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
Dynamic structure factors from lipid membrane molecular dynamics simulations
KTH, School of Engineering Sciences (SCI), Theoretical Physics.
KTH, School of Engineering Sciences (SCI), Theoretical Physics.ORCID iD: 0000-0002-7448-4664
2009 (English)In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 96, no 5, 1828-1838 p.Article in journal (Refereed) Published
Abstract [en]

Dynamic structure factors for a lipid bilayer have been calculated from molecular dynamics simulations. From trajectories of a system containing 1024 lipids we obtain wave vectors down to 0.34 nm(-1), which enables us to directly resolve the Rayleigh and Brillouin lines of the spectrum. The results confirm the validity of a model based on generalized hydrodynamics, but also improves the line widths and the position of the Brillouin lines. The improved resolution shows that the Rayleigh line is narrower than in earlier studies, which corresponds to a smaller thermal diffusivity. From a detailed analysis of the power spectrum, we can, in fact, distinguish two dispersive contributions to the elastic scattering. These translate to two exponential relaxation processes in separate time domains. Further, by including a first correction to the wave-vector-dependent position of the Brillouin lines, the results agree favorably to generalized hydrodynamics even up to intermediate wave vectors, and also yields a 20% higher adiabatic sound velocity. The width of the Brillouin lines shows a linear, not quadratic, dependence to low wave vectors.

Place, publisher, year, edition, pages
2009. Vol. 96, no 5, 1828-1838 p.
Keyword [en]
X-RAY-SCATTERING, LENNARD-JONES LIQUID, PARTICLE MESH EWALD, NEUTRON-SCATTERING, DENSITY-FLUCTUATIONS, COMPUTER EXPERIMENTS, CLASSICAL FLUIDS, BRILLOUIN-SCATTERING, COLLECTIVE DYNAMICS, CONSTANT-PRESSURE
National Category
Condensed Matter Physics
Identifiers
URN: urn:nbn:se:kth:diva-10294DOI: 10.1016/j.bpj.2008.11.044ISI: 000266376500014PubMedID: 19254541Scopus ID: 2-s2.0-65549120360OAI: oai:DiVA.org:kth-10294DiVA: diva2:214412
Note
QC 20101006Available from: 2009-05-05 Created: 2009-05-05 Last updated: 2017-12-13Bibliographically approved
In thesis
1. Interactions and dynamics in biophysical model systems
Open this publication in new window or tab >>Interactions and dynamics in biophysical model systems
2009 (English)Licentiate thesis, comprehensive summary (Other academic)
Abstract [en]

Computer simulations of simplified model systems provide understanding of how complex biological systems behave. The simulations give detailed information about the systems, with atomistic resolution, that can be used in combination with experimental knowledge to shed light on underlying physical principles. The thesis presents background information about the studies of two important model systems in biological physics.

First, metal ion-binding to proteins is investigated in a computational study on a zinc-binding synthetic peptide, to elucidate the binding details. The major scientific contributions from the study are the identification and mapping of the detailed contributions to the binding. A novel correction scheme is worked out, where classic free energy calculations are combined with density functional theory to adjust for quantum mechanical effects.  The sensitivity of the zinc-binding to a specific amino acid segment can be explained in terms of the zinc coordination.

Second, equilibrium density fluctuations in biological membranes are studied using computer simulations of the lipid bilayer. The fluctuations are linked to several processes; pore formation, membrane permeability and transport of small molecules across themembrane. Because the lipid bilayer behaves similar to a 2D fluid the density fluctuations can be described in the framework of generalized hydrodynamics. The major scientific contributions from the study are the direct calculation of the density-density autocorrelation function from raw data and the observation that the diffusive contribution to the power spectrum (the Rayleigh line) is not single-exponential. In addition, the accuracy of the approximate hydrodynamic solutions is questionable for the propagation of sound waves in the membrane.

Place, publisher, year, edition, pages
Stockholm: KTH, 2009. ix, 51 p.
Series
Trita-FYS, ISSN 0280-316X ; 2009:18
National Category
Condensed Matter Physics
Identifiers
urn:nbn:se:kth:diva-10300 (URN)978-91-7415-355-2 (ISBN)
Presentation
2009-05-29, FA32, Albanova Universitetscenter, Stockholm, 10:00 (English)
Opponent
Supervisors
Available from: 2009-05-18 Created: 2009-05-05 Last updated: 2010-11-03Bibliographically approved
2. 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 textPubMedScopus

Authority records BETA

Edholm, Olle

Search in DiVA

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

Search outside of DiVA

GoogleGoogle Scholar

doi
pubmed
urn-nbn

Altmetric score

doi
pubmed
urn-nbn
Total: 90 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