相关论文: Watson-Crick pairing, the Heisenberg group and Mil…
We define numerical link-homotopy invariants of link maps of any number of components, which naturally generalize the Kirk invariant. The Kirk invariant is a link-homotopy invariant of 2-component link maps given by linking numbers of loops…
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…
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 consider the Combinatorial RNA Design problem, a minimal instance of RNA design where one must produce an RNA sequence that adopts a given secondary structure as its minimal free-energy structure. We consider two free-energy models where…
This paper describes the relationship between the first non-vanishing Milnor invariants of a classical link and the intersection invariant of a twisted Whitney tower. This is a certain 2-complex in the 4-ball, built from immersed disks…
The first half of this paper is largely expository, wherein we present a systematic combinatorial approach to the theory of polynomial (semi)invariants and multilinear invariants of several vectors and covectors, for the classical groups.…
Based on some analogies with the Hodge theory of isolated hypersurface singularities, we define Hodge-type numerical invariants (called H-numbers) of any, not necessarily algebraic, link in $S^3$. They contain the same information as the…
Background: RNA exhibits a variety of structural configurations. Here we consider a structure to be tantamount to the noncrossing Watson-Crick and \pairGU-base pairings (secondary structure) and additional cross-serial base pairs. These…
Background: RNA exhibits a variety of structural configurations. Here we consider a structure to be tantamount to the noncrossing Watson-Crick and \pairGU-base pairings (secondary structure) and additional cross-serial base pairs. These…
We employ Hirzebruch-type invariants obtained from iterated p-covers to investigate concordance of links and string links. We show that the invariants naturally give various group homomorphisms of the string link concordance group into…
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…
A k-noncrossing RNA pseudoknot structure is a graph over $\{1,...,n\}$ without 1-arcs, i.e. arcs of the form (i,i+1) and in which there exists no k-set of mutually intersecting arcs. In particular, RNA secondary structures are 2-noncrossing…
Accurate prediction of RNA secondary structure underpins transcriptome annotation, mechanistic analysis of non-coding RNAs, and RNA therapeutic design. Recent gains from deep learning and RNA foundation models are difficult to interpret…
The homology cobordism group of homology cylinders is a generalization of the mapping class group and the string link concordance group. We study this group and its filtrations by subgroups by developing new homomorphisms. First, we define…
We reconfigure the Milnor invariant of links in terms of central group extensions and unipotent Magnus embeddings. We also develop a diagrammatic computation of the invariant and compute the first non-vanishing invariants of the Milnor link…
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…
We construct many examples of non-slice knots in 3-space that cannot be distinguished from slice knots by previously known invariants. Using Whitney towers in place of embedded disks, we define a geometric filtration of the 3-dimensional…
In a DNA sequence, we have the celebrated Watson-Crick complement $\overline{T}=A$, $\overline{A}=T$, $\overline{C}=G$, and $\overline{G}=C$. Given an integer $m\ge 2$, a secondary structure in a DNA sequence refers to the existence of two…
In this paper we enumerate $k$-noncrossing RNA pseudoknot structures with given minimum stack-length. We show that the numbers of $k$-noncrossing structures without isolated base pairs are significantly smaller than the number of all…
We describe a collection of computer scripts written in PARI/GP to compute, for reflection groups determined by finite-volume polyhedra in $\mathbb{H}^3$, the commensurability invariants known as the invariant trace field and invariant…