Biological Physics & Soft Matter - Tampere University of Technology

Department of Physics

Biological Physics and Soft Matter (BIO) Group

   

 

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Our team is the host to the ERC Advanced Grant Project CROWDED-PRO-LIPIDS granted to us by the European Research Council for 2012-2017.

We were chosen as Centre of Excellence (CoE) in Biomembrane Research by the Academy of Finland for 2014-2019. The Centre is comprised of three groups,one of them being our computational and theoretical team directed by Ilpo Vattulainen (vice-chair of the CoE), the others being directed by Academyprof. Elina Ikonen (chair, Univ Helsinki) and Prof. Pekka Lappalainen (partner, Univ Helsinki).

Biological physics, as many people call this discipline nowadays, is an excellent example of a cross-disciplinary field of science that bridges people with various backgrounds to work on problems whose proper understanding is crucial for life. Although much has been done, we are still on our early days of understanding the underlying physical principles that govern the behavior of biological systems.

The Biological Physics and Soft Matter Group focuses on the theory and modeling of biologically relevant soft and condensed matter systems. The work includes the development of theoretical and computational techniques for multiscale modeling, and applications of these methods to study physicochemical properties of soft and condensed matter systems over a multitude of scales.

The research covers lipid membranes (as well as interactions of these systems with e.g. drugs, alcohols, sterols, and nanoparticles), drug delivery, structure and dynamics of protein systems (in particular protein-membrane complexes), lipoproteins, glycosystems, and the non-equilibrium dynamics at soft interfaces and solid surfaces. The focus is more and more on cross-disciplinary problems in the field where the traditional borderlines between physics, chemistry, and computational and medical sciences tend to vanish.

Recent highlights

  • N-glycosylation as determinant of epidermal growth factor receptor conformation in membranes. K. Kazuba, M. Grzybek, A. Orlowski, R. Danne, T. Rog, K. Simons, U. Coskun, I. Vattulainen. Proceedings of the National Academy of Sciences USA (2015, in press).
  • Proton-coupled electron transfer and the role of water molecules in proton pumping by cytochrome c oxidase. V. Sharma, G. Enkavi, I. Vattulainen, T. Rog, M. Wikstrom. Proceedings of the National Academy of Sciences USA 112, 2040 (2015).
  • How anacetrapib inhibits the activity of the cholesteryl ester transfer protein? Perspective through atomistic simulations. T. Aijanen, A. Koivuniemi, M. Javanainen, S. Rissanen, T. Rog, I. Vattulainen. PLoS Computational Biology 10, e1003987 (2014).
  • Lipid exchange mechanism of the cholesteryl ester transfer protein clarified by atomistic and coarse-grained simulations. A. Koivuniemi, T. Vuorela, P. T. Kovanen, I. Vattulainen, M. T. Hyvonen. PLoS Computational Biology 8, e1002299 (2012).
  • Cholesterol modulates glycolipid conformation and receptor activity. D. Lingwood, B. Binnington, T. Rog, I. Vattulainen, M. Grzybek, U. Coskun, C. A. Lingwood, and K. Simons. Nature Chemical Biology vol. 7, 260-262 (2011).
  • Lateral sorting in model membranes by cholesterol-mediated hydrophobic matching. H. J. Kaiser, A. Orlowski, T. Rog, T. K. M. Nyholm, W. G. Chai, T. Feizi, D. Lingwood, I. Vattulainen, and K. Simons. Proceedings of the National Academy of Sciences USA 108, 16628-16633 (2011).
  • Association of lipidome remodelling in the adipocyte membrane with acquired obesity in humans. K. Pietilainen, T. Rog, T. Seppanen-Laakso, S. Virtue, P. Gopalacharyulu, J. Tang, S. Rodriguez-Cuenca, A. Maciejewski, J. Naukkarinen, A.-L. Ruskeepaa, P. Niemela, L. Yetukuri, C. Y. Tan, V. Velagapudi, S. Castillo, H. Nygren, T. Hyotylainen, A. Rissanen, J. Kaprio, H. Yki-Jarvinen, I. Vattulainen, A. Vidal-Plug, and M. Oresic. PLoS Biology 9, e1000623 (2011).
  • Defect-mediated trafficking across cell membranes. A. A. Gurtovenko, J. Anwar, and I. Vattulainen. Chemical Reviews vol. 110, 6077 (2010).
  • From local structure to nanosecond recrystallization dynamics in AgInSbTe phase-change materials. T. Matsunaga, J. Akola, S. Kohara, T. Honma, K. Kobayashi, E. Ikenaga, R. O. Jones, N. Yamada, M. Takata, and R. Kojima. Nature Materials vol. 10, 129 (2011).
  • Role of lipids in spheroidal high density lipoproteins. T. Vuorela, A. Catte, P. S. Niemela, A. Hall, M. T. Hyvonen, S. J. Marrink, M. Karttunen, and I. Vattulainen. PLoS Computational Biology vol. 6, e1000964 (2010).
  • Membrane proteins diffuse as dynamical complexes with lipids. P. Niemela, M. S. Miettinen, L. Monticelli, H. Hammaren, P. Bjelkmar, T. Murtola, E. Lindahl, and I. Vattulainen. Journal of the American Chemical Society vol. 132, 7574 (2010).
  • Quantum size effects in ambient CO oxidation catalysed by ligand-protected gold clusters. O. Lopez-Acevedo, K. A. Kacprzak, J. Akola, and H. Hakkinen. Nature Chemistry vol. 2, 329 (2010).
  • 3D Pressure Field in Lipid Membranes and Membrane-Protein Complexes. O. H. S. Ollila, J. Risselada, M. Louhivuori, E. Lindahl, I. Vattulainen, and S. J. Marrink. Physical Review Letters vol. 102, 078101 (2009).
  • Conformational changes and slow dynamics through microsecond polarized molecular simulation of an integral Kv1.2 ion channel. P. Bjelkmar, P. Niemela, I. Vattulainen, and E. Lindahl. PLoS Computational Biology vol. 5, e1000289 (2009).
  • BODIPY-cholesterol: A new tool to visualize sterol trafficking in living cells and organisms. M. Holtta-Vuori, R.-L. Uronen, J. Repakova, E. Salonen, I. Vattulainen, P. Panula, Z. Li, R. Bittman, and E. Ikonen. Traffic 9, 1839-1849 (2008).
  • Real-Time Translocation of Fullerene Reveals Cell Contraction. E. Salonen, S. Lin, M. L. Reid, M. Allegood, X. Wang, A. M. Rao, I. Vattulainen, and P.-C. Ke. Small 4, 1986-1992 (2008).
  • Lateral Diffusion in Lipid Membranes Through Collective Flows. E. Falck, T. Rog, M. Karttunen, and I. Vattulainen. Journal of the American Chemical Society 130, 44 (2008).
  • Lipid Transmembrane Asymmetry and Intrinsic Membrane Potential: Two Sides of the Same Coin. A. A. Gurtovenko and I. Vattulainen. Journal of the American Chemical Society 129, 5358 (2007).
  • Assessing the Nature of Lipid Raft Membranes. P. Niemela, S. Ollila, M. T. Hyvonen, M. Karttunen, and I. Vattulainen. PLoS Computational Biology 3, 304-312 (2007).

Updated by: Ilpo Vattulainen, 19.03.2015 15:40.
Content owner: Vattulainen Ilpo
Keywords: science and research, biological physics