The 20th century saw the first revolution of quantum mechanics, setting the rules for our understanding of light, matter, and their interaction. The 21st century is focused on using these quantum mechanical laws to develop technologies which allows us to solve challenging practical problems. One of the directions is the use quantum devices which promise to surpass the best computers and best known classical algorithms for solving certain tasks. Crucial to the design of realistic devices and technologies is to account for the open nature of quantum systems and to cope with their interactions with the environment. In the first part of this dissertation, we show how to tackle classical optimization problems of interest in the physical sciences within one of these quantum computing paradigms, known as quantum annealing (QA). We present the largest implementation of QA on a biophysical problem (six different experiments with up to 81 superconducting quantum bits). Although the cases presented here can be solved on a classical computer, we present the first implementation of lattice protein folding on a quantum device under the Miyazawa-Jernigan model. This is the first step towards studying optimization problems in biophysics and statistical mechanics using quantum devices. In the second part of this dissertation, we focus on the problem of excitonic energy transfer. We provide an intuitive platform for engineering exciton transfer dynamics and we show that careful consideration of the properties of the environment leads to opportunities to engineer the transfer of an exciton. Since excitons in nanostructures are proposed for use in quantum information processing and artificial photosynthetic designs, our approach paves the way for engineering a wide range of desired exciton dy- namics. Finally, we develop the theory for a two-dimensional electronic spectroscopic technique based on fluorescence (2DFS) and challenge previous theoretical results claiming its equivalence to the two-dimensional photon echo (2DPE) technique which is based on polarization. Experimental realization of this technique confirms our the- oretical predictions. The new technique is more sensitive than 2DPE as a tool for conformational determination of excitonically coupled chromophores and o↵ers the possibility of applying two-dimensional electronic spectroscopy to single-molecules
