A Minimal Mathematical Model of Cytoplasmic Mixing in Amoeba Chaos Carolinensis

Cytoplasmic mixing is essential for cellular function and is influenced by the cell’s motion, activity, shape changes, intracellular flows, and crowding. To better understand the physics of this process, we developed a minimal in silico model of an amoeba, chosen for its large cell size. The model consists of a cell membrane enclosing biopolymers, organelles, and tracer particles within a viscous fluid. Polymer-membrane interactions, steric interactions between intracellular structures, active transport, and pseudopod-driven bulk motion were included to replicate the cellular environment and dynamics. The interaction between the fluid and the cellular structures was modeled using the immersed boundary method. We characterized cytoplasmic mixing and transport by analyzing tracer particle trajectories and mean squared displacements. Our simulation results were compared with ongoing experiments in which fluorescent tracer particles are injected into the amoeba Chaos carolinensis and tracked via microscopy. This study provides valuable insights into the physical processes driving cytoplasmic mixing.