Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Determination of Electron Density Profiles and Area from Simulations of Undulating Membranes
KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical Biological Physics.
KTH, School of Engineering Sciences (SCI), Theoretical Physics.ORCID iD: 0000-0002-7448-4664
Show others and affiliations
2011 (English)In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 100, no 9, 2112-2120 p.Article in journal (Refereed) Published
Abstract [en]

The traditional method for extracting electron density and other transmembrane profiles from molecular dynamics simulations of lipid bilayers fails for large bilayer systems, because it assumes a flat reference surface that does not take into account long wavelength undulations. We have developed what we believe to be a novel set of methods to characterize these undulations and extract the underlying profiles in the large systems. Our approach first obtains an undulation reference surface for each frame in the simulation and subsequently isolates the long-wavelength undulations by filtering out the intrinsic short wavelength modes. We then describe two methods to obtain the appropriate profiles from the undulating reference surface. Most combinations of methods give similar results for the electron density profiles of our simulations of 1024 DMPC lipids. From simulations of smaller systems, we also characterize the finite size effect related to the boundary conditions of the simulation box. In addition, we have developed a set of methods that use the undulation reference surface to determine the true area per lipid which, due to undulations, is larger than the projected area commonly reported from simulations.

Place, publisher, year, edition, pages
2011. Vol. 100, no 9, 2112-2120 p.
Keyword [en]
MOLECULAR-DYNAMICS SIMULATIONS; X-RAY-SCATTERING; LIPID-BILAYERS; PHASE DMPC; COMPRESSIBILITY; FLUCTUATIONS
National Category
Biophysics
Identifiers
URN: urn:nbn:se:kth:diva-33983DOI: 10.1016/j.bpj.2011.03.009ISI: 000290360000007Scopus ID: 2-s2.0-79959770281OAI: oai:DiVA.org:kth-33983DiVA: diva2:419742
Funder
Swedish e‐Science Research Center
Note
QC 20110527Available from: 2011-05-27 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

Open Access in DiVA

No full text

Other links

Publisher's full textScopus

Authority records BETA

Edholm, Olle

Search in DiVA

By author/editor
Brandt, Erik G.Edholm, Olle
By organisation
Theoretical Biological PhysicsTheoretical Physics
In the same journal
Biophysical Journal
Biophysics

Search outside of DiVA

GoogleGoogle Scholar

doi
urn-nbn

Altmetric score

doi
urn-nbn
Total: 79 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf