The first radio surveys of the sky discovered that some large clusters of galaxies contained powerful sources of synchrotron emission. Optical images showed that long linear filaments with bizarre emission-line spectra permeated the intra-cluster medium. Recent observations in the infrared and radio show that these filaments have very strong emission lines of molecular hydrogen and carbon monoxide. The mass of molecular material is quite large, the gas is quite warm, and the filaments have not formed stars despite their ~Gyr age. I will discuss the general astrophysical context of large clusters of galaxies and how large masses of molecular gas can be heated to produce what we observe. The unique properties of the filaments are a result of the unique environment. Magnetically confined molecular filaments are surrounded by the hot intra-cluster medium. Thermal particles with keV energies enter atomic and molecular regions and produce a shower of secondary nonthermal electrons. These secondaries collisionally heat, excite, dissociate, and ionize the cool gas. While ionization is dominated by these secondary particles, recombination is controlled by charge exchange, which produces the unusual optical emission line spectrum. I will describe some of the physical processes that are unique to this environment and outline some of the atomic physics issues.