In this thesis, we investigate dynamics of many-body atomic systems coupled to electromagnetic fields. We find that collective effects present in cavity-mediated laser cooling and high temperatures of bubble in sonoluminescence can be explained using a two-stage model which combines quantum-optical models and thermodynamical processes. We show how the collective processes are strongly dependent on mutual atomic coherences and how these coherences need to be recreated for the continous collective processes to take place. The model mechanism behind both cavity-mediated laser cooling and sonoluminescence heating is alternating periods of thermalisation with cooling or heating cycles. The thermalisation stage is characterised by relatively weak interactions between the atomic system and its environment, while allowing the system to thermalise and to create phonon and electronic coherences necessary for the next stage. The second stage, when cooling or heating occurs, marks strong interactions of the atomic system with the surrounding radiation field, which renders interactions between the particles negligible. During this stage, the atomic coherences created earlier fuel the cooling or heating process, allowing the system to reach a more beneficial stationary state. For cavity-mediated laser cooling of an atomic gas, we show that dispersing cooling pulses with periods of thermalisation in an asymmetric potential can result in very low temperatures of the atomic gas. By applying this to atomic interactions of sonoluminescence, we can describe different parts of the lifecycle of the cavitating bubble and how very high temperatures arise inside of it.