Coarse-grained solvent-free simulation models enabling the study of self-assembling fluid lipid bilayers have been the goal of much recent modeling efforts, since their realization appeared to be quite intricate. This contribution reviews some of the challenges faced along the way, presents a surprisingly simple solution, and illustrates its capacity by means of three examples of biological interest.
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References
W.M. Gelbart, A. Ben-Shaul, D. Roux (Eds.), Micelles, Membranes, Microemulsions, and Monolayers. (Springer, New York 1994)
D.R. Nelson, T. Piran, S. Weinberg (Eds.), Statistical Mechanics of Membranes and Surfaces, 2nd edn. (World Scientific, Singapore 2004)
R. Lipowsky, E. Sackmann (Eds.), Structure and Dynamics of Membranes From Cells to Vesicles, vol. 1 of the Handbook of Biological Physics (Elsevier, Amsterdam 1995)
H. Lodish, A. Berk, S.L. Zipursky, P. Matsudaira, D. Baltimore, J. Darnell, Molecular Cell Biology. 2nd edn. (W.H. Freeman, New York, 2000)
D.P. Tieleman, S.J. Marrink, H.J.C. Berendsen, Biochim. Biophys. Acta 1331, 235 (1997); S.E. Feller, Curr. Opin. Colloid Interface Sci. 5, 217 (2000); L. Saiz, S. Bandyopadhyay, M.L. Klein, Biosci. Rep. 22, 151 (2002)
G. Gompper, D.M. Kroll, Chap. 12 in [2]
R. Goetz, R. Lipowsky, J. Chem. Phys. 108, 7397 (1998); R. Goetz, G. Gompper, R. Lipowsky, Phys. Rev. Lett. 82, 221 (1999); J.C. Shelley, M.Y. Shelley, R.C. Reeder, S. Bandyopadhyay, M.L. Klein, J. Phys. Chem. B 105, 4464 (2001); R.D. Groot, K.L. Rabone, Biophys. J. 81, 725 (2001); J. Shillcock, R. Lipowsky, J. Chem. Phys. 117, 5048 (2002); S.J. Marrink, A.E. Mark, J. Am. Chem. Soc. 125, 11144 (2003); M.J. Stevens, J. Chem. Phys. 121, 11942 (2004); R. Chang, G.S. Ayton, G.A. Voth, J. Chem. Phys. 122, 244716 (2005)
S. Yamamoto, S. Hyodo, J. Chem. Phys. 118, 7937 (2003)
M. Laradji, P.B. Sunil Kumar, Phys. Rev. Lett. 93, 198105 (2004)
J.-M. Drouffe, A.C. Maggs, S. Leibler, Science 254, 1353 (1991)
H. Noguchi, M. Takasu, Phys. Rev. E 64, 041913 (2001); J. Chem. Phys. 115, 9547 (2001); Biophys. J. 83, 299 (2002); Phys. Rev. E 65, 051907 (2002)
Z.-J. Wang, D. Frenkel, J. Chem. Phys. 122, 234711 (2005)
O. Farago, J. Chem. Phys. 119, 596 (2003)
G. Brannigan, F.L.H. Brown, J. Chem. Phys. 120, 1059 (2004); G. Brannigan, A.C. Tamboli, F.L.H. Brown, J. Chem. Phys. 121, 3259 (2004)
G. Brannigan, P.F. Philips, F.L.H. Brown, Phys. Rev. E 72, 011915 (2005)
I.R. Cooke, K. Kremer, M. Deserno, Phys. Rev. E 72, 011506 (2005)
I.R. Cooke, M. Deserno, J. Chem. Phys. 123, 224710 (2005)
K. Binder (Ed.), Monte Carlo and Molecular Dynamics Simulations in Polymer Science. (Oxford University Press, Oxford, 1995)
J.N. Israelachvili: Intermolecular and Surface Forces. 2nd edn. (Academic Press, London, San Diego, 1992)
N.T. Southall, K.A. Dill, A.D.J. Haymet, J. Phys. Chem. B 106, 521 (2002)
A.P. Gast, C.K. Hall, W.B. Russel, J. Coll. Interface Sci. 96, 251 (1983); M.H.J. Hagen, D. Frenkel, J. Chem. Phys. 101, 4093 (1994); A.A. Louis, Phil. Trans. R. Soc. Lond. A 359, 939 (2001)
I.R. Cooke, M. Deserno, Biophys. J. (submitted)
A. Arnold, B.A.F. Mann, H.J. Limbach, C. Holm, Comp. Phys. Comm. (in press); see also:http://www.espresso.mpg.de.
G.S. Grest, K. Kremer, Phys. Rev. A.33, 3628 (1986)
M.P. Allen, D.J. Tildesley:Computer Simulation of Liquids. (Clarendon, Oxford, 1990)
A. Kolb, B. Dünweg, J. Chem. Phys.111, 4453 (1999)
W. Helfrich, Phys. Lett. A50, 115 (1974)
P.B. Canham, J. Theoret. Biol.26, 61 (1970); W. Helfrich, Z. Naturforsch.28c, 693 (1973)
U. Seifert, R. Lipowsky: Chap. 8 in [3]
P.F. Fahey, W.W. Webb, Biochem.17, 3046 (1978)
E. Sackmann: Chap. 1 in [3]
R. Lipowsky, Biophys. J.64, 1133 (1993)
T. Baumgart, S.T. Hess, W.W. Webb, Nature425, 821 (2003)
P.B. Sunil Kumar, G. Gompper, R. Lipowsky, Phys. Rev. Lett.86, 3911 (2001)
K. Binder, D. Stauffer, Phys. Rev. Lett.33, 1006 (1974)
K. Simons, G. van Meer, Biochem.27, 6197 (1988)
S. Mukherjee, T.T. Soe, F.R. Maxfield, J. Cell. Biol.144, 1271 (1999)
H.T. McMahon, J.L. Gallop, Nature438, 590 (2005)
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Deserno, M. (2009). Solvent-Free Lipid-Bilayer Simulations: From Physics to Biology. In: Landau, D.P., Lewis, S.P., Schöttler, H.B. (eds) Computer Simulation Studies in Condensed-Matter Physics XIX. Springer Proceedings in Physics, vol 123. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-85625-2_20
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