Publications

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

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