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Molecular Simulation of Nonfacilitated Membrane Permeation

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110 Years of the Meyer–Overton Rule: Predicting Membrane Permeability of Gases and Other Small Compounds
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Development and testing of a general amber force field
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Scalable molecular dynamics with NAMD
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Efficient free energy calculation of water across lipid membranes
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THE weighted histogram analysis method for free‐energy calculations on biomolecules. I. The method
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Permeability of Fluid-Phase Phospholipid Bilayers: Assessment and Useful Correlations for Permeability Screening and Other Applications
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Umbrella sampling
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Zur Theorie der Alkoholnarkose
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Permeability of small nonelectrolytes through lipid bilayer membranes
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Interpretation of nonelectrolyte partition coefficients between dimyristoyl lecithin and water
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The movement of molecules across lipid membranes: A molecular theory
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A theory of membrane permeability: I
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The calculation of the potential of mean force using computer simulations
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Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes
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Breaching the skin barrier — Insights from molecular simulation of model membranes
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Membrane penetration of nitric oxide and its donor S-nitroso-N-acetylpenicillamine: a spin-label electron paramagnetic resonance spectroscopic study
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New insights into water?phospholipid model membrane interactions
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Behaviour of small solutes and large drugs in a lipid bilayer from computer simulations
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Membrane transport of hydrogen peroxide
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Oxygen permeability of the lipid bilayer membrane made of calf lens lipids
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Reactive oxygen species at phospholipid bilayers: Distribution, mobility and permeation
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The influence of cholesterol on interactions and dynamics of ibuprofen in a lipid bilayer
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Molecular Dynamics Simulations of a DMPC Bilayer Using Nonadditive Interaction Models
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Partitioning of Nonsteroidal Antiinflammatory Drugs in Lipid Membranes: A Molecular Dynamics Simulation Study
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Simulation of Nanoparticle Permeation through a Lipid Membrane
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Transfer of Arginine into Lipid Bilayers Is Nonadditive
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Local Partition Coefficients Govern Solute Permeability of Cholesterol-Containing Membranes
inferredcites →https://doi.org/10.1016/j.bpj.2013.12.027openalex-snapshot
Ion-Induced Defect Permeation of Lipid Membranes
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Interaction of neurotransmitters with a phospholipid bilayer: A molecular dynamics study
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A polarizable model of water for molecular dynamics simulations of biomolecules
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Free-energy change of inserting halothane into different depths of a hydrated DMPC bilayer
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Modelling the behavior of 5-aminolevulinic acid and its alkyl esters in a lipid bilayer
inferredcites →https://doi.org/10.1016/j.cplett.2011.04.052openalex-snapshot
Water permeation through DMPC lipid bilayers using polarizable charge equilibration force fields
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Thermal conductivity, shear viscosity and specific heat of rigid water models
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Drug permeation in biomembranes
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Mathematical models of skin permeability: An overview
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A comparison of sulfur mustard and heptane penetrating a dipalmitoylphosphatidylcholine bilayer membrane
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Determination of water permeability of paramagnetic liposomes of interest in MRI field
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Permeation Across Hydrated DPPC Lipid Bilayers: Simulation of the Titrable Amphiphilic Drug Valproic Acid
inferredcites →https://doi.org/10.1016/s0006-3495(04)74109-0openalex-snapshot
Distribution of Pentachlorophenol in Phospholipid Bilayers: A Molecular Dynamics Study
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Weak acid transport across bilayer lipid membrane in the presence of buffers. Theoretical and experimental pH profiles in the unstirred layers
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A molecular dynamics study of gating in dioxolane-linked gramicidin A channels
inferredcites →https://doi.org/10.1016/s0006-3495(97)78845-3openalex-snapshot
Molecular dynamics simulations of a fluid bilayer of dipalmitoylphosphatidylcholine at full hydration, constant pressure, and constant temperature
inferredcites →https://doi.org/10.1016/s0006-3495(98)77655-6openalex-snapshot
Effects of Anesthetics on the Structure of a Phospholipid Bilayer: Molecular Dynamics Investigation of Halothane in the Hydrated Liquid Crystal Phase of Dipalmitoylphosphatidylcholine
inferredcites →https://doi.org/10.1016/s0006-3495(99)76978-xopenalex-snapshot
An Analysis of the Size Selectivity of Solute Partitioning, Diffusion, and Permeation across Lipid Bilayers
inferredcites →https://doi.org/10.1016/s0302-4598(96)05097-0openalex-snapshot
Two mechanisms of permeation of small neutral molecules and hydrated ions across phospholipid bilayers
inferredcites →https://doi.org/10.1016/s0928-0987(97)10019-7openalex-snapshot
Estimation of permeability by passive diffusion through Caco-2 cell monolayers using the drugs' lipophilicity and molecular weight
inferredcites →https://doi.org/10.1021/acs.jpcb.5b02122openalex-snapshot
Membrane Permeation of a Peptide: It Is Better to be Positive
inferredcites →https://doi.org/10.1021/ar4002729openalex-snapshot
The Importance of Membrane Defects—Lessons from Simulations
inferredcites →https://doi.org/10.1021/bi00414a050openalex-snapshot
Solute partitioning into lipid bilayer membranes
inferredcites →https://doi.org/10.1021/bi060270fopenalex-snapshot
A Combined NMR and Molecular Dynamics Study of the Transmembrane Solubility and Diffusion Rate Profile of Dioxygen in Lipid Bilayers
inferredcites →https://doi.org/10.1021/ct100528uopenalex-snapshot
The Influence of Cholesterol on the Properties and Permeability of Hypericin Derivatives in Lipid Membranes
inferredcites →https://doi.org/10.1021/ct2009208openalex-snapshot
Convergence of Free Energy Profile of Coumarin in Lipid Bilayer
inferredcites →https://doi.org/10.1021/ct2009279openalex-snapshot
Theory and Simulation of Ion Conduction in the Pentameric GLIC Channel
inferredcites →https://doi.org/10.1021/ct300867eopenalex-snapshot
Calculating Position-Dependent Diffusivity in Biased Molecular Dynamics Simulations
inferredcites →https://doi.org/10.1021/ct301005bopenalex-snapshot
Accelerating Convergence in Molecular Dynamics Simulations of Solutes in Lipid Membranes by Conducting a Random Walk along the Bilayer Normal
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A Polarizable Force-Field for Cholesterol and Sphingomyelin
inferredcites →https://doi.org/10.1021/ct400690topenalex-snapshot
Passive Membrane Permeability: Beyond the Standard Solubility-Diffusion Model
inferredcites →https://doi.org/10.1021/ct500305uopenalex-snapshot
Acceleration of Lateral Equilibration in Mixed Lipid Bilayers Using Replica Exchange with Solute Tempering
inferredcites →https://doi.org/10.1021/ct501063aopenalex-snapshot
Evaluating Force Fields for the Computational Prediction of Ionized Arginine and Lysine Side-Chains Partitioning into Lipid Bilayers and Octanol
inferredcites →https://doi.org/10.1021/ct900302nopenalex-snapshot
Simulated Tempering Distributed Replica Sampling, Virtual Replica Exchange, and Other Generalized-Ensemble Methods for Conformational Sampling
inferredcites →https://doi.org/10.1021/ja000156zopenalex-snapshot
Calculation of the Free Energy Profile of H2O, O2, CO, CO2, NO, and CHCl3 in a Lipid Bilayer with a Cavity Insertion Variant of the Widom Method
inferredcites →https://doi.org/10.1021/ja0535099openalex-snapshot
Computer Simulation of the Distribution of Hexane in a Lipid Bilayer: Spatially Resolved Free Energy, Entropy, and Enthalpy Profiles
inferredcites →https://doi.org/10.1021/ja102133xopenalex-snapshot
Potentials of Mean Force and Permeabilities for Carbon Dioxide, Ammonia, and Water Flux across a Rhesus Protein Channel and Lipid Membranes
inferredcites →https://doi.org/10.1021/ja211929hopenalex-snapshot
Large Influence of Cholesterol on Solute Partitioning into Lipid Membranes
inferredcites →https://doi.org/10.1021/ja304007topenalex-snapshot
Flip-Flop of Steroids in Phospholipid Bilayers: Effects of the Chemical Structure on Transbilayer Diffusion
inferredcites →https://doi.org/10.1021/ja3064342openalex-snapshot
Structural Association of Nonsteroidal Anti-Inflammatory Drugs with Lipid Membranes
inferredcites →https://doi.org/10.1021/ja508063sopenalex-snapshot
Why Can Hydrogen Sulfide Permeate Cell Membranes?
inferredcites →https://doi.org/10.1021/ja806825gopenalex-snapshot
Many-Body Polarization Effects and the Membrane Dipole Potential
inferredcites →https://doi.org/10.1021/ja8081704openalex-snapshot
Free Energy for the Permeation of Na+ and Cl− Ions and Their Ion-Pair through a Zwitterionic Dimyristoyl Phosphatidylcholine Lipid Bilayer by Umbrella Integration with Harmonic Fourier Beads
inferredcites →https://doi.org/10.1021/ja902531kopenalex-snapshot
Permeation of Membranes by Ribose and Its Diastereomers
inferredcites →https://doi.org/10.1021/ja9540381openalex-snapshot
Mechanism of Unassisted Ion Transport across Membrane Bilayers
inferredcites →https://doi.org/10.1021/jm010289aopenalex-snapshot
Rational Determination of Transfer Free Energies of Small Drugs across the Water−Oil Interface
inferredcites →https://doi.org/10.1021/jm049711oopenalex-snapshot
Exploring the Role of Different Drug Transport Routes in Permeability Screening
inferredcites →https://doi.org/10.1021/jm970530eopenalex-snapshot
Physicochemical High Throughput Screening: Parallel Artificial Membrane Permeation Assay in the Description of Passive Absorption Processes
inferredcites →https://doi.org/10.1021/jp011001wopenalex-snapshot
Molecular Dynamics Simulations of Ubiquinone inside a Lipid Bilayer
inferredcites →https://doi.org/10.1021/jp021951xopenalex-snapshot
Effect of Cholesterol on the Properties of Phospholipid Membranes. 2. Free Energy Profile of Small Molecules
inferredcites →https://doi.org/10.1021/jp036508gopenalex-snapshot
Coarse Grained Model for Semiquantitative Lipid Simulations
inferredcites →https://doi.org/10.1021/jp108166kopenalex-snapshot
Cholesterol Flip-Flop: Insights from Free Energy Simulation Studies
inferredcites →https://doi.org/10.1021/jp112104ropenalex-snapshot
Permeation of Nucleosides through Lipid Bilayers
inferredcites →https://doi.org/10.1021/jp201611popenalex-snapshot
Cholesterol Effect on Water Permeability through DPPC and PSM Lipid Bilayers: A Molecular Dynamics Study
inferredcites →https://doi.org/10.1021/jp208145bopenalex-snapshot
Molecular Dynamics Simulation Study of the Effect of DMSO on Structural and Permeation Properties of DMPC Lipid Bilayers
inferredcites →https://doi.org/10.1021/jp2102447openalex-snapshot
Unassisted Transport of N-Acetyl- l -tryptophanamide through Membrane: Experiment and Simulation of Kinetics
inferredcites →https://doi.org/10.1021/jp301083hopenalex-snapshot
A Novel Approach to the Investigation of Passive Molecular Permeation through Lipid Bilayers from Atomistic Simulations
inferredcites →https://doi.org/10.1021/jp311802xopenalex-snapshot
Molecular Insight into Affinities of Drugs and Their Metabolites to Lipid Bilayers
inferredcites →https://doi.org/10.1021/jp3127829openalex-snapshot
Lipid Bilayer Membrane Affinity Rationalizes Inhibition of Lipid Peroxidation by a Natural Lignan Antioxidant
inferredcites →https://doi.org/10.1021/jp400264xopenalex-snapshot
How Warfarin’s Structural Diversity Influences Its Phospholipid Bilayer Membrane Permeation
inferredcites →https://doi.org/10.1021/jp402860eopenalex-snapshot
A Polarizable Force Field of Dipalmitoylphosphatidylcholine Based on the Classical Drude Model for Molecular Dynamics Simulations of Lipids
inferredcites →https://doi.org/10.1021/jp405418yopenalex-snapshot
The Different Interactions of Lysine and Arginine Side Chains with Lipid Membranes
inferredcites →https://doi.org/10.1021/jp502475eopenalex-snapshot
Benchmarking Quantum Chemical Methods for the Calculation of Molecular Dipole Moments and Polarizabilities
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Molecular Simulation of the Concentration-Dependent Interaction of Hydrophobic Drugs with Model Cellular Membranes
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Effects of Cholesterol on the Thermodynamics and Kinetics of Passive Transport of Water through Lipid Membranes
inferredcites →https://doi.org/10.1021/jp901088gopenalex-snapshot
Charge Equilibration Force Fields for Lipid Environments: Applications to Fully Hydrated DPPC Bilayers and DMPC-Embedded Gramicidin A
inferredcites →https://doi.org/10.1021/jp903248sopenalex-snapshot
Permeability of Small Molecules through a Lipid Bilayer: A Multiscale Simulation Study
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Current Status of the AMOEBA Polarizable Force Field
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Coarse-Grained Molecular Dynamics Study of Permeability Enhancement in DPPC Bilayers by Incorporation of Lysolipid
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Permeation Process of Small Molecules across Lipid Membranes Studied by Molecular Dynamics Simulations
inferredcites →https://doi.org/10.1021/jz400679zopenalex-snapshot
Homogeneous Hydrophobic–Hydrophilic Surface Patterns Enhance Permeation of Nanoparticles through Lipid Membranes
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Exploring the Free Energy Landscape of Solutes Embedded in Lipid Bilayers
inferredcites →https://doi.org/10.1021/jz401730sopenalex-snapshot
Driving Force for Water Permeation Across Lipid Membranes
inferredcites →https://doi.org/10.1021/la302879ropenalex-snapshot
Nanoparticle Permeation Induces Water Penetration, Ion Transport, and Lipid Flip-Flop
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Surface-Functionalized Nanoparticle Permeation Triggers Lipid Displacement and Water and Ion Leakage
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Simulation Study of the Permeability of a Model Lipid Membrane at the Fluid–Solid Phase Transition
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Dynamic Nuclear Polarization Enhanced Nuclear Magnetic Resonance and Electron Spin Resonance Studies of Hydration and Local Water Dynamics in Micelle and Vesicle Assemblies
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Nontrivial Behavior of Water in the Vicinity and Inside Lipid Bilayers As Probed by Molecular Dynamics Simulations
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Computer simulation study of fullerene translocation through lipid membranes
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Lipids on the frontier: a century of cell-membrane bilayers
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Membrane lipids: where they are and how they behave
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Passive Permeation Across Lipid Bilayers: a Literature Review
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Water permeation through stratum corneum lipid bilayers from atomistic simulations
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Effects of carbon nanoparticles on lipid membranes: a molecular simulation perspective
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Permeability of drugs and hormones through a lipid bilayer: insights from dual-resolution molecular dynamics
inferredcites →https://doi.org/10.1039/c1sm06405copenalex-snapshot
Penetration of lipid bilayers by nanoparticles with environmentally-responsive surfaces: simulations and theory
inferredcites →https://doi.org/10.1039/c2cp41581jopenalex-snapshot
Anesthetic molecules embedded in a lipid membrane: a computer simulation study
inferredcites →https://doi.org/10.1039/c3cs60093aopenalex-snapshot
Perspective on the Martini model
inferredcites →https://doi.org/10.1039/c3sm51225hopenalex-snapshot
Permeation of polystyrene nanoparticles across model lipid bilayer membranes
inferredcites →https://doi.org/10.1039/c4cc08527bopenalex-snapshot
Ethanol induces the formation of water-permeable defects in model bilayers of skin lipids
inferredcites →https://doi.org/10.1039/c4cp05466kopenalex-snapshot
Hydrophobic aggregation and collective absorption of dioxin into lipid membranes: insights from atomistic simulations
inferredcites →https://doi.org/10.1063/1.1589749openalex-snapshot
Modeling induced polarization with classical Drude oscillators: Theory and molecular dynamics simulation algorithm
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Comparative molecular dynamics study of ether- and ester-linked phospholipid bilayers
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A molecular-dynamics study of lipid bilayers: Effects of the hydrocarbon chain length on permeability
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A general purpose model for the condensed phases of water: TIP4P/2005
inferredcites →https://doi.org/10.1063/1.2764079openalex-snapshot
Stretching effects on the permeability of water molecules across a lipid bilayer
inferredcites →https://doi.org/10.1063/1.2978177openalex-snapshot
Statistically optimal analysis of samples from multiple equilibrium states
inferredcites →https://doi.org/10.1063/1.3129863openalex-snapshot
The role of lipid composition for insertion and stabilization of amino acids in membranes
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Free energy profiles for penetration of methane and water molecules into spherical sodium dodecyl sulfate micelles obtained using the thermodynamic integration method combined with molecular dynamics calculations
inferredcites →https://doi.org/10.1063/1.3677196openalex-snapshot
Transport coefficients of the TIP4P-2005 water model
inferredcites →https://doi.org/10.1063/1.445869openalex-snapshot
Comparison of simple potential functions for simulating liquid water
inferredcites →https://doi.org/10.1063/1.457480openalex-snapshot
Error estimates on averages of correlated data
inferredcites →https://doi.org/10.1063/1.4823500openalex-snapshot
One-dimensional potential of mean force underestimates activation barrier for transport across flexible lipid membranes
inferredcites →https://doi.org/10.1063/1.4904882openalex-snapshot
Extracting the diffusion tensor from molecular dynamics simulation with Milestoning
inferredcites →https://doi.org/10.1073/pnas.0408037102openalex-snapshot
Potential energy functions for atomic-level simulations of water and organic and biomolecular systems
inferredcites →https://doi.org/10.1073/pnas.0803720105openalex-snapshot
Quantitative visualization of passive transport across bilayer lipid membranes
inferredcites →https://doi.org/10.1073/pnas.0809606106openalex-snapshot
Passive transport across bilayer lipid membranes: Overton continues to rule
inferredcites →https://doi.org/10.1073/pnas.0902952106openalex-snapshot
No facilitator required for membrane transport of hydrogen sulfide
inferredcites →https://doi.org/10.1073/pnas.1103979108openalex-snapshot
Side-chain hydrophobicity scale derived from transmembrane protein folding into lipid bilayers
inferredcites →https://doi.org/10.1073/pnas.2635314100openalex-snapshot
Energetics of ion conduction through the gramicidin channel
inferredcites →https://doi.org/10.1080/00268976.2012.668964openalex-snapshot
Role of surface ligands in nanoparticle permeation through a model membrane: a coarse-grained molecular dynamics simulations study
inferredcites →https://doi.org/10.1080/00268976.2013.842010openalex-snapshot
Computational study of peptide permeation through membrane: searching for hidden slow variables
inferredcites →https://doi.org/10.1080/00268978500103111openalex-snapshot
Temperature and size dependence for Monte Carlo simulations of TIP4P water
inferredcites →https://doi.org/10.1080/08927020600726708openalex-snapshot
Fluctuating charge force fields: recent developments and applications from small molecules to macromolecular biological systems
inferredcites →https://doi.org/10.1080/08927020902763839openalex-snapshot
Exploring gas permeability of lipid membranes using coarse-grained molecular dynamics
inferredcites →https://doi.org/10.1085/jgp.200709819openalex-snapshot
Lonely Arginine Seeks Friendly Environment
inferredcites →https://doi.org/10.1085/jgp.200709848openalex-snapshot
Structural Determinants of Water Permeability through the Lipid Membrane
inferredcites →https://doi.org/10.1085/jgp.200709849openalex-snapshot
Theory of Passive Permeability through Lipid Bilayers
inferredcites →https://doi.org/10.1085/jgp.201010577openalex-snapshot
Ion selectivity in channels and transporters
inferredcites →https://doi.org/10.1103/physreve.86.036707openalex-snapshot
Calculating diffusion and permeability coefficients with the oscillating forward-reverse method
inferredcites →https://doi.org/10.1111/cbdd.12074openalex-snapshot
Back to the Future: Can Physical Models of Passive Membrane Permeability Help Reduce Drug Candidate Attrition and Move Us Beyond QSPR?
inferredcites →https://doi.org/10.1126/science.182.4118.1258openalex-snapshot
Diffusion of Weak Acids across Lipid Bilayer Membranes: Effects of Chemical Reactions in the Unstirred Layers
inferredcites →https://doi.org/10.1134/s1990747809020172openalex-snapshot
Molecular dynamics investigation of nitric oxide (II) interaction with a model biological membrane
inferredcites →https://doi.org/10.1146/annurev.bb.15.060186.000333openalex-snapshot
INTERPRETATION OF BIOLOGICAL ION CHANNEL FLUX DATA—Reaction-Rate versus Continuum Theory
inferredcites →https://doi.org/10.1351/pac199365122513openalex-snapshot
Molecular dynamics of water transport through membranes: Water from solvent to solute
inferredcites →https://doi.org/10.1371/journal.pcbi.1000810openalex-snapshot
Polarizable Water Model for the Coarse-Grained MARTINI Force Field
inferredcites →https://doi.org/10.1371/journal.pone.0023187openalex-snapshot
Permeation through the Cell Membrane of a Boron-Based β-Lactamase Inhibitor
inferredcites →https://doi.org/10.1371/journal.pone.0122468openalex-snapshot
A Permeability Study of O2 and the Trace Amine p-Tyramine through Model Phosphatidylcholine Bilayers
inferredcites →https://doi.org/10.1529/biophysj.104.052399openalex-snapshot
2H-NMR Study and Molecular Dynamics Simulation of the Location, Alignment, and Mobility of Pyrene in POPC Bilayers
inferredcites →https://doi.org/10.1529/biophysj.105.060871openalex-snapshot
Permeation of Aromatic Carboxylic Acids across Lipid Bilayers: The pH-Partition Hypothesis Revisited
inferredcites →https://doi.org/10.1529/biophysj.105.080275openalex-snapshot
Indole Localization in Lipid Membranes Revealed by Molecular Simulation
inferredcites →https://doi.org/10.1529/biophysj.106.084343openalex-snapshot
A New Model of Weak Acid Permeation through Membranes Revisited: Does Overton Still Rule?
inferredcites →https://doi.org/10.1529/biophysj.107.105395openalex-snapshot
Intermonolayer Friction and Surface Shear Viscosity of Lipid Bilayer Membranes
inferredcites →https://doi.org/10.1529/biophysj.107.112805openalex-snapshot
Distribution of Amino Acids in a Lipid Bilayer from Computer Simulations
inferredcites →https://doi.org/10.3109/10715769609088032openalex-snapshot
Permeability of Nitric Oxide through Lipid Bilayer Membranes
inferredcites →https://doi.org/10.3866/pku.whxb201408271openalex-snapshot
Molecular Dynamics Simulation of the Permeation of Methyldopa through POPC Phospholipid Bilayer Membrane

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1063/5.0033476openalex-snapshot
Sampling efficiency of the counting method for permeability calculations estimated with the inhomogeneous solubility–diffusion model
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