91 research outputs found
Upward Three-Dimensional Grid Drawings of Graphs
A \emph{three-dimensional grid drawing} of a graph is a placement of the
vertices at distinct points with integer coordinates, such that the straight
line segments representing the edges do not cross. Our aim is to produce
three-dimensional grid drawings with small bounding box volume. We prove that
every -vertex graph with bounded degeneracy has a three-dimensional grid
drawing with volume. This is the broadest class of graphs admiting
such drawings. A three-dimensional grid drawing of a directed graph is
\emph{upward} if every arc points up in the z-direction. We prove that every
directed acyclic graph has an upward three-dimensional grid drawing with
volume, which is tight for the complete dag. The previous best upper
bound was . Our main result is that every -colourable directed
acyclic graph ( constant) has an upward three-dimensional grid drawing with
volume. This result matches the bound in the undirected case, and
improves the best known bound from for many classes of directed
acyclic graphs, including planar, series parallel, and outerplanar
Track Layouts of Graphs
A \emph{-track layout} of a graph consists of a (proper) vertex
-colouring of , a total order of each vertex colour class, and a
(non-proper) edge -colouring such that between each pair of colour classes
no two monochromatic edges cross. This structure has recently arisen in the
study of three-dimensional graph drawings. This paper presents the beginnings
of a theory of track layouts. First we determine the maximum number of edges in
a -track layout, and show how to colour the edges given fixed linear
orderings of the vertex colour classes. We then describe methods for the
manipulation of track layouts. For example, we show how to decrease the number
of edge colours in a track layout at the expense of increasing the number of
tracks, and vice versa. We then study the relationship between track layouts
and other models of graph layout, namely stack and queue layouts, and geometric
thickness. One of our principle results is that the queue-number and
track-number of a graph are tied, in the sense that one is bounded by a
function of the other. As corollaries we prove that acyclic chromatic number is
bounded by both queue-number and stack-number. Finally we consider track
layouts of planar graphs. While it is an open problem whether planar graphs
have bounded track-number, we prove bounds on the track-number of outerplanar
graphs, and give the best known lower bound on the track-number of planar
graphs.Comment: The paper is submitted for publication. Preliminary draft appeared as
Technical Report TR-2003-07, School of Computer Science, Carleton University,
Ottawa, Canad
Networks, (K)nots, Nucleotides, and Nanostructures
Designing self-assembling DNA nanostructures often requires the identification of a route for a scaffolding strand of DNA through the target structure. When the target structure is modeled as a graph, these scaffolding routes correspond to Eulerian circuits subject to turning restrictions imposed by physical constraints on the strands of DNA. Existence of such Eulerian circuits is an NP-hard problem, which can be approached by adapting solutions to a version of the Traveling Salesperson Problem. However, the author and collaborators have demonstrated that even Eulerian circuits obeying these turning restrictions are not necessarily feasible as scaffolding routes by giving examples of nontrivially knotted circuits which cannot be traced by the unknotted scaffolding strand.
Often, targets of DNA nanostructure self-assembly are modeled as graphs embedded on surfaces in space. In this case, Eulerian circuits obeying the turning restrictions correspond to A-trails, circuits which turn immediately left or right at each vertex. In any graph embedded on the sphere, all A-trails are unknotted regardless of the embedding of the sphere in space. We show that this does not hold in general for graphs on the torus. However, we show this property does hold for checkerboard-colorable graphs on the torus, that is, those graphs whose faces can be properly 2-colored, and provide a partial converse to this result. As a consequence, we characterize (with one exceptional family) regular triangulations of the torus containing unknotted A-trails. By developing a theory of sums of A-trails, we lift constructions from the torus to arbitrary n-tori, and by generalizing our work on A-trails to smooth circuit decompositions, we construct all torus links and certain sums of torus links from circuit decompositions of rectangular torus grids.
Graphs embedded on surfaces are equivalent to ribbon graphs, which are particularly well-suited to modeling DNA nanostructures, as their boundary components correspond to strands of DNA and their twisted ribbons correspond to double-helices. Every ribbon graph has a corresponding delta-matroid, a combinatorial object encoding the structure of the ribbon-graph\u27s spanning quasi-trees (substructures having exactly one boundary component). We show that interlacement with respect to quasi-trees can be generalized to delta-matroids, and use the resulting structure on delta-matroids to provide feasible-set expansions for a family of delta-matroid polynomials, both recovering well-known expansions of this type (such as the spanning-tree expansion of the Tutte polynnomial) as well as providing several previously unknown expansions. Among these are expansions for the transition polynomial, a version of which has been used to study DNA nanostructure self-assembly, and the interlace polynomial, which solves a problem in DNA recombination
Web-based drawing software for graphs in 3D and two layout algorithms
A new web-based software system for visualization and manipulation of graphs in 3D,
named We3Graph is presented with a focus on accessibility, customizability for applications
of graph drawing, usability and extendibility. The software system allows multiple
users to work on the same graph at the same time and is accessible through web browsers.
The software can be extended using plugins written in any programming language and
custom render engines written in the Javascript language. Also two new algorithms are
proposed to answer the following question, previously raised in [53]:
Given a graph G with n vertices, V = fv1;v2; : : : ;vng, and given a set of n
distinct points P = fp1; p2; : : : ; png each with integer coordinates in three dimensions,
can G be drawn crossing-free on P with vi at pi and with a number
of bends polynomial in n and in a volume polynomial in n and the dimension
of P
Layout of Graphs with Bounded Tree-Width
A \emph{queue layout} of a graph consists of a total order of the vertices,
and a partition of the edges into \emph{queues}, such that no two edges in the
same queue are nested. The minimum number of queues in a queue layout of a
graph is its \emph{queue-number}. A \emph{three-dimensional (straight-line
grid) drawing} of a graph represents the vertices by points in
and the edges by non-crossing line-segments. This paper contributes three main
results:
(1) It is proved that the minimum volume of a certain type of
three-dimensional drawing of a graph is closely related to the queue-number
of . In particular, if is an -vertex member of a proper minor-closed
family of graphs (such as a planar graph), then has a drawing if and only if has O(1) queue-number.
(2) It is proved that queue-number is bounded by tree-width, thus resolving
an open problem due to Ganley and Heath (2001), and disproving a conjecture of
Pemmaraju (1992). This result provides renewed hope for the positive resolution
of a number of open problems in the theory of queue layouts.
(3) It is proved that graphs of bounded tree-width have three-dimensional
drawings with O(n) volume. This is the most general family of graphs known to
admit three-dimensional drawings with O(n) volume.
The proofs depend upon our results regarding \emph{track layouts} and
\emph{tree-partitions} of graphs, which may be of independent interest.Comment: This is a revised version of a journal paper submitted in October
2002. This paper incorporates the following conference papers: (1) Dujmovic',
Morin & Wood. Path-width and three-dimensional straight-line grid drawings of
graphs (GD'02), LNCS 2528:42-53, Springer, 2002. (2) Wood. Queue layouts,
tree-width, and three-dimensional graph drawing (FSTTCS'02), LNCS
2556:348--359, Springer, 2002. (3) Dujmovic' & Wood. Tree-partitions of
-trees with applications in graph layout (WG '03), LNCS 2880:205-217, 200
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