ArticleFrontiers in molecular biosciences2022
Unifying Single-Channel Permeability From Rare-Event Sampling and Steady-State Flux.
Article in Frontiers in molecular biosciences, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed.
- Estimating Permeabilities from Biased Molecular Dynamics with a Green-Kubo Formalism for Transport across the Blood-Brain Barrier.Journal of chemical information and modeling · 2026Article
- Molecular permeation through large pore channels: computational approaches and insights.The Journal of physiology · 2025Review
- Dissecting current rectification through asymmetric nanopores.Biophysical journal · 2025Article
- Permeability Benchmarking: Guidelines for ComparingJournal of chemical information and modeling · 2025Review
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Authors and funding
2 authors.
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Abstract
Various all-atom molecular dynamics (MD) simulation methods have been developed to compute free energies and crossing rates of ions and small molecules through ion channels. However, a systemic comparison across different methods is scarce. Using a carbon nanotube as a model of small conductance ion channel, we computed the single-channel permeability for potassium ion using umbrella sampling, Markovian milestoning, and steady-state flux under applied voltage. We show that a slightly modified inhomogeneous solubility-diffusion equation yields a single-channel permeability consistent with the mean first passage time (MFPT) based method. For milestoning, applying cylindrical and spherical bulk boundary conditions yield consistent MFPT if factoring in the effective bulk concentration. The sensitivity of the MFPT to the output frequency of collective variables is highlighted using the convergence and symmetricity of the inward and outward MFPT profiles. The consistent transport kinetic results from all three methods demonstrated the robustness of MD-based methods in computing ion channel permeation. The advantages and disadvantages of each technique are discussed, focusing on the future applications of milestoning in more complex systems.
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Registered trials
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