Tutorial for Atomistic and Coarse-Grained Simulations of Membrane-Nanoplastic Interactions Using GROMACS

Area of Science:

• Biophysics
• Computational Chemistry
• Materials Science

Background:

• Molecular dynamics (MD) simulations are crucial for studying membrane properties and interactions with plastic particles.
• Understanding nanoplastic-membrane interactions is vital due to environmental and health concerns.

Purpose of the Study:

• To provide a practical tutorial for simulating nanoplastic-membrane interactions using atomistic and coarse-grained MD.
• To guide users in modeling and analyzing systems involving polystyrene (PS) nanoplastics and POPC membranes.

Main Methods:

• Utilized CHARMM-GUI for system preparation and GROMACS for molecular dynamics simulations.
• Performed simulations at both atomistic and coarse-grained levels for PS in water, POPC membrane in water, and POPC-PS complex.
• Employed GROMACS analysis tools and Tcl scripts for property calculations.

Main Results:

• Successfully modeled and simulated three distinct systems involving nanoplastics and membranes.
• Calculated key biophysical properties such as radius of gyration, membrane thickness, area per lipid, order parameters, and lipid diffusion coefficients.
• Demonstrated a comprehensive workflow for analyzing complex membrane-nanoplastic interactions.

Conclusions:

• The presented workflow offers a practical guide for researchers to model, simulate, and analyze their own systems involving membranes and nanoplastics.
• This tutorial facilitates deeper understanding of nanoplastic interactions with biological membranes through computational methods.