Ion fluxes through nano-pores and transmembrane channels
  We introduce an implicit solvent Molecular Dynamics approach for calculating ionic fluxes through narrow nano-pores and transmembrane channels. The method relies on a dual-control- volume grand-canonical molecular dynamics (DCV-GCMD) simulation and the analytical solution for the electrostatic potential inside a cylindrical nano-pore recently obtained by Levin [Europhys. Lett., 76, 163 (2006)]. The theory is used to calculate the ionic fluxes through an artificial trans-membrane c hannel which mimics the antibacterial gramicidin A channel. Both current-voltage and current-concentration relations are calculated under various experimental conditions. We show that our results are comparable to the characteristics associated to the gramicidin A pore, specially the existence of two binding sites inside the pore and the observed saturation in the current-concentration profiles. 
Jos\'e Rafael Bordin, Alexandre Diehl, Marcia C. Barbosa and Yan Levin
cond-mat.soft physics.bio-ph q-bio.BM