## 4 Conclusions  
The adsorption of bacteriorhodopsin onto graphene has the potential to improve the yield of its Q photostate and, hence, its effectiveness for applications in optical memory devices. This notion is supported through both the stability and energetics data analysis. Higher deviation and less fluctuations in the RMSD data indicates more conformational changes that occur for bacteriorhodopsin due to its adsorption onto the graphene surface, and based on the graphene and bR interface study, it can be concluded that the optimal distance for these interactions to be maximized is ~4.2 A. Due to the presence of graphene, a greater number of hydrogen bonds are formed around the retinal as a result of an increased number of water molecules and the regulation of the interface by these interfacial water molecules. This suggests the occurrence of conformational changes and the subsequent stability of the protein, which is also evident from the greater deformation of salt bridges in the presence of graphene, specifically in the deformation of the ASP85-ARG82 salt bridge. This results in the release of ARG82, which triggers the conformational changes in the bR and the retinal itself. Furthermore, the conformational changes are also found to be a byproduct of the increasing total and electrostatic energy of bR, which are deemed to be facilitators for the photocycle. Finally, the dihedral calculations for both angles and energies indicate greater stability and beneficial conformational changes of bacteriorhodopsin in the presence of graphene. In other words, rather than bR decaying to rest, graphene would help promote the advancement of photoisomer states and, in turn, it is postulated that this will mean a greater yield of the branched photocycle, the mechanism for binary data storage.  
The following are available online at [[https://www.mdpi.com/article/10.3390/app11209698/s1](https://www.mdpi.com/article/10.3390/app11209698/s1)]([https://www.mdpi.com/article/10.3390/app11209698/s1](https://www.mdpi.com/article/10.3390/app11209698/s1)), Figure S1: Initial (0 ns) and Final (100 ns) orientations of bR and graphene, Figure S2: Salt bridges for bR control and bR--graphene simulations, Figure S3: Timeline of secondary structure of bR protein in presence of graphene, Figure S4: Timeline of secondary structure of bR protein in absence of graphene, Figure S5: Color key for secondary structure plot, Figure S6: Timeline of the secondary structure of the 'O' state of BR protein, Figure S7: 3D spatial distribution of hydrogen bonds within bR protein, Table S1: List of angles and dihedrals between retinal and LYS216, Table S2: Parameter for bonds, angles and dihedrals between retinal and LYS216.  
Conceptualization, I.M.; methodology, R.P. and I.M.; software, R.P. and I.M.; validation, I.M., R.P. and G.S.; formal analysis, R.P. and G.S.; investigation, R.P. and G.S.; resources, I.M.; data curation, I.M., G.S. and R.P.; writing--original draft preparation, R.P. and G.S.; writing--review and editing, G.S. and I.M.; supervision, I.M.; project administration, I.M. All authors have read and agreed to the published version of the manuscript.  
This research received no external funding.  
\begin{table}
\begin{tabular}{c c c} \hline \hline
**Residue Name** & **Residue ID** & **Residue Type** \\ \hline Alanine & 2 & Non-polar, aliphatic \\ \hline Isoleucine & 4 & Non-polar, aliphatic \\ \hline Phenylalanine & 71 & Non-polar, aromatic \\ \hline Glycine & 6, 72, 73 & Non-polar, aliphatic \\ \hline Valine & 69, 130 & Non-polar, aliphatic \\ \hline Tyrosine & 131, 133 & Non-polar, aromatic \\ \hline Glutamine & 3, 75 & Polar, uncharged \\ \hline Threonine & 5, 67 & Polar, uncharged \\ \hline Proline & 70 & Polar, uncharged \\ \hline Lysine & 129 & Polar, positive \\ \hline \hline \end{tabular}
\end{table}
Table 3: Amino acids (residues) of Bacteriorhodopsin adsorbed (within 5 Å) on the surface of Graphene.