Related papers: Asymptotic Enumeration of RNA Structures with Pseu…
We enumerate the number of RNA contact structures according to their genus, i.e. the topological character of their pseudoknots. By using a recently proposed matrix model formulation for the RNA folding problem, we obtain exact results for…
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…
Computational prediction of RNA structures is an important problem in computational structural biology. Studies of RNA structure formation often assume that the process starts from a fully synthesized sequence. Experimental evidence,…
This paper analyzes over 30 types of q-series and the asymptotic behavior of their expansions. A method is described for deriving further asymptotic formulas using convolutions of generating functions with subexponential growth. All…
The paper investigates the computational problem of predicting RNA secondary structures. The general belief is that allowing pseudoknots makes the problem hard. Existing polynomial-time algorithms are heuristic algorithms with no…
In this paper, we study the structure of the complete asymptotic expansion of the probability that a large combinatorial object is connected or consists of a given number of connected components. For rapidly growing labeled families of…
Let $\{a_\rr : \rr \in (\Z^+)^d \}$ be a $d$-dimensional array of numbers, for which the generating function $F(\zz) := \sum_\rr a_\rr \zz^\rr$ is meromorphic in a neighborhood of the origin. For example, $F$ may be a rational multivariate…
Phylogenetic networks provide a general framework for modeling reticulate evolutionary processes such as hybridization, recombination, and horizontal gene transfer. In this paper, we study the asymptotic counting of binary phylogenetic…
It is a classical result of Stein and Waterman that the asymptotic number of RNA secondary structures is $1.104366 \cdot n^{-3/2} \cdot 2.618034^n$. Motivated by the kinetics of RNA secondary structure formation, we are interested in…
The contact map of a protein fold is a graph that represents the patterns of contacts in the fold. It is known that the contact map can be decomposed into stacks and queues. RNA secondary structures are special stacks in which the degree of…
The algebraic properties of formal power series, whose coefficients show factorial growth and admit a certain well-behaved asymptotic expansion, are discussed. It is shown that these series form a subring of $\mathbb{R}[[x]]$. This subring…
We explain a discontinuous drop in the exponential growth rate for certain multivariate generating functions at a critical parameter value, in even dimensions d at least 4. This result depends on computations in the homology of the…
We examine the sum of modified Bessel functions with argument depending non-linearly on the summation index given by \[S_{\nu,p}(a)=\sum_{n\geq 1} (an^p/2)^{-\nu} K_\nu(an^p)\qquad (a>0,\ 0\leq\nu<1)\] as the parameter $a\to 0+$, where $p$…
A representation for the Riemann zeta function valid for arbitrary complex $s=\sigma+it$ is $\zeta(s)=\sum_{n=0}^\infty A(n,s)$, where \[A(n,s)=\frac{2^{-n-1}}{1-2^{1-s}} \sum_{k=0}^n \left(\!\begin{array}{c}n\\k\end{array}\!\right)…
We examine the sum of modified Bessel functions with argument depending quadratically on the summation index given by \[S_\nu(a)=\sum_{n\geq 1} (\frac{1}{2} an^2)^{-\nu} K_\nu(an^2)\qquad (|\arg\,a|<\pi/2)\] as the parameter $|a|\to 0$. It…
This is the second in a series of articles devoted to showing that a typical covering map of large degree to a fixed, regular graph has its new adjacency eigenvalues within the bound conjectured by Alon for random regular graphs. The first…
In this paper we study properties of topological RNA structures, i.e.~RNA contact structures with cross-serial interactions that are filtered by their topological genus. RNA secondary structures within this framework are topological…
We examine the exponential generating function for the number of symmetric involutions (A000898 in OEIS) and point out that Robinson's asymptotic formula for its coefficients is incorrect. We further supply the correct formula.
In this paper we consider the problem of RNA folding with pseudoknots. We use a graphical representation in which the secondary structures are described by planar diagrams. Pseudoknots are identified as non-planar diagrams. We analyze the…
A hypergraph is simple if it has no loops and no repeated edges, and a hypergraph is linear if it is simple and each pair of edges intersects in at most one vertex. For $n\geq 3$, let $r= r(n)\geq 3$ be an integer and let $\boldsymbol{k} =…