Effect of elastic colored noise in the hopping dynamics of single molecules in stretching experiments

Abstract

The influence of colored noise induced by elastic fluctuations in single-molecule stretching experiments is theoretically and numerically studied. Unlike in the thermal white noise case currently considered in the literature, elastically induced hopping dynamics between folded and unfolded states is manifested through critical oscillations showing smaller end-to-end distance fluctuations (δx∼1.25nm) within the free energy wells corresponding to both states. Our results are derived by analyzing the elastic coupling between the Handle-Molecule-Handle system and the laser optical tweezers (LOT) array. It is shown that an Ornstein-Uhlenbeck process related to this elastic coupling may trigger the hopping transitions via a colored noise with an intensity proportional to the elastic constant of the LOT array. Evolution equations of the variables of the system were derived by using the irreversible thermodynamics of small systems recently proposed. Theoretical expressions for the corresponding stationary probability densities are provided and the viability of inferring the shape of the free energy from direct measurements is discussed.