CHARMM36 All-Atom Gas Model for Lipid Nanobubble Simulation

Lipid nanobubbles with different gas cores may integrate the biocompatibility of lipids, powerful physicochemical properties of nanobubbles, and therapeutic effects of gas molecules, which thus promote enormous biomedical applications such as ultrasound molecular imaging, gene/drug delivery, and gas therapy. In order for further more precise applications, the exact molecular mechanisms for the interactions between lipid nanobubbles and biological systems should be studied. Molecular dynamics (MD) simulation provides a powerful computational tool for this purpose. However, previous state-of-the-art MD simulations of free gas nanobubble/lipid nanobubble employed the vacuum as their gas cores, which is not suitable for studying the interactions between functional lipid nanobubbles and biological systems and revealing the biological roles of gas molecules. Hence, in this work, we developed and optimized the CHARMM36 all-atom gas parameters for six gases including N₂, O₂, H₂, CO, CO₂, and SO₂, which accurately reproduced the gas density at different pressures as well as the spontaneous formation of gas nanobubbles. Subsequent applications of these gas parameters for lipid nanobubble simulations also reproduced the self-assembly process of the lipid nanobubble. We further developed a Python script to generate all-atom lipid nanobubble simulation systems, which was proven to be efficient for all-atom MD simulations of lipid nanobubbles and to be able to capture the exact dynamics of gas molecules at the gas-lipid and lipid-water interfaces of the lipid nanobubble. In summary, the all-atom gas models proposed in this work are suitable for simulating free gas nanobubbles and lipid nanobubbles, which are supposed to overcome the shortcomings of previous state-of-the-art MD simulations with the vacuum replacing the gas core and play key roles in revealing the molecular-level interactions between lipid nanobubbles and biological systems.