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:	Zemba, Guillermo Raúl
Publicado:	2009
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:	https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_15393755_v79_n1_p_DellErba 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

id	paper:paper_15393755_v79_n1_p_DellErba
record_format	dspace
spelling	paper:paper_15393755_v79_n1_p_DellErba2023-06-08T16:20:38Z Thermodynamics of a model for RNA folding Zemba, Guillermo Raúl 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 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. Fil:Zemba, G.R. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. 2009 https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_15393755_v79_n1_p_DellErba http://hdl.handle.net/20.500.12110/paper_15393755_v79_n1_p_DellErba
institution	Universidad de Buenos Aires
institution_str	I-28
repository_str	R-134
collection	Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA)
topic	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
spellingShingle	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 Zemba, Guillermo Raúl Thermodynamics of a model for RNA folding
topic_facet	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
description	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.
author	Zemba, Guillermo Raúl
author_facet	Zemba, Guillermo Raúl
author_sort	Zemba, Guillermo Raúl
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
publishDate	2009
url	https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_15393755_v79_n1_p_DellErba http://hdl.handle.net/20.500.12110/paper_15393755_v79_n1_p_DellErba
work_keys_str_mv	AT zembaguillermoraul thermodynamicsofamodelforrnafolding
_version_	1768543963326709760

Thermodynamics of a model for RNA folding

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