Shock-wave induced damage in lipid bilayers: a dissipative particle dynamics simulation study

Abstract

The effects of shock-wave impact on the damage of lipid bilayer membranes are investigated with dissipative particle simulations at constant energy (DPDE). A coarse-grained model for the phospholipid bilayer in aqueous environment is employed, which models single lipids as short chains consisting of a hydrophilic head and two hydrophobic tail beads. Water is modeled by mapping four H 2 O molecules to one water bead. Using the DPDE method enables us to faithfully simulate the nonequilibrium shock-wave process with a coarse-grained model as the correct heat capacity can be recovered. At equilibrium, we obtain self-stabilizing bilayer structures that exhibit bending stiffness and compression modulus comparable to experimental measurements under physiological conditions. We study in detail the damage behavior of the coarse-grained lipid bilayer upon high-speed shock-wave impact as a function of shock impact velocity and bilayer stability. A single damage parameter based on an orientation dependent correlation function is introduced. We observe that mechanical bilayer stability has only small influence on the resulting damage after shock-wave impact, and inertial effects play almost no role. At shock-front velocities below ( 3000 ms À1 , we observe reversible damage, whereas for speeds T 3900 ms À1 no such recovery, or self-repair of the bilayer, could be observed.

Consistent Temperature Coupling with Thermal Fluctuations of Smooth Particle Hydrodynamics and Molecular Dynamics

“…This stems from the observation that the temperature increase across a shock-wave front cannot be described using ordinary CG MD, as the heat capacity of such a system would be incorrect, see refs. [31], [32] for further details. In order to further improve computational efficiency, we use a graded resolution within the SPH domain, increasing the smoothing length with increasing distance from the bilayer, see Fig.…”

“…Therefore, . The amplitude of the DPDE forces, , was parametrized by requiring that the temperature rise across a shock-wave travelling with 1000 m/s is the same in both a fully atomistic simulation of SPC water and the CG MD water model used here, a procedure detailed in [32]. All CG MD particles carry a mass of 72 g/mol.…”

Ligands influence a carbon nanotube penetration through a lipid bilayer

“…Dissipative particle dynamics (DPD) is a coarse-grained computer simulation method extensively applied to study bio-membrane systems (Ganzenmüller et al 2011;Goetz and Lipowsky 1998;Goicochea 2014;Peng et al 2014).…”

Damage in spherical cellular membrane generated by the shock waves: Coarse-grained molecular dynamics simulation of lipid vesicle

“…The longer simulation time obtainable by these models also makes it possible to study the time evolution of the shocked membranes, where the shock front can travel for a longer period of time. 28 The DPD approach, which is a mesoscale technique for complex fluids, correctly captures hydrodynamic behavior. A DPD system is composed of coarse-grained soft particles, each representing a cluster of molecules rather than individual atoms, moving continuously in space and discreetly in time according to Newton's equations of motion.…”

“…As a consequence, it may prove particularly helpful to elucidate the microscopic structural details and dynamics with computer simulations. Recently, there have been several computational studies on structural changes of lipid bilayers induced by shock waves, 13,[26][27][28][29] high-speed stretching, 30 and ultrasound radiation. 31 Santo and Berkowitz 29 observed that a shock wave passing through a lipid bilayer in water induced nanobubble collapse, where they discerned transient damage to the bilayer and pore creation.…”