Related papers: Enumeration of RNA complexes via random matrix the…
We introduce and study the Hermitian matrix model with potential V(x)=x^2/2-stx/(1-tx), which enumerates the number of linear chord diagrams of fixed genus with specified numbers of backbones generated by s and chords generated by t. For…
We enumerate the number of RNA contact structures according to their genus, i.e. the topological character of their pseudoknots. By using a recently proposed matrix model formulation for the RNA folding problem, we obtain exact results for…
We propose a new topological characterization of RNA secondary structures with pseudoknots based on two topological invariants. Starting from the classic arc-representation of RNA secondary structures, we consider a model that couples both…
A topological RNA structure is derived from a diagram and its shape is obtained by collapsing the stacks of the structure into single arcs and by removing any arcs of length one. Shapes contain key topological, information and for fixed…
We compute the complete topological expansion of the formal hermitian two-matrix model. For this, we refine the previously formulated diagrammatic rules for computing the 1/ N expansion of the nonmixed correlation functions and give a new…
Shapes of interacting RNA complexes are studied using a filtration via their topological genus. A shape of an RNA complex is obtained by (iteratively) collapsing stacks and eliminating hairpin loops. This shape-projection preserves the…
We present a novel topological classification of RNA secondary structures with pseudoknots. It is based on the topological genus of the circular diagram associated to the RNA base-pair structure. The genus is a positive integer number,…
Combinatorial analysis of a certain abstract of RNA structures has been studied to investigate their statistics. Our approach regards the backbone of secondary structures as an alternate sequence of paired and unpaired sets of nucleotides,…
In this paper we study multi-matrix models whose potentials are perturbations of the quadratic potential associated with independent GUE random matrices. More precisely, we compute the free energy and the expectation of the trace of…
In this paper we consider the enumeration of orientable and non-orientable chord diagrams. We show that this enumeration is encoded in appropriate expectation values of the $\beta$-deformed Gaussian and RNA matrix models. We evaluate these…
We present a method, based on loop equations, to compute recursively all the terms in the large $N$ topological expansion of the free energy for the 2-hermitian matrix model. We illustrate the method by computing the first subleading term,…
We analyze the thermodynamic properties of a simplified model for folded RNA molecules recently studied by G. Vernizzi, H. Orland, A. Zee (in {\it Phys. Rev. Lett.} {\bf 94} (2005) 168103). The model consists of a chain of one-flavor base…
We present a method, based on loop equations, to compute recursively, all the terms in the large $N$ topological expansion of the free energy for the 2-hermitian matrix model, in the case where the support of the density of eigenvalues is…
Interacting RNA complexes are studied via bicellular maps using a filtration via their topological genus. Our main result is a new bijection for RNA-RNA interaction structures and linear time uniform sampling algorithm for RNA complexes of…
An RNA sequence is a word over an alphabet on four elements $\{A,C,G,U\}$ called bases. RNA sequences fold into secondary structures where some bases match one another while others remain unpaired. Pseudoknot-free secondary structures can…
We formulate the RNA folding problem as an $N\times N$ matrix field theory. This matrix formalism allows us to give a systematic classification of the terms in the partition function according to their topological character. The theory is…
We solve the loop equations to all orders in $1/N^2$, for the Chain of Matrices matrix model (with possibly an external field coupled to the last matrix of the chain). We show that the topological expansion of the free energy, is, like for…
The loop equations for a chain of hermitian random matrices are computed explicitely, including the 1/N^2 corrections. To leading order, the master loop equation reduces to an algebraic equation, whose solution can be written in terms of…
Random matrices are used in fields as different as the study of multi-orthogonal polynomials or the enumeration of discrete surfaces. Both of them are based on the study of a matrix integral. However, this term can be confusing since the…
We obtain the topological expansion of the hermitian matrix model using its representation as a CFT on a hyperelliptic Riemann surface. To each branch point of the Riemann surface we associate an operator which represents a twist field…