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We relate two concepts in graph theory and algorithmic complexity, namely the search number and the vertex separation of a graph. Let s (G ) denote the search number and vs (G ) denote the vertex separation of a connected, undirected graph G . We show that vs (G ) s (G ) vs (G ) + 2 and we give a simple transformation from G to G such that vs (G ) = s (G ). We characterize those trees having a given vertex separation and describe the smallest such trees. We also note that there exist trees for which the difference between search number and vertex separation is indeed 2. We give algorithms that, for any tree T , compute vs (T ) in linear time and compute an optimal layout with respect to vertex separation in time O (n log n ). Vertex separation has previously been related to progressive black/white pebble demand and has been shown to be identical to a variant of search number, node search number, and to path width, which has been related directly to gate matrix layout cost. All these...

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Physical Mapping is a central problem in molecular biology ... and the human genome project. The problem is to reconstruct the relative position of fragments of DNA along the genome from information on their pairwise overlaps. We show that four simplified models of the problem lead to NP-complete decision problems: Colored unit interval graph completion, the maximum interval (or unit interval) subgraph, the pathwidth of a bipartite graph, and the k-consecutive ones problem for k >= 2. These models have been chosen to reflect various features typical in biological data, including false negative and positive errors, small width of the map and chimericism.

Consider a team of mobile software agents deployed to capture a (possibly hostile) intruder in a network. All agents, including the intruder move along the network links; the intruder could be arbitrarily fast, and aware of the positions of all the agents. The problem is to design the agents' strategy for capturing the intruder. The main eciency parameter is the size of the team. This is an instance of the well known graph-searching problem whose many variants have been extensively studied in the literature. In all existing solutions, and in all the variants of the problem, it is assumed that agents can be removed from their current location and placed in another network site arbitrarily and at any time. As a consequence, the existing optimal strategies cannot be employed in situations for which agents cannot access the network at any point, or cannot "jump" across the network, or cannot reach an arbitrary point of the network via an internal travel through insecure zones. This motivates the contiguous search problem in which agents cannot be removed from the network, and clear links must form a connected sub-network at any time, providing safety of movements. This new problem is NP-complete in general. We study it for tree networks, and we consider its more general version, the weighted case, which arises naturally when considering networks whose nodes and links are of different nature and thus require a different number of agents to be explored. We give a linear-time algorithm that computes, for any tree T , the minimum number of agents to capture the intruder, and the corresponding search strategy. Beside its optimality in time, our algorithm is naturally distributed: if T is a processor-network...

We study two related problems motivated by molecular biology: ffl Given a graph G and a constant k, does there exist a supergraph G of G which is a unit interval graph and has clique size at most k? ffl Given a graph G and a proper k-coloring c of G, does there exist a supergraph We show that those problems are polynomial for fixed k. On the other hand we prove that the first problem is equivalent to deciding if the bandwidth of G is at most k \Gamma 1. Hence, it is NP-hard, and W [t]-hard for all t. We also show that the second problem is W [1]-hard. This implies that for fixed k, both of the problems are unlikely to have an O(n ) algorithm, where ff is a constant independent of k.

This thesis addresses the topic of secure distributed computation, a general and powerful tool for balancing cooperation and mistrust among independent agents. We study many related models, which differ as to the allowable communication among agents, the ways in which agents may misbehave, and the complexity (cryptographic) assumptions that are made. We present new protocols, both for general secure computation (i.e., of any function over a finite domain) and for specific tasks (e.g., electronic money). We investigate fundamental relationships among security needs and various resource requirements, with an emphasis on communication complexity. A number of mathematical methods are employed for our investigations, including algebraic, graph-theoretic, and cryptographic techniques.

We analyze a randomized pursuit-evasion game on graphs. This game is played by two players, a hunter and a rabbit. Let G be any connected, undirected graph with n nodes. The game is played in rounds and in each round both the hunter and the rabbit are located at a node of the graph. Between rounds both the hunter and the rabbit can stay at the current node or move to another node. The hunter is assumed to be restricted to the graph G: in every round, the hunter can move using at most one edge. For the rabbit we investigate two models: in one model the rabbit is restricted to the same graph as the hunter, and in the other model the rabbit is unrestricted, i.e., it can jump to an arbitrary node in every round. We say that the rabbit is caught as soon as hunter and rabbit are located at the same node in a round. The goal of the hunter is to catch the rabbit in as few rounds as possible, whereas the rabbit aims to maximize the number of rounds until it is caught. Given a randomized hunter strategy for G, the escape length for that strategy is the worst case expected number of rounds it takes the hunter to catch the rabbit, where the worst case is with regards to all (possibly randomized) rabbit strategies. Our main result is a hunter strategy for general graphs with an escape length of only O(n log(diam(G))) against restricted as well as unrestricted rabbits. This bound is close to optimal since Ω(n) is a trivial lower bound on the escape length in both models. Furthermore, we prove that our upper bound is optimal up to constant factors against unrestricted rabbits. 1

This paper addresses memory requirement issues arising in implementations of algorithms on graphs of bounded treewidth. Such dynamic programming algorithms require a large data table for each vertex of a treedecomposition T of the input graph. We give a linear-time algorithm that finds the traversal order of T minimizing the number of tables stored simultaneously. We show that this minimum value is lower-bounded by the pathwidth of T plus one, and upper bounded by twice the pathwidth of T plus one. We also give a linear-time algorithm finding the depth-first traversal order minimizing the sum of the sizes of tables stored simultaneously.

We present a linear time algorithm which, given a tree, computes a linear layout optimal with respect to vertex separation. As a consequence optimal edge search strategies, optimal node search strategies, and optimal interval augmentations can be computed also in O(n) for trees. This improves the running time of former algorithms from O(n log n) to O(n) and answers two related open questions raised in [7] and [15].