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Interpretation of Fluctuation Spectra in Lipid Bilayer Simulations
KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical Biological Physics.
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2011 (English)In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 100, no 9, 2104-2111 p.Article in journal (Refereed) Published
Abstract [en]

Atomic resolution and coarse-grained simulations of dimyristoylphosphatidylcholine lipid bilayers were analyzed for fluctuations perpendicular to the bilayer using a completely Fourier-based method. We find that the fluctuation spectrum of motions perpendicular to the bilayer can be decomposed into just two parts: 1), a pure undulation spectrum proportional to q(-4) that dominates in the small-q regime; and 2), a molecular density structure factor contribution that dominates in the large-q regime. There is no need for a term proportional to q(-2) that has been postulated for protrusion fluctuations and that appeared to have been necessary to fit the spectrum for intermediate q. We suggest that earlier reports of such a term were due to the artifact of binning and smoothing in real space before obtaining the Fourier spectrum. The observability of an intermediate protrusion regime from the fluctuation spectrum is discussed based on measured and calculated material constants.

Place, publisher, year, edition, pages
2011. Vol. 100, no 9, 2104-2111 p.
Keyword [en]
MOLECULAR-DYNAMICS SIMULATIONS; ENTROPY-DRIVEN TENSION; COARSE-GRAINED MODEL; PARTICLE MESH EWALD; THERMAL FLUCTUATIONS; BENDING ELASTICITY; CONSTANT-PRESSURE; MEMBRANES; HYDRATION; SCATTERING
National Category
Biophysics
Identifiers
URN: urn:nbn:se:kth:diva-33982DOI: 10.1016/j.bpj.2011.03.010ISI: 000290360000006Scopus ID: 2-s2.0-79959741351OAI: oai:DiVA.org:kth-33982DiVA: diva2:419844
Funder
Swedish e‐Science Research Center
Note
QC 20110530Available from: 2011-05-30 Created: 2011-05-23 Last updated: 2017-12-11Bibliographically approved
In thesis
1. Molecular Dynamics Simulations of Fluid Lipid Membranes
Open this publication in new window or tab >>Molecular Dynamics Simulations of Fluid Lipid Membranes
2011 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Lipid molecules form thin biological membranes that envelop all living cells, and behave as two-dimensional liquid sheets immersed in bulk water. The interactions of such biomembranes with their environment lay the foundation of a plethora of biological processes rooted in the mesoscopic domain - length scales of 1-1000 nm and time scales of 1-1000 ns. Research in this intermediate regime has for a long time been out of reach for conventional experiments, but breakthroughs in computer simulation methods and scattering experimental techniques have made it possible to directly probe static and dynamic properties of biomembranes on these scales.

Biomembranes are soft, with a relatively low energy cost of bending, and are thereby influenced by random, thermal fluctuations of individual molecules. Molecular dynamics simulations show how in-plane (density fluctuations) and out-of-plane (undulations) motions are intertwined in the bilayer in the mesoscopic domain. By novel methods, the fluctuation spectra of lipid bilayers can be calculated withdirect Fourier analysis. The interpretation of the fluctuation spectra reveals a picture where density fluctuations and undulations are most pronounced on different length scales, but coalesce in the mesoscopic regime. This analysis has significant consequences for comparison of simulation data to experiments. These new methods merge the molecular fluctuations on small wavelengths, with continuum fluctuations of the elastic membrane sheet on large wavelengths, allowing electron density profiles (EDP) and area per lipid to be extracted from simulations with high accuracy.

Molecular dynamics simulations also provide insight on the small-wavelength dynamics of lipid membranes. Rapidly decaying density fluctuations can be described as propagating sound waves in the framework of linearized hydrodynamics, but there is a slow, dispersive, contribution that needs to be described by a stretched exponential over a broad range of length- and time scales - recent experiments suggest that this behavior can prevail even on micrometer length scales. The origin of this behavior is discussed in the context of fluctuations of the bilayer interface and the molecular structure of the bilayer itself. Connections to recent neutron scattering experiments are highlighted.

Place, publisher, year, edition, pages
Stockholm: KTH Royal Institute of Technology, 2011. xi, 90 p.
Series
Trita-FYS, ISSN 0280-316X ; 2011:48
Keyword
biological fluid dynamics, biomembranes, hydrodynamics, lipid bilayers, molecular dynamics, neutron spin echo
National Category
Biophysics
Identifiers
urn:nbn:se:kth:diva-42586 (URN)978-91-7501-125-7 (ISBN)
Public defence
2011-11-04, FB42, AlbaNova Universitetscentrum, Stockholm, 10:00 (English)
Opponent
Supervisors
Projects
Modelling of biological membranes
Funder
Swedish e‐Science Research Center
Note
QC 20111014Available from: 2011-10-14 Created: 2011-10-11 Last updated: 2012-05-24Bibliographically approved

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