Molecular Simulation/Membrane permeability

The flux of a solute across a membrane is calculated from its permeability coefficient, P, and the concentration gradient across the bilayer (ΔC)

A 0.1 ns molecular dynamics simulation of a dipalmitoylphosphatidylcholine bilayer. The simulation was performed using NAMD 2.10 and the CHARMM36 lipid force field. Hydrogen atoms on the lipid tails are omitted for clarity.

P can be calculated using molecular simulation using the solubility-diffusion model,[1][2]

w(z) is the potential of mean force of the solute along the transmembrane axes, z. D(z) is the diffusion coefficient profile. The interval [L,-L] spans the membrane.

Derivation edit

The solubility diffusion model can be derived from the Nernst-Planck equation,


In this equation, J(z) is the flux of the solute through the membrane at the depth z . C(z) is the concentration of the solute. w(z) and D(z) are the potential of mean force and diffusivity, respectively.

References edit

  1. Marrink, Siewert-Jan; Berendsen, Herman J. C. (1994). "Simulation of water transport through a lipid membrane". The Journal of Physical Chemistry. 98 (15): 4155–68. doi:10.1021/j100066a040.
  2. Awoonor-Williams, Ernest; Rowley, Christopher N. (2016). "Molecular simulation of nonfacilitated membrane permeation". Biochimica et Biophysica Acta (BBA) - Biomembranes. 1858 (7): 1672–87. doi:10.1016/j.bbamem.2015.12.014.