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From kinematics to molecular machines, biologically inspired technologies harness and enhance the intrinsic properties of naturally occurring materials and systems for applied technologies. Bacteriorhodopsin (BR) represents the most studied protein for photonic applications, and has found use in artificial retinas, associative and volumetric memories, optical limiters, photovoltaic cells and other devices. The native BR protein is rarely optimal for device applications, and genetic engineering plays an important role in the optimization process. In addition, new retinal proteins such as proteorhodopsin and channelrhodopsin-2 have been discovered which provide new options and opportunities.

Vision in vertebrates is a complex and involved process. Small organic molecules, known as chromophores, become electronically excited upon the absorption of a photon of light. In the excited state exists a barrier-less potential energy surface for some torsional movement about a double bond. The conformational change in the chromophore moiety induces a corresponding conformational change in the covalently bound polypeptide, thereby triggering a messenger cascade within the photoreceptor cell that results in the transmission of signals to the appropriate neurons. These signals are transmitted along the optic nerve to the visual centers of the brain, which allows the brain to process the visual input and perceive a visual image. The study of chromophores and photoreceptors in vitro is dominantly focused on theoretical computational calculations and spectroscopy. The focus of this chapter is to elucidate these methods, with emphasis on their application to the study of biological systems.