Behavior of random RNA secondary structures near the glass transition
نویسندگان
چکیده
منابع مشابه
Glass transition in secondary structures formed by random RNA sequences
Formation of RNA secondary structures is an example of the sequence-structure problem omnipresent in biopolymers. A theoretical question of recent interest is whether a random RNA sequence undergoes a finite temperature glass transition. We answer this question affirmatively by first establishing the perturbative stability of the high temperature phase via a two replica calculation. Subsequentl...
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RNA molecules form a sequence-specific self-pairing pattern at low temperatures. We analyze this problem using a random pairing energy model as well as a random sequence model that includes a base stacking energy in favor of helix propagation. The free energy cost for separating a chain into two equal halves offers a quantitative measure of sequence specific pairing. In the low temperature glas...
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The free energy of a single-stranded RNA can be calculated by adding the free energies of the components: basepairs, bulges, and loops. Basepairs receive negative free energy while the unpaired bases receive positive free energy. The minimum free energy of a random RNA secondary structure with one domain has value Fn where the sequence length is n. Under simplifying assumptions, we show that fo...
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The formation of secondary structures by a random RNA sequence is studied as a model system for the sequence-structure problem omnipresent in biopolymers. Several toy energy models are introduced to allow detailed analytical and numerical studies. First, a two-replica calculation is performed. By mapping the two-replica problem to the denaturation of a single homogeneous RNA molecule in six-dim...
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ژورنال
عنوان ژورنال: Physical Review E
سال: 2019
ISSN: 2470-0045,2470-0053
DOI: 10.1103/physreve.99.022415