<title>Analysis of bacteriorhodopsin and its applications in photonics</title>

Abstract

A comprehensive analysis of the light induced processes in the bacteriorhodopsin (BR) molecule is. presented based on the rate equations approach. A simplified energy level scheme is proposed to represent the complex photochemical cycle of the BR molecule. Light intensity-induced population densities in various states of the molecule at steady-state are computed and used to derive an analytic expression for the absorption coefficient of the modulation beam passing through the medium containing the BR molecules. This coefficient encompasses all possible photochromic transitions of the BR molecule and can be used to analyse various nonlinear processes exhibited by the BR molecules. The analysis is used to study the spatial light modulation and the mode-locking applications of BR molecules. It is shown that for a probe beam at 412 nm upto 82% modulation can be achieved using a modulating laser of intensity 3.2 W/cm2 at 570 nm. For temperatures ~77 K, the transmission at 610 nm can be switched from the initial 13% to 96% for modulating laser intensity of 11 W/cm2. The analysis demonstrates the feasibility of constructing a molecular spatial light modulator using BR molecules with a dynamic range of 0.12 and sensitivity of 0.66 cm^/W for the read beam at 412 nm. The analysis of mode-locking demonstrates the possibility of producing pulses of 64 fs duration and 7 nJ energy by passively mode-locking a laser in the visible region using the BR molecules.