Molecular dynamics simulation of structural changes of lipid bilayers induced by shock waves: Effects of incident angles

Abstract

Unsteady and nonequilibrium molecular dynamics simulations of the response of dipalmitoylphosphatidylcholine (DPPC) bilayers to the shock waves of various incident angles are presented. The action of an incident shock wave is modeled by adding a momentum in an oblique direction to water molecules adjacent to a bilayer. We thereby elucidate the effects of incident shock angles on (i) collapse and rebound of the bilayer, (ii) lateral displacement of headgroups, (iii) tilts of lipid molecules, (iv) water penetration into the hydrophobic region of the bilayer, and (v) momentum transfer across the bilayer. The number of water molecules delivered into the hydrophobic region is found to be insensitive to incident shock angles. The most important structural changes are the lateral displacement of headgroups and tilts of lipid molecules, which are observed only in the half of the bilayer directly exposed to a shock wave for all incident shock angles studied here. As a result, only the normal component of the added oblique momentum is substantially transferred across the bilayer. This also suggests that the irradiation by shock waves may induce a jet-like streaming of the cytoplasm toward the nucleus.

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

“…This approach constitutes a successful example of a multi-scale simulation. It has enabled us to study the water penetration phenomena using a system size which is almost two order of magnitude larger in size and three order of magnitude larger in simulation time than preceding fully atomistic MD simulations [29], [30]. The results of our simulations verify the predictions and observations made in those studies.…”

“…Explicit simulation of this solvent requires a much larger part of computational resources than actually spent on the bilayer, even though one is, in general, not interested in the structure of the solvent. This computational bottleneck is so severe that the largest atomistic simulations published to date [29], [30] only considered a system size of 128 phospholipids, with simulation box lengths parallel, and perpendicular to the bilayer plane of and , i.e., comparable to the bilayer thickness which is .…”

Molecular dynamics simulations of pore formation dynamics during the rupture process of a phospholipid bilayer caused by high-speed equibiaxial stretching

“…The l t is the length between the peaks of the phosphate groups of the lipid molecules across the bilayer system as defined in previous studies (Koshiyama et al, , 2008. We define the stretch ratio l i ¼(l i /l i0 ), where l i0 is the initial value, and the areal strain e A ¼ lxlyÀ1 ¼ ðl 2…”

“…Additionally, the apparent stretching force F resulted from stretching is estimated by F¼ ÀP lat l t l x , where the P lat ¼ ((P x þP y )/2) is the instantaneous lateral pressure exerted on the simulation box calculated from the Virial theorem. The values of the pressure are smoothed by taking running averages and sample averages for 20 calculations, since the statistical fluctuation of pressure is considerable and a long-time average cannot be implemented in unsteady MD simulations (Koshiyama et al, , 2008. The instantaneous surface tension g at the interfaces between the bilayer and the water layer is calculated by using boundary pressures, i.e.…”

“…On the other hand, with bubbles, the leakage is enhanced and large-sized molecules can be diffused into cells (Kodama et al, 2000). This suggests that pore formation under shock waves with bubbles may be induced not only by the high-speed deformation but also by other mechanisms, e.g., spontaneous pore formation after water penetration by repetitive impacts of shock waves from bubbles (Koshiyama et al, , 2008(Koshiyama et al, , 2010.…”