Abstract: In this paper, we consider a system of two linear
parabolic partial differential equations with nonlinear boundary conditions
describing the diffusion of cytoplasmic signaling molecules cGMP and in the rod outer segment (ROS) of
the photoreceptors. A semi-implicit numerical scheme with super time-stepping
based on Finite Volume discretization of the partial differential equations and
boundary conditions for the system in a 3-dimensional intricate geometry of the
ROS is developed. Exploiting the layered geometry of the computational domain,
the numerical scheme is parallelized for distributed memory clusters of
processors via domain decomposition and implemented in MPI/FORTRAN. Finally some
simulation results on a typical salamander rod (taking disc incisure into
account) are presented.
