Pattern Recognition of Adsorbing HP Lattice Proteins

Protein adsorption is relevant in fields ranging from medicine to industry, and the qualitative behavior exhibited by course-grained models could shed insight for further research in such fields. Our study on the selective adsorption of lattice proteins utilizes the Wang-Landau algorithm to simulate the Hydrophobic-Polar (H-P) model\footnote{K. A. Dill, Biochemistry 24, 1501 (1985); K. F. Lau and K. A. Dill, Macromolecules 22, 3986 (1989).} with an efficient set of Monte Carlo moves\footnote{T. W\"ust and D. P. Landau, Phys. Rev. Lett. 102, 178101 (2009); J. Chem. Phys. 137, 064903 (2012).}. Each substrate is modeled as a square pattern of 9 lattice sites which attract either H or P monomers, and are located on an otherwise neutral surface. The fully enumerated set of 102 unique surfaces is simulated with each protein sequence. A collection of 27-monomer sequences\footnote{M. Mann, D. Maticzka, R. Saunders, and R. Backofen. HFSP Journal 2. 396. Special issue on protein folding: experimental and theoretical approaches.(2008).} is used-- each of which is non-degenerate and protein-like. Thermodynamic quantities such as the specific heat and free energy are calculated from the density of states, and are used to investigate the adsorption of lattice proteins on patterned substrates.