Carbon fullerenes are emerging as effective devices for different biomedical applications, including the transportation of nanosized drugs and the extraction of harmful oxidants and radicals. It has been proposed that fullerenes could be used as novel antibacterial agents, given the realization that the nanoparticles can kill pathogenic Gram-negative bacteria. To explore this at the molecular level, we simulated C 60 fullerenes with bacterial membranes using the coarse-grain (CG) molecular dynamics (MD) Martini force field. We find that pristine C 60 has a limited tendency to penetrate (incomplete core) Re mutant lipopolysaccharide (LPS) leaflets, but the translocation of C 60 fullerenes into (complete core) Ra mutant LPS leaflets is not thermodynamically favored. Moreover, we show that the permeability of Re LPS bilayers depends sensitively on system temperature, the charge of ambient ions, and the prevalence of POPE defect domains. The different permeabilities are rationalized in terms of transitory head group pore formation, which underpins the translocation of C 60 into the lipid core. The Re LPS lipids readily form transient micropores when they are linked with monovalent cations, or when they are heated to a high temperature. POPE lipids are shown to be particularly adept at forming these transient surface cavities, and their inclusion into Re LPS membranes facilitates the formation of particularly large pores that are tunneled by C 60 aggregates of significant size (~ 5 nm wide). After inserting into the lipid core, the aggregates dissociate, and the disbanded nanoparticles migrate to the interface between separate POPE and LPS domains, where they weaken the boundaries between the coexisting lipid fractions and thereby promoting lipid mixing.