First coarse grain then scale: How to estimate diffusion coefficients of confined molecules

Area of Science:

• Fluid dynamics
• Computational physics
• Polymer science

Background:

• Understanding molecular diffusion is crucial in various scientific fields.
• Geometric confinement significantly alters diffusion behavior.
• Accurate modeling of diffusion near boundaries remains a challenge.

Purpose of the Study:

• To propose a novel method for approximating position and orientation-dependent diffusion coefficients.
• To extend existing near-wall diffusion schemes to arbitrary boundary geometries.
• To simplify hydrodynamic calculations involving molecular diffusion under confinement.

Main Methods:

• Shape-based coarse-graining of rigid molecules.
• Scaling of mobility matrix components using energy dissipation arguments for Stokes flows.
• Application to various molecular shapes (capsule, dumbbell) and boundary types (sphere, cylinder, parallel planes).

Main Results:

• The proposed method accurately approximates translational and rotational diffusion coefficients.
• Excellent agreement was achieved between detailed and coarse-grained models, even near boundaries.
• The method effectively handles complex geometries and molecular shapes.

Conclusions:

• The developed approach offers a simplified and accurate way to model diffusion under confinement.
• It reduces errors associated with coarse-graining molecular shapes in hydrodynamic simulations.
• This method has broad applicability in studying molecular behavior in confined environments.