Confined & Hydrodynamically Interacting Colloids

Many-body hydrodynamic interactions, Brownian motion, and confinement are rigorously modeled in our model biological cell via “Confined Stokesian Dynamics” (Aponte-Rivera & Zia, Phys. Rev. Fluids 2016; Aponte-Rivera, Su & Zia, J. Fluid Mech. 2018). Ongoing implementation of bio-fidelic particle interactions has led to our “Cellular Stokesian Dynamics” model.

Cellular Stokesian Dynamics. Biological cells are packed with macromolecules that diffuse, react, and self-assemble. Modeling these colloidal-scale physics requires accurately representing confinement, reactions, many-body solvent-mediated interactions, patchy attractions, and Brownian motion. Prior attempts neglected confinement, hydrodynamics, Brownian motion, or all three. Our aim was to explicitly model a spherically confined macromolecular suspension with Brownian motion, hydrodynamic interactions, and chemical reactions for a large number of macromolecules at any concentration. Our Cellular Stokesian dynamics model is the world’s first accurate model of a spherically-confined colloidal suspension Related publications: Aponte-Rivera & Zia, Phys. Rev. Fluids 2016; Aponte-Rivera, Su & Zia, J. Fluid Mech. 2018.

We explicitly represent individual macromolecules and their Brownian motion, hydrodynamics, surface chemistry, and patchy attractions while we track reactions, self-assembly, and ordering, resulting in a model biological cell that recovers cytoplasmic streaming, nuclear migration, gradient diffusion, and ternary complex–ribosome reactions. Our work established that diffusion in cells is anisotropic and that hydrodynamic interactions remain strong for all particle sizes and concentrations, disproving prior assertions that hydrodynamics are screened. We showed that size polydispersity leads to layered particle structure and increases diffusivity. In this way, biological cells can speed up diffusion of smaller biomolecules by surrounding them with larger ones.