You pointed it out correctly. For short time dynamics, equilibrium approach does not hold good and a probability based non-equilibrium approach is rather required. Lattice Boltzmann simulation is a good tool to simulate such phenomena.

Thank you for your answer.

I will consider using Lattice Boltzmann simulation. But my question remains how to change these laws in itself? because I think that if I use these laws as-is, the problem will remain. I think there must have terms to add up towards the Boltzmann equation in each case. Unless Lattice Boltzmann simulation incorporates these terms.

Well LBM is a kind of direct numerical simulation where you do not need to use constitutive relationships for processes like heat transfer/mass transfer. All the physical phenomena are solved by the "collision integral" and the "relaxation time". Since, at the core, all physical phenomena can be explained by molecular motion and collisions between molecules e.g. heat transfer by conduction process; such macroscopic representations can be avoided if LBM or DNS is used.