In this paper, we introduce a new computational method for solving the diffusion equation. In particular, we construct a "generalized" state-space system and compute the impulse response of an equivalent truncated state-space system. In this effort, we use a 3-D Finite Element Method (FEM) to obtain the state space system. Secondly, we use the Arnoldi iteration to approximate the state impulse response by projecting on the dominant controllable subspace. The idea exploited here is the approximation of the impulse response of the linear system. The homogeneous and heterogeneous cases are studied and the approximation error is discussed. Finally, we compare our computational results to our experimental set up.