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Understanding the process of protein unfolding plays a crucial role invarious applications such as design of folding-based protein engines. Using thewell-established kinetostatic compliance (KCM)-based method for modeling ofprotein conformation dynamics and a recent nonlinear control theoretic approachto KCM-based protein folding, this paper formulates protein unfolding as adestabilizing control analysis/synthesis problem. In light of this formulation,it is shown that the Chetaev instability framework can be used to investigatethe KCM-based unfolding dynamics. In particular, a Chetaev function foranalysis of unfolding dynamics under the effect of optical tweezers and a classof control Chetaev functions for synthesizing control inputs that elongateprotein strands from their folded conformations are presented. Based on thepresented control Chetaev function, an unfolding input is derived from theArtstein-Sontag universal formula and the results are compared against opticaltweezer-based unfolding.

Chetaev Instability Framework for Kinetostatic Compliance-Based Protein Unfolding