The lack of lightning strike protection (LSP) for the nanocomposite materials limits their use in many applications including aircrafts. As a result, there is a continuous interest in understanding the heterogeneous thermoelectric behavior of mixtures with carbon fibers/nanotubes of these materials. Currently available methodologies, including computer simulation of finite different method (FDM) with periodic boundary conditions, to assess the thermoelectric behavior of composite materials are extremely time consuming, expensive, and ineffectual. In this work, we propose a fast and effective simulation model using NVIDIA general purpose graphics processing unit (GPGPU) and compute unified device architecture (CUDA) technology which is targeted to LSP analysis on nanocomposite aircrafts. Preliminary results using FDM based steady state heat equation and Laplace's equation demonstrate that the optimized shared memory CUDA/GPGPU implementation has potential to significantly reduce the simulation execution time.