Thermodynamics of a model for RNA folding
Abstract: We analyze the thermodynamic properties of a simplified model for folded RNA molecules recently studied by G. Vernizzi, H. Orland, A. Zee (in Phys. Rev. Lett. 94 (2005) 168103). The model consists of a chain of one-flavor base molecules with a flexible backbone and all possible pairing interactions equally allowed. The spatial pseudoknot structure of the model can be effi- ciently studied by introducing a N × N hermitian random matrix model at each chain site, and associating Feynman diagrams of these models to spatial configurations of the molecules. We obtain an exact expression for the topo- logical expansion of the partition function of the system. We calculate exact and asymptotic expressions for the free energy, specific heat, entanglement and chemical potential and study their behavior as a function of temperature. Our results are consistent with the interpretation of 1/N as being a measure of the concentration of Mg++ in solution.
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Format: | Artículo biblioteca |
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American Institute of Physics
2009
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Subjects: | MOLECULAS DE ARN, PROPIEDADES TERMODINAMICAS, BIOLOGIA, DIAGRAMA DE FEYNMAN, Vernizzi, Graziano, Zee, Anthony, Orland, Henri, |
Online Access: | https://repositorio.uca.edu.ar/handle/123456789/18411 |
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oai:ucacris:123456789-184112024-07-19T05:01:21Z Thermodynamics of a model for RNA folding Dell'Erba, Matías G. Zemba, Guillermo Raúl MOLECULAS DE ARN PROPIEDADES TERMODINAMICAS BIOLOGIA DIAGRAMA DE FEYNMAN Vernizzi, Graziano Zee, Anthony Orland, Henri Abstract: We analyze the thermodynamic properties of a simplified model for folded RNA molecules recently studied by G. Vernizzi, H. Orland, A. Zee (in Phys. Rev. Lett. 94 (2005) 168103). The model consists of a chain of one-flavor base molecules with a flexible backbone and all possible pairing interactions equally allowed. The spatial pseudoknot structure of the model can be effi- ciently studied by introducing a N × N hermitian random matrix model at each chain site, and associating Feynman diagrams of these models to spatial configurations of the molecules. We obtain an exact expression for the topo- logical expansion of the partition function of the system. We calculate exact and asymptotic expressions for the free energy, specific heat, entanglement and chemical potential and study their behavior as a function of temperature. Our results are consistent with the interpretation of 1/N as being a measure of the concentration of Mg++ in solution. 2024-07-18T10:33:52Z 2024-07-18T10:33:52Z 2009 Artículo Dell'Erba MG, Zemba GR. Thermodynamics of a model for RNA folding [en línea]. Physical review E. 2009, E 79 (011913). doi: 10.1103/PhysRevE.79.011913. Disponible en: https://repositorio.uca.edu.ar/handle/123456789/18411 2470-0045 (impreso) 2470-0053 (online) https://repositorio.uca.edu.ar/handle/123456789/18411 10.1103/PhysRevE.79.011913 eng Atribución-NoComercial-CompartirIgual 4.0 Internacional http://creativecommons.org/licenses/by-nc-sa/4.0/ application/pdf American Institute of Physics Physical review. 2008, E 79 (011913). |
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MOLECULAS DE ARN PROPIEDADES TERMODINAMICAS BIOLOGIA DIAGRAMA DE FEYNMAN Vernizzi, Graziano Zee, Anthony Orland, Henri MOLECULAS DE ARN PROPIEDADES TERMODINAMICAS BIOLOGIA DIAGRAMA DE FEYNMAN Vernizzi, Graziano Zee, Anthony Orland, Henri |
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MOLECULAS DE ARN PROPIEDADES TERMODINAMICAS BIOLOGIA DIAGRAMA DE FEYNMAN Vernizzi, Graziano Zee, Anthony Orland, Henri MOLECULAS DE ARN PROPIEDADES TERMODINAMICAS BIOLOGIA DIAGRAMA DE FEYNMAN Vernizzi, Graziano Zee, Anthony Orland, Henri Dell'Erba, Matías G. Zemba, Guillermo Raúl Thermodynamics of a model for RNA folding |
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Abstract: We analyze the thermodynamic properties of a simplified model for folded RNA molecules recently studied by G. Vernizzi, H. Orland, A. Zee (in Phys. Rev. Lett. 94 (2005) 168103). The model consists of a chain of one-flavor base molecules with a flexible backbone and all possible pairing interactions equally allowed. The spatial pseudoknot structure of the model can be effi- ciently studied by introducing a N × N hermitian random matrix model at each chain site, and associating Feynman diagrams of these models to spatial configurations of the molecules. We obtain an exact expression for the topo- logical expansion of the partition function of the system. We calculate exact and asymptotic expressions for the free energy, specific heat, entanglement and chemical potential and study their behavior as a function of temperature. Our results are consistent with the interpretation of 1/N as being a measure of the concentration of Mg++ in solution. |
format |
Artículo |
topic_facet |
MOLECULAS DE ARN PROPIEDADES TERMODINAMICAS BIOLOGIA DIAGRAMA DE FEYNMAN Vernizzi, Graziano Zee, Anthony Orland, Henri |
author |
Dell'Erba, Matías G. Zemba, Guillermo Raúl |
author_facet |
Dell'Erba, Matías G. Zemba, Guillermo Raúl |
author_sort |
Dell'Erba, Matías G. |
title |
Thermodynamics of a model for RNA folding |
title_short |
Thermodynamics of a model for RNA folding |
title_full |
Thermodynamics of a model for RNA folding |
title_fullStr |
Thermodynamics of a model for RNA folding |
title_full_unstemmed |
Thermodynamics of a model for RNA folding |
title_sort |
thermodynamics of a model for rna folding |
publisher |
American Institute of Physics |
publishDate |
2009 |
url |
https://repositorio.uca.edu.ar/handle/123456789/18411 |
work_keys_str_mv |
AT dellerbamatiasg thermodynamicsofamodelforrnafolding AT zembaguillermoraul thermodynamicsofamodelforrnafolding |
_version_ |
1806028984250531840 |