paper

Modeling single-molecule stretching experiments using statistical thermodynamics

arXiv:2309.01009 · doi:10.1103/PhysRevE.108.064503

Abstract

Single-molecule stretching experiments are widely utilized within the fields of physics and chemistry to characterize the mechanics of individual bonds or molecules, as well as chemical reactions. Analytic relations describing these experiments are valuable, and these relations can be obtained through the statistical thermodynamics of idealized model systems representing the experiments. Since the specific thermodynamic ensembles manifested by the experiments affect the outcome, primarily for small molecules, the stretching device must be included in the idealized model system. Though the model for the stretched molecule might be exactly solvable, including the device in the model often prevents analytic solutions. In the limit of large or small device stiffness, the isometric or isotensional ensembles can provide effective approximations, but the device effects are missing. Here, a dual set of asymptotically correct statistical thermodynamic theories are applied to develop accurate approximations for the full model system that includes both the molecule and the device. The asymptotic theories are first demonstrated to be accurate using the freely jointed chain model, and then using molecular dynamics calculations of a single polyethylene chain.

arXiv commentAssociated code implementation indexed at https://doi.org/10.5281/zenodo.7041983

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