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Particle-based simulations of bilayer membranes: self-assembly, structural analysis, and shock-wave damage

Abstract

We report on the results of particle-based, coarse-grained molecular dynamics simulations of amphiphilic lipid molecules in aqueous environment where the membrane structures at equilibrium are subsequently exposed to strong shock waves, and their damage is analyzed. The lipid molecules self-assemble from unbiased random initial configurations to form stable bilayer membranes, including closed vesicles. During self-assembly of lipid molecules, we observe several stages of clustering, starting with many small clusters of lipids, gradually merging together to finally form one single bilayer membrane. We find that the clustering of lipids sensitively depends on the hydrophobic interaction \(h_\mathrm{c}\) of the lipid tails in our model and on temperature T of the system. The self-assembled bilayer membranes are quantitatively analyzed at equilibrium with respect to their degree of order and their local structure. We also show that—by analyzing the membrane fluctuations and using a linearized theory— we obtain area compression moduli \(K_\mathrm{A}\) and bending stiffnesses \(\kappa _\mathrm{B}\) for our bilayer membranes which are within the experimental range of in vivo and in vitro measurements of biological membranes. We also discuss the density profile and the pair correlation function of our model membranes at equilibrium which has not been done in previous studies of particle-based membrane models. Furthermore, we present a detailed phase diagram of our lipid model that exhibits a sol–gel transition between quasi-solid and fluid domains, and domains where no self-assembly of lipids occurs. In addition, we present in the phase diagram the conditions for temperature T and hydrophobicity \(h_\mathrm{c}\) of the lipid tails of our model to form closed vesicles. The stable bilayer membranes obtained at equilibrium are then subjected to strong shock waves in a shock tube setup, and we investigate the damage in the membranes due to their interaction with shock waves. Here, we find a transition from self-repairing membranes (reducing their damage after impact) and permanent (irreversible) damage, depending on the shock front speed. The here presented idea of using coarse-grained (CG) particle models for soft matter systems in combination with the investigation of shock-wave effects in these systems is a quite new approach.

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Funding

This study was funded by the Fraunhofer-Gesellschaft, e.V., Germany, under grant no. 400017 “Extracorporeal, Focused Ultrasound Therapy: Effectiveness, Simulation, and Planning of New Therapies” and grant no. 600016, Vintage Class Program: “Shock Wave Induced Destruction of Tumor Cells”.

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Correspondence to Martin O. Steinhauser.

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Steinhauser, M.O., Schindler, T. Particle-based simulations of bilayer membranes: self-assembly, structural analysis, and shock-wave damage. Comp. Part. Mech. 4, 69–86 (2017). https://doi.org/10.1007/s40571-016-0126-3

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Keywords

  • Molecular dynamics simulation
  • Biological membrane
  • Particle simulation
  • Shock-wave physics
  • Cell research
  • Multiscale modeling