相关论文: Central and Local Limit Theorems for RNA Structure…

We investigate Gaussian Laplacian eigenfunctions (Arithmetic Random Waves) on the three-dimensional standard flat torus, in particular the asymptotic distribution of the nodal intersection length against a fixed regular reference surface.…

The combinatorics of RNA plays a central role in biology. Mathematical biologists have several commonly-used models for RNA: words in a fixed alphabet (representing the primary sequence of nucleotides) and plane trees (representing the…

Integrative biomolecular modeling of RNA relies on structural refined collections and accurate experimental data that reflect binding and folding behavior. However, the prediction of such collections remains challenging due to the rugged…

Motivation: RNA design aims to find RNA sequences that fold into a given target secondary structure, a problem also known as RNA inverse folding. However, not all target structures are designable. Recent advances in RNA designability have…

We propose a new deterministic methodology to predict RNA sequence and protein folding. Is stem enough for structure prediction? The main idea is to consider all possible stem formation in the given sequence. With the stem loop energy and…

Accurate prediction of RNA properties, such as stability and interactions, is crucial for advancing our understanding of biological processes and developing RNA-based therapeutics. RNA structures can be represented as 1D sequences, 2D…

RNA secondary structure folding kinetics is known to be important for the biological function of certain processes, such as the hok/sok system in E. coli. Although linear algebra provides an exact computational solution of secondary…

Noncrossing arc diagrams are combinatorial models for permutations that encode information about lattice congruences of the weak order and about the associated discrete geometry. In this paper, we consider two related, analogous models for…

Real-world networks exhibit prominent hierarchical and modular structures, with various subgraphs as building blocks. Most existing studies simply consider distinct subgraphs as motifs and use only their numbers to characterize the…

The problem of estimating the structure of a graph from observed data is of growing interest in the context of high-throughput genomic data, and single-cell RNA sequencing in particular. These, however, are challenging applications, since…

The prevalent method for RNA secondary structure prediction for a single sequence is free energy minimization based on the nearest neighbor thermodynamic model (NNTM). One of the least well-developed parts of the model is the energy…

The incipient infinite cluster appearing at the bond percolation threshold can be decomposed into singly-connected ``links'' and multiply-connected ``blobs.'' Here we decompose blobs into objects known in graph theory as 3-blocks. A 3-block…

In this paper we compute the loop homology of bi-secondary structures. Bi-secondary structures were introduced by Haslinger and Stadler and are pairs of RNA secondary structures, i.e. diagrams having non-crossing arcs in the upper…

In this work, we investigate a challenging problem, which has been considered to be an important criterion in designing codewords for DNA computing purposes, namely secondary structure avoidance in single-stranded DNA molecules. In short,…

Phylogenetic networks provide a more general description of evolutionary relationships than rooted phylogenetic trees. One way to produce a phylogenetic network is to randomly place $k$ arcs between the edges of a rooted binary phylogenetic…

In this paper we study the asymptotic behavior of a structure made of curved rods of thickness 2\delta when \delta rightarrow 0. This study is carried on within the frame of linear elasticity by using the unfolding method. It is based on…

A pseudodiagram is a diagram of a knot with some crossing information missing. We review and expand the theory of pseudodiagrams introduced by R. Hanaki. We then extend this theory to the realm of virtual knots, a generalization of knots.…

Decomposing a graph into a hierarchical structure via $k$-core analysis is a standard operation in any modern graph-mining toolkit. $k$-core decomposition is a simple and efficient method that allows to analyze a graph beyond its mere…

Statistical inference for exponential-family models of random graphs with dependent edges is challenging. We stress the importance of additional structure and show that additional structure facilitates statistical inference. A simple…

Let $D$ be a division ring with infinite center, $K$ a proper division subring of $D$ and $N$ an almost subnormal subgroup of the multiplicative group $D^*$ of $D$. The aim of this paper is to show that if $K$ is $N$-invariant and $N$ is…