Semi-automatic computer construction of three-dimensional shapes for the finite element method

Precise estimation of spatio-temporal distribution of ions (or other constitutives) in three-dimensional geometrical configuration plays a major role in biology. Since a direct experimental information regarding the free intracellular Ca2+ spatio-temporal distribution is not available to date, mathematical models have been developed. Most of the existing models are based on the classical numerical method of finite-difference (FD). Using this method one is limited when dealing with complicated geometry, general boundary conditions and variable or non-linear material properties. These difficulties are easily solved when the finite-element-method (FEM) is employed. The first step in the implementation of the FEM procedure is the mesh generation which is the single most tedious, time consuming task and vulnerable to mistake. In order to overcome these limitations we developed a new interface called AUTOMESH. This tool is used as a preprocessor program which generates two- and three-dimensional meshes for some known and often-used shapes in neurobiology. AUTOMESH creates an appropriate mesh by using the mesh generator commercial tool of FIDAP.