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<p>We compare the free energies of adsorption (∆Aads) and the structural preferences of amino
acids obtained using the force fields — Amberff99SB-ILDN/TIP3P, CHARMM36/modified-TIP3P,
OPLS-AA/M/TIP3P, and Amber03w/TIP4P/2005. The amino acid–graphene interactions are favorable irrespective of the force field. While the magnitudes of ∆Aads differ between the force
fields, the trends in the free energy of adsorption with amino acids are similar across the studied
force fields. ∆Aads positively correlates with amino acid–graphene and negatively correlates with
graphene–water interaction energies. Using a combination of principal component analysis and
density-based clustering technique, we grouped the structures observed in the graphene adsorbed
state. The resulting population of clusters, and the conformation in each cluster indicate that the
structures of the amino acid in the graphene adsorbed state vary across force fields. The differences
in the conformations of amino acids are more severe in the graphene adsorbed state compared to the
bulk state for all the force fields. Our findings suggest that while the thermodynamics of adsorption
of proteins and peptides would be described consistently across different force fields, the structural
preferences of peptides and proteins on graphene will be force field dependent.
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Order-preserving optimization of twig queries with structural preferences
