A beta(1-40) and A beta(1-42) are the main forms of amyloid beta(A beta) peptides in the brain of Alzheimer's patients; however, the latter possesses much stronger aggregation and deposition propensity than the former, which is partially attributed to the more unfolded C-terminus of A beta(1-42) than that of A beta(1-40). To explore the physical basis underlying the different dynamic behaviors of both A beta peptides, parallel molecular dynamics (MD) simulations on A beta(1-40) and A beta(1-42) were performed to investigate their thermal unfolding processes. It is revealed that the addition of residues 41 and 42 in A beta(1-42) disrupts the C-terminal hydrophobic core, which triggers the unraveling of the C-terminal helix of A beta(1-42). This conclusion is supported by the MD simulation on the I41A mutant of A beta(1-42), in which the C-terminal helix possesses relatively higher conformational stability than that of wild type A beta(1-42) owing to the change in hydrophobic interaction patterns.