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Hydrodynamic coupling for particle-based solvent-free membrane models.

Mohsen Sadeghi1, Frank Noé1

  • 1Department of Mathematics and Computer Science, Freie Universität Berlin, Arnimallee 6, 14195 Berlin, Germany.

The Journal of Chemical Physics
|September 23, 2021
PubMed
Summary
This summary is machine-generated.

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We developed a new framework for coarse-grained membrane simulations that accurately models hydrodynamic interactions. This method improves the realism of membrane dynamics, crucial for understanding cellular processes.

Area of Science:

  • Biophysics
  • Computational Biology
  • Materials Science

Background:

  • Biological membranes involve diverse scales, from nanometers/picoseconds to micrometers/milliseconds.
  • Current solvent-free coarse-grained models offer convenience but often lack realistic kinetics.
  • Introducing hydrodynamic coupling in these models is computationally expensive and challenging.

Purpose of the Study:

  • To introduce a computationally efficient framework for modeling hydrodynamic coupling in coarse-grained membrane simulations.
  • To improve the accuracy of kinetic descriptions in large-scale membrane dynamics.
  • To provide insights into slow cellular signaling processes involving membranes.

Main Methods:

  • Anisotropic Langevin dynamics framework.

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  • Modeling hydrodynamic effects using friction and diffusion tensors derived from Stokes equations.
  • Integration with a recently developed coarse-grained membrane model.
  • Analysis of dispersion relations for planar membrane patches.

    • Main Results:

    • Accurate dispersion relations for free-standing and wall-confined membrane patches were obtained.
    • The framework successfully models in-plane and out-of-plane hydrodynamic effects.
    • Non-equilibrium dynamics were analyzed concerning hydrodynamic interactions.
    • Surface viscosity of the model membrane was measured and dissipative mechanisms discussed.

    Conclusions:

    • The proposed anisotropic Langevin dynamics framework effectively incorporates hydrodynamic coupling into coarse-grained membrane models.
    • This approach enhances the realism of membrane simulations, enabling more accurate studies of biological processes.
    • The method provides a balance between computational efficiency and physical accuracy for large-scale membrane dynamics.