In the present quantum optics and laser physics study, the non-linear interaction of electromagnetic fields with atomic, molecular and biomolecular media is analyzed. Particular emphasis is given to coherent phenomena, while propagation and dispersion effects are also extensively investigated. The fields involved vary from ultra short pulses to continuous waves; while their energies range from the very strong that are addressed classically, to the very weak which are described quantum mechanically. Applications and problems addressed span a wide range. A scheme for a real time detector of chemical and biological hazards, like anthrax spores, is presented; in it, a strong spectroscopic signature is obtained from complex molecules by using ultrashort, femtosecond, laser pulses and inducing vibrational coherence on them. Furthermore, a way of reversing the phase matching condition in coherent spectroscopy, based on dispersion, is developed; which allows for the use of such spectroscopic methods in remote detection. More fundamental questions addressed include a resolution of the centennial old paradox of Maxwell's demon via quantum thermodynamics, and the role of atomic coherence in enhancing the efficiency of a heat engine as well as in obtaining lasing without population inversion. Additionally, a quantum storage scheme is presented, in which the information contained in an optical pulse is stored and restored via photon echoes.