ArticleThe Journal of chemical physics2020
Membrane permeability of small molecules from unbiased molecular dynamics simulations.
Article in The Journal of chemical physics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- Deep learning of position-dependent diffusivity from umbrella sampling molecular dynamics simulations.The Journal of chemical physics · 2026Article
- Article
- In Silico Prediction and Validation of the Permeability of Small Molecules Across the Blood-Brain Barrier.International journal of molecular sciences · 2026Article
- Influence of Breast Tumor-Associated Lipids on Oxygen Transport Across Model Cell Membranes (Part B: Saturated Phospholipids and Cholesterol).Advances in experimental medicine and biology · 2026Article
- Probing Passive Permeation of Tetracycline: Are Simulations Ready for beyond-Rule-of-Five Drug Permeability Calculation?The journal of physical chemistry. B · 2025Article
- Influence of Membrane Composition on the Passive Membrane Penetration of Industrially Relevant NSO-Heterocycles.International journal of molecular sciences · 2025Article
- 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
- Insights into Dermal Permeation of Skin Oil Oxidation Products from Enhanced Sampling Molecular Dynamics Simulation.The journal of physical chemistry. B · 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
- Generating Concentration Gradients across Membranes for Molecular Dynamics Simulations of Periodic Systems.International journal of molecular sciences · 2024Article
- Ion-Induced PIP2 Clustering with Martini3: Modification of Phosphate-Ion Interactions and Comparison with CHARMM36.The journal of physical chemistry. B · 2024Article
- tICA-Metadynamics for Identifying Slow Dynamics in Membrane Permeation.Journal of chemical theory and computation · 2023Article
- Advances in Computational Approaches for Estimating Passive Permeability in Drug Discovery.Membranes · 2023Review
- Combining SILCS and Artificial Intelligence for High-Throughput Prediction of the Passive Permeability of Drug Molecules.Journal of chemical information and modeling · 2023Article
- 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
- 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
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Permeation of many small molecules through lipid bilayers can be directly observed in molecular dynamics simulations on the nano- and microsecond timescale. While unbiased simulations provide an unobstructed view of the permeation process, their feasibility for computing permeability coefficients depends on various factors that differ for each permeant. The present work studies three small molecules for which unbiased simulations of permeation are feasible within less than a microsecond, one hydrophobic (oxygen), one hydrophilic (water), and one amphiphilic (ethanol). Permeabilities are computed using two approaches: counting methods and a maximum-likelihood estimation for the inhomogeneous solubility diffusion (ISD) model. Counting methods yield nearly model-free estimates of the permeability for all three permeants. While the ISD-based approach is reasonable for oxygen, it lacks precision for water due to insufficient sampling and results in misleading estimates for ethanol due to invalid model assumptions. It is also demonstrated that simulations using a Langevin thermostat with collision frequencies of 1/ps and 5/ps yield oxygen permeabilities and diffusion constants that are lower than those using Nosé-Hoover by statistically significant margins. In contrast, permeabilities from trajectories generated with Nosé-Hoover and the microcanonical ensemble do not show statistically significant differences. As molecular simulations become more affordable and accurate, calculation of permeability for an expanding range of molecules will be feasible using unbiased simulations. The present work summarizes theoretical underpinnings, identifies pitfalls, and develops best practices for such simulations.
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