Statistical Physics of RNA-folding

Details Statistical Physics of RNA-folding Statistical Physics of RNA-folding

2002-06-13

arxiv.org/abs/cond-mat/0206225v2

Phys. Rev. E 67, 021914 (2003)

Physics

Condensed Matter

Statistical Mechanics

accepted for publication in Phys. Rev. E

Scientific paper

10.1103/PhysRevE.67.021914

We discuss the physics of RNA as described by its secondary structure. We examine the static properties of a homogeneous RNA-model that includes pairing and base stacking energies as well as entropic costs for internal loops. For large enough costs the model exhibits a thermal denaturation transition which we analyze in terms of the radius of gyration. We point out an inconsistency in the standard approach to RNA secondary structure prediction for large molecules. Under an external force a second order phase transition between a globular and an extended phase takes place. A Harris-type criterion shows that sequence disorder does not affect the correlation length exponent while the other critical exponents are modified in the glass phase. However, at high temperatures, on a coarse-grained level, disordered RNA is well described by a homogeneous model. The characteristics of force-extension curves are discussed as a function of the energy parameters. We show that the force transition is always second order. A re-entrance phenomenon relevant for real disordered RNA is predicted.

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