<p>FRET-enabled optical computing is a new computing paradigm that uses the energy of incident photons to perform computation in molecular-scale circuits composed of inter-communicating photoactive molecules. Unlike conventional computing approaches, computation in these circuits does not require any electric current; instead, it relies on the controlled-migration of energy in the circuit through a phenomenon called Förster Resonance Energy Transfer (FRET). This, coupled with other unique features of FRET circuits can enable computing in new domains that are unachievable by the conventional semiconductor-based computing, such as in-cell computing or targeted drug delivery. In this thesis, we explore novel FRET-based multiplexing techniques to significantly increase the storage density of optical storage media. Further, we develop analysis algorithms, and computer-aided design tools for FRET circuits.</p><p>Existing computer-aided design tools for FRET circuits are predominantly ad hoc and specific to particular functionalities. We develop a generic design-automation framework for FRET-circuit optimization that is not limited to any particular functionality. We also show that within a fixed time-budget, the low-speed of Monte-Carlo-based FRET-simulation (MCS) algorithms can have a potentially-significant negative impact on the quality of the design process, and to address this issue, we design and implement a fast FRET-simulation algorithm which is up to several million times faster than existing MCS algorithms. We finally exploit the unique features of FRET-enabled optical computing to develop novel multiplexing techniques that enable orders of magnitude higher storage density compared to conventional optical storage media, such as DVD or Blu-Ray.</p> / Dissertation