Related papers: A combinatorial framework for RNA tertiary interac…
We propose a method for obtaining parsimonious decompositions of networks into higher order interactions which can take the form of arbitrary motifs.The method is based on a class of analytically solvable generative models, where vertices…
We present a statistical approach to protein structure by introducing a representation of protein folds based on simple observables defined as frequencies of oriented cycles in contact graphs. Motivated by the idea that these cycles may…
This contribution focuses on the fascinating RNA molecule, its sequence-dependent folding driven by base-pairing interactions, the interplay between these interactions and natural evolution, and its multiple regulatory roles. The four of us…
We propose an unexpected twist to description of the geometry and topology of configurations of n straight lines considered as a whole 3D entity (because the lines are inseparably linked pairwise while having linking numbers 1/2 or -1/2)…
The high-throughput short-reads RNA-seq protocols often produce paired-end reads, with the middle portion of the fragments being unsequenced. We explore if the full-length fragments can be computationally reconstructed from the sequenced…
Counterterms that are not reducible to $\zeta_{n}$ are generated by ${}_3F_2$ hypergeometric series arising from diagrams for which triangle and uniqueness relations furnish insufficient data. Irreducible double sums, corresponding to the…
Random graph models have been instrumental in characterizing complex networks, but chemical reaction networks (CRNs) are better represented as hypergraphs. Traditional models of random CRNs often reduce CRNs to bipartite graphs,…
We give a parity reversing involution on noncrossing trees that leads to a combinatorial interpretation of a formula on noncrossing trees and symmetric ternary trees in answer to a problem proposed by Hough. We use the representation of…
Quantum simulation of spin models can provide insight into complex problems that are difficult or impossible to study with classical computers. Trapped ions are an established platform for quantum simulation, but only systems with fewer…
We describe in detail the implementation of the relativistic three-neutron finite-volume quantization condition derived in Ref. [1]. In particular, we show how the complications due to Wigner rotations acting on spins are included, and…
We extend an hypergraph representation, introduced by Finkelstein and Roytberg, to unify dynamic programming algorithms in the context of RNA folding with pseudoknots. Classic applications of RNA dynamic programming energy minimization,…
It has been shown that inter-spin interaction strengths in a spins-1/2 chain can be evaluated by accessing one of the edge spins only. We demonstrate this experimentally for the simplest case, a three-spin chain, with nuclear magnetic…
The group $PGL(2,q)$ has an embedding into $PGL(3,q)$ such that it acts as the group fixing a nonsingular conic in $PG(2,q)$. This action affords a coherent configuration $R(q)$ on the set $L(q)$ of non-tangent lines of the conic. We show…
We conjecture that the distribution of the edge-disjoint union of two random regular graphs on the same vertex set is asymptotically equivalent to a random regular graph of the combined degree, provided it grows as the number of vertices…
We give diagrammatic algorithms for computing the group trisection, homology groups, and intersection form of a closed, orientable, smooth 4-manifold, presented as a branched cover of a bridge-trisected surface in $\mathbb{S}^{4}$. The…
Entangled photons generated by spontaneous parametric down conversion inside a nonlinear crystal exhibit a complex spatial photon count distribution. A quantitative description of this distribution helps with the interpretation of…
Real 3-manifold triangulations can be uniquely represented by isomorphism signatures. Databases of these isomorphism signatures are generated for a variety of 3-manifolds and knot complements, using SnapPy and Regina, then these…
Rydberg atoms trapped by optical tweezers have emerged as a versatile platform to emulate lattices with different geometries, in which long-range interacting spins lead to fascinating phenomena, ranging from spin liquids to topological…
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…
In this study we consider the problem of triangulated graphs. Precisely we give a necessary and sufficient condition for a graph to be triangulated. This give an alternative characterization of triangulated graphs. Our method is based on…