In the environment, the process of combustion is the dominant pathway through which mankind continuously injects particles into the atmosphere at the present time. The most direct and serious risk related to these emissions is the direct absorption of these particles into the living systems of humans and animals through the process of respiration, especially in more urban environments. Little is known about the potential of low-level exposures to alter key biophysical functions, such as membrane form and function. This study employs molecular dynamics simulations to reconstruct the free energy landscapes of the mechanisms of entry of nanoparticles into biological cells. Specifically, we investigate the behavior of two nanoparticles produced in combustion conditions with different amphiphilic properties to assess the effect of chemical composition on the interactions with cellular membranes. Free energy calculations of nanoparticles interacting with a lipid bilayer composed of dimyristoylphosphatidyl-choline and cholesterol show that the presence of hydroxyl groups on the nanoparticle makes the region where the lipids' heads are solvated by water the most favorable position for these species. The hydrophobic nanoparticle shows a strong affinity for the center of the membrane. This study shows the importance of surface composition and suggests different mechanisms of interactions of nanoparticles with cellular membranes.