Generalized Langevin Methods for Calculating Transmembrane Diffusivity.
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Summary
Roux and Hummer have derived expressions for the diffusion coefficient from the velocity autocorrelation function (VACF) and position autOCorrelationfunction (PACF), respectively, and these methods are validated by calculating the diffusivity of H2O and O2 in homogeneous liquids.
- Type
- article
- Published
- 2016-10-12
- Cited by
- 57
- References
- 49
- Access
- Open access
- OpenAlex
- https://openalex.org/W2432414111
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:46827595
Keywords
Thermal diffusivity, Mass diffusivity, Autocorrelation, Lipid bilayer, Diffusion
References
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- An alternative approach to dissipative particle dynamics
- Algorithm 748: enclosing zeros of continuous functions
- Calculating Position-Dependent Diffusivity in Biased Molecular Dynamics Simulations.
- A method to predict blood-brain barrier permeability of drug-like compounds using molecular dynamics simulations.
- Molecular-dynamics study of a three-dimensional one-component model for distortive phase transitions
- Molecular dynamics simulation of the gramicidin channel in a phospholipid bilayer.
- Position-dependent diffusion coefficients and free energies from Bayesian analysis of equilibrium and replica molecular dynamics simulations
- Diffusive reaction dynamics on invariant free energy profiles
- High throughput artificial membrane permeability assay for blood-brain barrier.
- All-atom empirical potential for molecular modeling and dynamics studies of proteins.
- Calculation of Lipid-Bilayer Permeabilities Using an Average Force.
- Simulation of Water Transport through a Lipid Membrane
- Calculation of dynamic friction on intramolecular degrees of freedom
Cited by
- C-terminal kink formation is required for lateral gating in BamA
- Shedding light on the puzzle of drug-membrane interactions: Experimental techniques and molecular dynamics simulations.
- Influence of Cholesterol on the Oxygen Permeability of Membranes: Insight from Atomistic Simulations.
- Computed free energies of peptide insertion into bilayers are independent of computational method
- Simulations of lipid bilayers using the CHARMM36 force field with the TIP3P-FB and TIP4P-FB water models
- Effects of lipid composition on membrane permeation.
- Molecular Dynamics Simulations of Membrane Permeability
- Simulations of gasotransmitter permeation through lipid bilayers
- The asymmetry of plasma membranes and their cholesterol content influence the uptake of cisplatin
- The CHARMM36 Force Field for Lipids Can Be Used With More Accurate Water Models
- Water hydrogen-bonding structure and dynamics near lipid multibilayer surface: Molecular dynamics simulation study with direct experimental comparison.
- The Chemical Langevin Equation for Complex Reactions.
- Polarizable molecular dynamics simulations of ionic liquids: Influence of temperature control
- Molecular dynamics simulation of the interaction of small molecules with biological membranes.
- Molecular Dynamics Simulations of Micelle Properties and Behaviors of Sodium Lauryl Ether Sulfate Penetrating Ceramide and Phospholipid Bilayers.
- Membrane permeability of small molecules from unbiased molecular dynamics simulations.
- Molecular dynamics simulations of ethanol permeation through single and double-lipid bilayers.
- Structural insight into toxin secretion by contact-dependent growth inhibition transporters
- Molecular dynamics simulations of liquid-liquid interfaces in an electric field: The water-1,2-dichloroethane interface.
- Position-Dependent Diffusion Constant of Molecules in Heterogeneous Systems as Evaluated by the Local Mean Squared Displacement.
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