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Computational modeling of three-dimensional electrodiffusion in biological systems: application to the node of Ranvier.

ABSTRACT: A computational model is presented for the simulation of three-dimensional electrodiffusion of ions. Finite volume techniques were used to solve the Poisson-Nernst-Planck equation, and a dual Delaunay-Voronoi mesh was constructed to evaluate fluxes of ions, as well as resulting electric potentials. The algorithm has been validated and applied to a generalized node of Ranvier, where numerical results for computed action potentials agree well with cable model predictions for large clusters of voltage-gated ion channels. At smaller channel clusters, however, the three-dimensional electrodiffusion predictions diverge from the cable model predictions and show a broadening of the action potential, indicating a significant effect due to each channel's own local electric field. The node of Ranvier complex is an elaborate organization of membrane-bound aqueous compartments, and the model presented here represents what we believe is a significant first step in simulating electrophysiological events with combined realistic structural and physiological data.

SUBMITTER: Lopreore CL

PROVIDER: S-EPMC2527256 | biostudies-other | 2008 Sep

REPOSITORIES: biostudies-other

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Project description:Assessing the efficacy of specific porous materials for use in various applications has been a central focus for many experimental studies over the years, with a view to altering the material properties according to the desired characteristics. The application potential for one such class of nanoporous materials-organic resorcinol-formaldehyde (RF) gels-is of particular interest, due to their attractive and adjustable properties. In this work, we simulate adsorption analysis using lattice-based mean field theory, both in individual pores and within three-dimensional porous materials generated from a kinetic Monte Carlo cluster aggregation model. We investigate the impacts of varying pore size and geometry on the adsorptive behavior, with results agreeing with those previously postulated in the literature. The adsorption analysis is carried out for porous materials simulated with varying catalyst concentrations and solids contents, allowing their structural properties to be assessed from resulting isotherms and the adsorption and desorption processes visualized using density color maps. Isotherm analysis indicated that both low catalyst concentrations and low solids contents resulted in structures with open transport pores that were larger in width, while high catalyst concentrations and solids contents resulted in structures with bottleneck pores that were narrower. We present results from both the simulated isotherms and pore size analysis distributions, in addition to results from RF gels synthesized in the lab and analyzed experimentally, with significant similarities observed between the two. Not only do the results of this comparison validate the kinetic Monte Carlo model's ability to successfully capture the formation of RF gels under varying synthesis parameters, but they also show significant promise for the tailoring of material properties in an efficient and computationally inexpensive manner-something which would be pivotal in realizing their full application potential, and could be applied to other porous materials whose formation mechanism operates under similar principles.

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Computational modeling of three-dimensional electrodiffusion in biological systems: application to the node of Ranvier.

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