David Marreiro et al 2007 J. Phys.: Condens. Matter 19 215203 doi:10.1088/0953-8984/19/21/215203
David Marreiro1, Marco Saraniti1 and Shela Aboud2
Show affiliationsIn this work, we study the suitability of a P3M force field scheme coupled with a Brownian dynamics simulation engine for the accurate modelling of charge transport in ion channels. The proposed simulation algorithm (Aboud et al 2004 J. Comput. Electron. 3 117–33) is briefly discussed, and its validation for the electrodynamic description of aqueous solutions (Marreiro et al 2005 J. Comput. Electron. 4 179–83; 2006 J. Comput. Electron. at press) is presented. The algorithm is applied to the simulation of ion channel systems where the influence of the dielectric representation and the diffusion coefficients are computed and compared to experimental (Van Der Straaten et al 2003 J. Comput. Electron. 2 29–47) and simulated (Van Der Straaten et al 2003 J. Comput. Electron. 2 29–47; Miedema et al 2004 Biophys. J. 87 3137–47) data. The results show that while the bulk parameters do not correctly apply to the channel, the model can be refined by a careful choice of parameters in order to yield accurate charge transport properties while remaining extremely effective from the computational viewpoint.
87.16.Uv Active transport processes
87.16.A- Theory, modeling, and simulations
87.16.D- Membranes, bilayers, and vesicles
82.39.Wj Ion exchange, dialysis, osmosis, electro-osmosis, membrane processes
Issue 21 (30 May 2007)
Received 13 October 2006, in final form 13 December 2006
Published 1 May 2007
David Marreiro et al 2007 J. Phys.: Condens. Matter 19 215203
C Q Geng et al JCAP09(2007)010
E G Adelberger 2001 Class. Quantum Grav. 18 2397
W. C. Jones et al. 2006 ApJ 647 823
T. E. Montroy et al. 2006 ApJ 647 813
F. Piacentini et al. 2006 ApJ 647 833
Nimesh A. Patel et al. 2009 ApJ 692 1205
Y Arntz et al 2003 Nanotechnology 14 86
Kook-Nyung Lee et al 2003 J. Micromech. Microeng. 13 18
R F Sabirianov et al 2007 J. Phys.: Condens. Matter 19 082201