Related papers: Canonical RNA pseudoknot structures
Given a random RNA secondary structure, $S$, we study RNA sequences having fixed ratios of nuclotides that are compatible with $S$. We perform this analysis for RNA secondary structures subject to various base pairing rules and minimum arc-…
Let $\crs(K_n)$ be the minimum number of crossings over all rectilinear drawings of the complete graph on $n$ vertices on the plane. In this paper we prove that $\crs(K_n) < 0.380473\binom{n}{4}+\Theta(n^3)$; improving thus on the previous…
Functional or non-coding RNAs are attracting more attention as they are now potentially considered valuable resources in the development of new drugs intended to cure several human diseases. The identification of drugs targeting the…
Combinatorial analysis of a certain abstract of RNA structures has been studied to investigate their statistics. Our approach regards the backbone of secondary structures as an alternate sequence of paired and unpaired sets of nucleotides,…
In this article, we investigate short topological decompositions of non-orientable surfaces and provide algorithms to compute them. Our main result is a polynomial-time algorithm that for any graph embedded in a non-orientable surface…
Suppose $c_n(\sigma)$ denotes the number of cyclic permutations in $\mathcal{S}_n$ that avoid a pattern $\sigma$. In this paper, we define partial groupoid structures on cyclic pattern-avoiding permutations that allow us to build larger…
For a generic anti-canonical hypersurface in each smooth toric Fano 4-fold with rank 2 Picard group, we prove there exist three isolated rational curves in it. Moreover, for all these 4-folds except one, the contractions of generic…
We construct the K=8 fractional superconformal algebras. There are two such extended Virasoro algebras, one of which was constructed earlier, involving a fractional spin (equivalently, conformal dimension) 6/5 current. The new algebra…
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…
In this paper we consider left-invariant pseudo-K\"{a}hler structures on six-dimensional nilpotent Lie algebras. The explicit expressions of the canonical complex structures are calculated, and the curvature properties of the associated…
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…
No existing algorithm can start with arbitrary RNA sequences and return the precise, three-dimensional structures that ensures their biological function. This chapter outlines current algorithms for automated RNA structure prediction…
Let T_n denote the set of log canonical thresholds of pairs (X,Y), with X a nonsingular variety of dimension n, and Y a nonempty closed subscheme of X. Using non-standard methods, we show that every limit of a decreasing sequence in T_n…
A new N=4 superconformal algebra (SCA) is presented. Its internal affine Lie algebra is based on the seven-dimensional Lie algebra su(2)\oplus g, where g should be identified with a four-dimensional non-reductive Lie algebra. Thus, it is…
The linear canonical transform (LCT) has attained respectable status within a short span and is being broadly employed across several disciplines of science and engineering including signal processing, optical and radar systems, electrical…
Motivated by the work of Anstee, Griggs, and Sali on forbidden submatrices and the extremal sat-function for graphs, we introduce sat-type problems for matrices. Let F be a family of k-row matrices. A matrix M is called F-admissible if M…
In this paper, we use semidefinite programming and representation theory to compute new lower bounds on the crossing number of the complete bipartite graph $K_{m,n}$, extending a method from de Klerk et al. [SIAM J. Discrete Math. 20…
We consider the problem of counting the copies of a length-$k$ pattern $\sigma$ in a sequence $f \colon [n] \to \mathbb{R}$, where a copy is a subset of indices $i_1 < \ldots < i_k \in [n]$ such that $f(i_j) < f(i_\ell)$ if and only if…
In the abstract pseudodifferential setup of Connes and Moscovici, we prove a general formula for the discrepancies of zeta-regularised traces associated with certain spectral triples, and we introduce a canonical trace on operators, whose…
We describe a method to compute the Culler-Shalen seminorms of a knot, using the (-3,3,4) pretzel knot as an illustrative example. We deduce that the SL2(C)-character variety of this knot consists of three algebraic curves and that it…