To give a correct description of plutonium resorption from lungs to blood in case of inhalation intake of the radionuclide as a dioxide, it is important to understand physical process of plutonium transition from aerosol solid phase into lung liquid. Interaction of recoil nucleus generating after 239Pu nucleus alpha-decay, with crystal lattice of aerosol solid phase material is regarded as a main mechanism of such transition. The interaction is modeled by three-dimensional molecular dynamics method. Ion motion equations, their integration technique and system temperature control method are described. The justification for intermolecular interaction potential choice is given. The results of molecular simulation as a displacement stages development and plutonium dioxide molecules escape pattern are provided. Particles are able to escape from a crystal in the form of separate ions of plutonium and oxygen, plutonium dioxide molecules and electroneutral clusters of Pu dioxide. Alpha-decay of nuclei present in near-surface layer 10 nm thick from crystal surface makes the main contribution to Pu sputtering.