Strong coupling between a quantum system and its many-body environment is becoming an increasingly important topic for many branches of physics. Numerous systems of experimental and technological relevance demonstrate strong system-environment coupling, leading to complex dynamical behaviour. This thesis is concerned with two particular examples of such systems, namely quantum dots (QDs) and excitonic energy transfer (EET) in molecular systems. Traditional quantum optics treatments are often

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... ufficient to describe the transient, steady state, and optical properties of QDs due to system-environment correlations. In contrast, we present a modified theory of quantum optics capable of capturing the influence of a thermal environment on the behaviour of QDs. Using this framework we demonstrate a striking departure of the emission spectra and photon measurement statistics of a classically driven QD when compared to an analogous atomic system. Furthermore, in contradiction to accepted notions of decoherence and dissipation, we show that the interaction between a QD and its thermal environment induces non-classical light-matter correlations in an otherwise semi-classical regime of cavity quantum electrodynamics. Away from QDs, we develop the reaction coordinate (RC) formalism to describe the dynamics of a system coupled to a low frequency environment — a regime important to EET systems. We do so by identifying and incorporating important environmental degrees of freedom into an enlarged system Hamiltonian. Uniquely, this approach gives insight directly into the dynamical evolution of the environment and correlations accumulated between the system and environment. Furthermore, it is demonstrated that these corre- lations persist into the steady state, generating non-canonical equilibrium states of the system and environment. We then apply the RC model to describe EET in a molecular dimer, highlighting the effect that under- and over-damped environments have on the excitation dynamics. In doing so, we show interactions b [...]