Protein viscoelastic dynamics: a model system

Abstract

A model system inspired by recent experiments on the dynamics of a folded protein under the influence of a sinusoidal force is investigated and found to replicate many of the response characteristics of such a system. The essence of the model is a strongly over-damped oscillator described by a harmonic restoring force for small displacements that reversibly yields to stress under sufficiently large displacement. This simple dynamical system also reveals unexpectedly rich behavior, exhibiting a series of dynamical transitions and analogies with equilibrium thermodynamic phase transitions. The effects of noise and of inertia are briefly considered and described.