Chaos in biomolecular dynamics

An analysis of molecular dynamics simulation of a model alpha-helix indicates that the motion of the helix system is chaotic. This system's behavior is due to an intrinsic sensitivity to initial conditions, which makes initially similar conformations of the helix evolve into completely different conformations. The chaotic properties of the system can be clearly identified in terms of nonzero Lyapunov exponents, broad-band power spectra, and strange attractors. The dominant factors resulting in the chaos are found to be (1) the nonlinear interactions inherent in the system's force field, (2) the restraints (such as the restraints on temperature, dihedral angles, and bond lengths), and (3) the stochastic forces generated by the solvent. These results suggest a limitation for the predictive capabilities of the molecular dynamics simulation method in studies of biomolecules and, especially, have important implications to the studies of the protein-folding problem.