  Colonies of bacteria endowed with a pili-based self-propulsion machinery are
ideal models for investigating the structure and dynamics of active
many-particle systems. We study Neisseria gonorrhoeae colonies with a
molecular-dynamics-based approach. A generic, adaptable simulation method for
particle systems with fluctuating bond-like interactions is devised. The
simulations are employed to investigate growth of bacterial colonies and the
dependence of the colony structure on cell-cell interactions. In colonies,
pilus retraction enhances local ordering. For colonies consisting of different
types of cells, the simulations show a segregation depending on the
pili-mediated interactions among different cells. These results agree with
experimental observations. Next, we quantify the power-spectral density of
colony-shape fluctuations in silico. Simulations predict a strong violation of
the equilibrium fluctuation-response relation. Furthermore, we show that active
force generation enables colonies to spread on surfaces and to invade narrow
channels. The methodology can serve as a foundation for future studies of
active many-particle systems at boundaries with complex shape.
