Modeling a hybrid peptide-silicon interface

Seeking further confirmation of this amazing observation, we also introduce a new sequence obtained by interchanging Pro4 (P) and Thr9 (T) in SI. This sequence shall be denoted by SI AQNTSDNNPHTH. As expected, it turns out that this transposition of SI leads to a behavior similar to that of S3, as is illustrated by Fig. 14.6, which confirms the importance of the position of proline in all these sequences. 

But how important is all this for the understanding of the adsorption behavior at a silicon substrate After these exciting preliminary considerations of the peptide behavior in solvent, we are now in a position to extend the peptide model by introdncing the interaction with the substrate and discuss the apparently different binding behavior of these short peptides. 

The trade-off may be a model that consists of a combination of coarse-grained and atomic interactions. Such a model will not only be computationally feasible, it will also allow to treat essential specific properties of hybrid interfaces of proteins and solid 

It is important to review properties of sihcon surfaces and the sample preparation in experiments, because this information is necessary input for modeling the peptide-Si(lOO) interface. In these experiments [275,276], the Si(lOO) surfaces were first cleaned in a solution of ammonium fluoride (NH4F) and hydrofluoric acid (HF) and then the adsorption experiments were performed in distilled water. This standard procedure ensures that the Si surface is widely free of oxide, which causes strong hydrophobic properties [359,361], The initial Si-F bonds after etching are replaced by Si H bonds in the rinsing process in de-ionized water. Although the oxidation proceeds also in water [361,362], it was found that the hydrophobicity of the Si samples is widely sustained during the peptide adsorption process. 

Experimental cPAC values for SI and S3 at bare and oxidized Si(100) substrates. From 340]. 

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