Related papers: Stacks in canonical RNA pseudoknot structures
Consider a weighted branching process generated by the lengths of intervals obtained by stick-breaking of unit length (a.k.a. the residual allocation model) and associate with each weight a `box'. Given the weights `balls' are thrown…
The primary structure of a ribonucleic acid (RNA) molecule can be represented as a sequence of nucleotides (bases) over the alphabet {A, C, G, U}. The secondary or tertiary structure of an RNA is a set of base pairs which form bonds between…
In this paper, we introduce the $k\times n$ (with $k\leq n$) truncated, supplemented Pascal matrix which has the property that any $k$ columns form a linearly independent set. This property is also present in Reed-Solomon codes; however,…
We demonstrate analytically and numerically the possibility that the fractal property of a scale-free network cannot be characterized by a unique fractal dimension and the network takes a multifractal structure. It is found that the mass…
We initiate an investigation into the local structure of simple nonnuclear C$^*$-crossed products by showing that stable rank one is generic within two natural classes of minimal actions of free groups on the Cantor set. The arguments also…
In this paper, we are interested in sequences of q-tuple of N-by-N random matrices having a strong limiting distribution (i.e. given any non-commutative polynomial in the matrices and their conjugate transpose, its normalized trace and its…
In a general stochastic multistate promoter model of dynamic mRNA/protein interactions, we identify the stationary joint distribution of the promoter state, mRNA, and protein levels through an explicit `stick-breaking' construction of…
The notion of a pseudoknot is defined as an equivalence class of knot diagrams that may be missing some crossing information. We provide here a topological invariant schema for pseudoknots and their relatives, 4-valent rigid vertex spatial…
For a class $\mathcal C$ of graphs $G$ equipped with functions $f_G$ defined on subsets of $E(G)$ or $V(G)$, we say that $\mathcal{C}$ is $k$-scattered with respect to $f_G$ if there exists a constant $\ell$ such that for every graph $G\in…
A graph is a $k$-leaf power of a tree $T$ if its vertices are leaves of $T$ and two vertices are adjacent in $T$ if and only if their distance in $T$ is at most $k$. Then $T$ is a $k$-leaf root of $G$. This notion was introduced by…
Ara\'ujo, Kinyon and Konieczny (2011) pose several problems concerning the construction of arbitrary commuting graphs of semigroups. We observe that every star-free graph is the commuting graph of some semigroup. Consequently, we suggest…
We investigate bifurcations in feedforward coupled cell networks. Feedforward structure (the absence of feedback) can be defined by a partial order on the cells. We use this property to study generic one-parameter steady state bifurcations…
In Part I of this series we described three algorithms that construct canonical tree-decompositions of graphs which distinguish all their k-blocks and tangles of order k. We now establish bounds on the number of parts in these…
It has been observed that mutualistic bipartite networks have a nested structure of interactions. In addition, the degree distributions associated with the two guilds involved in such networks (e.g. plants & pollinators or plants & seed…
A random overlap structure (ROSt) is a measure on pairs (X,Q) where X is a locally finite sequence in the real line with a maximum and Q a positive semidefinite matrix of overlaps intrinsic to the particles X. Such a measure is said to be…
We study $t$-intersecting and $t$-cross-intersecting families of $k$-dimensional subspaces in finite vector spaces of dimension $n$. We show that all large $t$-intersecting families admit a governing low-dimensional structure for $n \ge…
We continue to study the squared Frobenius norm of a submatrix of a $n \times n$ random unitary matrix. When the choice of the submatrix is deterministic and its size is $[ns] \times [nt]$, we proved in a previous paper that, after…
We present a structural approach of some results about jumps in the behavior of the profile (alias generating function) of hereditary classes of finite structures. We consider the following notion due to N.Thi\'ery and the second author. A…
For an integer $k\geq 2$, a spanning tree of a graph without vertices of degree from $2$ to $k$ is called a {\it $[2,k]$-ST} of the graph. The concept of $[2,k]$-STs is a natural extension of a homeomorphically irreducible spanning tree (or…
We study the relations between the invariants $\tau_{RT}$, $\tau_{HKR}$, and $\tau_L$ of Reshetikhin-Turaev, Hennings-Kauffman-Radford, and Lyubashenko, respectively. In particular, we discuss explicitly how $\tau_L$ specializes to…