ArticleJournal of chemical theory and computation2018
BUMPy: A Model-Independent Tool for Constructing Lipid Bilayers of Varying Curvature and Composition.
Article in Journal of chemical theory and computation, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 63 citations in OpenAlex.
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- TS2CG as a Membrane Builder.Journal of chemical theory and computation · 2025Article
- Local enrichment of cardiolipin to transient membrane undulations.Biophysical journal · 2025Article
- Enabling Atomistic Modeling and Simulation of Complex Curved Cellular Membranes with xMAS Builder.bioRxiv : the preprint server for biology · 2025Article
- Local Stress in Cylindrically Curved Lipid Membrane: Insights into Local Versus Global Lateral Fluidity Models.Biomolecules · 2024Article
- Article
- Exploring the Properties of Curved Lipid Membranes: Comparative Analysis of Atomistic and Coarse-Grained Force Fields.The journal of physical chemistry. B · 2024Article
- Diffusion Analyses along Mean and Gaussian-Curved Membranes with CurD.The journal of physical chemistry letters · 2024Article
- Curvature sensing lipid dynamics in a mitochondrial inner membrane model.Communications biology · 2024Article
- Understanding Virus Structure and Dynamics through Molecular Simulations.Journal of chemical theory and computation · 2023Review
- Nanoscale membrane curvature sorts lipid phases and alters lipid diffusion.Biophysical journal · 2023Article
- Defining permeability of curved membranes in molecular dynamics simulations.Biophysical journal · 2023Article
- CHARMM-GUIJournal of chemical theory and computation · 2023Review
- Molecular Dynamics Simulations of Curved Lipid Membranes.International journal of molecular sciences · 2022Review
- Assembly and Analysis of Cell-Scale Membrane Envelopes.Journal of chemical information and modeling · 2022Article
- Backmapping triangulated surfaces to coarse-grained membrane models.Nature communications · 2020Article
- Understanding the synergistic effect of physicochemical properties of nanoparticles and their cellular entry pathways.Communications biology · 2020Article
- Computational Modeling of Realistic Cell Membranes.Chemical reviews · 2019Review
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.