ArticleJournal of chemical theory and computation2017
Position-Dependent Diffusion Tensors in Anisotropic Media from Simulation: Oxygen Transport in and through Membranes.
Article in Journal of chemical theory and computation, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed, 67 citations in OpenAlex.
- 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
- Molecular Principles of Proton-Coupled Quinone Reduction in the Membrane-Bound Superoxide Oxidase.Journal of the American Chemical Society · 2025Article
- Permeability Benchmarking: Guidelines for ComparingJournal of chemical information and modeling · 2025Review
- Validation of a Coarse-Grained Martini 3 Model for Molecular Oxygen.Journal of chemical theory and computation · 2025Article
- Understanding Oxygen "Buffering" by Caveolae Using Coarse-Grained Molecular Dynamics Simulations.Advances in experimental medicine and biology · 2024Article
- Biophysical Modelling for Insight into Oxygen Diffusion, Distribution, and Measurement.Advances in experimental medicine and biology · 2024Article
- Path sampling with memory reduction and replica exchange to reach long permeation timescales.Biophysical journal · 2023Article
- Lipid packing in biological membranes governs protein localization and membrane permeability.Biophysical journal · 2023Article
- Defining permeability of curved membranes in molecular dynamics simulations.Biophysical journal · 2023Article
- How Azide Ion/Hydrazoic Acid Passes Through Biological Membranes: An Experimental and Computational Study.The protein journal · 2023Article
- Understanding the Role of Caveolae in Oxygen Buffering: The Effect of Membrane Curvature.Advances in experimental medicine and biology · 2023Article
- Molecular simulation of lignin-related aromatic compound permeation through gram-negative bacterial outer membranes.The Journal of biological chemistry · 2022Article
- Oxygen Storage in Stacked Phospholipid Membranes Under an Oxygen Gradient as a Model for Myelin Sheaths.Advances in experimental medicine and biology · 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
- Updated Evaluation of Cholesterol's Influence on Membrane Oxygen Permeability.Advances in experimental medicine and biology · 2021Article
- Simulation Study of Breast Cancer Lipid Changes Affecting Membrane Oxygen Permeability: Effects of Chain Length and Cholesterol.Advances in experimental medicine and biology · 2021Article
- Membrane permeability of small molecules from unbiased molecular dynamics simulations.The Journal of chemical physics · 2020Article
- Molecular dynamics simulations of ethanol permeation through single and double-lipid bilayers.The Journal of chemical physics · 2020Article
- Pathways of Oxygen Diffusion in Cells and Tissues : Hydrophobic Channeling via Networked Lipids.Advances in experimental medicine and biology · 2020Review
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Authors and funding
4 authors at 3 institutions in 3 countries.
Funding
Abstract
A Bayesian-based methodology is developed to estimate diffusion tensors from molecular dynamics simulations of permeants in anisotropic media, and is applied to oxygen in lipid bilayers. By a separation of variables in the Smoluchowski diffusion equation, the multidimensional diffusion is reduced to coupled one-dimensional diffusion problems that are treated by discretization. The resulting diffusivity profiles characterize the membrane transport dynamics as a function of the position across the membrane, discriminating between diffusion normal and parallel to the membrane. The methodology is first validated with neat water, neat hexadecane, and a hexadecane slab surrounded by water, the latter being a simple model for a lipid membrane. Next, a bilayer consisting of pure 1-palmitoyl 2-oleoylphosphatidylcholine (POPC), and a bilayer mimicking the lipid composition of the inner mitochondrial membrane, including cardiolipin, are investigated. We analyze the detailed time evolution of oxygen molecules, in terms of both normal diffusion through and radial diffusion inside the membrane. Diffusion is fast in the more loosely packed interleaflet region, and anisotropic, with oxygen spreading more rapidly in the membrane plane than normal to it. Visualization of the propagator shows that oxygen enters the membrane rapidly, reaching its thermodynamically favored center in about 1 ns, despite the free energy barrier at the headgroup region. Oxygen transport is quantified by computing the oxygen permeability of the membranes and the average radial diffusivity, which confirm the anisotropy of the diffusion. The position-dependent diffusion constants and free energies are used to construct compartmental models and test assumptions used in estimating permeability, including Overton's rule. In particular, a hexadecane slab surrounded by water is found to be a poor model of oxygen transport in membranes because the relevant energy barriers differ substantially.
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