  The activity of biological cells is primarily based on chemical reactions and
typically modeled as a reaction-diffusion system. Cells are, however, highly
crowded with macromolecules, including a variety of molecular machines such as
enzymes. The working cycles of these machines are often coupled with their
internal motion (conformational changes). In the crowded environment of a cell,
motion interference between neighboring molecules is not negligible, and this
interference can affect the reaction dynamics through machine operation. To
simulate such a situation, we propose a reaction-diffusion model consisting of
particles whose shape depends on an internal state variable, for crowds of
nano- to micro-machines. The interference between nearby particles is naturally
introduced through excluded volume repulsion. In the simulations, we observed
segregation and flow-like patterns enhanced by crowding out of relevant
molecules, as well as molecular synchronization waves and phase transitions.
The presented model is simple and extensible for diverse molecular machinery,
and may serve as a framework to study the interplay between the mechanical
stress/strain network and the chemical reaction network in the cell.
Applications to more macroscopic systems, e.g., crowds of cells, are also
discussed.
