Theoretical Design of All-Optical Universal Logic via Multistage FRET-STED Energy Cascades in Fluorescent Protein Nanoclusters.

The scaling limits of conventional electronics necessitate a shift toward alternative physical computing substrates. We present a universal logic design based on a novel materials platform employing FRET-coupled Fluorescent Protein (FP) NOR gates. By leveraging the nonlinear dynamics of Stimulated Emission Depletion (STED) to bypass slow protein backbone rearrangements, this system enables all-optical switching at speeds ranging from 1 GHz to potentially even 1 THz. We developed a dynamic multistage model of a three-protein FRET-STED cascade to evaluate performance. While a "lifetime bottleneck" initially limits standard operation, we demonstrate that engineering the plasmonic environment via Nanometal Surface Energy Transfer (NSET) enables 1 GHz operation with current protein variants. Analysis of fundamental electronic transitionsspecifically vibrational relaxationconfirms a theoretical bandwidth of ∼3.15 THz for optimized synthetic chromoproteins. This work establishes a robust foundation for high-speed, nanoscale, all-optical computing using DNA origami as a molecular breadboard for precise sub-10 nm positioning.