vattulainen, I. Coarse-grained model for phospholipid/cholesterol bilayer employing inverse Monte Carlo with thermodynamic constraints. The Journal of Chemical Physics 126, 075101 (2007). DOI: http://dx.doi.org/10.1063/1.2646614
Masin, M., Vattulainen, I., Ala-Nissila, T. and Chvoj, Z. Interplay between steps and nonequilibrium effects in surface diffusion for a lattice-gas model of OW(110). The Journal of Chemical Physics 126, 114705 (2007). DOI: http://dx.doi.org/10.1063/1.2713100
Degtyarenko, I. M., Jalkanen, K. J., Gurtovenko, A. A. and Nieminen, R. M. L-Alanine in a Droplet of Water: A Density-Functional Molecular Dynamics Study. The Journal of Physical Chemistry B 111, 4227–4234 (2007). DOI: http://dx.doi.org/10.1021/jp0676991
Curdova, J., Capkova, P., Plasek, J., Repakova, J. and Vattulainen, I. Free Pyrene Probes in Gel and Fluid Membranes: Perspective through Atomistic Simulations. The Journal of Physical Chemistry B 111, 3640–3650 (2007). DOI: http://dx.doi.org/10.1021/jp065956w
Samuli Ollila, O., Rog, T., Karttunen, M. and Vattulainen, I. Role of sterol type on lateral pressure profiles of lipid membranes affecting membrane protein functionality: Comparison between cholesterol, desmosterol, 7-dehydrocholesterol and ketosterol. Journal of Structural Biology 159, 311–323 (2007). DOI: http://dx.doi.org/10.1016/j.jsb.2007.01.012
Ollila, S., Hyvonen, M. T. and Vattulainen, I. Polyunsaturation in Lipid Membranes: Dynamic Properties and Lateral Pressure Profiles. The Journal of Physical Chemistry B 111, 3139–3150 (2007). DOI: http://dx.doi.org/10.1021/jp065424f
Rog, T., Pasenkiewicz-Gierula, M., Vattulainen, I. and Karttunen, M. What Happens if Cholesterol Is Made Smoother. Biophysical Journal 92, 3346–3357 (2007). DOI: http://dx.doi.org/10.1529/biophysj.106.095497
Gurtovenko, A. A. and Vattulainen, I. Ion Leakage through Transient Water Pores in Protein-Free Lipid Membranes Driven by Transmembrane Ionic Charge Imbalance. Biophysical Journal 92, 1878–1890 (2007). DOI: http://dx.doi.org/10.1529/biophysj.106.094797
Niemela, P. S., Ollila, S., Hyvonen, M. T., Karttunen, M. and Vattulainen, I. Assessing the Nature of Lipid Raft Membranes. PLoS Computational Biology 3, e34 (2007). DOI: http://dx.doi.org/10.1371/journal.pcbi.0030034
Aittoniemi, J., Niemela, P. S., Hyvonen, M. T., Karttunen, M. and Vattulainen, I. Insight into the Putative Specific Interactions between Cholesterol, Sphingomyelin, and Palmitoyl-Oleoyl Phosphatidylcholine. Biophysical Journal 92, 1125–1137 (2007). DOI: http://dx.doi.org/10.1529/biophysj.106.088427
Zhao, W., Rog, T., Gurtovenko, A. A., Vattulainen, I. and Karttunen, M. Atomic-Scale Structure and Electrostatics of Anionic Palmitoyloleoylphosphatidylglycerol Lipid Bilayers with Na+ Counterions. Biophysical Journal 92, 1114–1124 (2007). DOI: http://dx.doi.org/10.1529/biophysj.106.086272
Murtola, T., Kupiainen, M., Falck, E. and Vattulainen, I. Conformational analysis of lipid molecules by self-organizing maps. The Journal of Chemical Physics 126, 054707 (2007). DOI: http://dx.doi.org/10.1063/1.2429066
Nikunen, P., Vattulainen, I. and Karttunen, M. Reptational dynamics in dissipative particle dynamics simulations of polymer melts. Physical Review E 75, 036713 (2007). DOI: http://dx.doi.org/10.1103/PhysRevE.75.036713
Schneider, R., Rai, A., Mutzke, A., Warrier, M., Salonen, E. and Nordlund, K. Dynamic Monte-Carlo modeling of hydrogen isotope reactive-diffusive transport in porous graphite. Journal of Nuclear Materials 367-370, 1238–1242 (2007). DOI: http://dx.doi.org/10.1016/j.jnucmat.2007.03.226
Patra, M., Hyvonen, M. T., Falck, E., Sabouri-Ghomi, M., Vattulainen, I. and Karttunen, M. Long-range interactions and parallel scalability in molecular simulations. Computer Physics Communications 176, 14–22 (2007). DOI: http://dx.doi.org/10.1016/j.cpc.2006.07.017
Murtola, T., Rog, T., Falck, E., Karttunen, M. and Vattulainen, I. Transient Ordered Domains in Single-Component Phospholipid Bilayers. Physical Review Letters 97, 238102 (2006). DOI: http://dx.doi.org/10.1103/PhysRevLett.97.238102
Repakova, J., Holopainen, J. M., Karttunen, M. and Vattulainen, I. Influence of Pyrene-Labeling on Fluid Lipid Membranes. The Journal of Physical Chemistry B 110, 15403–15410 (2006). DOI: http://dx.doi.org/10.1021/JP061300R
Aittoniemi, J., Rog, T., Niemela, P., Pasenkiewicz-Gierula, M., Karttunen, M. and Vattulainen, I. Tilt: Major Factor in Sterols’ Ordering Capability in Membranes. The Journal of Physical Chemistry B 110, 25562–25564 (2006). DOI: http://dx.doi.org/10.1021/jp064931u
Falck, E., Hautala, J. T., Karttunen, M., Kinnunen, P. K., Patra, M., Saaren-Seppala, H., Vattulainen, I., Wiedmer, S. K. and Holopainen, J. M. Interaction of Fusidic Acid with Lipid Membranes: Implications to the Mechanism of Antibiotic Activity. Biophysical Journal 91, 1787–1799 (2006). DOI: http://dx.doi.org/10.1529/biophysj.106.084525
Gurtovenko, A. A., Lyulin, S. V., Karttunen, M. and Vattulainen, I. Molecular dynamics study of charged dendrimers in salt-free solution: Effect of counterions. The Journal of Chemical Physics 124, 094904 (2006). DOI: http://dx.doi.org/10.1063/1.2166396
Nordlund, K., Salonen, E., Krasheninnikov, A. V. and Keinonen, J. Swift chemical sputtering of covalently bonded materials. Pure and Applied Chemistry 78 (2006). DOI: http://dx.doi.org/10.1351/pac200678061203
WARRIER, M., SCHNEIDER, R., SALONEN, E. and NORDLUND, K. Multi-scale modeling of hydrogen isotope transport in porous graphite. Journal of Plasma Physics 72, 799 (2006). DOI: http://dx.doi.org/10.1017/S0022377806004909
Heikela, M., Vattulainen, I. and Hyvnen, M. T. Atomistic Simulation Studies of Cholesteryl Oleates: Model for the Core of Lipoprotein Particles. Biophysical Journal 90, 2247–2257 (2006). DOI: http://dx.doi.org/10.1529/biophysj.105.069849
Punkkinen, J., Konkka, I., Punkkinen, O., Korppi-Tommola, T., Farkkila, M. and Koskenpato, J. Measuring Gastric Emptying: Comparison of 13C-Octanoic Acid Breath Test and Scintigraphy. Digestive Diseases and Sciences 51, 262–267 (2006). DOI: http://dx.doi.org/10.1007/s10620-006-3122-2
Niemela, P. S., Hyvonen, M. T. and Vattulainen, I. Influence of Chain Length and Unsaturation on Sphingomyelin Bilayers. Biophysical Journal 90, 851–863 (2006). DOI: http://dx.doi.org/10.1529/biophysj.105.067371
Patra, M., Salonen, E., Terama, E., Vattulainen, I., Faller, R., Lee, B. W., Holopainen, J. and Karttunen, M. Under the Influence of Alcohol: The Effect of Ethanol and Methanol on Lipid Bilayers. Biophysical Journal 90, 1121–1135 (2006). DOI: http://dx.doi.org/10.1529/biophysj.105.062364
Masin, M. and Vattulainen, I. Computer Simulation Studies for Collective Adatom Diffusion Stepped Surfaces. Focus on Surface Science Research 1, 183–203 (2006). DOI: http://www.novapublishers.com/catalog/product_info.php?products_id=3685
Vattulainen, I. and Karttunen, M. Modeling of biologically motivated soft matter systems. In Rieth, M., De Gennes, P. and Schommers, W. (eds.) Handbook of Theoretical and Computational Nanotechnology, no. 1 in Handbook of Theoretical and Computational Nanotechnology, 361–417 (American Scientific Publishers, 2006). DOI: http://books.google.fi/books?id=p7VbjgEACAAJ
Vainio, S., Jansen, M., Koivusalo, M., Rog, T., Karttunen, M., Vattulainen, I. and Ikonen, E. Significance of sterol structural specificity: DESMOSTEROL CANNOT REPLACE CHOLESTEROL IN LIPID RAFTS. Journal of Biological Chemistry 281, 348–355 (2005). DOI: http://dx.doi.org/10.1074/jbc.M509530200
Juslin, N., Erhart, P., Traskelin, P., Nord, J., Henriksson, K. O. E., Nordlund, K., Salonen, E. and Albe, K. Analytical interatomic potential for modeling nonequilibrium processes in the WCH system. Journal of Applied Physics 98, 123520 (2005). DOI: http://dx.doi.org/10.1063/1.2149492
Masin, M., Vattulainen, I., Ala-Nissila, T. and Chvoj, Z. Nonequilibrium effects in diffusion of interacting particles on vicinal surfaces. The Journal of Chemical Physics 122, 214728 (2005). DOI: http://dx.doi.org/10.1063/1.1924695
Falck, E., Patra, M., Karttunen, M., Hyvonen, M. T. and Vattulainen, I. Response to Comment by Almeida et al.: Free Area Theories for Lipid BilayersPredictive or Not? Biophysical Journal 89, 745–752 (2005). DOI: http://dx.doi.org/10.1529/biophysj.105.065714
Stimson, L. M., Vattulainen, I., Rog, T. and Karttunen, M. EXPLORING THE EFFECT OF XENON ON BIOMEMBRANES. Cellular and Molecular Biology Letters 10, 563–569 (2005). DOI: http://www.cmbl.org.pl/pdf/Vol10_p563.pdf
Gurtovenko, A. A. and Vattulainen, I. Pore Formation Coupled to Ion Transport through Lipid Membranes as Induced by Transmembrane Ionic Charge Imbalance: Atomistic Molecular Dynamics Study. Journal of the American Chemical Society 127, 17570–17571 (2005). DOI: http://dx.doi.org/10.1021/ja053129n
Gurtovenko, A. A. Asymmetry of lipid bilayers induced by monovalent salt: Atomistic molecular-dynamics study. The Journal of Chemical Physics 122, 244902 (2005). DOI: http://dx.doi.org/10.1063/1.1942489
Rog, T., Vattulainen, I. and Karttunen, M. MODELING GLYCOLIPIDS: TAKE ONE. Cellular and Molecular Biology Letters 10, 625–630 (2005). DOI: http://www.cmbl.org.pl/pdf/Vol10_p625.pdf
Gurtovenko, A. A., Miettinen, M., Karttunen, M. and Vattulainen, I. Effect of Monovalent Salt on Cationic Lipid Membranes As Revealed by Molecular Dynamics Simulations. The Journal of Physical Chemistry B 109, 21126–21134 (2005). DOI: http://dx.doi.org/10.1021/jp053667m
Vattulainen, I. Molecules dancing in membranes. In Karger, J. (ed.) Diffusion Fundamentals, t. 1, 509–523 (Leipziger Univ.-Verlag, 2005). DOI: https://books.google.fi/books?id=4YKWiN2TMbQC
Kupiainen, M., Falck, E., Ollila, S., Niemela, P., Gurtovenko, A. A., Hyvonen, M. T., Patra, M., Karttunen, M. and Vattulainen, I. Free Volume Properties of Sphingomyelin, DMPC, DPPC, and PLPC Bilayers. Journal of Computational and Theoretical Nanoscience 2, 401–413 (2005). DOI: http://dx.doi.org/10.1166/jctn.2005.211
Punkkinen, O., Hansen, P. L., Miao, L. and Vattulainen, I. DNA Overstretching Transition: Ionic Strength Effects. Biophysical Journal 89, 967–978 (2005). DOI: http://dx.doi.org/10.1529/biophysj.105.063099
Hyvonen, M. T. and Kovanen, P. T. Molecular dynamics simulations of unsaturated lipid bilayers: effects of varying the numbers of double bonds. European Biophysics Journal 34, 294–305 (2005). DOI: http://dx.doi.org/10.1007/s00249-004-0455-7
Gurtovenko, A. A. and Blumen, A. Polymer Analysis Polymer Theory, chap. Generalized Gaussian Structures: Models for Polymer Systems with Complex Topologies, 171–282 (Springer Berlin Heidelberg, Berlin, Heidelberg, 2005). DOI: http://dx.doi.org/10.1007/b135561
Salonen, E., Terama, E., Vattulainen, I. and Karttunen, M. Dielectrophoresis of nanocolloids: A molecular dynamics study. The European Physical Journal E 18, 133–142 (2005). DOI: http://dx.doi.org/10.1140/epje/i2004-10157-2
Repakova, J., Holopainen, J. M., Morrow, M. R., McDonald, M. C., Capkova, P. and Vattulainen, I. Influence of DPH on the Structure and Dynamics of a DPPC Bilayer. Biophysical Journal 88, 3398–3410 (2005). DOI: http://dx.doi.org/10.1529/biophysj.104.055533
Punkkinen, O., Falck, E., Vattulainen, I. and Ala-Nissila, T. Dynamics and scaling of polymers in a dilute solution: Analytical treatment in two and higher dimensions. The Journal of Chemical Physics 122, 094904 (2005). DOI: http://dx.doi.org/10.1063/1.1855876
Warrier, M., Schneider, R., Salonen, E. and Nordlund, K. Multi-scale modeling of hydrogen isotope transport in porous graphite. Journal of Nuclear Materials 337-339, 580–584 (2005). DOI: http://dx.doi.org/10.1016/j.jnucmat.2004.10.017
Vattulainen, I. and Mouritsen, O. Diffusion in membranes. In Heitjans, P. and Krger, J. (eds.) Diffusion in Condensed Matter: Methods, Materials, Models, 471–512 (2005). DOI: http://dx.doi.org/10.1007/3-540-30970-5
Satmarel, C., Gurtovenko, A. A. and Blumen, A. Relaxation of Copolymeric Dendrimers Built from Alternating Monomers. Macromolecular Theory and Simulations 13, 487–496 (2004). DOI: http://dx.doi.org/10.1002/mats.200400020
Falck, E., Patra, M., Karttunen, M., Hyvonen, M. T. and Vattulainen, I. Impact of cholesterol on voids in phospholipid membranes. The Journal of Chemical Physics 121, 12676 (2004). DOI: http://dx.doi.org/10.1063/1.1824033
Murtola, T., Falck, E., Patra, M., Karttunen, M. and Vattulainen, I. Coarse-grained model for phospholipid/cholesterol bilayer. The Journal of Chemical Physics 121, 9156 (2004). DOI: http://dx.doi.org/10.1063/1.1803537
Niemela, P., Hyvonen, M. T. and Vattulainen, I. Structure and Dynamics of Sphingomyelin Bilayer: Insight Gained through Systematic Comparison to Phosphatidylcholine. Biophysical Journal 87, 2976–2989 (2004). DOI: http://dx.doi.org/10.1529/biophysj.104.048702
Repakova, J., Capkova, P., Holopainen, J. M. and Vattulainen, I. Distribution, Orientation, and Dynamics of DPH Probes in DPPC Bilayer. The Journal of Physical Chemistry B 108, 13438–13448 (2004). DOI: http://dx.doi.org/10.1021/JP048381G
Lee, B. W., Faller, R., Sum, A. K., Vattulainen, I., Patra, M. and Karttunen, M. Structural effects of small molecules on phospholipid bilayers investigated by molecular simulations. Fluid Phase Equilibria 225, 63–68 (2004). DOI: http://dx.doi.org/10.1016/j.fluid.2004.07.008
Falck, E., Patra, M., Karttunen, M., Hyvonen, M. T. and Vattulainen, I. Lessons of Slicing Membranes: Interplay of Packing, Free Area, and Lateral Diffusion in Phospholipid/Cholesterol Bilayers. Biophysical Journal 87, 1076–1091 (2004). DOI: http://dx.doi.org/10.1529/biophysj.104.041368
Gurtovenko, A. A., Patra, M., Karttunen, M. and Vattulainen, I. Cationic DMPC/DMTAP Lipid Bilayers: Molecular Dynamics Study. Biophysical Journal 86, 3461–3472 (2004). DOI: http://dx.doi.org/10.1529/biophysj.103.038760
Salonen, E. Overview of the Atomistic Modeling of the Chemical Erosion of Carbon. Physica Scripta T111, 133 (2004). DOI: http://dx.doi.org/10.1238/Physica.Topical.111a00133
Warrier, M., Schneider, R., Salonen, E. and Nordlund, K. Multiscale modeling of hydrogen isotope diffusion in graphite. Contributions to Plasma Physics 44, 307–310 (2004). DOI: http://dx.doi.org/10.1002/ctpp.200410047
Masin, M., Vattulainen, I., Ala-Nissila, T. and Chvoj, Z. Diffusion and mobility of interacting particles on stepped surfaces along the ledges. Surface Science 566-568, 143–147 (2004). DOI: http://dx.doi.org/10.1016/j.susc.2004.05.036
Zuckermann, M. J., Ipsen, J. H., Miao, L., Mouritsen, O. G., Nielsen, M., Polson, J., Thewalt, J., Vattulainen, I. and Zhu, H. Modeling lipidsterol bilayers: Applications to structural evolution, lateral diffusion, and rafts. In Numerical Computer Methods, Part D, vol. 383 of Methods in Enzymology, 198 – 229 (Academic Press, 2004). DOI: http://www.sciencedirect.com/science/article/pii/S007668790483009X
Patra, M., Karttunen, M., Hyvonen, M. T., Falck, E. and Vattulainen, I. Lipid Bilayers Driven to a Wrong Lane in Molecular Dynamics Simulations by Subtle Changes in Long-Range Electrostatic Interactions. The Journal of Physical Chemistry B 108, 4485–4494 (2004). DOI: http://dx.doi.org/10.1021/jp031281a
Falck, E., Lahtinen, J. M., Vattulainen, I. and Ala-Nissila, T. Influence of hydrodynamics on many-particle diffusion in 2D colloidal suspensions. The European Physical Journal E - Soft Matter 13, 267–275 (2004). DOI: http://dx.doi.org/10.1140/epje/i2003-10075-9
Satmarel, C., Gurtovenko, A. A. and Blumen, A. Viscoelastic Relaxation of Cross-Linked, Alternating Copolymers in the Free-Draining Limit. Macromolecules 36, 486–494 (2003). DOI: http://dx.doi.org/10.1021/ma0214409
Gotlib, Y. Y., Gurtovenko, A. A., Torchinskii, I. A., Shevelev, V. A. and Toshchevikov, V. P. The relaxation spectra of polymer networks with different types of topology, ordering, heterogeneity. Macromolecular Symposia 191, 131–140 (2003). DOI: http://dx.doi.org/10.1002/masy.200390003
Masin, M., Vattulainen, I., Ala-Nissila, T. and Chvoj, Z. Diffusion and mobility of interacting particles on stepped surfaces. Surface Science 544, L703–L708 (2003). DOI: http://dx.doi.org/10.1016/j.susc.2003.07.014
Gurtovenko, A. A., Markelov, D. A., Gotlib, Y. Y. and Blumen, A. Dynamics of dendrimer-based polymer networks. The Journal of Chemical Physics 119, 7579 (2003). DOI: http://dx.doi.org/10.1063/1.1606675
Falck, E., Punkkinen, O., Vattulainen, I. and Ala-Nissila, T. Dynamics and scaling of 2D polymers in a dilute solution. Physical Review E 68, 050102 (2003). DOI: http://dx.doi.org/10.1103/PhysRevE.68.050102
Hyvonen, M. T. and Kovanen, P. T. Molecular Dynamics Simulation of Sphingomyelin Bilayer. The Journal of Physical Chemistry B 107, 9102–9108 (2003). DOI: http://dx.doi.org/10.1021/jp035319v
Patra, M., Karttunen, M., Hyvonen, M., Falck, E., Lindqvist, P. and Vattulainen, I. Molecular dynamics simulations of lipid bilayers: Major artifacts due to truncating electrostatic interactions. Biophysical Journal 84, 3636 – 3645 (2003). DOI: http://www.sciencedirect.com/science/article/pii/S0006349503750942
Masin, M., Vattulainen, I., Ala-Nissila, T. and Chvoj, Z. Non-equilibrium effects in profile spreading on stepped surfaces. Surface Science 529, L256 – L262 (2003). DOI: http://www.sciencedirect.com/science/article/pii/S0039602803002681
Nikunen, P., Karttunen, M. and Vattulainen, I. How would you integrate the equations of motion in dissipative particle dynamics simulations? Computer Physics Communications 153, 407 – 423 (2003). DOI: http://www.sciencedirect.com/science/article/pii/S0010465503002029
Nikunen, P., Vattulainen, I. and Ala-Nissila, T. Effects of quenched impurities on surface diffusion, spreading, and ordering of O/W(110). The Journal of Chemical Physics 117, 6757 (2002). DOI: http://dx.doi.org/10.1063/1.1505856
Karttunen, M., Vattulainen, I. and Lukkarinen, A. SoftSimu 2002 - Novel Methods in Soft Matter Simulations. Applied Rheology 12, 200 (2002). DOI: http://dx.doi.org/10.3933/ApplRheol-12-200
Lyubartsev, A. P., Karttunen, M., Vattulainen, I. and Laaksonen, A. On Coarse-Graining by the Inverse Monte Carlo Method: Dissipative Particle Dynamics Simulations Made to a Precise Tool in Soft Matter Modeling. Soft Materials 1, 121–137 (2002). DOI: http://dx.doi.org/10.1081/SMTS-120016746
Masin, M., Chvoj, Z., Jelinek, P. and Heinonen, J. Monte-Carlo simulation of diffusion in a two barriers system. Surface Science 516, 169 – 178 (2002). DOI: http://www.sciencedirect.com/science/article/pii/S0039602802020307
Vattulainen, I., Karttunen, M., Besold, G. and Polson, J. M. Integration schemes for dissipative particle dynamics simulations: From softly interacting systems towards hybrid models. The Journal of Chemical Physics 116, 3967 (2002). DOI: http://dx.doi.org/10.1063/1.1450554
Nikunen, P., Vattulainen, I. and Ala-Nissila, T. Density profile evolution and nonequilibrium effects in partial and full spreading measurements of surface diffusion. The Journal of Chemical Physics 114, 6335 (2001). DOI: http://dx.doi.org/10.1063/1.1355765
Falck, E., Ala-Nissila, T., Granato, E. and Ying, S.-C. Dynamic scaling in c(22) reconstruction on w(0 0 1). Surface Science 482-485, Part 1, 413 – 417 (2001). DOI: http://www.sciencedirect.com/science/article/pii/S0039602801007919
Hjelt, T., Vattulainen, I., Lahtinen, J., Ala-Nissila, T. and Ying, S. How to measure velocity correlations from surface diffusion experiments by STM. Surface Science 482-485, Part 1, 381 – 385 (2001). DOI: http://www.sciencedirect.com/science/article/pii/S0039602801009402