ArticleJournal of chemical theory and computation2014
Determining Structural and Mechanical Properties from Molecular Dynamics Simulations of Lipid Vesicles.
Article in Journal of chemical theory and computation, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Review
- Understanding the Mechanical Properties of Ultradeformable Liposomes Using Molecular Dynamics Simulations.The journal of physical chemistry. B · 2023Article
- Translocating Peptides of Biomedical Interest Obtained from the Spike (S) Glycoprotein of the SARS-CoV-2.Membranes · 2022Article
- Full scale structural, mechanical and dynamical properties of HIV-1 liposomes.PLoS computational biology · 2022Article
- Location and Conformational Ensemble of Menaquinone and Menaquinol, and Protein-Lipid Modulations in Archaeal Membranes.The journal of physical chemistry. B · 2021Article
- Effect of Amyloid-β Monomers on Lipid Membrane Mechanical Parameters-Potential Implications for Mechanically Driven Neurodegeneration in Alzheimer's Disease.International journal of molecular sciences · 2020Article
- Mechanical Properties Determination of DMPC, DPPC, DSPC, and HSPC Solid-Ordered Bilayers.Langmuir : the ACS journal of surfaces and colloids · 2020Article
- High-Performance Analysis of Biomolecular Containers to Measure Small-Molecule Transport, Transbilayer Lipid Diffusion, and Protein Cavities.Journal of chemical information and modeling · 2019Article
- Nanovesicles Versus Nanoparticle-Supported Lipid Bilayers: Massive Differences in Bilayer Structures and in Diffusivities of Lipid Molecules and Nanoconfined Water.Langmuir : the ACS journal of surfaces and colloids · 2019Article
- Hydrogen Bonding Regulates the Rigidity of Liposome-Encapsulated Chlorin Photosensitizers.ChemistryOpen · 2018Article
- Physical properties of the HIV-1 capsid from all-atom molecular dynamics simulations.Nature communications · 2017Article
- Membrane remodeling and mechanics: Experiments and simulations of α-Synuclein.Biochimica et biophysica acta · 2016Review
- The Role of the Membrane in the Structure and Biophysical Robustness of the Dengue Virion Envelope.Structure (London, England : 1993) · 2016Article
- Article
- α-Synuclein Reduces Tension and Increases Undulations in Simulations of Small Unilamellar Vesicles.Biophysical journal · 2015Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We have developed an algorithm to determine membrane structure, area per lipid, and bending rigidity from molecular dynamics simulations of lipid vesicles. Current methods to extract structure from vesicle simulations define densities relative to the global center of mass of the vesicle. This approach ignores the long-wavelength fluctuations (undulations) that develop across the sphere and broaden the underlying structure. Our method establishes a local reference frame by defining a radially undulating reference surface (URS) and thereby removes the broadening effect of the undulations. Using an arc-length low-pass filter, we render the URS by defining the bilayer midplane on an equi-angular
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