arXiv subjects

Christian M. Reidys

Publications and source records attributed to Christian M. Reidys.

At least 37 records · Page 2Linked to original sources

arXiv2017

The boundary length and point spectrum enumeration of partial chord diagrams using cut and join recursion

We introduce the boundary length and point spectrum, as a joint generalization of the boundary length spectrum and boundary point spectrum in arXiv:1307.0967. We establish by cut-and-join methods that the number of partial chord diagrams filtered by the boundary length and point spectrum satisfies a recursion relation, which combined with an initial condition determines these numbers uniquely. This recursion relation is equivalent to a second order, non-linear, algebraic partial differential equation for the generating function of the numbers of partial chord diagrams filtered by the boundary length and point spectrum.

math-ph↗

arXiv2016

Sequence-structure relations of biopolymers

Motivation: DNA data is transcribed into single-stranded RNA, which folds into specific molecular structures. In this paper we pose the question to what extent sequence- and structure-information correlate. We view this correlation as structural semantics of sequence data that allows for a different interpretation than conventional sequence alignment. Structural semantics could enable us to identify more general embedded "patterns" in DNA and RNA sequences. Results: We compute the partition function of sequences with respect to a fixed structure and connect this computation to the mutual information of a sequence-structure pair for RNA secondary structures. We present a Boltzmann sampler and obtain the a priori probability of specific sequence patterns. We present a detailed analysis for the three PDB-structures, 2JXV (hairpin), 2N3R (3-branch multi-loop) and 1EHZ (tRNA). We localize specific sequence patterns, contrast the energy spectrum of the Boltzmann sampled sequences versus those sequences that refold into the same structure and derive a criterion to identify native structures. We illustrate that there are multiple sequences in the partition function of a fixed structure, each having nearly the same mutual information, that are nevertheless poorly aligned. This indicates the possibility of the existence of relevant patterns embedded in the sequences that are not discoverable using alignments.

math.CO↗

arXiv2016

Plane permutations and applications to a result of Zagier-Stanley and distances of permutations

In this paper, we introduce plane permutations, i.e. pairs $\mathfrak{p}=(s,π)$ where $s$ is an $n$-cycle and $π$ is an arbitrary permutation, represented as a two-row array. Accordingly a plane permutation gives rise to three distinct permutations: the permutation induced by the upper horizontal ($s$), the vertical $π$) and the diagonal ($D_{\mathfrak{p}}$) of the array. The latter can also be viewed as the three permutations of a hypermap. In particular, a map corresponds to a plane permutation, in which the diagonal is a fixed point-free involution. We study the transposition action on plane permutations obtained by permuting their diagonal-blocks. We establish basic properties of plane permutations and study transpositions and exceedances and derive various enumerative results. In particular, we prove a recurrence for the number of plane permutations having a fixed diagonal and $k$ cycles in the vertical, generalizing Chapuy's recursion for maps filtered by the genus. As applications of this framework, we present a combinatorial proof of a result of Zagier and Stanley, on the number of $n$-cycles $ω$, for which the product $ω(1~2~\cdots ~n)$ has exactly $k$ cycles. Furthermore, we integrate studies on the transposition and block-interchange distance of permutations as well as the reversal distance of signed permutations. Plane permutations allow us to generalize and recover various lower bounds for transposition and block-interchange distances and to connect reversals with block-interchanges.

math.CO↗

arXiv2016

Statistics of topological RNA structures

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 structures having genus zero. We derive a new bivariate generating function whose singular expansion allows us to analyze the distributions of arcs, stacks, hairpin- , interior- and multi-loops. We then extend this analysis to H-type pseudoknots, kissing hairpins as well as $3$-knots and compute their respective expectation values. Finally we discuss our results and put them into context with data obtained by uniform sampling structures of fixed genus.

math.CO↗

arXiv2016

Topological language for RNA

In this paper we introduce a novel, context-free grammar, {\it RNAFeatures$^*$}, capable of generating any RNA structure including pseudoknot structures (pk-structure). We represent pk-structures as orientable fatgraphs, which naturally leads to a filtration by their topological genus. Within this framework, RNA secondary structures correspond to pk-structures of genus zero. {\it RNAFeatures$^*$} acts on formal, arc-labeled RNA secondary structures, called $λ$-structures. $λ$-structures correspond one-to-one to pk-structures together with some additional information. This information consists of the specific rearrangement of the backbone, by which a pk-structure can be made cross-free. {\it RNAFeatures$^*$} is an extension of the grammar for secondary structures and employs an enhancement by labelings of the symbols as well as the production rules. We discuss how to use {\it RNAFeatures$^*$} to obtain a stochastic context-free grammar for pk-structures, using data of RNA sequences and structures. The induced grammar facilitates fast Boltzmann sampling and statistical analysis. As a first application, we present an $O(n log(n))$ runtime algorithm which samples pk-structures based on ninety tRNA sequences and structures from the Nucleic Acid Database (NDB).

cs.FL↗

arXiv2016

RNA secondary structures having a compatible sequence of certain nucleotide ratios

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- and stack-length restrictions. Our main result reads as follows: in the simplex of the nucleotide ratios there exists a convex region in which, in the limit of long sequences, a random structure a.a.s.~has compatible sequence with these ratios and outside of which a.a.s.~a random structure has no such compatible sequence. We localize this region for RNA secondary structures subject to various base pairing rules and minimum arc- and stack-length restrictions. In particular, for {\bf GC}-sequences having a ratio of {\bf G} nucleotides smaller than $1/3$, a random RNA secondary structure without any minimum arc- and stack-length restrictions has a.a.s.~no such compatible sequence. For sequences having a ratio of {\bf G} nucleotides larger than $1/3$, a random RNA secondary structure has a.a.s. such compatible sequences. We discuss our results in the context of various families of RNA structures.

math.CO↗

arXiv2016

On the local genus distribution of graph embeddings

The $2$-cell embeddings of graphs on closed surfaces have been widely studied. It is well known that ($2$-cell) embedding a given graph $G$ on a closed orientable surface is equivalent to cyclically ordering the edges incident to each vertex of $G$. In this paper, we study the following problem: given a genus $g$ embedding $ε$ of the graph $G$ and a vertex of $G$, how many different ways of reembedding the vertex such that the resulting embedding $ε'$ is of genus $g+Δg$? We give formulas to compute this quantity and the local minimal genus achieved by reembedding. In the process we obtain miscellaneous results. In particular, if there exists a one-face embedding of $G$, then the probability of a random embedding of $G$ to be one-face is at least $\prod_{ν\in V(G)}\frac{2}{deg(ν)+2}$, where $deg(ν)$ denotes the vertex degree of $ν$. Furthermore we obtain an easy-to-check necessary condition for a given embedding of $G$ to be an embedding of minimum genus.

math.CO↗

arXiv2015

Narayana polynomials and some generalizations

In this note, by counting some colored plane trees we obtain several binomial identities. These identities can be viewed as specific evaluations of certain generalizations of the Narayana polynomials. As consequences, it provides combinatorial proofs for a bijective problem in Stanley's collection "Bijective Proof Problems", a new formula for the Narayana polynomials as well as a new expression for the Harer-Zagier formula enumerating unicellular maps, in a unified way. Furthermore, we identify a class of plane trees, whose enumeration is closely connected to the Schröder numbers. Many other binomial identities are presented as well.

math.CO↗

arXiv2015

On plane permutations

In this paper we generalize permutations to plane permutations. We employ this framework to derive a combinatorial proof of a result of Zagier and Stanley, that enumerates the number of $n$-cycles $ω$, for which $ω(12\cdots n)$ has exactly $k$ cycles. This quantity is $0$, if $n-k$ is odd and $\frac{2C(n+1,k)}{n(n+1)}$, otherwise, where $C(n,k)$ is the unsigned Stirling number of the first kind. The proof is facilitated by a natural transposition action on plane permutations which gives rise to various recurrences. Furthermore we study several distance problems of permutations. It turns out that plane permutations allow to study transposition and block-interchange distance of permutations as well as the reversal distance of signed permutations. Novel connections between these different distance problems are established via plane permutations.

math.CO↗

arXiv2015

A simple framework on sorting permutations

In this paper we present a simple framework to study various distance problems of permutations, including the transposition and block-interchange distance of permutations as well as the reversal distance of signed permutations. These problems are very important in the study of the evolution of genomes. We give a general formulation for lower bounds of the transposition and block-interchange distance from which the existing lower bounds obtained by Bafna and Pevzner, and Christie can be easily derived. As to the reversal distance of signed permutations, we translate it into a block-interchange distance problem of permutations so that we obtain a new lower bound. Furthermore, studying distance problems via our framework motivates several interesting combinatorial problems related to product of permutations, some of which are studied in this paper as well.

math.CO↗

arXiv2015

Variation of the local topological structure of graph embeddings

The $2$-cell embeddings of graphs on closed surfaces have been widely studied. It is well known that ($2$-cell) embedding a given graph $G$ on a closed orientable surface is equivalent to cyclically ordering the edges incident to each vertex of $G$. In this paper, we study the following problem: given a genus $g$ embedding $\mathbb{E}$ of the graph $G$, if we randomly rearrange the edges around a vertex, i.e., re-embedding, what is the probability of the resulting embedding $\mathbb{E}'$ having genus $g+Δg$? We give a formula to compute this probability. Meanwhile, some other known and unknown results are also obtained. For example, we show that the probability of preserving the genus is at least $\frac{2}{deg(v)+2}$ for re-embedding any vertex $v$ of degree $deg(v)$ in a one-face embedding; and we obtain a necessary condition for a given embedding of $G$ to be an embedding with the minimum genus.

math.CO↗

arXiv2014

A topological framework for signed permutations

In this paper we present a topological framework for studying signed permutations and their reversal distance. As a result we can give an alternative approach and interpretation of the Hannenhalli-Pevzner formula for the reversal distance of signed permutations. Our approach utlizes the Poincaré dual, upon which reversals act in a particular way and obsoletes the notion of "padding" of the signed permutations. To this end we construct a bijection between signed permutations and an equivalence class of particular fatgraphs, called $π$-maps, and analyze the action of reversals on the latter. We show that reversals act via either slicing, gluing or half-flipping of external vertices, which implies that any reversal changes the topological genus by at most one. Finally we revisit the Hannenhalli-Pevzner formula employing orientable and non-orientable, irreducible, $π$-maps.

math.CO↗

arXiv2014

A combinatorial interpretation of the $κ^{\star}_{g}(n)$ coefficients

Studying the virtual Euler characteristic of the moduli space of curves, Harer and Zagier compute the generating function $C_g(z)$ of unicellular maps of genus $g$. They furthermore identify coefficients, $κ^{\star}_{g}(n)$, which fully determine the series $C_g(z)$. The main result of this paper is a combinatorial interpretation of $κ^{\star}_{g}(n)$. We show that these enumerate a class of unicellular maps, which correspond $1$-to-$2^{2g}$ to a specific type of trees, referred to as O-trees. O-trees are a variant of the C-decorated trees introduced by Chapuy, Féray and Fusy. We exhaustively enumerate the number $s_{g}(n)$ of shapes of genus $g$ with $n$ edges, which is a specific class of unicellular maps with vertex degree at least three. Furthermore we give combinatorial proofs for expressing the generating functions $C_g(z)$ and $S_g(z)$ for unicellular maps and shapes in terms of $κ^{\star}_{g}(n)$, respectively. We then prove a two term recursion for $κ^{\star}_{g}(n)$ and that for any fixed $g$, the sequence $\{κ_{g,t}\}_{t=0}^g$ is log-concave, where $κ^{\star}_{g}(n)= κ_{g,t}$, for $n=2g+t-1$.

math.CO↗

arXiv2014

Shapes of interacting RNA complexes

Shapes of interacting RNA complexes are studied using a filtration via their topological genus. A shape of an RNA complex is obtained by (iteratively) collapsing stacks and eliminating hairpin loops. This shape-projection preserves the topological core of the RNA complex and for fixed topological genus there are only finitely many such shapes.Our main result is a new bijection that relates the shapes of RNA complexes with shapes of RNA structures.This allows to compute the shape polynomial of RNA complexes via the shape polynomial of RNA structures. We furthermore present a linear time uniform sampling algorithm for shapes of RNA complexes of fixed topological genus.

math.CO↗

arXiv2014

Uniform generation of RNA-RNA interaction structures of fixed topological genus

Interacting RNA complexes are studied via bicellular maps using a filtration via their topological genus. Our main result is a new bijection for RNA-RNA interaction structures and linear time uniform sampling algorithm for RNA complexes of fixed topological genus. The bijection allows to either reduce the topological genus of a bicellular map directly, or to lose connectivity by decomposing the complex into a pair of single stranded RNA structures. Our main result is proved bijectively. It provides an explicit algorithm of how to rewire the corresponding complexes and an unambiguous decomposition grammar. Using the concept of genus induction, we construct bicellular maps of fixed topological genus $g$ uniformly in linear time. We present various statistics on these topological RNA complexes and compare our findings with biological complexes. Furthermore we show how to construct loop-energy based complexes using our decomposition grammar.

math.CO↗

arXiv2014

Shapes of topological RNA structures

A topological RNA structure is derived from a diagram and its shape is obtained by collapsing the stacks of the structure into single arcs and by removing any arcs of length one. Shapes contain key topological, information and for fixed topological genus there exist only finitely many such shapes. We shall express topological RNA structures as unicellular maps, i.e. graphs together with a cyclic ordering of their half-edges. In this paper we prove a bijection of shapes of topological RNA structures. We furthermore derive a linear time algorithm generating shapes of fixed topological genus. We derive explicit expressions for the coefficients of the generating polynomial of these shapes and the generating function of RNA structures of genus $g$. Furthermore we outline how shapes can be used in order to extract essential information of RNA structure databases.

math.CO↗

arXiv2013

On the genus filtration of diagrams over two backbones

In this paper we compute the bivariate generating function of $γ$-matchings over two backbones, filtered by the number of arcs and the topological genus. $γ$-matchings over two backbones are chord-diagrams, obtained via concatenation and nesting of irreducible shapes of topological genus $\le γ$. We show that the key information is contained in the polynomials counting these shapes and provide recursions that allow to compute the latter. In particular we give a bijection between such irreducible shapes over one and two backbones. We present two applications of our results. The first is concerned with RNA-RNA interaction structures, obtained from the $γ$-matchings via symbolic methods. We secondly show that, using analytic-combinatorial methods, the topological genus satisfies a central limit theorem.

math.CO↗

arXiv2013

Combinatorics of $γ$-structures

In this paper we study canonical $γ$-structures, a class of RNA pseudoknot structures that plays a key role in the context of polynomial time folding of RNA pseudoknot structures. A $γ$-structure is composed by specific building blocks, that have topological genus less than or equal to $γ$, where composition means concatenation and nesting of such blocks. Our main result is the derivation of the generating function of $γ$-structures via symbolic enumeration using so called irreducible shadows. We furthermore recursively compute the generating polynomials of irreducible shadows of genus $\le γ$. $γ$-structures are constructed via $γ$-matchings. For $1\le γ\le 10$, we compute Puiseux-expansions at the unique, dominant singularities, allowing us to derive simple asymptotic formulas for the number of $γ$-structures.

math.CO↗