dorsal/arxiv
View SchemaGround state and glass transition of the RNA secondary structure
| Authors | Sheng Hui, Lei-Han Tang |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0608020 |
| URL | https://arxiv.org/abs/q-bio/0608020 |
| DOI | 10.1140/epjb/e2006-00347-x |
Abstract
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 glass phase, this quantity grows quadratically with the logarithm of the chain length, but it switches to a linear behavior of entropic origin in the high temperature molten phase. Transition between the two phases is continuous, with characteristics that resemble those of a disordered elastic manifold in two dimensions. For designed sequences, however, a power-law distribution of pairing energies on a coarse-grained level may be more appropriate. Extreme value statistics arguments then predict a power-law growth of the free energy cost to break a chain, in agreement with numerical simulations. Interestingly, the distribution of pairing distances in the ground state secondary structure follows a remarkable power-law with an exponent -4/3, independent of the specific assumptions for the base pairing energies.
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"abstract": "RNA molecules form a sequence-specific self-pairing pattern at low\ntemperatures. We analyze this problem using a random pairing energy model as\nwell as a random sequence model that includes a base stacking energy in favor\nof helix propagation. The free energy cost for separating a chain into two\nequal halves offers a quantitative measure of sequence specific pairing. In the\nlow temperature glass phase, this quantity grows quadratically with the\nlogarithm of the chain length, but it switches to a linear behavior of entropic\norigin in the high temperature molten phase. Transition between the two phases\nis continuous, with characteristics that resemble those of a disordered elastic\nmanifold in two dimensions. For designed sequences, however, a power-law\ndistribution of pairing energies on a coarse-grained level may be more\nappropriate. Extreme value statistics arguments then predict a power-law growth\nof the free energy cost to break a chain, in agreement with numerical\nsimulations. Interestingly, the distribution of pairing distances in the ground\nstate secondary structure follows a remarkable power-law with an exponent -4/3,\nindependent of the specific assumptions for the base pairing energies.",
"arxiv_id": "q-bio/0608020",
"authors": [
"Sheng Hui",
"Lei-Han Tang"
],
"categories": [
"q-bio.BM",
"cond-mat.dis-nn"
],
"doi": "10.1140/epjb/e2006-00347-x",
"title": "Ground state and glass transition of the RNA secondary structure",
"url": "https://arxiv.org/abs/q-bio/0608020"
},
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