BUMPy: A Model-Independent Tool for Constructing Lipid Bilayers of Varying Curvature and Composition
| Autor: | Eric R. May, Kevin J. Boyd |
|---|---|
| Rok vydání: | 2018 |
| Předmět: |
Materials science
Lipid Bilayers Molecular Conformation 02 engineering and technology Molecular Dynamics Simulation Curvature 01 natural sciences Force field (chemistry) Article Quantitative Biology::Subcellular Processes Molecular dynamics User-Computer Interface 0103 physical sciences Monolayer Physical and Theoretical Chemistry Lipid bilayer Mesoscopic physics Physics::Biological Physics 010304 chemical physics Bilayer 021001 nanoscience & nanotechnology Computer Science Applications Condensed Matter::Soft Condensed Matter Model resolution Classical mechanics Programming Languages 0210 nano-technology |
| Zdroj: | Journal of chemical theory and computation. 14(12) |
| ISSN: | 1549-9626 |
| Popis: | Molecular dynamics is a powerful tool to investigate atomistic and mesoscopic phenomena in lipid bilayer systems. These studies have progressed with the advent of increased computational power, and efforts are now increasingly being directed toward investigating the role of curvature and bilayer morphology, as these are critical features of biological processes. Computational studies of lipid bilayers benefit from tools that can create starting configurations for molecular dynamics simulations, but the majority of such tools are restricted to generating flat bilayers. Generating curved bilayer configurations comes with practical complications and potential ramifications on physical properties in the simulated system if the bilayer is initiated in a high-strain state. We present a new tool for creating curved lipid bilayers that combines flexibility of shape, force field, model resolution, and bilayer composition. A key aspect of our approach is the use of the monolayer pivotal plane location to accurately estimate interleaflet area differences in a curved bilayer. Our tool is named BUMPy (Building Unique Membranes in Python), is written in Python, is fast, and has a simple command line interface. |
| Databáze: | OpenAIRE |
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