Examining the characteristics of chaos in biomolecular dynamics: a random matrix approximation

We apply a random matrix method to study the chaotic character of dynamics of biomolecules in the native state, where the fluctuations in the matrix elements were modelled as a stochastic process and represented by coloured noise. We found that the chaotic nature of the dynamics increases with an increase in the system size and the cutoff length of non-bonded interactions. The cutoff length seems to be less important than the fluctuation in the elements in determining the rate of divergence of trajectories. Also, increased temporal correlation in the random elements leads to increased chaos for a small amount of correlation.