The significance of fuzzy boundaries of the barrier regions in single-molecule measurements of failed barrier crossing attempts

• Published in: The Journal of chemical physics 2024-09, Vol.161 (10)
• Main Authors: Berezhkovskii, Alexander M., Makarov, Dmitrii E.
• Format: Article
• Language: English
• Subjects: Boundaries; Temporal resolution
• ISSN: 0021-9606; 1089-7690; 1089-7690
• DOI: 10.1063/5.0227497

A recent ground-breaking experimental study [Lyons et al., Phys. Rev. X 14(1), 011017 (2024)] reports on measuring the temporal duration and the spatial extent of failed attempts to cross an activation barrier (i.e., “loops”) for a folding transition in a single molecule and for a Brownian particle trapped within a bistable potential. Within the model of diffusive dynamics, however, both of these quantities are, on average, exactly zero because of the recrossings of the barrier region boundary. That is, an observer endowed with infinite spatial and temporal resolution would find that finite loops do not exist (or, more precisely, form a set of measure zero). Here we develop a description of the experiment that takes the “fuzziness” of the boundaries caused by finite experimental resolution into account and show how the experimental uncertainty of localizing the point, in time and space, where the barrier is crossed leads to observable distributions of loop times and sizes. Although these distributions generally depend on the experimental resolution, this dependence, in certain cases, may amount to a simple resolution-dependent factor and, therefore, the experiments do probe inherent properties of barrier crossing dynamics.