Protein viscoelastic dynamics: a model system

TL;DR

This paper introduces a simple yet rich dynamical model inspired by protein behavior under sinusoidal forces, revealing complex transitions and thermodynamic analogies, with considerations of noise and inertia effects.

Contribution

It presents a novel over-damped oscillator model capturing key features of protein viscoelastic dynamics and uncovering unexpected dynamical transitions.

Findings

Model replicates experimental response characteristics

Reveals dynamical transitions analogous to phase transitions

Shows effects of noise and inertia on system behavior

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.