Dependence of RNA secondary structure on the energy model

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