The Particle and Heavy Ion Transport code System, PHITS, has been developed under the collaboration of several research institutes in Japan and Europe. This system can simulate the transport of most particles with energy levels up to 1 TeV (per nucleon for ion) using different nuclear reaction models and data libraries. More than 2,500 registered researchers and technicians have used this system for various applications such as accelerator design, radiation shielding and protection, medical physics, and space- and geo-sciences. This paper summarizes the physics models and functions recently implemented in PHITS, between versions 2.52 and 2.88, especially those related to source generation useful for simulating brachytherapy and internal exposures of radioisotopes.