相关论文: Combinatorics Of RNA Structures With Pseudoknots

In the combinatorics of finite finite Coxeter groups, there is a simple formula giving the number of maximal chains of noncrossing partitions. It is a reinterpretation of a result by Deligne which is due to Chapoton, and the goal of this…

We investigate which chordal graphs have a representation as intersection graphs of pseudosegments. For positive we have a construction which shows that all chordal graphs that can be represented as intersection graph of subpaths on a tree…

We review a derivation of the numbers of RNA complexes of an arbitrary topology. These numbers are encoded in the free energy of the hermitian matrix model with potential V(x)=x^2/2-stx/(1-tx), where s and t are respective generating…

We generalize the notion of linear chord diagrams to the case of matched sets of size $k$, which we call $k$-chord diagrams. We provide formal generating functions and recurrence relations enumerating these $k$-chord diagrams by the number…

RNA design shows growing applications in synthetic biology and therapeutics, driven by the crucial role of RNA in various biological processes. A fundamental challenge is to find functional RNA sequences that satisfy given structural…

The manuscript studies configurations of non-overlapping non-bonding dominoes on finite rectangular boards of unit squares characterized by row and column number. The non-bonding dominoes are defined here by the requirement that any domino…

In this paper, we find an explicit formula for the generating function that counts the circular permutations of length n avoiding the pattern 23 4 1 whose enumeration was raised as an open problem by Rupert Li. This then completes in all…

The multiplicative structure of the trivial symplectic groupoid over $\mathbb R^d$ associated to the zero Poisson structure can be expressed in terms of a generating function. We address the problem of deforming such a generating function…

A knot is a closed loop in space without self-intersection. Two knots are equivalent if there is a self homeomorphism of space bringing one onto the other. An arc presentation is an embedding of a knot in the union of finitely many half…

Families of alternating knots (links) and tangles are studied using as building block the conway defined as the twisting of two strands. The regular representation of knots assumes the projection has the minimal number of overpassings, and…

The Kinetoplast DNA (kDNA) is a two-dimensional Olympic-ring-like network of mutually linked 2.5 kb-long DNA minicircles found in certain parasites called Trypanosomes. Understanding the self-assembly and replication of this structure are…

Recently, imposing the gauge-symmetry and the T-duality constraints on the string frame effective actions of type II superstring theories, the NS-NS cuplings have been found in a particular scheme which has 445 couplings in 15 different…

RNA design is the search for a sequence or set of sequences that will fold into predefined structures, also known as the inverse problem of RNA folding. While numerous RNA design methods have been invented to find sequences capable of…

It is known that the majority of the human genome consists of repeated sequences. Furthermore, it is believed that a significant part of the rest of the genome also originated from repeated sequences and has mutated to its current form. In…

The unique properties of topological semimetals have strongly driven efforts to seek for new topological phases and related materials. Here, we identify a critical condition for the existence of linked nodal rings (LNRs) in symmorphic…

We extend recent methods for parametric sequence alignment to the parameter space for scoring RNA folds. This involves the construction of an RNA polytope. A vertex of this polytope corresponds to RNA secondary structures with common…

In this work, we prove the existence of linear recurrences of order M with a non-trivial solution vanishing exactly on the set of gaps (or a subset) of a numerical semigroup S finitely generated by a1 < a2 <...< aN and M = aN. Keywords:…

Algorithms to generate various combinatorial structures find tremendous importance in computer science. In this paper, we begin by reviewing an algorithm proposed by Rohl that generates all unique permutations of a list of elements which…

Cellular Automata (CA) are an interesting computational model for designing Pseudorandom Number Generators (PRNG), due to the complex dynamical behavior they can exhibit depending on the underlying local rule. Most of the CA-based PRNGs…

The revelation of the supreme authority of nucleic acids in the cellular landscape has precipitated the recognition of the versatility of RNAs in cells. The subsequent discovery of non-coding RNAs was a major breakthrough that revealed…