On the behavior of random RNA secondary structures near the glass transition

Abstract

RNA forms elaborate secondary structures through intramolecular base pairing. These structures perform critical biological functions within each cell. Due to the availability of a polynomial algorithm to calculate the partition function over these structures, they are also a suitable system for the statistical physics of disordered systems. In this model, below the denaturation temperature, random RNA secondary structures exist in one of two phases: a strongly disordered, low-temperature glass phase, and a weakly disordered, high-temperature molten phase. The probability of two bases to pair decays with their distance with an exponent 3/2 in the molten phase, and about 4/3 in the glass phase. Inspired by previous results from a renormalized field theory of the glass transition separating the two phases, we numerically study this transition. We introduce distinct order parameters for each phase, that both vanish at the critical point. We finally explore the driving mechanism behind this transition.

References in corpus (10)

• Statistical mechanics of secondary structures formed by random RNA sequences
• Glassy transition in a disordered model for the RNA secondary structure
• The secondary structure of RNA under tension
• Nature of the glassy phase of RNA secondary structure
• The Freezing of Random RNA
• Zero Temperature Properties of RNA Secondary Structures
• Systematic Field Theory of the RNA Glass Transition
• Ground state and glass transition of the RNA secondary structure
• Analytical description of finite size effects for RNA secondary structures
• Field Theory of the RNA Freezing Transition

Cited by in corpus (2)

• Theory and Experiments for Disordered Elastic Manifolds, Depinning, Avalanches, and Sandpiles
• Pseudo-RNA with parallel aligned single-strands and periodic base sequence as a new universality class