Thermodynamics of a model for RNA folding

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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Detalles Bibliográficos
Autores principales: Dell'Erba, M.G., Zemba, G.R.
Formato: JOUR
Lenguaje:English
Materias:
Nucleic acids
Probability density function
RNA
Thermodynamic properties
Thermodynamics
Asymptotic expressions
Concentration of
Feynman diagrams
Hermitian
Pairing interactions
Partition functions
Pseudoknot
Random matrix models
RNA folding
Rna molecules
Simplified models
Spatial configurations
Topological expansions
Molecules
Acceso en línea:http://hdl.handle.net/20.500.12110/paper_15393755_v79_n1_p_DellErba
Aporte de:
Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) de Universidad de Buenos Aires
Descripción
Sumario: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.

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