Dependence of RNA secondary structure on the energy model.
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 behavior 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, at both zero temperature and finite temperatures. All calculations can be done efficiently in polynomial time by a dynamic programming algorithm. We do not find a sign for the 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-energy excitations. The exponent theta describing the energy scaling of the excitations seems to depend not much on the energy model.
Burghardt
Bernd
B
Institut für Theoretische Physik, Universität Göttingen, Friedrich-Hund-Platz 1, D-37077 Göttingen, Germany. burghard@theorie.physik.uni-goettingen.de
Hartmann
Alexander K
AK
D000465:Algorithms; D003198:Computer Simulation; D004735:Energy Transfer; D008956:Models, Chemical; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012313:RNA / Q000032:analysis / Q000737:chemistry* / Q000648:ultrastructure*; D013329:Structure-Activity Relationship; D013696:Temperature
D012313:RNA