A random matrix approach to RNA folding

with interaction

I GARG and N DEO^*

Department of Physics & Astrophysics, University of

Delhi, Delhi 110 007, India

^*Corresponding author. E-mail: ndeo@physics.du.ac.in

Abstract. In the matrix model of RNA [G Vernizzi, H Orland and

A Zee, {\it Phys. Rev. Lett.} {\bf 94}, 168103 (2005)] we introduce external

interactions on $n$ bases in the action of the partition function

where $n \leq L$ and $L$ is the length of the

polymer chain. The RNA structures found in the model can be

separated into two regimes: (i) $0 \leq \alpha \leq 1$, $n<L$

and $0 \leq \alpha < 1$, $n=L$ where unpaired and paired base

structures exist and (ii) $\alpha=1$, $n=L$ with only completely

paired base structures. Figures for the genus distribution

functions show differences at small lengths. We consider the

situation when the strength of external perturbation is different

on different bases in the polymer chain.

Keywords. RNA folding; random matrix model; external perturbation.

PACS Nos 02.10.Yn; 87.10.-e; 87.14.gn; 87.15.Cc