## 2 Materials and Methods  
To study the behavior of the bacteriorhodopsin protein in the presence and absence of a monolayer graphene sheet, NAMD (Nanoscale Molecular Dynamics) software [23] integrated with a molecular visualization graphics software VMD (Visual Molecular Dynamics) was utilized [24]. In an all-atom isothermal and isobaric (NPT) ensemble of the NAMD software, 100 ns molecular trajectories were simulated for the bR control and experimental simulations (Figure S1). The all-atom system, containing the bR protein (230 residues) and the graphene sheet (3936 atoms), was structurally modeled using the CHARMM force field parameters available from the MacKerell lab at the University of Maryland [25]. The coordinate file (PDB) of the bR protein (1 AT9) used in the study was acquired from the protein data bank [26]. The armchair graphene sheet with a size of 100 A \(\times\) 100 A [27] was modeled using the graphene builder plugin in the VMD program. The structural parameters for the graphene sheet and those between the carbon C15 atom of the retinal chromophore and Lys216 were modeled using a topology manipulating plugin, TopoTools, and Molefacture [28; 29]. The relative position of bR molecule was kept at ~15 A from the surface of graphene to provide enough room between the molecules to ensure either adsorption or repulsion. Furthermore, the orientation was such that the retinal would be closest to the graphene sheet, even though it would not come in direct contact with graphene due to the presence of the surrounding amino acids. It was ensured that the adsorption occurs closest to the retinal site so that a direct effect of this adsorption can be captured on the dihedral angles of the retinal. Additionally, the state of the bR molecule was chosen such that it is in the ground state with the Schiff Base and ASP96 protonated. Both the systems (with and without graphene) were solvated using the TIP3 water model containing 81,699 and 11,724 molecules, respectively [30], and a neutralizing concentration of sodium chloride was used to compensate for the overall net charge in the system. Additionally, based on the CHARMM topology parameters, there was no net charge modeled on bR or graphene molecules.  
After setting the periodic boundary conditions, first, a 2500-step minimization using the steepest descent algorithm was carried out to remove the bad contacts and achieve minimum potential energy. This was followed by 500,000 steps of equilibration [31]. In all simulations, the temperature was maintained at 300 K by a Langevin thermostat and a pressure of 1 atm through a Nose-Hoover Langevin piston barostat with a period of 100 ps and a decay rate of 50 ps. Multiple HP 2Z30 systems with eight cores, each using an Intel Xeon processor and a Quadro K620 CUDA acceleration capability, were used to perform all simulations. All simulations employed an integrated time step of 2 fs. A cut-off of 10-12 A designated the short-range forces, while the long-range forces were calculated using the Particle Mesh Ewald (PME) algorithm. Root Mean Square Deviation (RMSD) and NAMD energy extensions were used to determine the interaction energy between bR and graphene. The VMD Timeline tool was used to analyze the secondary structure of the bR. TCL scripting was used to determine the number of atoms and interaction energies with respect to the cutoff distance from the surface of graphene and the optimal adsorption distance.