Many graphs arising in practice can be represented in a concise and intuitive way that conveys their structure. For example: A planar graph can be represented in the plane with points for vertices and non-crossing curves for edges. An interval graph can be represented on the real line with intervals for vertices and intersection of intervals representing edges. The concept of ``simultaneity'' applies for several types of graphs: the idea is to find representations for two graphs that share some common vertices and edges, and ensure that the common vertices and edges are represented the same way. Simultaneous representation problems arise in any situation where two related graphs should be represented consistently. A main instance is for temporal relationships, where an old graph and a new graph share some common parts. Pairs of related graphs arise in many other situations. For example, two social networks that share some members; two schedules that share some events, overlap graphs of DNA fragments of two similar organisms, circuit graphs of two adjacent layers on a computer chip etc. In this thesis, we study the simultaneous representation problem for several graph classes. For planar graphs the problem is defined as follows. Let G1 and G2 be two graphs sharing some vertices and edges. The simultaneous planar embedding problem asks whether there exist planar embeddings (or drawings) for G1 and G2 such that every vertex shared by the two graphs is mapped to the same point and every shared edge is mapped to the same curve in both embeddings. Over the last few years there has been a lot of work on simultaneous planar embeddings, which have been called `simultaneous embeddings with fixed edges'. A major open question is whether simultaneous planarity for two graphs can be tested in polynomial time. We give a linear-time algorithm for testing the simultaneous planarity of any two graphs that share a 2-connected subgraph. Our algorithm also extends to the case of k planar graphs, where each vertex [edge] is either common to all graphs or belongs to exactly one of them. Next we introduce a new notion of simultaneity for intersection graph classes (interval graphs, chordal graphs etc.) and for comparability graphs. For interval graphs, the problem is defined as follows. Let G1 and G2 be two interval graphs sharing some vertices I and the edges induced by I. G1 and G2 are said to be `simultaneous interval graphs' if there exist interval representations of G1 and G2 such that any vertex of I is assigned to the same interval in both the representations. The `simultaneous representation problem' for interval graphs asks whether G1 and G2 are simultaneous interval graphs. The problem is defined in a similar way for other intersection graph classes. For comparability graphs and any intersection graph class, we show that the simultaneous representation problem for the graph class is equivalent to a graph augmentation problem: given graphs G1 and G2, sharing vertices I and the corresponding induced edges, do there exist edges E' between G1-I and G2-I such that the graph G1 U G_2 U E' belongs to the graph class. This equivalence implies that the simultaneous representation problem is closely related to other well-studied classes in the literature, namely, sandwich graphs and probe graphs. We give efficient algorithms for solving the simultaneous representation problem for interval graphs, chordal graphs, comparability graphs and permutation graphs. Further, our algorithms for comparability and permutation graphs solve a more general version of the problem when there are multiple graphs, any two of which share the same common graph. This version of the problem also generalizes probe graphs.

Many graphs arising in practice can be represented in a concise and intuitive way that conveys their structure. For example: A planar graph can be represented in the plane with points for vertices and non-crossing curves for edges. An interval graph can be represented on the real line with intervals for vertices and intersection of intervals representing edges. The concept of ``simultaneity'' applies for several types of graphs: the idea is to find representations for two graphs that share some common vertices and edges, and ensure that the common vertices and edges are represented the same way. Simultaneous representation problems arise in any situation where two related graphs should be represented consistently. A main instance is for temporal relationships, where an old graph and a new graph share some common parts. Pairs of related graphs arise in many other situations. For example, two social networks that share some members; two schedules that share some events, overlap graphs of DNA fragments of two similar organisms, circuit graphs of two adjacent layers on a computer chip etc. In this thesis, we study the simultaneous representation problem for several graph classes. For planar graphs the problem is defined as follows. Let G1 and G2 be two graphs sharing some vertices and edges. The simultaneous planar embedding problem asks whether there exist planar embeddings (or drawings) for G1 and G2 such that every vertex shared by the two graphs is mapped to the same point and every shared edge is mapped to the same curve in both embeddings. Over the last few years there has been a lot of work on simultaneous planar embeddings, which have been called `simultaneous embeddings with fixed edges'. A major open question is whether simultaneous planarity for two graphs can be tested in polynomial time. We give a linear-time algorithm for testing the simultaneous planarity of any two graphs that share a 2-connected subgraph. Our algorithm also extends to the case of k planar graphs, where each vertex [edge] is either common to all graphs or belongs to exactly one of them. Next we introduce a new notion of simultaneity for intersection graph classes (interval graphs, chordal graphs etc.) and for comparability graphs. For interval graphs, the problem is defined as follows. Let G1 and G2 be two interval graphs sharing some vertices I and the edges induced by I. G1 and G2 are said to be `simultaneous interval graphs' if there exist interval representations of G1 and G2 such that any vertex of I is assigned to the same interval in both the representations. The `simultaneous representation problem' for interval graphs asks whether G1 and G2 are simultaneous interval graphs. The problem is defined in a similar way for other intersection graph classes. For comparability graphs and any intersection graph class, we show that the simultaneous representation problem for the graph class is equivalent to a graph augmentation problem: given graphs G1 and G2, sharing vertices I and the corresponding induced edges, do there exist edges E' between G1-I and G2-I such that the graph G1 U G_2 U E' belongs to the graph class. This equivalence implies that the simultaneous representation problem is closely related to other well-studied classes in the literature, namely, sandwich graphs and probe graphs. We give efficient algorithms for solving the simultaneous representation problem for interval graphs, chordal graphs, comparability graphs and permutation graphs. Further, our algorithms for comparability and permutation graphs solve a more general version of the problem when there are multiple graphs, any two of which share the same common graph. This version of the problem also generalizes probe graphs.

Let F be a family of sets. A graph G is an intersection graph of sets from the family F if there exists a mapping f : V (G)→ F such that, An interval graph is an intersection graph of a family of closed intervals on the real line. Interval graphs find application in diverse fields ranging from DNA analysis to VLSI design. An interval on the real line can be generalized to a k dimensional box or k-box. A k-box B = (R1.R2….Rk) is defined to be the Cartesian product R1 × R2 × …× Rk, where each Ri is a closed interval on the real line. If each Ri is a unit length interval, we call B a k-cube. Thus, an interval is a 1-box and a unit length interval is a 1-cube. A graph G has a k-box representation, if G is an intersection graph of a family of k-boxes in Rk. Similarly, G has a k-cube representation, if G is an intersection graph of a family of k-cubes in Rk. The boxicity of G, denoted by box(G), is the minimum positive integer k such that G has a k-box representation. Similarly, the cubicity of G, denoted by cub(G), is the minimum positive integer k such that G has a k-cube representation. Thus, interval graphs are the graphs with boxicity equal to 1 and unit interval graphs are the graphs with cubicity equal to 1. The concepts of boxicity and cubicity were introduced by F.S. Roberts in 1969. Deciding whether the boxicity (or cubicity) of a graph is at most k is NP-complete even for a small positive integer k. Box representation of graphs finds application in niche overlap (competition) in ecology and to problems of fleet maintenance in operations research. Given a low dimensional box representation, some well known NP-hard problems become polynomial time solvable. Attempts to find efficient box and cube representations for special classes of graphs can be seen in the literature. Scheinerman [6] showed that the boxicity of outerplanar graphs is at most 2. Thomassen [7] proved that the boxicity of planar graphs is bounded from above by 3. Cube representations of special classes of graphs like hypercubes and complete multipartite graphs were investigated in [5, 3, 4]. In this thesis, we present several bounds for boxicity and cubicity of special classes of graphs in terms of other graph parameters. The following are the main results shown in this work. 1. It was shown in [2] that, for a graph G with maximum degree Δ, cub(G) ≤ [4(Δ+ 1) log n]. We show that, for a k-degenerate graph G, cub(G) ≤ (k + 2)[2e log n]. Since k is at most Δ and can be much lower, this clearly is a stronger result. This bound is tight up to a constant factor. 2. For a k-degenerate graph G, we give an efficient deterministic algorithm that runs in O(n2k) time to output an O(k log n) dimensional cube representation. 3. Crossing number of a graph G is the minimum number of crossing pairs of edges, over all drawings of G in the plane. We show that if crossing number of G is t, then box(G) is O(t1/4 log3/4 t). This bound is tight up to a factor of O((log t)1/4 ). 4. We prove that almost all graphs have cubicity O(dav log n), where dav denotes the average degree. 5. Boxicity of a k-leaf power is at most k -1. For every k, there exist k-leaf powers whose boxicity is exactly k - 1. Since leaf powers are a subclass of strongly chordal graphs, this result implies that there exist strongly chordal graphs with arbitrarily high boxicity 6. Otachi et al. [8] conjectured that chordal bipartite graphs (CBGs) have boxicity at most 2. We disprove this conjecture by exhibiting an infinite family of CBGs that have unbounded boxicity. We first prove that the bipartite power of a tree (which is a CBG) is a CBG and then show that there exist trees whose bipartite powers have high boxicity. Later in Chapter ??, we prove a more generic result in bipartite powering. We prove that, for every k ≥ 3, the bipartite power of a bipartite, k-chordal graph is bipartite and k-chordal thus implying that CBGs are closed under bipartite powering. 7. Boxicity of a line graph with maximum degree Δ is O(Δ log2 log2 Δ). This is a log2 Δ log log Δ factor improvement over the best known upper bound for boxicity of any graph [1]. We also prove a non-trivial lower bound for the boxicity of a d-dimensional hypercube.

In this thesis we consider two sets of combinatorial structures defined on an Eulerian graph: the Eulerian orientations and Euler tours. We are interested in the computational problems of counting (computing the number of elements in the set) and sampling (generating a random element of the set). Specifically, we are interested in the question of when there exists an efficient algorithm for counting or sampling the elements of either set. The Eulerian orientations of a number of classes of planar lattices are of practical significance as they correspond to configurations of certain models studied in statistical physics. In 1992 Mihail and Winkler showed that counting Eulerian orientations of a general Eulerian graph is #P-complete and demonstrated that the problem of sampling an Eulerian orientation can be reduced to the tractable problem of sampling a perfect matching of a bipartite graph. We present a proof that this problem remains #Pcomplete when the input is restricted to being a planar graph, and analyse a natural algorithm for generating random Eulerian orientations of one of the afore-mentioned planar lattices. Moreover, we make some progress towards classifying the range of planar graphs on which this algorithm is rapidly mixing by exhibiting an infinite class of planar graphs for which the algorithm will always take an exponential amount of time to converge. The problem of counting the Euler tours of undirected graphs has proven to be less amenable to analysis than that of Eulerian orientations. Although it has been known for many years that the number of Euler tours of any directed graph can be computed in polynomial time, until recently very little was known about the complexity of counting Euler tours of an undirected graph. Brightwell and Winkler showed that this problem is #P-complete in 2005 and, apart from a few very simple examples, e.g., series-parellel graphs, there are no known tractable cases, nor are there any good reasons to believe the problem to be intractable. Moreover, despite several unsuccessful attempts, there has been no progress made on the question of approximability. Indeed, this problem was considered to be one of the more difficult open problems in approximate counting since long before the complexity of exact counting was resolved. By considering a randomised input model, we are able to show that a very simple algorithm can sample or approximately count the Euler tours of almost every d-in/d-out directed graph in expected polynomial time. Then, we present some partial results towards showing that this algorithm can be used to sample or approximately count the Euler tours of almost every 2d-regular graph in expected polynomial time. We also provide some empirical evidence to support the unproven conjecture required to obtain this result. As a sideresult of this work, we obtain an asymptotic characterisation of the distribution of the number of Eulerian orientations of a random 2d-regular graph.

We used a divide-and-conquer algorithm to recursively solve the two-dimensional problem of protein folding of an HP sequence with the maximum number of H-H contacts. We derived both lower and upper bounds for the algorithmic complexity by using the newly introduced concept of multi-directional width-bounded geometric separator. We proved that for a grid graph G with n grid points P, there exists a balanced separator A subseteq P$ such that A has less than or equal to 1.02074 sqrt{n} points, and G-A has two disconnected subgraphs with less than or equal to {2over 3}n nodes on each subgraph. We also derive a 0.7555sqrt {n} lower bound for our balanced separator. Based on our multidirectional width-bounded geometric separator, we found that there is an O(n^{5.563sqrt{n}}) time algorithm for the 2D protein folding problem in the HP model. We also extended the upper bound results to rectangular and triangular lattices.

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's 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.

<p>This thesis is a study on the confluence of algebraic structures and graph theory. Its aim is to consider groupoids from factorisations of complete graphs. We are especially interested in the cases where the factors are isomorphic. We analyse the loops obtained from homogeneous factorisations and ask if homogeneity is reflected in the kind of loops that are obtained. In particular, we are interested to see if we obtain either groups or quasi-associative Cayley sets from these loops. November 2008.</p>

Combinatorial auctions (CAs) are an important mechanism for allocating multiple items while allowing agents to specify preferences over bundles of items. In order to communicate these preferences, agents submit bids, which consist of one or more items and a value indicating the agent’s preference for these items. The process of determining the allocation of items is known as the winner determination problem (WDP). WDP for CAs is known to be NP-complete in the general case. We consider two distinct graph representations of a CA; the bid graph and the item graph. In a bid graph, vertices represent bids, and two vertices are adjacent if and only if the bids share items in common. In an item graph, each vertex represents a unique item, there is a vertex for each item, and any bid submitted by any agent must induce a connected subgraph of the item graph. We introduce a new definition of combinatorial auction equivalence by declaring two CAs equivalent if and only if their bid graphs are isomorphic. Parameterized complexity theory can be used to further distinguish between NP-hard problems. In order to make use of parameterized complexity theory in the investigation of a problem, we aim to find one or more parameters that describe some aspect of the problem such that if we fix these parameters, then either the problem is still hard (fixed-parameter intractable), or the problem can be solved in polynomial time (fixed-parameter tractable). We analyze WDP using bid graphs from within the formal scope of parameterized complexity theory. This approach has not previously been used to analyze WDP for CAs, although it has been used to solve set packing, which is related to WDP for CAs and is discussed in detail. We investigate a few parameterizations of WDP; some of the parameterizations are shown to be fixed-parameter intractable, while others are fixed-parameter tractable. We also analyze WDP when the graph class of a bid graph is restricted. We also discuss relationships between item graphs and bid graphs. Although both graphs can represent the same problem, there is little previous work analyzing direct relationships between them. Our discussion on these relationships begins with a result by Conitzer et al. [7], which focuses on the item graph representation and its treewidth, a property of a graph that measures how close the graph is to a tree. From a result by Gavril, if an item graph has treewidth one, then the bid graph must be chordal [16]. To apply the other direction of Gavril’s theorem, we use our new definition of CA equivalence. With this new definition, Gavril’s result shows that if a bid graph of a CA is chordal, then we can construct an item graph that has treewidth one for some equivalent CA.

Combinatorial auctions (CAs) are an important mechanism for allocating multiple items while allowing agents to specify preferences over bundles of items. In order to communicate these preferences, agents submit bids, which consist of one or more items and a value indicating the agent’s preference for these items. The process of determining the allocation of items is known as the winner determination problem (WDP). WDP for CAs is known to be NP-complete in the general case. We consider two distinct graph representations of a CA; the bid graph and the item graph. In a bid graph, vertices represent bids, and two vertices are adjacent if and only if the bids share items in common. In an item graph, each vertex represents a unique item, there is a vertex for each item, and any bid submitted by any agent must induce a connected subgraph of the item graph. We introduce a new definition of combinatorial auction equivalence by declaring two CAs equivalent if and only if their bid graphs are isomorphic. Parameterized complexity theory can be used to further distinguish between NP-hard problems. In order to make use of parameterized complexity theory in the investigation of a problem, we aim to find one or more parameters that describe some aspect of the problem such that if we fix these parameters, then either the problem is still hard (fixed-parameter intractable), or the problem can be solved in polynomial time (fixed-parameter tractable). We analyze WDP using bid graphs from within the formal scope of parameterized complexity theory. This approach has not previously been used to analyze WDP for CAs, although it has been used to solve set packing, which is related to WDP for CAs and is discussed in detail. We investigate a few parameterizations of WDP; some of the parameterizations are shown to be fixed-parameter intractable, while others are fixed-parameter tractable. We also analyze WDP when the graph class of a bid graph is restricted. We also discuss relationships between item graphs and bid graphs. Although both graphs can represent the same problem, there is little previous work analyzing direct relationships between them. Our discussion on these relationships begins with a result by Conitzer et al. [7], which focuses on the item graph representation and its treewidth, a property of a graph that measures how close the graph is to a tree. From a result by Gavril, if an item graph has treewidth one, then the bid graph must be chordal [16]. To apply the other direction of Gavril’s theorem, we use our new definition of CA equivalence. With this new definition, Gavril’s result shows that if a bid graph of a CA is chordal, then we can construct an item graph that has treewidth one for some equivalent CA.

No description available.