ArticleThe Journal of chemical physics2015
Strong influence of periodic boundary conditions on lateral diffusion in lipid bilayer membranes.
Article in The Journal of chemical physics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers.
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Who cites it
50 citing papers in PubMed, 117 citations in OpenAlex.
- Tutorial for Atomistic and Coarse-Grained Simulations of Membrane-Nanoplastic Interactions Using GROMACS.The journal of physical chemistry. B · 2026Article
- Elucidating the mechanical properties of asymmetric membranes by direct derivation of their energetics.Faraday discussions · 2025Article
- Molecular Dynamics Simulations of Self-Assembled EACS physical chemistry Au · 2025Article
- Understanding the coarse-grained free energy landscape of phospholipids and their phase separation.Biophysical journal · 2025Article
- Effects of a Polarizable Force Field on Membrane Dynamics: Surface Viscosity, Lipid Diffusion, and Peptide Induced Pore Formation.Journal of computational chemistry · 2025Article
- Permeability Benchmarking: Guidelines for ComparingJournal of chemical information and modeling · 2025Review
- CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.The journal of physical chemistry. B · 2024Review
- System size effects on the free energy landscapes from molecular dynamics of phase-separating bilayers.The Journal of chemical physics · 2024Article
- Simulating Bacterial Membrane Models at the Atomistic Level: A Force Field Comparison.Journal of chemical theory and computation · 2024Article
- Exploring How System Dimensions and Periodic Boundary Conditions Influence the Molecular Dynamics Simulation of AThe journal of physical chemistry. B · 2024Article
- Quantitative Comparison against Experiments Reveals Imperfections in Force Fields' Descriptions of POPC-Cholesterol Interactions.Journal of chemical theory and computation · 2023Article
- Drude Polarizable Lipid Force Field with Explicit Treatment of Long-Range Dispersion: Parametrization and Validation for Saturated and Monounsaturated Zwitterionic Lipids.Journal of chemical theory and computation · 2023Article
- Protein Crowding and Cholesterol Increase Cell Membrane Viscosity in a Temperature Dependent Manner.Journal of chemical theory and computation · 2023Article
- Surface viscosities of lipid bilayers determined from equilibrium molecular dynamics simulations.Biophysical journal · 2023Article
- Modeling Receptor Motility along Advecting Lipid Membranes.Membranes · 2022Review
- Spider Toxin SNX-482 Gating Modifier Spontaneously Partitions in the Membrane Guided by Electrostatic Interactions.Membranes · 2022Article
- Article
- Assembly and Analysis of Cell-Scale Membrane Envelopes.Journal of chemical information and modeling · 2022Article
- Correlated diffusion in lipid bilayers.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Subdiffusive-Brownian crossover in membrane proteins: a generalized Langevin equation-based approach.Biophysical journal · 2021Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
The Saffman-Delbrück hydrodynamic model for lipid-bilayer membranes is modified to account for the periodic boundary conditions commonly imposed in molecular simulations. Predicted lateral diffusion coefficients for membrane-embedded solid bodies are sensitive to box shape and converge slowly to the limit of infinite box size, raising serious doubts for the prospects of using detailed simulations to accurately predict membrane-protein diffusivities and related transport properties. Estimates for the relative error associated with periodic boundary artifacts are 50% and higher for fully atomistic models in currently feasible simulation boxes. MARTINI simulations of LacY membrane protein diffusion and LacY dimer diffusion in DPPC membranes and lipid diffusion in pure DPPC bilayers support the underlying hydrodynamic model.
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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.