ArticleJournal of chemical theory and computation2015
Density-biased sampling: a robust computational method for studying pore formation in membranes.
Article in Journal of chemical theory and computation, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
5 citing papers in PubMed.
- Sequential Water and Headgroup Merger: Membrane Poration Paths and Energetics from MD Simulations.Biophysical journal · 2020Article
- Free energy of hydrophilic and hydrophobic pores in lipid bilayers by free energy perturbation of a restraint.The Journal of chemical physics · 2020Article
- Direct Derivation of Free Energies of Membrane Deformation and Other Solvent Density Variations From Enhanced Sampling Molecular Dynamics.Journal of computational chemistry · 2020Article
- Article
- Interactions of amino acid side-chain analogs within membrane environments.The journal of physical chemistry. B · 2015Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
A new reaction coordinate to bias molecular dynamics simulation is described that allows enhanced sampling of density-driven processes, such as mixing and demixing two different molecular species. The methodology is validated by comparing the theoretical entropy of demixing two ideal gas species and then applied to induce deformation and pore formation in phospholipid membranes within an umbrella sampling framework. Comparison with previous biased simulations of membrane pore formation suggests overall quantitative agreement, but the density-based biasing potential results in a different, more realistic transition pathway than that in previous studies.
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Registered trials
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