Reaction-diffusion condensation generates a regulatable landscape for self-organizing subcellular structures

Cells self-organize complex internal architectures through an interplay between biochemical signaling and physical structure. Within this paradigm, reaction-diffusion signaling mechanisms create local concentration gradients, and protein condensates assemble in a concentration-dependent manner, providing a natural coupling for a landscape of composite active structures to emerge. Here, we systematically chart this landscape in human cells at scale using RIPPLE (Reaction-diffusion IDR Platform for Producing Living Emulsions), a synthetic modular system that tethers disordered, condensate-forming IDR sequences to a programmable, two-protein wave-generating reaction-diffusion (RD) circuit. Fusing IDRs to the RD Activator, its partner ATPase, or both, generates a vast array of self-organizing subcellular architectures—ranging from traveling condensation waves to oscillating droplet networks to persistent phase-separated macrostructures that pattern the entire cell. By systematically tuning the frequency and amplitude of the underlying RD waveforms, we reveal frequency-dependent transitions regulating dilute, condensed, and aggregated states specified by IDR sequence chemistry and miscibility. RIPPLE provides a platform for understanding and engineering protein condensation far from equilibrium, revealing how signaling and structure can cooperate in a minimal, two-protein system to generate a tunable spectrum of dynamic cellular structures.