We present the structural analysis of single peptide molecules,folding structures of the amyloid peptides,interaction modes between peptide and dye or drug molecules,and modulation of peptide assemblies by small molecules.By using scanning tunneling microscopy(STM),molecularly resolved core regions of the amyloid peptide assembly structures are identified.The effects of mutation and phosphorylation on the folding structures and core regions were also revealed in the assembly characteristics.