arXiv subjects

Robert Brijder

Publications and source records attributed to Robert Brijder.

35 records · Page 2Linked to original sources

arXiv2015

Dominance and Deficiency for Petri Nets and Chemical Reaction Networks

Inspired by Anderson et al. [J. R. Soc. Interface, 2014] we study the long-term behavior of discrete chemical reaction networks (CRNs). In particular, using techniques from both Petri net theory and CRN theory, we provide a powerful sufficient condition for a structurally-bounded CRN to have the property that none of the non-terminal reactions can fire for all its recurrent configurations. We compare this result and its proof with a related result of Anderson et al. and show its consequences for the case of CRNs with deficiency one.

cs.DC↗

arXiv2014

Quaternary Bicycle Matroids and the Penrose Polynomial for Delta-Matroids

In contrast to matroids, vf-safe delta-matroids have three kinds of minors and are closed under the operations of twist and loop complementation. We show that the delta-matroids representable over GF(4) with respect to the nontrivial automorphism of GF(4) form a subclass of the vf-safe delta-matroids closed under twist and loop complementation. In particular, quaternary matroids are vf-safe. Using this result, we show that the matroid of a bicycle space of a quaternary matroid M is obtained from M by using loop complementation. As a consequence, the matroid of a bicycle space of a quaternary matroid M is independent of the chosen representation. This also leads to, e.g., an extension of a known parity-type characterization of the bicycle dimension, a generalization of the tripartition of Rosenstiehl and Read [Ann. Disc. Math. (1978)], and a suitable generalization of the dual notions of bipartite and Eulerian binary matroids to a vf-safe delta-matroids. Finally, we generalize a number of results concerning the Penrose polynomial from binary matroids to vf-safe delta-matroids. In this general setting the Penrose polynomial turns out to have a recursive relation much like the recursive relation of the Tutte polynomial.

math.CO↗

arXiv2014

Quaternary matroids are vf-safe

Binary delta-matroids are closed under vertex flips, which consist of the natural operations of twist and loop complementation. In this note we provide an extension of this result from GF(2) to GF(4). As a consequence, quaternary matroids are "safe" under vertex flips (vf-safe for short). As an application, we find that the matroid of a bicycle space of a quaternary matroid is independent of the chosen representation. This extends a result of Vertigan [J. Comb. Theory B (1998)] concerning the bicycle dimension of quaternary matroids.

math.CO↗

arXiv2014

Interlace Polynomials for Multimatroids and Delta-Matroids

We provide a unified framework in which the interlace polynomial and several related graph polynomials are defined more generally for multimatroids and delta-matroids. Using combinatorial properties of multimatroids rather than graph-theoretical arguments, we find that various known results about these polynomials, including their recursive relations, are both more efficiently and more generally obtained. In addition, we obtain several interrelationships and results for polynomials on multimatroids and delta-matroids that correspond to new interrelationships and results for the corresponding graphs polynomials. As a tool we prove the equivalence of tight 3-matroids and delta-matroids closed under the operations of twist and loop complementation, called vf-safe delta-matroids. This result is of independent interest and related to the equivalence between tight 2-matroids and even delta-matroids observed by Bouchet.

math.CO↗

arXiv2013

The Nullity Theorem for Principal Pivot Transform

We generalize the nullity theorem of Gustafson [Linear Algebra Appl. (1984)] from matrix inversion to principal pivot transform. Several special cases of the obtained result are known in the literature, such as a result concerning local complementation on graphs. As an application, we show that a particular matrix polynomial, the so-called nullity polynomial, is invariant under principal pivot transform.

math.CO↗

arXiv2012

Nullity and Loop Complementation for Delta-Matroids

We show that the symmetric difference distance measure for set systems, and more specifically for delta-matroids, corresponds to the notion of nullity for symmetric and skew-symmetric matrices. In particular, as graphs (i.e., symmetric matrices over GF(2)) may be seen as a special class of delta-matroids, this distance measure generalizes the notion of nullity in this case. We characterize delta-matroids in terms of equicardinality of minimal sets with respect to inclusion (in addition we obtain similar characterizations for matroids). In this way, we find that, e.g., the delta-matroids obtained after loop complementation and after pivot on a single element together with the original delta-matroid fulfill the property that two of them have equal "null space" while the third has a larger dimension.

math.CO↗

arXiv2012

The adjacency matroid of a graph

If $G$ is a looped graph, then its adjacency matrix represents a binary matroid $M_{A}(G)$ on $V(G)$. $M_{A}(G)$ may be obtained from the delta-matroid represented by the adjacency matrix of $G$, but $M_{A}(G)$ is less sensitive to the structure of $G$. Jaeger proved that every binary matroid is $M_{A}(G)$ for some $G$ [Ann. Discrete Math. 17 (1983), 371-376]. The relationship between the matroidal structure of $M_{A}(G)$ and the graphical structure of $G$ has many interesting features. For instance, the matroid minors $M_{A}(G)-v$ and $M_{A}(G)/v$ are both of the form $M_{A}(G^{\prime}-v)$ where $G^{\prime}$ may be obtained from $G$ using local complementation. In addition, matroidal considerations lead to a principal vertex tripartition, distinct from the principal edge tripartition of Rosenstiehl and Read [Ann. Discrete Math. 3 (1978), 195-226]. Several of these results are given two very different proofs, the first involving linear algebra and the second involving set systems or delta-matroids. Also, the Tutte polynomials of the adjacency matroids of $G$ and its full subgraphs are closely connected to the interlace polynomial of Arratia, Bollobás and Sorkin [Combinatorica 24 (2004), 567-584].

math.CO↗

arXiv2011

The Group Structure of Pivot and Loop Complementation on Graphs and Set Systems

We study the interplay between principal pivot transform (pivot) and loop complementation for graphs. This is done by generalizing loop complementation (in addition to pivot) to set systems. We show that the operations together, when restricted to single vertices, form the permutation group S_3. This leads, e.g., to a normal form for sequences of pivots and loop complementation on graphs. The results have consequences for the operations of local complementation and edge complementation on simple graphs: an alternative proof of a classic result involving local and edge complementation is obtained, and the effect of sequences of local complementations on simple graphs is characterized.

cs.DM↗

arXiv2010

Maximal Pivots on Graphs with an Application to Gene Assembly

We consider principal pivot transform (pivot) on graphs. We define a natural variant of this operation, called dual pivot, and show that both the kernel and the set of maximally applicable pivots of a graph are invariant under this operation. The result is motivated by and applicable to the theory of gene assembly in ciliates.

math.CO↗

arXiv2010

Nullity Invariance for Pivot and the Interlace Polynomial

We show that the effect of principal pivot transform on the nullity values of the principal submatrices of a given (square) matrix is described by the symmetric difference operator (for sets). We consider its consequences for graphs, and in particular generalize the recursive relation of the interlace polynomial and simplify its proof.

cs.DM↗

arXiv2009

Non-Confluent NLC Graph Grammar Inference by Compressing Disjoint Subgraphs

Grammar inference deals with determining (preferable simple) models/grammars consistent with a set of observations. There is a large body of research on grammar inference within the theory of formal languages. However, there is surprisingly little known on grammar inference for graph grammars. In this paper we take a further step in this direction and work within the framework of node label controlled (NLC) graph grammars. Specifically, we characterize, given a set of disjoint and isomorphic subgraphs of a graph $G$, whether or not there is a NLC graph grammar rule which can generate these subgraphs to obtain $G$. This generalizes previous results by assuming that the set of isomorphic subgraphs is disjoint instead of non-touching. This leads naturally to consider the more involved ``non-confluent'' graph grammar rules.

cs.LG↗

arXiv2008

Pivots, Determinants, and Perfect Matchings of Graphs

We give a characterization of the effect of sequences of pivot operations on a graph by relating it to determinants of adjacency matrices. This allows us to deduce that two sequences of pivot operations are equivalent iff they contain the same set S of vertices (modulo two). Moreover, given a set of vertices S, we characterize whether or not such a sequence using precisely the vertices of S exists. We also relate pivots to perfect matchings to obtain a graph-theoretical characterization. Finally, we consider graphs with self-loops to carry over the results to sequences containing both pivots and local complementation operations.

math.CO↗

arXiv2007

Extending the Overlap Graph for Gene Assembly in Ciliates

Gene assembly is an intricate biological process that has been studied formally and modeled through string and graph rewriting systems. Recently, a restriction of the general (intramolecular) model, called simple gene assembly, has been introduced. This restriction has subsequently been defined as a string rewriting system. We show that by extending the notion of overlap graph it is possible to define a graph rewriting system for two of the three types of rules that make up simple gene assembly. It turns out that this graph rewriting system is less involved than its corresponding string rewriting system. Finally, we give characterizations of the `power' of both types of graph rewriting rules. Because of the equivalence of these string and graph rewriting systems, the given characterizations can be carried over to the string rewriting system.

cs.LO↗

arXiv2007

How Overlap Determines the Macronuclear Genes in Ciliates

Formal models for gene assembly in ciliates have been developed, in particular the string pointer reduction system (SPRS) and the graph pointer reduction system (GPRS). The reduction graph is a valuable tool within the SPRS, revealing much information about how gene assembly is performed for a given gene. The GPRS is more abstract than the SPRS and not all information present in the SPRS is retained in the GPRS. As a consequence the reduction graph cannot be defined for the GPRS in general, but we show that it can be defined (in an equivalent manner as defined for the SPRS) if we restrict ourselves to so-called realistic overlap graphs. Fortunately, only these graphs correspond to genes occurring in nature. Defining the reduction graph within the GPRS allows one to carry over several results within the SPRS that rely on the reduction graph.

cs.LO↗

arXiv2007

The Fibers and Range of Reduction Graphs in Ciliates

The biological process of gene assembly has been modeled based on three types of string rewriting rules, called string pointer rules, defined on so-called legal strings. It has been shown that reduction graphs, graphs that are based on the notion of breakpoint graph in the theory of sorting by reversal, for legal strings provide valuable insights into the gene assembly process. We characterize which legal strings obtain the same reduction graph (up to isomorphism), and moreover we characterize which graphs are (isomorphic to) reduction graphs.

cs.LO↗

arXiv2006

Strategies of Loop Recombination in Ciliates

Gene assembly in ciliates is an extremely involved DNA transformation process, which transforms a nucleus, the micronucleus, to another functionally different nucleus, the macronucleus. In this paper we characterize which loop recombination operations (one of the three types of molecular operations that accomplish gene assembly) can possibly be applied in the transformation of a given gene from its micronuclear form to its macronuclear form. We also characterize in which order these loop recombination operations are applicable. This is done in the abstract and more general setting of so-called legal strings.

cs.LO↗

arXiv2006

Reducibility of Gene Patterns in Ciliates using the Breakpoint Graph

Gene assembly in ciliates is one of the most involved DNA processings going on in any organism. This process transforms one nucleus (the micronucleus) into another functionally different nucleus (the macronucleus). We continue the development of the theoretical models of gene assembly, and in particular we demonstrate the use of the concept of the breakpoint graph, known from another branch of DNA transformation research. More specifically: (1) we characterize the intermediate gene patterns that can occur during the transformation of a given micronuclear gene pattern to its macronuclear form; (2) we determine the number of applications of the loop recombination operation (the most basic of the three molecular operations that accomplish gene assembly) needed in this transformation; (3) we generalize previous results (and give elegant alternatives for some proofs) concerning characterizations of the micronuclear gene patterns that can be assembled using a specific subset of the three molecular operations.

cs.LO↗