Skip to main content
NCBI home page
Biophysical Journal logoLink to Biophysical Journal
. 2002 Dec;83(6):3357–3370. doi: 10.1016/S0006-3495(02)75336-8

Bridging microscopic and mesoscopic simulations of lipid bilayers.

Gary Ayton 1, Gregory A Voth 1
PMCID: PMC1302411  PMID: 12496103

Abstract

A lipid bilayer is modeled using a mesoscopic model designed to bridge atomistic bilayer simulations with macro-scale continuum-level simulation. Key material properties obtained from detailed atomistic-level simulations are used to parameterize the meso-scale model. The fundamental length and time scale of the meso-scale simulation are at least an order of magnitude beyond that used at the atomistic level. Dissipative particle dynamics cast in a new membrane formulation provides the simulation methodology. A meso-scale representation of a dimyristoylphosphatidylcholine membrane is examined in the high and low surface tension regimes. At high surface tensions, the calculated modulus is found to be slightly less than the atomistically determined value. This result agrees with the theoretical prediction that high-strain thermal undulations still persist, which have the effect of reducing the value of the atomistically determined modulus. Zero surface tension simulations indicate the presence of strong thermal undulatory modes, whereas the undulation spectrum and the calculated bending modulus are in excellent agreement with theoretical predictions and experiment.

Full Text

The Full Text of this article is available as a PDF (204.9 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Ayton Gary, Smondyrev Alexander M., Bardenhagen Scott G., McMurtry Patrick, Voth Gregory A. Calculating the bulk modulus for a lipid bilayer with nonequilibrium molecular dynamics simulation. Biophys J. 2002 Mar;82(3):1226–1238. doi: 10.1016/S0006-3495(02)75479-9. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Ayton Gary, Smondyrev Alexander M., Bardenhagen Scott G., McMurtry Patrick, Voth Gregory A. Interfacing molecular dynamics and macro-scale simulations for lipid bilayer vesicles. Biophys J. 2002 Aug;83(2):1026–1038. doi: 10.1016/S0006-3495(02)75228-4. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Bagatolli L. A., Gratton E. Two photon fluorescence microscopy of coexisting lipid domains in giant unilamellar vesicles of binary phospholipid mixtures. Biophys J. 2000 Jan;78(1):290–305. doi: 10.1016/S0006-3495(00)76592-1. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Bagatolli L. A., Parasassi T., Gratton E. Giant phospholipid vesicles: comparison among the whole lipid sample characteristics using different preparation methods: a two photon fluorescence microscopy study. Chem Phys Lipids. 2000 Apr;105(2):135–147. doi: 10.1016/s0009-3084(00)00118-3. [DOI] [PubMed] [Google Scholar]
  5. Boey S. K., Boal D. H., Discher D. E. Simulations of the erythrocyte cytoskeleton at large deformation. I. Microscopic models. Biophys J. 1998 Sep;75(3):1573–1583. doi: 10.1016/S0006-3495(98)74075-5. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Discher D. E., Boal D. H., Boey S. K. Simulations of the erythrocyte cytoskeleton at large deformation. II. Micropipette aspiration. Biophys J. 1998 Sep;75(3):1584–1597. doi: 10.1016/S0006-3495(98)74076-7. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Español P. Dissipative particle dynamics for a harmonic chain: A first-principles derivation. Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics. 1996 Feb;53(2):1572–1578. doi: 10.1103/physreve.53.1572. [DOI] [PubMed] [Google Scholar]
  8. Español P. Hydrodynamics from dissipative particle dynamics. Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics. 1995 Aug;52(2):1734–1742. doi: 10.1103/physreve.52.1734. [DOI] [PubMed] [Google Scholar]
  9. Evans E, Rawicz W. Entropy-driven tension and bending elasticity in condensed-fluid membranes. Phys Rev Lett. 1990 Apr 23;64(17):2094–2097. doi: 10.1103/PhysRevLett.64.2094. [DOI] [PubMed] [Google Scholar]
  10. Forrest L. R., Sansom M. S. Membrane simulations: bigger and better? Curr Opin Struct Biol. 2000 Apr;10(2):174–181. doi: 10.1016/s0959-440x(00)00066-x. [DOI] [PubMed] [Google Scholar]
  11. Groot R. D., Rabone K. L. Mesoscopic simulation of cell membrane damage, morphology change and rupture by nonionic surfactants. Biophys J. 2001 Aug;81(2):725–736. doi: 10.1016/S0006-3495(01)75737-2. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Hallett F. R., Marsh J., Nickel B. G., Wood J. M. Mechanical properties of vesicles. II. A model for osmotic swelling and lysis. Biophys J. 1993 Feb;64(2):435–442. doi: 10.1016/S0006-3495(93)81384-5. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Hoover WG. Canonical dynamics: Equilibrium phase-space distributions. Phys Rev A Gen Phys. 1985 Mar;31(3):1695–1697. doi: 10.1103/physreva.31.1695. [DOI] [PubMed] [Google Scholar]
  14. Koenig B. W., Strey H. H., Gawrisch K. Membrane lateral compressibility determined by NMR and x-ray diffraction: effect of acyl chain polyunsaturation. Biophys J. 1997 Oct;73(4):1954–1966. doi: 10.1016/S0006-3495(97)78226-2. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Lindahl E., Edholm O. Mesoscopic undulations and thickness fluctuations in lipid bilayers from molecular dynamics simulations. Biophys J. 2000 Jul;79(1):426–433. doi: 10.1016/S0006-3495(00)76304-1. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Noguchi Hiroshi, Takasu Masako. Adhesion of nanoparticles to vesicles: a Brownian dynamics simulation. Biophys J. 2002 Jul;83(1):299–308. doi: 10.1016/S0006-3495(02)75170-9. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Rawicz W., Olbrich K. C., McIntosh T., Needham D., Evans E. Effect of chain length and unsaturation on elasticity of lipid bilayers. Biophys J. 2000 Jul;79(1):328–339. doi: 10.1016/S0006-3495(00)76295-3. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Sackmann E. The seventh Datta Lecture. Membrane bending energy concept of vesicle- and cell-shapes and shape-transitions. FEBS Lett. 1994 Jun 6;346(1):3–16. doi: 10.1016/0014-5793(94)00484-6. [DOI] [PubMed] [Google Scholar]
  19. Smondyrev A. M., Berkowitz M. L. Molecular dynamics simulation of the structure of dimyristoylphosphatidylcholine bilayers with cholesterol, ergosterol, and lanosterol. Biophys J. 2001 Apr;80(4):1649–1658. doi: 10.1016/S0006-3495(01)76137-1. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Tieleman D. P., Marrink S. J., Berendsen H. J. A computer perspective of membranes: molecular dynamics studies of lipid bilayer systems. Biochim Biophys Acta. 1997 Nov 21;1331(3):235–270. doi: 10.1016/s0304-4157(97)00008-7. [DOI] [PubMed] [Google Scholar]

Articles from Biophysical Journal are provided here courtesy of The Biophysical Society

RESOURCES