First-passage-time analysis of atomic-resolution simulations of the ionic transport in a bacterial porin
comunitat-uji-handle:10234/9
comunitat-uji-handle2:10234/2507
comunitat-uji-handle3:10234/6973
comunitat-uji-handle4:
INVESTIGACIONMetadatos
Título
First-passage-time analysis of atomic-resolution simulations of the ionic transport in a bacterial porinFecha de publicación
2011-02-16Editor
American Physical SocietyISSN
1539-3755; 1550-2376Cita bibliográfica
Physical Review E (2011) vol. 83, no. 2Tipo de documento
info:eu-repo/semantics/articleVersión de la editorial
http://pre.aps.org/abstract/PRE/v83/i2/e021908Versión
info:eu-repo/semantics/publishedVersionPalabras clave / Materias
Ions | Porin | Dynamics of the ions | Ions | Cell membranes | Biophysics | Ions | Membranes cel·lulars | Biofísica
Resumen
We have studied the dynamics of chloride and potassium ions in the interior of the Outer membrane porin F (OmpF) under the influence of an external electric field. From the results of extensive all-atom molecular ... [+]
We have studied the dynamics of chloride and potassium ions in the interior of the Outer membrane porin F (OmpF) under the influence of an external electric field. From the results of extensive all-atom molecular dynamics (MD) simulations of the system, we computed several first-passage-time (FPT) quantities to characterize the dynamics of the ions in the interior of the channel. Such FPT quantities obtained from MD simulations demonstrate that it is not possible to describe the dynamics of chloride and potassium ions inside the whole channel with a single constant diffusion coefficient. However, we showed that a valid, statistically rigorous description in terms of a constant diffusion coefficient D and an effective deterministic force Feff can be obtained after appropriate subdivison of the channel in different regions suggested by the x-ray structure. These results have important implications for popular simplified descriptions of channels based on the one-dimensional Poisson- Nernst-Planck equations. Also, the effect of entropic barriers on the diffusion of the ions is identified and briefly discussed. [-]
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