CA3D: A Monte Carlo code to simulate 3D buffered diffusion of ions in sub-membrane domains

CA3D is a simulation program, based on Monte Carlo techniques, which simula tes the buffered diffusion of ions in the submembrane domain of cells. Two geometries of submembrane domains are considered. The first, a conical doma in, applies to spherical cells with a locally uniform distribution of chann els while the second, a cylindrical domain, is intended to model ciliar cel ls and presynaptic terminals. Other domains can be implemented in the code with ease. The entry of ions takes place through discrete entry points (cha nnel pores). Ions diffuse inside the cell and react with endogenous or exog enous buffers, mobile or fixed, The diffusion of ions and binding molecules is modeled as a 3D random walk process by moving each individual ion and m olecule. The reaction of ions with the binding molecules is also modeled pr obabilistically. The outputs of the code are concentration time courses and 2D maps of concentration of ions in the sub-membrane domain of cells. (C) 2001 Published by Elsevier Science B.V.