Breathing is one internal function that the conscious mind can control with comparative ease. The effect of controlled breathing is almost like communication with all conscious parts of one's being saying to them, "Simmer down and listen; there is something beyond the turmoil". It is communication in action that often works when words merely go in one ear and out the other, not even changing the cognitive mind. In essence, the effect is to turn all the elements of our will toward stillness and waiting.
The highest level of prayer is not a prayer FOR anything. It is a deep and profound silence, in which we allow ourselves to be still and know God. In that silence, we are changed. We are calmed. We are illumined. Prayer is meant to dissolve the worldly focus, to dissolve our sense of a separate self, to help us detach from the noisy world order.
Prayer is like pouring hot water on an ice cube, melting the cold and encrusted thought forms that still surround our hearts.