Thermodynamics of a model for RNA folding

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We analyze the thermodynamic properties of a simplified model for folded RNA molecules recently studied by Vernizzi, Orland, and Zee [Phys. Rev. Lett. 94, 168103 (2005)]. The model consists of a chain of one-flavor base molecules with a flexible backbone and all possible pairing interactions equally...

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Autor principal: Dell'Erba, M.G
Otros Autores: Zemba, G.R
Formato: Capítulo de libro
Lenguaje:Inglés
Publicado: 2009
Acceso en línea:Registro en Scopus
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245 1 0 |a Thermodynamics of a model for RNA folding 
260 |c 2009 
270 1 0 |m Dell'Erba, M. G.; Departamento de Física, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, Funes 3350, 7600 Mar del Plata, Argentina 
506 |2 openaire  |e Política editorial 
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504 |a Müller, M., (2003) Phys. Rev. e, 67, p. 021914. , 10.1103/PhysRevE.67.021914 
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504 |a Dellâerba, M.G., Zemba, G.R., Müller, M., Krzakala, F., Mãzard, M., (2002) Eur. Phys. J. e, 9, p. 67 
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520 3 |a We analyze the thermodynamic properties of a simplified model for folded RNA molecules recently studied by Vernizzi, Orland, and Zee [Phys. Rev. Lett. 94, 168103 (2005)]. 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 efficiently 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 topological 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 Mg2+ in solution. © 2009 The American Physical Society.  |l eng 
593 |a Departamento de Física, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, Funes 3350, 7600 Mar del Plata, Argentina 
593 |a Facultad de Ciencias Fisicomatemáticas e Ingeniería, Pontificia Universidad Católica Argentina, Avenida A. Moreau de Justo 1500, Buenos Aires, Argentina 
593 |a Departamento de Fisica, CNEA, Avenida Libertador 8250, 1429 Buenos Aires, Argentina 
593 |a CONICET, Argentina 
690 1 0 |a NUCLEIC ACIDS 
690 1 0 |a PROBABILITY DENSITY FUNCTION 
690 1 0 |a RNA 
690 1 0 |a THERMODYNAMIC PROPERTIES 
690 1 0 |a THERMODYNAMICS 
690 1 0 |a ASYMPTOTIC EXPRESSIONS 
690 1 0 |a CONCENTRATION OF 
690 1 0 |a FEYNMAN DIAGRAMS 
690 1 0 |a HERMITIAN 
690 1 0 |a PAIRING INTERACTIONS 
690 1 0 |a PARTITION FUNCTIONS 
690 1 0 |a PSEUDOKNOT 
690 1 0 |a RANDOM MATRIX MODELS 
690 1 0 |a RNA FOLDING 
690 1 0 |a RNA MOLECULES 
690 1 0 |a SIMPLIFIED MODELS 
690 1 0 |a SPATIAL CONFIGURATIONS 
690 1 0 |a TOPOLOGICAL EXPANSIONS 
690 1 0 |a MOLECULES 
700 1 |a Zemba, G.R. 
773 0 |d 2009  |g v. 79  |k n. 1  |p Phys. Rev. E Stat. Nonlinear Soft Matter Phys.  |o Nro. del artículo: 011913  |x 15393755  |t Physical Review E - Statistical, Nonlinear, and Soft Matter Physics 
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856 4 0 |u https://doi.org/10.1103/PhysRevE.79.011913  |y DOI 
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