Estimating near-wall diffusion coefficients of arbitrarily shaped rigid macromolecules

Area of Science:

• Computational physics
• Macromolecular science
• Fluid dynamics

Background:

• Accurate prediction of macromolecular diffusion near surfaces is crucial for understanding biological and chemical processes.
• Existing methods for calculating near-wall diffusion coefficients can be computationally intensive, especially for complex molecular shapes.

Purpose of the Study:

• To develop a computationally efficient method for approximating near-wall diffusion coefficients of arbitrarily shaped rigid macromolecules.
• To validate the accuracy of the proposed method using biomolecular examples.

Main Methods:

• Utilized extremum principles for Stokes flows and hydrodynamic interactions of rigid bodies near a no-slip boundary.
• Employed a coarse-grained molecular model with Rotne-Prager-Yamakawa hydrodynamics and Blake's image construction for boundary effects.
• Scaled mobility matrix components using ratios of bulk to near-wall values for improved accuracy.

Main Results:

• The developed approach provides accurate approximations of near-wall diffusion coefficients for macromolecules.
• The method's performance was successfully assessed for two biomolecules at varying coarse-graining levels.
• Demonstrated the effectiveness of incorporating boundary effects through image construction and scaling.

Conclusions:

• The computationally efficient method accurately predicts near-wall diffusion coefficients for complex macromolecules.
• This approach offers a valuable tool for simulating and understanding macromolecular behavior in confined environments.
• The findings have implications for fields requiring precise modeling of particle transport near interfaces.