2011/08/26 by José Rafael Bordin, Alexandre Diehl, Bordin, José Rafael +6
Biochemistry, Genetics and Molecular Biology · Engineering · Physics and Astronomy · #Biological Physics (physics.bio-ph) #Biomolecules (q-bio.BM) #FOS: Biological sciences #FOS: Physical sciences #Lipid Membrane Structure and Behavior #Microfluidic and Capillary Electrophoresis Applications #Nanopore and Nanochannel Transport Studies #Soft Condensed Matter (cond-mat.soft) #cond-mat.soft #physics.bio-ph #q-bio.BM
paper · pdf · doi:10.48550/arxiv.1108.5366
15 pages, 8 figures, accepted for publication in Physical Review E
openalex publication_date 2011/08/26 · arxiv created 2012/03/12 · arxiv updated 2012/03/13 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/01
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.