Journal
PHYSICAL REVIEW LETTERS
Volume 98, Issue 2, Pages -Publisher
AMERICAN PHYSICAL SOC
DOI: 10.1103/PhysRevLett.98.028102
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Classical molecular dynamics simulations of the folding of alanine peptides in aqueous solution are analyzed by constructing a deterministic model of the dynamics, using methods from nonlinear time series analysis. While the dimension of the free energy landscape increases with system size, a Lyapunov analysis shows that the effective dimension of the dynamic system is rather small and even decreases with chain length. The observed reduction of phase space is a nonlinear cooperative effect that is caused by intramolecular hydrogen bonds that stabilize the secondary structure of the peptides.
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