Context <p>Lipid nanoparticles (LNPs) are a novel type of drug delivery carrier, which play a protective role in nucleic acid drug delivery. LNPs are composed of various organic materials and these compositions assume corresponding tasks. Among these components, ionizable lipids undergo localized accumulation of lipids after exposure to the acidic pH environment of endosomes due to electrostatic interactions between lipid nanoparticles and phospholipids in endosomal membranes, which contributes to membrane fusion-disruption, endosomal escape, and cargo release. However, these extrapolations lack intuitive evidence at the molecular level, so we perform computational simulations to provide a microscopic view of molecular and cellular biological events. In this work, we performed molecular dynamics (MD) simulations to study the microscopic mechanism of membrane disruption induced by the protonation of ionizable lipids. Models containing different concentrations of ionizable lipids were obtained by simulating the uptake process of ionizable lipids by the endosomal membrane. The simulated results showed that the protonated ionizable lipids accumulated on one side of the endosomal membrane. Through the analysis of intermolecular interactions, it was found that the accumulation was due to the strong association of the head groups of the protonated ionizable lipids with the membrane lipids. Whereas the unprotonated ionizable lipids were dispersed on both sides of the bilayer, which served to stabilize the nanoparticles. The accumulation of ionizable lipids caused a sustained effect on lipid order parameters and the thickness of the simulated bilayer, which may be responsible for endosomal membrane rupture.</p> Methods <p>In this study, we employed MD simulations and used the GROMOS 54A7 united-atom force field to investigate the passive diffusion process of ionizable lipids. MD simulations were performed using the GROMACS 2019 software, focusing on the changes in the energy and molecular distribution of the system during the uptake process of ionizable lipids. Characteristics such as SDC, thickness, and energy of the system configuration at the end of the process are also analyzed. These configurations of the simulations were visualized using VMD. The GridMAT-MD package was adopted to analyze the thickness of the membrane. The other characters such as density distribution profiles and energies were analyzed using the tools within the GROMACS package.</p>