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OnderzoekZernike (ZIAM)

Refereed academic publications of 2009

Molecular Dynamics
  1. Bennett, W.F.D., MacCallum, J.L., Hinner, M.J., Marrink, S.J. & Tieleman, D.P. Molecular view of cholesterol flip-flop and chemical potential in different membrane environments. Journal of the American Chemical Society 131 (35) 12714-12720 (2009)

  2. Berntsson, R.P.A., Doeven, M.K., Fusetti, F., Duurkens, R.H., Sengupta, D., Marrink, S.J., Thunnissen, A.M.W.H., Poolman, B. & Slotboom, D.J. The structural basis for peptide selection by the transport receptor OppA. Embo Journal 28 (9) 1332-1340 (2009)

  3. Esteban-Martin, S., Risselada, H.J., Salgado, J. & Marrink, S.J. Stability of asymmetric lipid bilayers assessed by molecular dynamics simulations. Journal of the American Chemical Society 131 (42) 15194-15202 (2009)

  4. Fuhrmans, M., Knecht, V. & Marrink, S.J. A single bicontinuous cubic phase induced by fusion peptides. Journal of the American Chemical Society 131 (26) 9166-+ (2009)

  5. Hinner, M.J., Marrink, S.J. & de Vries, A.H. Location, tilt, and binding: A molecular dynamics study of voltage-sensitive dyes in biomembranes. Journal of Physical Chemistry B 113 (48) 15807-15819 (2009)

  6. Kucerka, N., Gallova, J., Uhrikova, D., Balgavy, P., Bulacu, M., Marrink, S.J. & Katsaras, J. Areas of monounsaturated diacylphosphatidylcholines. Biophysical Journal 97 (7) 1926-1932 (2009)

  7. Lee, H., de Vries, A.H., Marrink, S.J. & Pastor, R.W. A coarse-grained model for polyethylene oxide and polyethylene glycol: Conformation and hydrodynamics. Journal of Physical Chemistry B 113 (40) 13186-13194 (2009)

  8. Lopez, C.A., Rzepiela, A.J., de Vries, A.H., Dijkhuizen, L., Hunenberger, P.H. & Marrink, S.J. Martini coarse-grained force field: Extension to carbohydrates. Journal of Chemical Theory and Computation 5 (12) 3195-3210 (2009)

  9. Marrink, S.J., de Vries, A.H. & Tieleman, D.P. Lipids on the move: Simulations of membrane pores, domains, stalks and curves. Biochimica et Biophysica Acta-Biomembranes 1788 (1) 149-168 (2009)

  10. Masman, M.F., Eisel, U.L.M., Csizmadia, I.G., Penke, B., Enriz, R.D., Marrink, S.J. & Luiten, P.G.M. In silico study of full-length amyloid beta 1-42 tri- and penta-oligomers in solution. Journal of Physical Chemistry B 113 (34) 11710-11719 (2009)

  11. Mulder, F.A.A. Leucine side-chain conformation and dynamics in proteins from C-13 NMR chemical shifts. Chembiochem 10 (9) 1477-1479 (2009)

  12. Ollila, O.H.S., Risselada, H.J., Louhivuori, M., Lindahl, E., Vattulainen, I. & Marrink, S.J. 3D pressure field in lipid membranes and membrane-protein complexes. Physical Review Letters 102 (7) art. 078101 (2009)

  13. Otten, R., Wood, K. & Mulder, F.A.A. Comprehensive determination of (3)J(HNH alpha) for unfolded proteins using C-13'-resolved spin-echo difference spectroscopy. Journal of Biomolecular Nmr 45 (4) 343-349 (2009)

  14. Periole, X., Cavalli, M., Marrink, S.J. & Ceruso, M.A. Combining an elastic network with a coarse-grained molecular force field: Structure, dynamics, and intermolecular recognition. Journal of Chemical Theory and Computation 5 (9) 2531-2543 (2009)

  15. Periole, X., Rampioni, A., Vendruscolo, M. & Mark, A.E. Factors that affect the degree of twist in beta-sheet structures: A molecular dynamics simulation study of a cross-beta filament of the GNNQQNY peptide. Journal of Physical Chemistry B 113 (6) 1728-1737 (2009)

  16. Periole, X., Allen, L.R., Tamiola, K., Mark, A.E. & Paci, E. Probing the free energy landscape of the FBP28 WW domain using multiple techniques. Journal of Computational Chemistry 30 (7) 1059-1068 (2009)

  17. Risselada, H.J. & Marrink, S.J. Curvature effects on lipid packing and dynamics in liposomes revealed by coarse grained molecular dynamics simulations. Physical Chemistry Chemical Physics 11 (12) 2056-2067 (2009)

  18. Risselada, H.J. & Marrink, S.J. The freezing process of small lipid vesicles at molecular resolution. Soft Matter 5 (22) 4531-4541 (2009)

  19. Sengupta, D., Rampioni, A. & Marrink, S.J. Simulations of the c-subunit of ATP-synthase reveal helix rearrangements. Molecular Membrane Biology 26 (8) 410-421 (2009)

  20. Siwko, M.E., de Vries, A.H., Mark, A.E., Kozubek, A. & Marrink, S.J. Disturb or stabilize? A molecular dynamics study of the effects of resorcinolic lipids on phospholipid bilayers. Biophysical Journal 96 (8) 3140-3153 (2009)

  21. Smith, L.J., Berendsen, H.J.C. & Gunsteren, W.F.v. Computer simulation of urea-water mixtures: A test of force field parameters for use in biomolecular simulation. Journal of Physical Chemistry B 108 1065-1071 (2009)

  22. Yesylevskyy, S., Marrink, S.J. & Mark, A.E. Alternative mechanisms for the interaction of the cell-penetrating peptides penetratin and the TAT peptide with lipid bilayers. Biophysical Journal 97 (1) 40-49 (2009)

Last modified:22 October 2012 2.30 p.m.