The Raspberry model for protein-like particles: ellipsoids and confinement in cylindrical pores

TL;DR

This paper introduces an advanced raspberry model for simulating protein-like colloidal particles, accurately capturing their diffusive behavior and resistance in confined geometries using coarse-grained lattice Boltzmann methods.

Contribution

The study develops a raspberry model for ellipsoidal and spherical particles that accurately reproduces resistance and rotational dynamics in confined environments, enabling efficient large-scale simulations.

Findings

Reproduces linear resistance to motion versus particle size.

Accurately models enhanced drag in cylindrical pores.

Captures body-frame rotations during diffusion.

Abstract

The study of protein mass transport via atomistic simulation requires time and length scales beyond the computational capabilities of modern computer systems. The raspberry model for colloidal particles in combination with the mesoscopic hydrodynamic method of lattice Boltzmann facilitates coarse-grained simulations that are on the order of microseconds and hundreds of nanometers for the study of diffusive transport of protein-like colloid particles. The raspberry model reproduces linearity in resistance to motion versus particle size and correct enhanced drag within cylindrical pores at off-center coordinates for spherical particles. Owing to the high aspect ratio of many proteins, ellipsoidal raspberry colloid particles were constructed and reproduced the geometric resistance factors of Perrin and of Happel and Brenner in the laboratory-frame and in the moving body-frame. Accurate body-frame rotations during diffusive motion have been captured for the first time using projections of displacements.