Article Dans Une Revue Journal of Colloid and Interface Science Année : 2022

Polystyrene perturbs the structure, dynamics, and mechanical properties of DPPC membranes: An experimental and computational study

Davide Bochicchio
  • Fonction : Auteur
Laura Cantu
  • Fonction : Auteur
Maria Vittoria Cadario
  • Fonction : Auteur
Leonardo Palchetti
  • Fonction : Auteur
Francesca Natali
Giulia Rossi
Elena del Favero
  • Fonction : Auteur

Résumé

Abstract Molecular dynamics simulations play an increasingly important role in the rational design of (nano)-materials and in the study of biomacromolecules. However, generating input files and realistic starting coordinates for these simulations is a major bottleneck, especially for high throughput protocols and for complex multi-component systems. To eliminate this bottleneck, we present the polyply software suite that provides 1) a multi-scale graph matching algorithm designed to generate parameters quickly and for arbitrarily complex polymeric topologies, and 2) a generic multi-scale random walk protocol capable of setting up complex systems efficiently and independent of the target force-field or model resolution. We benchmark quality and performance of the approach by creating realistic coordinates for polymer melt simulations, single-stranded as well as circular single-stranded DNA. We further demonstrate the power of our approach by setting up a microphase-separated block copolymer system, and by generating a liquid-liquid phase separated system inside a lipid vesicle.

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Dates et versions

hal-05023560 , version 1 (07-04-2025)

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Citer

Davide Bochicchio, Laura Cantu, Maria Vittoria Cadario, Leonardo Palchetti, Francesca Natali, et al.. Polystyrene perturbs the structure, dynamics, and mechanical properties of DPPC membranes: An experimental and computational study. Journal of Colloid and Interface Science, 2022, 605 (1), pp.110-119. ⟨10.1016/j.jcis.2021.07.069⟩. ⟨hal-05023560⟩
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