Solvent-free simulations of fluid membrane bilayers.

A molecular level model for lipid bilayers is presented. Lipids are represented by rigid, asymmetric, soft spherocylinders in implicit solvent. A simple three parameter potential between pairs of lipids gives rise to a rich assortment of phases including (but not limited to) micelles, fluid bilayers, and gel-like bilayers. Monte Carlo simulations have been carried out to verify self-assembly, characterize the phases corresponding to different potential parametrizations, and to quantify the physical properties associated with those parameter sets corresponding to fluid bilayer behavior. The studied fluid bilayers have compressibility moduli in agreement with experimental systems, but display bending moduli at least three times larger than typical biological membranes without cholesterol.

[1]  Bagchi,et al.  Computer simulation study of the melting transition in two dimensions. , 1996, Physical review letters.

[2]  Reinhard Lipowsky,et al.  Structure and dynamics of membranes , 1995 .

[3]  T. Lubensky,et al.  Principles of condensed matter physics , 1995 .

[4]  Udo Seifert,et al.  Configurations of fluid membranes and vesicles , 1997 .

[5]  M. Bloom,et al.  Physical properties of the fluid lipid-bilayer component of cell membranes: a perspective , 1991, Quarterly Reviews of Biophysics.

[6]  Fisher,et al.  Thermodynamic behavior of two-dimensional vesicles. , 1987, Physical review letters.

[7]  P. Gennes,et al.  The physics of liquid crystals , 1974 .

[8]  Smith,et al.  Structure of the L beta phases in a hydrated phosphatidylcholine multimembrane. , 1988, Physical Review Letters.

[9]  F. Brown.  Regulation of protein mobility via thermal membrane undulations. , 2003, Biophysical journal.

[10]  R. Lipowsky,et al.  Binding and unbinding of lipid membranes: A Monte Carlo study. , 1989, Physical review letters.

[11]  O. Farago.  “Water-free” computer model for fluid bilayer membranes , 2003, cond-mat/0304203.

[12]  Carlos Vega,et al.  A Fast Algorithm to Evaluate the Shortest Distance Between Rods , 1994, Comput. Chem..

[13]  E. Sackmann,et al.  On defects in different phases of two-dimensional lipid bilayers , 1983 .

[14]  S. Hyodo,et al.  Dissipative particle dynamics study of spontaneous vesicle formation of amphiphilic molecules , 2002 .

[15]  David R. Nelson,et al.  Theory of Two-Dimensional Melting , 1978 .

[16]  Peter A. J. Hilbers,et al.  Computer simulations of surfactant self-assembly. , 1993 .

[17]  J. Kirkwood,et al.  The Statistical Mechanical Theory of Surface Tension , 1949 .

[18]  Berend Smit,et al.  Understanding molecular simulation: from algorithms to applications , 1996 .

[19]  K. Schulten,et al.  Molecular dynamics simulation of a bilayer of 200 lipids in the gel and in the liquid crystal phase , 1993 .

[20]  S. Safran,et al.  NONLINEAR RESPONSE OF MEMBRANES TO PINNING SITES , 1997 .

[21]  J. Israelachvili.  Intermolecular and surface forces , 1985 .

[22]  Alan E. Mark,et al.  Effect of Undulations on Surface Tension in Simulated Bilayers , 2001 .

[23]  E. Lindahl,et al.  Molecular dynamics simulations of phospholipid bilayers with cholesterol. , 2003, Biophysical journal.

[24]  Gregory A. Voth,et al.  Interfacing continuum and molecular dynamics: An application to lipid bilayers , 2001 .

[25]  Nelson,et al.  Tethered surfaces: Statics and dynamics. , 1987, Physical review. A, General physics.

[26]  D. Chandler,et al.  Introduction To Modern Statistical Mechanics , 1987 .

[27]  A C Maggs,et al.  Computer simulations of self-assembled membranes. , 1991, Science.

[28]  D. Frenkel,et al.  Do cylinders exhibit a cubatic phase , 1999, cond-mat/9903324.

[29]  Reinhard Lipowsky,et al.  Computer simulations of bilayer membranes - self-assembly and interfacial tension. , 1998 .

[30]  Samuel A. Safran,et al.  Membrane-induced interactions between inclusions , 1993 .

[31]  FREEZING FLEXIBLE VESICLES , 1997 .

[32]  W. Helfrich.  Elastic Properties of Lipid Bilayers: Theory and Possible Experiments , 1973, Zeitschrift fur Naturforschung. Teil C: Biochemie, Biophysik, Biologie, Virologie.

[33]  Samuel A. Safran,et al.  Statistical Thermodynamics Of Surfaces, Interfaces, And Membranes , 1994 .

[34]  Milner,et al.  Dynamical fluctuations of droplet microemulsions and vesicles. , 1987, Physical review. A, General physics.

[35]  Gregory A Voth,et al.  Bridging microscopic and mesoscopic simulations of lipid bilayers. , 2002, Biophysical journal.

[36]  Gerhard Gompper,et al.  Mobility and elasticity of self-assembled membranes. , 1999 .

[37]  Ho,et al.  Crumpling of fluid vesicles. , 1990, Physical review. A, Atomic, molecular, and optical physics.

[38]  Yun Peng,et al.  Computational Models for the Formation of Protocell Structures , 1998, Artificial Life.

[39]  John S. Rowlinson,et al.  Molecular Theory of Capillarity , 1983 .

[40]  G. Oster,et al.  Curvature-mediated interactions between membrane proteins. , 1998, Biophysical journal.

[41]  G. Oster,et al.  Effect of protein shape on multibody interactions between membrane inclusions. , 2000, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.

[42]  John C. Shelley,et al.  Computer simulation of surfactant solutions , 2000 .

[43]  B. Ninham,et al.  Theory of self-assembly of hydrocarbon amphiphiles into micelles and bilayers , 1976 .

[44]  Ho,et al.  Observation of two-dimensional hexatic behavior in free-standing liquid-crystal thin films. , 1988, Physical review letters.

[45]  R. D. Groot,et al.  Mesoscopic simulation of cell membrane damage, morphology change and rupture by nonionic surfactants. , 2001, Biophysical journal.

[46]  David R. Nelson,et al.  Statistical mechanics of membranes and surfaces , 2004 .

[47]  Electrostatic analogy for surfactant assemblies , 1992 .

[48]  S. Weisberg.  Plots, transformations, and regression , 1985 .

[49]  Thomas Soddemann,et al.  A generic computer model for amphiphilic systems , 2001 .

[50]  Daan Frenkel,et al.  The hard ellipsoid-of-revolution fluid I. Monte Carlo simulations , 1985 .

[51]  K Schulten,et al.  VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.

[52]  U. Essmann,et al.  The origin of the hydration interaction of lipid bilayers from MD simulation of dipalmitoylphosphatidylcholine membranes in gel and liquid crystalline phases , 1995 .

[53]  M. Sansom,et al.  Interactions of alpha-helices with lipid bilayers: a review of simulation studies. , 1999, Biophysical chemistry.

[54]  M. Caffrey,et al.  Phases and phase transitions of the phosphatidylcholines. , 1998, Biochimica et biophysica acta.

[55]  J. Goodby,et al.  X-Ray Observation of a Stacked Hexatic Liquid-CrystalBPhase , 1981 .

[56]  Jonathan W. Essex,et al.  Molecular dynamics simulation of the hydrocarbon region of a biomembrane using a reduced representation model , 2001, J. Comput. Chem..

[57]  Douglas J. Tobias,et al.  Atomic-scale molecular dynamics simulations of lipid membranes , 1997 .

[58]  W. Gelbart,et al.  Curvature defects in lamellar phases of amphiphile–water systems , 1991 .

[59]  F. Brochard,et al.  Frequency spectrum of the flicker phenomenon in erythrocytes , 1975 .

[60]  Richard W. Pastor,et al.  Molecular dynamics and Monte Carlo simulations of lipid bilayers , 1994 .

[61]  L. F. Rull,et al.  Monte Carlo study of liquid crystal phases of hard and soft spherocylinders , 2002 .

[62]  J. Ho,et al.  Simulations of Fluid Self-Avoiding Membranes , 1990 .

[63]  Frenkel,et al.  Phase diagram of a system of hard spherocylinders by computer simulation. , 1990, Physical review. A, Atomic, molecular, and optical physics.

[64]  S. Feller,et al.  Molecular dynamics simulations of lipid bilayers , 2000 .

[65]  E. Lindahl,et al.  Mesoscopic undulations and thickness fluctuations in lipid bilayers from molecular dynamics simulations. , 2000, Biophysical journal.

[66]  M. Costello,et al.  Defect structures in lyotropic smectic phases revealed by freeze-fracture electron microscopy , 1977 .

[67]  Reinhard Lipowsky,et al.  Equilibrium structure and lateral stress distribution of amphiphilic bilayers from dissipative particle dynamics simulations , 2002 .

[68]  M. Klein,et al.  Computer simulation studies of biomembranes using a coarse grain model , 2002 .

[69]  Molecular dynamics studies of smectic B liquid crystals of soft parallel spherocylinders with sixfold bond orientational order. , 1992, Physical review letters.

[70]  Fluctuation-induced interactions between rods on membranes and interfaces , 1995, cond-mat/9509071.

[71]  M. Plischke,et al.  Molecular dynamics of tethered membranes. , 1989, Physical review letters.

[72]  W. Helfrich.  Effect of thermal undulations on the rigidity of fluid membranes and interfaces , 1985 .

[73]  D P Tieleman,et al.  A computer perspective of membranes: molecular dynamics studies of lipid bilayer systems. , 1997, Biochimica et biophysica acta.

[74]  H. Lodish.  Molecular Cell Biology , 1986 .

[75]  Fluctuation-induced interactions between rods on a membrane. , 1996, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.

[76]  Jay T. Groves,et al.  Synaptic pattern formation during cellular recognition , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[77]  Hiroshi Noguchi,et al.  Fusion pathways of vesicles: A Brownian dynamics simulation , 2001 .

[78]  P. Canham.  The minimum energy of bending as a possible explanation of the biconcave shape of the human red blood cell. , 1970, Journal of theoretical biology.

[79]  G. S. Smith,et al.  X-ray structural studies of freely suspended ordered hydrated DMPC multimembrane films , 1990 .

[80]  Mark Goulian,et al.  Long-Range Forces in Heterogeneous Fluid Membranes , 1993 .

[81]  G. Ranieri,et al.  Structure of the lamellar lyo-mesophase in water/ammonium perfluorononanoate mixtures: PFG NMR and 2H-NMR investigations , 1988 .

[82]  Charles Tanford,et al.  The hydrophobic effect , 1980 .

[83]  M. C. Holmes,et al.  Smectic-nematic transition in a lyotropic liquid crystal , 1984 .

[84]  Lipowsky,et al.  Shape fluctuations of polymerized or solidlike membranes. , 1990, Physical review letters.