My PhD involved computer simulations of various non-equilibrium active systems: systems which may be far from thermal equilibrium for sustained periods of time. These systems generally have some input of external energy, for example via conversion of chemical energy into mechanical work by biological organisms.
The work I did in particular consisted of agent-based simulations of simplified models of motile bacteria in confining environments, such as two-dimensional traps, mazes, and three-dimensional water droplets. The non-equilibrium nature of such systems makes their behaviour difficult to predict, and complex phenomena are frequently observed.
I don't work on these things any more.