CHAOS IN BIOMOLECULAR DYNAMICS

An analysis of molecular dynamics simulation of a model alpha-helix in dicates that the motion of the helix system is chaotic. This system's behavior is due to an intrinsic sensitivity to initial conditions, whi ch makes initially similar conformations of the helix evolve into comp letely different conformations. The chaotic properties of the system c an be clearly identified in terms of nonzero Lyapunov exponents, broad -band power spectra, and strange attractors. The dominant factors resu lting in the chaos are found to be (1) the nonlinear interactions inhe rent in the system's force field, (2) the restraints (such as the rest raints on temperature, dihedral angles, and bond lengths), and (3) the stochastic forces generated by the solvent. These results suggest a l imitation for the predictive capabilities of the molecular dynamics si mulation method in studies of biomolecules and, especially, have impor tant implications to the studies of the protein-folding problem.