 Abstract optogenetics is a technique which combines externally applied light signals and genetically engineered photoreceptors to control cellular processes with unprecedented precision. This paper developed a mathematical model of wavelength, an intensity-dependent photoconversion, signalling, and output gene expression for two recently engineered light-sensing bacterial two-component systems. The model was then validated experimentally by testing it against a variety of light sources and signals. Additionally, the authors developed a novel method for programming two simultaneous and independent gene expression signals within the same cell. This method enables powerful new interrogations of how metabolic, signalling, and decision-making pathways integrate multiple inputs. This article was authored by Evan J. Olson, Konstantin N. Suanas, and Jeffrey J. Tabba.