Abstract: Quantum simulation methods are used to encode the quantum response of a molecular system so as to improve the sensitivity for detection of a target material, while rejecting background. The perturbation and response information may be used to discover the system function of a quantum system, or more generally, of a complex system, such as a physiological system. The approach may be applied to medical non-invasive, real-time, continuous molecular detection and quantification techniques through coherent Raman spectroscopy to enable a significantly more attractive course of therapy than existing protocols.