With gravity, there is a density gradient in the vertical direction. The strength of the gradient depends on the mass of the species. Since the atmosphere has a mixture of different species, you get a separation between different components in the vertical direction, that you would not get if you just mixed all the same gases together in free space (or in a chamber where you could ignore gravity).
A simple model of this is the isothermal atmosphere. The pressure of a gas varies with height $z$ as
\begin{equation}
p(z) = p_0 e^{-z/z_0}
\end{equation}
where $p_0$ is the "sea level" pressure and the scale height $z_0$ is
\begin{equation}
z_0 = \frac{R T}{\mu g}
\end{equation}
where $R$ is the gas constant, $T$ is the temperature, $g$ is the acceleration due to gravity, and $\mu$ is the molecular weight of the gas. If the molecular weight of a gas is smaller than that of air, it will tend to be more dense than air at higher altitudes.
This equation also implies that if the temperature of a gas $T$ is larger than the ambient air temperature, it will be denser than air at larger heights -- hence "hot air rises." I suspect this latter point explains the behavior of the smoke in the simulation.