We consider a lattice polymer model of the two-tolerant type (i.e., a random walk allowed to visit lattice bondsat most twice), in which doubly visited bonds yield an attractive energy term (pairing energy). Such a model has been previously proposed as a rough, nonspecific description of the RNA folding mechanism. Indeed, the model predicts, besides the usual theta collapse, an extra transition to a low-temperature fully paired state. In the current work, we propose an extension of the model, in which a "micromolecular" chemical species can bind the polymer and locally forbid segment pairing. We investigate equilibrium thermodynamics in the grand-canonical picture, at the level of a Bethe approximation, which is, a refined mean-field technique, equivalent to the exact solution on a random-regular graph. The general trend we observe is that expected from the mechanism implemented in the model (increasing micromolecule concentration favors unfolding and lowers the transition temperature), but the resulting phase diagram turns out to be remarkably interesting and rich.

Chemically controlled unfolding of a RNA-like polymer model

Pretti M
2012

Abstract

We consider a lattice polymer model of the two-tolerant type (i.e., a random walk allowed to visit lattice bondsat most twice), in which doubly visited bonds yield an attractive energy term (pairing energy). Such a model has been previously proposed as a rough, nonspecific description of the RNA folding mechanism. Indeed, the model predicts, besides the usual theta collapse, an extra transition to a low-temperature fully paired state. In the current work, we propose an extension of the model, in which a "micromolecular" chemical species can bind the polymer and locally forbid segment pairing. We investigate equilibrium thermodynamics in the grand-canonical picture, at the level of a Bethe approximation, which is, a refined mean-field technique, equivalent to the exact solution on a random-regular graph. The general trend we observe is that expected from the mechanism implemented in the model (increasing micromolecule concentration favors unfolding and lowers the transition temperature), but the resulting phase diagram turns out to be remarkably interesting and rich.
2012
Istituto dei Sistemi Complessi - ISC
Bethe approximation; Equilibrium thermodynamics; Exact solution; Lattice polymers; Mean-field; Micromolecule; Polymer models; Random Walk; RNA folding
File in questo prodotto:
File Dimensione Formato  
prod_197775-doc_43116.pdf

solo utenti autorizzati

Descrizione: Chemically controlled unfolding of a RNA-like polymer model
Tipologia: Versione Editoriale (PDF)
Licenza: NON PUBBLICO - Accesso privato/ristretto
Dimensione 435.04 kB
Formato Adobe PDF
435.04 kB Adobe PDF   Visualizza/Apri   Richiedi una copia

I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.

Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/20.500.14243/236068
Citazioni
  • ???jsp.display-item.citation.pmc??? ND
  • Scopus 0
  • ???jsp.display-item.citation.isi??? 0
social impact