# Artificial Photosynthesis: Is Computation Ready for the Challenge Ahead?
## 4 Protein/Surface Interactions
### Adsorption on Low Dimensional Materials  
Low 1D and 2D dimensional materials are emerging as promising candidates not only as support layers due to their peculiar electronic properties, but also for active center for charge separation and storage [191]. The archetype for this materials are carbon allotropes, in particular carbon nanotubes (CNT) and single layer graphene (SLG) and due to their extremely high surface area, they are optimal candidates for the design of highly efficient biosensor applications [192]. The unique electronic characteristics of these materials is the presence of a strongly delocalized \(\pi\) electrons clouds which strongly favor the creation of van der Waals interactions with organic molecules and proteins. As for the previous section, computational approaches and methods has been mainly used to describe protein/low dimensional material interaction in terms of MD simulations, to describe the adsorption process. In the last few years, rigorous approaches have been developed in order to meet the strong demands of conformational samplings [193] needed for this kind of protein/material interactions since they are often intrinsically disordered. Moreover, the size of the system pushes classical MD to its boundary, and to have meaningful results, MD should be long enough to let the protein fully adsorb and relax on the surface. To overcome these bottlenecks, [PERSON] et al. developed an \"economical\" polarizable all-atom force field to describe a graphene/water/peptide interface used in combination with replica exchange solute tempering MD (REST-MD) simulations [194]. This method is based on a replica exchange Hamiltonian-based approach that allows for efficient conformational sampling of complex interfaces. As results, the authors found that a strong binding is obtained not only for aromatic residues of the peptide, but also for residues possessing amide groups, like Asn and Gln, of a short peptide sequence. This study was performed in diluted solution for one (short) peptide chain, in order to avoid peptide-peptide interactions, which might complicate the description of the force field. In a subsequent study [195], the same authors considered the presence of multiple peptides to study their aggregation and organization on SLG/water interface, for the first time in an all-atom approach focused on advanced conformational sampling. They concluded that despite the presence of a considerable degree of peptide-peptide interactions, the interaction with the surface still resemble the one obtained from the monopeptide system, without leading to self-organization. Moving a step forward toward complexity, [PERSON] et al. investigated the adsorption of a peptide on SLG supported on gold as well as on multilayer graphene [196]. The result of this study was the negligible influence of the supporting layers (either gold or SLG) on the adsorption properties of short peptides. Yet, the authors did not consider the SLG/Au interactions explicitly, which might be important in the determination of the adsorption process. Challenges are still present when modeling these interfaces, such as how to consider the commensuration of the SLG/Au lattice parameters and to what point a mismatch between the two lattices is acceptable. As already shown in previous Sections 3 and 4.1, MD simulations strongly focus on the adsorption of proteins on different substrates. These simulations address the problem in two ways; (1) the study of the dynamic of the adsorption process of a (small) protein or peptide sequence at liquid/solid interfaces [197; 198], in which the process is divided into three phases, namely the (biased) diffusion, the anchoring to the surface and the lockdown (or relaxation) phase. (2) The study of already adsorbed protein on a surface using thermodynamic methods, in which different interactions such as hydrophobic, \(\pi-\pi\) staking or hydrogen bond play an important role.