BPS2026 – Configurational temperature and entropy changes of RNA unfolding from Brownian dynamics simulations

We analyzed a set of three-dimensional RNA structures of varying molecular weights from the Protein Data Bank to determine key chain parameters, including the radius of gyration, contour length, and persistence length. Pair distribution functions were used to derive effective potentials describing nucleotide center-of-mass interactions, which were subsequently refined via Iterative Boltzmann Inversion. These optimized potentials enabled the development of a novel coarse-grained force field for investigating the mechanical unfolding of RNA chains. Brownian dynamics simulations, combined with theoretical analysis, were employed to quantify free energy and entropy changes, which were then compared with theoretical predictions. Furthermore, we monitored the configurational temperature of the simulated molecules throughout the unfolding process.