相关论文: Loop Homology of Bi-secondary Structures
In this paper we further describe the features of the topological space $K(R)$ obtained from the loop nerve of $R$, for $R=(S,T)$ a bi-secondary structure. We will first identify certain distinct combinatorial structures in the arc diagram…
Enumerative studies of RNA secondary structures were initiated four decades ago by Waterman and his coworkers. Since then, RNA secondary structures have been explored according to many different structural characteristics, for instance,…
A quantitative characterization of the relationship between molecular sequence and structure is essential to improve our understanding of how function emerges. This particular genotype-phenotype map has been often studied in the context of…
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…
In this paper we study properties of topological RNA structures, i.e.~RNA contact structures with cross-serial interactions that are filtered by their topological genus. RNA secondary structures within this framework are topological…
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,…
We introduce a commutative product of degree $-n$ on the homology $H_\ast(X)$ of an $n$-dimensional special cubical set $X$ and lift it on the free loop homology $H_\ast(\Lambda M)$ for $M=|X|$ to be the geometric realization. These…
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…
Arone and Turchin defined graph-complexes computing the rational homotopy of the spaces of long embeddings. The graph-complexes split into a direct sum by the number of loops in graphs. In this paper we compute the homology of its two-loop…
In his Inventiones paper, Ziller (Invent. Math: 1-22, 1977) computed the integral homology as a graded abelian group of the free loop space of compact, globally symmetric spaces of rank 1. Chas and Sullivan (String Topology, 1999)showed…
We view the folding of RNA-sequences as a map that assigns a pattern of base pairings to each sequence, known as secondary structure. These preimages can be constructed as random graphs (i.e. the neutral networks associated to the structure…
We consider the inverse-folding problem for RNA secondary structures: for a given (pseudo-knot-free) secondary structure find a sequence that has that structure as its ground state. If such a sequence exists, the structure is called…
In the paper we describe complexes whose homologies are naturally isomorphic to the first term of the Vassiliev spectral sequence computing (co)homology of the spaces of long knots in R^d, d>=3. The first term of the Vassiliev spectral…
The contact map of a protein fold is a graph that represents the patterns of contacts in the fold. It is known that the contact map can be decomposed into stacks and queues. RNA secondary structures are special stacks in which the degree of…
This is the second paper in our series of papers dedicated to the study of the generalized loop Heisenberg-Virasoro algebra. The first paper is dedicated to the study of maps on the generalized loop Heisenberg-Virasoro algebra, including…
Dual graphs have been applied to model RNA secondary structures with pseudoknots, or intertwined base pairs. In previous works, a linear-time algorithm was introduced to partition dual graphs into maximally connected components called…
We study the statistical mechanics of RNA secondary structures designed to have an attraction between two different types of structures as a model system for heteropolymer aggregation. The competition between the branching entropy of the…
The bispectrum is the leading non-Gaussian statistic in large-scale structure, carrying valuable information on cosmology that is complementary to the power spectrum. To access this information, we need to model the bispectrum in the weakly…
Chas and Sullivan recently defined an intersection product on the homology $H_*(LM)$ of the space of smooth loops in a closed, oriented manifold $M$. In this paper we will use the homotopy theoretic realization of this product described by…
An RNA molecule is structured on several layers. The primary and most obvious structure is its sequence of bases, i.e. a word over the alphabet {A,C,G,U}. The higher structure is a set of one-to-one base-pairings resulting in a…