Collective behavior of penetrable self-propelled rods in two dimensions

Collective behavior of self-propelled particles is observed on a microscale for swimmers such as sperm and bacteria as well as for protein filaments in motility assays. The properties of such systems depend both on their dimensionality and the interactions between their particles. We introduce a model for self-propelled rods in two dimensions that interact via a separation-shifted Lennard-Jones potential. Due to the finite potential barrier, the rods are able to cross. This model allows us to efficiently simulate systems of self-propelled rods that effectively move in two dimensions but can occasionally escape to the third dimension in order to pass each other. Our quasi-two-dimensional self-propelled particles describe a class of active systems that encompasses microswimmers close to a wall and filaments propelled on a substrate. Using Monte Carlo simulations, we first determine the isotropic-nematic transition for passive rods. Using Brownian dynamics simulations, we characterize cluster formation of self-propelled rods as a function of propulsion strength, noise, and energy barrier. Contrary to rods with an infinite potential barrier, an increase of the propulsion strength does not only favor alignment but also effectively decreases the potential barrier that prevents crossing of rods. We thus find a clustering window with a maximum cluster size at medium propulsion strengths.