We investigate and model the collisions and the self diffusion processes of dilute Helium gas in nanometric graphite channels using molecular dynamics. At high temperature, collisions are mostly specular with short resident time. At temperature as low as 50 K-75 K, the gas atoms stay longer near the surface and the surface diffusion becomes dominant. Both ballistic and diffusive transport regimes are present before the desorption. A waiting time model based on the residence time distribution and coupled with ballistic-diffusive surface motion of atoms and with Cercignani-Lampis scattering model is proposed. The stochastic simulation of self diffusion based on the waiting time model agrees with the MD simulations and theoretical results in literature. The Arrhenius law is used to model the variation of the obtained Knudsen diffusivity as functions of temperature.