Shock Wave Induced Collapse of Arrays of Nanobubbles Located Next to a Lipid Membrane: Coarse-Grained Computer Simulations

We used molecular dynamics simulations to study creation of pores in lipid bilayer membranes by inducing shock waves in systems containing arrays of nanobubbles next to these membranes. Shock waves impinged on the bubbles imploding them and produced nanojets that subsequently hit the bilayers making pores in them. Our simulations were performed using the MARTINI coarse-grained force field. The emphasis in our study was on the interaction of shock waves with two-bubble arrays when the bubbles were placed in different alignments. We observed that the largest damage to the bilayer was produced when two bubbles were positioned in a serial alignment and the bubbles touched each other. When two touching each other bubbles were located parallel to the membrane surface and at the same distance from the surface, the membrane damage was reduced, compared to the damage done by explosion of two independent nanobubbles. When two nanobubbles were placed in slanted configurations, the damage was intermediate between damages produced by two bubbles in parallel or serial alignment. Damage to the membrane produced by arrays containing more than two bubbles can be understood as a combination of damage produced by all three alignments of two bubbles.