Temperature and Viscosity Tune the Intermediates during the Collapse of a Polymer

Abstract

Dynamics of a polymer chain in solution gets significantly affected by the temperature and frictional forces arising due to viscosity of the solvent. Here, using an explicit solvent framework for polymer simulation with the liberty to tune the viscous drag of the system, we study the nonequilibrium dynamics of a flexible homopolymer when it is suddenly quenched from an extended random-coil state in good solvent to poor solvent conditions. Results from our extensive simulations reveal that depending on the temperature T and viscous drag, one encounters long-lived sausage-like intermediates following the usual pearl-necklace intermediates. Using shape factors of the polymer we disentangle these two distinct stages of the overall collapse process. This allows us to extract the corresponding relaxation times and their respective scaling behaviors as a function of the length of the polymer. The relaxation time τ_s of the sausage stage, which is the rate-limiting stage of the overall collapse process, follows an anti-Arrhenius behavior in the high-T limit, and the Arrhenius behavior in the low-T limit. Furthermore, the variation of τ_s with the viscous drag provides evidence of internal friction of the polymer, that modulates the overall collapse significantly, analogous to what is observed for relaxation rates of proteins during their folding. This suggests that the origin of internal friction in proteins is plausibly intrinsic to its polymeric backbone rather than other specifications.