In this article, we present a stochastic model for the movement of Helium particles within a graphite channel, focusing on Knudsen diffusion. We develop a semi-Markov model to describe the movement of the particle, derive the stationary distribution of its mean position, and analyze the model's asymptotic properties. To validate the model, we compare its theoretical outcomes with Monte Carlo simulations. As temperature significantly influences on the movement of particles, two situations are studied for high and low temperature. In both cases, theoretical and simulation results by Monte Carlo coincide. Furthermore, we propose estimation methods for the local parameters of the model and demonstrate its application using data from Molecular Dynamics simulations.