Related papers: RNA Folding and Large N Matrix Theory
In cond-mat/9907125 the low-temperature behavior of a model for RNA secondary structure was studied. It is claimed that the model exhibits a breaking of the replica symmetry, since the width of the distribution P(q) of overlaps may converge…
The coverage depth problem in DNA data storage is about computing the expected number of reads needed to recover all encoded strands. Given a generator matrix of a linear code, this quantity equals the expected number of randomly drawn…
Many computerized methods for RNA-RNA interaction structure prediction have been developed. Recently, $O(N^6)$ time and $O(N^4)$ space dynamic programming algorithms have become available that compute the partition function of RNA-RNA…
The lattice definition of a two-dimensional topological field theory (TFT) is given generically, and the exact solution is obtained explicitly. In particular, the set of all lattice topological field theories is shown to be in one-to-one…
The properties of nuclear matter are studied in the cut-off field theory. It is found that, under the Hartree approximation, the small cut-off makes the equations of state hard, especially at higher densities. The theory is modified in the…
We construct the $Z_{N}$ symmetry extended fusion ring of bulk and chiral theories and the corresponding modular partition functions with nonanomalous subgroup $Z_{n}(\subset Z_{N})$. The chiral fusion ring provides fundamental data for…
We investigate an integrable property and observables of 2 dimensional N=(4,4) topological field theory defined on a discrete lattice by using the "orbifolding" and "deconstruction" methods. We show that our lattice model possesses the…
Deep Learning using the eponymous deep neural networks (DNNs) has become an attractive approach towards various data-based problems of theoretical physics in the past decade. There has been a clear trend to deeper architectures containing…
We compute genus two partition functions in two dimensional conformal field theories at large central charge, focusing on surfaces that give the third Renyi entropy of two intervals. We compute this for generalized free theories and for…
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…
A new formulation of four dimensional quantum field theories, such as scalar field theory, is proposed as a large N limit of a special NxN matrix model. Our reduction scheme works beyond planar approximation and applies for QFT with finite…
Large RNA molecules often carry multiple functional domains whose spatial arrangement is an important determinant of their function. Pre-mRNA splicing, furthermore, relies on the spatial proximity of the splice junctions that can be…
DNA nanoparticles with three-fold coordination have been observed to self-assemble in experiment into a network equivalent to the hexagonal (6.6.6) tiling, and a network equivalent to the 4.8.8 Archimedean tiling. Both networks are built…
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…
After a short introduction to Matrix theory, we explain how can one generalize matrix models to describe toroidal compactifications of M-theory and the heterotic vacua with 16 supercharges. This allows us, for the first time in history, to…
Topological quantum matter exhibits a range of exotic phenomena when enriched by subdimensional symmetries. This includes new features beyond those that appear in the conventional setting of global symmetry enrichment. A recently discovered…
Prior results for tRNA and 5S rRNA demonstrated that secondary structure prediction accuracy can be significantly improved by modifying the parameters in the multibranch loop entropic penalty function. However, for reasons not well…
Non-coding RNA sequences play a great role in controlling a number of cellular functions, thus raising the need to understand their complex conformational dynamics in quantitative detail. In this perspective, we first show that single…
Braiding matrices in rational conformal field theory are considered. The braiding matrices for any two block four point function are computed, in general, using the holomorphic properties of the blocks and the holomorphic properties of…
In this paper, we study the interaction of an antisense RNA and its target mRNA, based on the model introduced by Alkan {\it et al.} (Alkan {\it et al.}, J. Comput. Biol., Vol:267--282, 2006). Our main results are the derivation of the…