ArticleBiophysical journal2011
Determination of electron density profiles and area from simulations of undulating membranes.
Article in Biophysical journal, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed.
- ThebioRxiv : the preprint server for biology · 2026Article
- Low-THz Vibrations of Biological Membranes.Membranes · 2023Article
- Design and simulation of the liposomal model by using a coarse-grained molecular dynamics approach towards drug delivery goals.Scientific reports · 2022Article
- All-Atom Molecular Dynamics Elucidating Molecular Mechanisms of Single-Transmembrane Model Peptide Dimerization in a Lipid Bilayer.ACS omega · 2021Article
- Location of the Hydrophobic Surfactant Proteins, SP-B and SP-C, in Fluid-Phase Bilayers.The journal of physical chemistry. B · 2020Article
- Lipid Head Group Parameterization for GROMOS 54A8: A Consistent Approach with Protein Force Field Description.Journal of chemical theory and computation · 2019Article
- Accelerating Membrane Simulations with Hydrogen Mass Repartitioning.Journal of chemical theory and computation · 2019Article
- Molecular Dynamics Simulations of Membrane Permeability.Chemical reviews · 2019Review
- Revisiting Volumes of Lipid Components in Bilayers.The journal of physical chemistry. B · 2019Article
- Simulation Best Practices for Lipid Membranes [Article v1.0].Living journal of computational molecular science · 2019Article
- Membrane Permeability: Characteristic Times and Lengths for Oxygen and a Simulation-Based Test of the Inhomogeneous Solubility-Diffusion Model.Journal of chemical theory and computation · 2018Article
- All n-3 PUFA are not the same: MD simulations reveal differences in membrane organization for EPA, DHA and DPA.Biochimica et biophysica acta. Biomembranes · 2018Article
- Polyunsaturated chains in asymmetric lipids disorder raft mixtures and preferentially associate with α-Synuclein.Biochimica et biophysica acta. Biomembranes · 2017Article
- α-Synuclein's Uniquely Long Amphipathic Helix Enhances its Membrane Binding and Remodeling Capacity.The Journal of membrane biology · 2017Article
- Membrane remodeling and mechanics: Experiments and simulations of α-Synuclein.Biochimica et biophysica acta · 2016Review
- The Lipid Bilayer Provides a Site for Cortisone Crystallization at High Cortisone Concentrations.Scientific reports · 2016Article
- Article
- Biological Membranes in Extreme Conditions: Simulations of Anionic Archaeal Tetraether Lipid Membranes.PloS one · 2016Article
- Mechanical properties of lipid bilayers from molecular dynamics simulation.Chemistry and physics of lipids · 2015Review
- Penetration of HIV-1 Tat47-57 into PC/PE Bilayers Assessed by MD Simulation and X-ray Scattering.Membranes · 2015Article
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Authors and funding
5 authors.
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Abstract
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.
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