## 1 Introduction  
Bacteriorhodopsin (bR) is a widely explored photoactive protein for a variety of biomolecular electronics applications, including optical memory storage [1, 2]. bR is a membrane protein found in the salt marsh archaeon, Halobacterium salinarum, and comprises a photoactive moiety called retinal chromophore (C\({}_{20}\)H\({}_{28}\)O) in the middle of a channel formed by seven transmembrane alpha helices (A-G) [3]. It has a primary role of facilitating proton transportation and, therefore, generating a proton gradient across the cell membrane through a photochemical cycle [3]. This photocycle is a series of conformational changes caused by photoexcitation and de-excitation of covalently linked retinal chromophore atoms with the amino acid Lys216 via a protonated Schiff base linkage [1]. When bR is exposed to yellow light (\(\sim\)570 nm), it undergoes photoisomerization from an all-trans to 13-cis isomer and deprotonates by donating its extra hydrogen to the proton accepter Asp85 amino acid [4,5]. This protonation causes a proton release to the extracellular surface from the Asp212, Arg82, Glu204 or Glu194 amino acids [4,6,7,8,9,10,11,12], after which a re-protonation occurs by the proton donor Asp96 amino acid [4,13]. This cyclic reaction leads to the formation of different conformational and photochemical intermediate states (photostates J, K, L, M, N and O) before returning to the ground state (bR) in around 4-5 ms. This results in a net translocation of one proton across the membrane (Figure 1a) [1,14]. The remarkable level of photochemical stability makes bR a powerful choice for optical memory storage devices. This stability is strongly correlated to its cyclicity, which is measured by the number of times the protein can undergo a photocycle before \(\sim\)37% of it denatures (Figure 1b). Native bR protein has a cyclicity of \(\sim\)10\({}^{6}\), which is higher than any other photochemical proteins (e.g., blue proteorhodopsin has a cyclicity of \(\sim\)10\({}^{4}\)) [14]. The second important property of bR in such an application is its thermal stability, as the protein has been observed to be structurally and functionally stable above 80 \({}^{\circ}\)C [15,16]. In order to store or record binary data, it is required to have two stable states. In bR, the ground (bR) state is appropriate to designate bit 0, as it remains stable until a yellow light activates the photocycle. Similarly, another stable state is the branched photocycle Q state, which can be assigned a bit 1 [1,14]. The protein enters the branched photocycle only when the all-trans O intermediate (where Asp85 is still protonated) is illuminated with red light (\(\sim\)640 nm). Here, bacteriorhodopsin photoconverts to an unstable 9-cis conformation called P state, which ultimately undergoes a thermal decay and forms free (hydrolyzed from Lys216) 9-cis retinal chromophore called the Q state [17]. This Q state is a highly stable intermediate state at ambient temperatures with a lifetime of 7-12 years and will only convert back to the bR state when it is exposed to near-UV light (\(\sim\)390 nm) [1]. These properties of the bR and Q states make the bR protein suitable for long-term memory storage devices, similar to semiconductor memories [1,14]. The challenge in realizing such a device comes in accessing the branched photostates to produce volumetric long term optical memory storage. The low yield of the O state (\(\sim\)3%) during the photocycle results in an even lower yield of the branched photoproducts (P  
Figure 1: Proton transfer mechanism and binary logic in bR: (**a**) Location of key residues within bR and around the retinal showing the proton path from cytoplasm to extracellular environment; (**b**) Photochemical states of bR highlighting the ‘Branched photocycle’ that is responsible for binary state ‘1’ (9-cis) for the molecule. Binary state ‘0’ (all-trans) is also highlighted as the ground state. and Q) [1].