Dependence of RNA secondary structure on the energy model

Abstract

We analyze a microscopic RNA model, which includes two widely used models as limiting cases, namely it contains terms for bond as well as for stacking energies. We numerically investigate possible changes in the qualitative and quantitative behaviour while going from one model to the other; in particular we test, whether a transition occurs, when continuously moving from one model to the other. For this we calculate various thermodynamic quantities, both at zero temperature as well as at finite temperatures. All calculations can be done efficiently in polynomial time by a dynamic programming algorithm. We do not find a sign for transition between the models, but the critical exponent $\nu$ of the correlation length, describing the phase transition in all models to an ordered low-temperature phase, seems to depend continuously on the model. Finally, we apply the epsilon-Coupling method, to study low excitations. The exponent $\theta$ describing the energy-scaling of the excitations seems to depend not much on the energy model.