ArticleJournal of chemical theory and computation2018
Membrane Permeability: Characteristic Times and Lengths for Oxygen and a Simulation-Based Test of the Inhomogeneous Solubility-Diffusion Model.
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 20 papers.
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Who cites it
20 citing papers in PubMed, 40 citations in OpenAlex.
- Impact of Lipid Composition on Membrane Partitioning and Permeability of Gas Molecules.Membranes · 2026Article
- Membrane Permeability of Sucrose Calculated from Equilibrium Time-Correlation Functions Using Molecular Dynamics Simulations with Enhanced Sampling.The journal of physical chemistry. B · 2025Article
- Myelin sheaths can act as compact temporary oxygen storage units as modeled by an electrical RC circuit model.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Validation of a Coarse-Grained Martini 3 Model for Molecular Oxygen.Journal of chemical theory and computation · 2025Article
- Statistical Mechanical Theories of Membrane Permeability.The journal of physical chemistry. B · 2024Article
- Biophysical Modelling for Insight into Oxygen Diffusion, Distribution, and Measurement.Advances in experimental medicine and biology · 2024Article
- Understanding Oxygen "Buffering" by Caveolae Using Coarse-Grained Molecular Dynamics Simulations.Advances in experimental medicine and biology · 2024Article
- Path sampling with memory reduction and replica exchange to reach long permeation timescales.Biophysical journal · 2023Article
- Defining permeability of curved membranes in molecular dynamics simulations.Biophysical journal · 2023Article
- Molecular simulation of lignin-related aromatic compound permeation through gram-negative bacterial outer membranes.The Journal of biological chemistry · 2022Article
- Lipid Composition Is Critical for Accurate Membrane Permeability Prediction of Cyclic Peptides by Molecular Dynamics Simulations.Journal of chemical information and modeling · 2022Article
- OCellular and molecular life sciences : CMLS · 2021Article
- Atomistic simulations modify interpretation of spin-label oximetry data. Part 1: intensified water-lipid interfacial resistances.Applied magnetic resonance · 2021Article
- Membrane permeability of small molecules from unbiased molecular dynamics simulations.The Journal of chemical physics · 2020Article
- Molecular dynamics trajectories for 630 coarse-grained drug-membrane permeations.Scientific data · 2020Article
- Pathways of Oxygen Diffusion in Cells and Tissues : Hydrophobic Channeling via Networked Lipids.Advances in experimental medicine and biology · 2020Review
- Permeability of membranes in the liquid ordered and liquid disordered phases.Nature communications · 2019Article
- Effects of Cholesterol on Water Permittivity of Biomimetic Ion Pair Amphiphile Bilayers: Interplay between Membrane Bending and Molecular Packing.International journal of molecular sciences · 2019Article
- Molecular Dynamics Simulations of Membrane Permeability.Chemical reviews · 2019Review
- The Evolution of Cholesterol-Rich Membrane in Oxygen Adaption: The Respiratory System as a Model.Frontiers in physiology · 2019Review
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 3 countries.
Funding
Abstract
The balance of normal and radial (lateral) diffusion of oxygen in phospholipid membranes is critical for biological function. Based on the Smoluchowski equation for the inhomogeneous solubility-diffusion model, Bayesian analysis (BA) can be applied to molecular dynamics trajectories of oxygen to extract the free energy and the normal and radial diffusion profiles. This paper derives a theoretical formalism to convert these profiles into characteristic times and lengths associated with entering, escaping, or completely crossing the membrane. The formalism computes mean first passage times and holds for any process described by rate equations between discrete states. BA of simulations of eight model membranes with varying lipid composition and temperature indicate that oxygen travels 3 to 5 times further in the radial than in the normal direction when crossing the membrane in a time of 15 to 32 ns, thereby confirming the anisotropy of passive oxygen transport in membranes. Moreover, the preceding times and distances estimated from the BA are compared to the aggregate of 280 membrane exits explicitly observed in the trajectories. BA predictions for the distances of oxygen radial diffusion within the membrane are statistically indistinguishable from the corresponding simulation values, yet BA oxygen exit times from the membrane interior are approximately 20% shorter than the simulation values, averaged over seven systems. The comparison supports the BA approach and, therefore, the applicability of the Smoluchowski equation to membrane diffusion. Given the shorter trajectories required for the BA, these results validate the BA as a computationally attractive alternative to direct observation of exits when estimating characteristic times and radial distances. The effect of collective membrane undulations on the BA is also discussed.
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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.