Notes on molecular fragmentation and parameter settings for a dissipative particle dynamics study of a C10E4/water mixture with lamellar bilayer formation

Journal of Cheminformatics

Research

Christoph Steinbeck¹  Achim Zielesny²  Felix Bänsch³ 

[1] Institute for Analytical Chemistry, Friedrich-Schiller-University, Jena, Germany;Institute for Bioinformatics and Chemoinformatics, Westphalian University of Applied Sciences, August-Schmidt-Ring 10, 45665, Recklinghausen, Germany;Institute for Bioinformatics and Chemoinformatics, Westphalian University of Applied Sciences, August-Schmidt-Ring 10, 45665, Recklinghausen, Germany;Institute for Analytical Chemistry, Friedrich-Schiller-University, Jena, Germany;

关键词: Dissipative particle dynamics;    DPD;    Surfactant;    Bilayer;    Lamellar;    Simulation;    Mesoscopic;   

DOI  :  10.1186/s13321-023-00697-w

 received in 2022-06-10, accepted in 2023-02-07,  发布年份 2023

来源: Springer

【 摘 要 】

The influence of molecular fragmentation and parameter settings on a mesoscopic dissipative particle dynamics (DPD) simulation of lamellar bilayer formation for a C10E4/water mixture is studied. A “bottom-up” decomposition of C10E4 into the smallest fragment molecules (particles) that satisfy chemical intuition leads to convincing simulation results which agree with experimental findings for bilayer formation and thickness. For integration of the equations of motion Shardlow’s S1 scheme proves to be a favorable choice with best overall performance. Increasing the integration time steps above the common setting of 0.04 DPD units leads to increasingly unphysical temperature drifts, but also to increasingly rapid formation of bilayer superstructures without significantly distorted particle distributions up to an integration time step of 0.12. A scaling of the mutual particle–particle repulsions that guide the dynamics has negligible influence within a considerable range of values but exhibits apparent lower thresholds beyond which a simulation fails. Repulsion parameter scaling and molecular particle decomposition show a mutual dependence. For mapping of concentrations to molecule numbers in the simulation box particle volume scaling should be taken into account. A repulsion parameter morphing investigation suggests to not overstretch repulsion parameter accuracy considerations.

【 授权许可】

CC BY   
© The Author(s) 2023

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