Comparison of Dynamic Lattice Monte Carlo Simulations and the Dielectric Self-Energy Poisson-Nernst-Planck Continuum Theory for Model Ion Channels

Journal of Physical Chemistry B

Volumn 108, Issue 6, 2004, Pages 2006-2015

  Graf, Peter ^a   Kurnikova, Maria G ^b   Coalson, Rob D ^c   Nitzan, Abraham ^a  

^a TEL AVIV UNIVERSITY   (Israel)

^b CARNEGIE MELLON UNIVERSITY   (United States)

^c UNIVERSITY OF PITTSBURGH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; BIOLOGICAL MEMBRANES; BROWNIAN MOVEMENT; COMPUTER SIMULATION; CURRENT DENSITY; CURRENT VOLTAGE CHARACTERISTICS; DIELECTRIC MATERIALS; ELECTROSTATICS; MONTE CARLO METHODS; PROTEINS; RELAXATION PROCESSES;

DIELECTRIC SELF ENERGY (DSE); DYNAMIC LATTICE MONTE CARLO (DLMC) SIMULATIONS; POISSON-NERNST-PLANCK (PNP) THEORY;

IONIC CONDUCTION;

EID: 1342344804     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp0355307     Document Type: Article

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44. In reality, D is expected to be different in the bulk and inside the channel, but this distinction is not important in the present context.
45. To obtain each point on this curve, an average was taken over the central point (along the z axis) and its four nearest-neighbor grid points in the x - y plane.
46. Such a finite-sized ion model has the following advantages: (1) It renders all self-energies, and forces derived from these, finite, Therefore, a renormalization of infinite self-energies is not necessary, (2) It inherently encompasses the "Bom solvation energy" for a nonuniform dielectric.
47. These surface terms can be discarded because of the boundary condition that φ = 0 on all bounding surfaces Note also that the Poisson equation (eq A1.2) has been invoked in older to obtain eq A1.3.
48. This derivation parallels the treatment of M. K. Gilson, M. E. Davis, B. A. Luty, and J. A. McCammon (J. Phys. Chem. 1993, 97, 3591), who were interested in the force on a macroion in an electrolytic solution.
49. → are related to φ in the usual manner.
50. This assumes no changes in the dielectric function as the charged body in question moves This assumption is valid for the case of a point ion moving through a medium that is locally uniform (e.g., the solvent)
51. 0)