Influence of particle smoothness and substrate mechanics on the clustering of self-propelled rods

Motile rod-shaped cells are common in biology. It is now well established that dry systems of motile rods show a rich variety of dynamic phases. Furthermore, the colonization of a soft, passive material by these motile cells, such as bacteria or cancer cells, is widely observed. This thesis explores the role of particle smoothness on the collective behavior of anisotropic self-propelled particles and the tendency of these particles to form clusters of different kinds in the elasto-plastic environment, using a computational model in LAMMPS. These studies are crucial for understanding the morphodynamics of colonization of bacterial colonies.