195859283
On fixed edges and edge-reconstruction of series-parallel networks
A graph configuration is a vertex labeled simple graph. We say a configuration is exclusive for graphs with a property in a class of graphs if every graph in the class containing the configuration has the property. We use the method of exclusive configurations to search for graphs without fixed edges and forced edges investigate the fixed edges. An edge e of a graph G is said to be a fixed edge if G-e+e'/spl cong/G implies that e'=e, and a forced edge if G-e+e' is an edge-reconstruction of G implies that e'=e. It is proved that all series-parallel networks contain fixed edges and forced edge except P/sub 2//spl times/K/sub 1/ and P/sub 3//spl times/K/sub 1/. A similar method is used to investigate the alternative wire problem in circuit design. Let G be a Boolean network and w a wire in G. Wire w' is said to be an alternative wire of w if w'/spl ne/w and G-w+w' has the same functionality as that of G. A wire is said to be fixed if it has no alternative wire. We present a set of exclusive configurations for Boolean networks in which every wire is fixed.
15615911
Time-varying shortest path problems with constraints
The shortest path problem is considered with yet another extension. The transit times b(x,y,u) and the arc costs c(x,y,u) on arc (x,y) vary as a function of the departure time u at the beginning vertex of the arc. The problem considered is to find the shortest path between a pair of nodes such that the total traverse time is lesser than some specified value T. Waiting times at nodes are considered as decision variables in this paper as well. Three variations of the problem are analyzed in which the waiting times are allowed to be arbitrary, the waiting times are zero and the waiting time has an upper bound at each vertex. Algorithms are also discussed to solve the problem. Some of the applications of the problem are encountered in communication networks and freight delivery problems. Suppose that some freight is to be sent from one city to another in a network before a deadline T. Different types of freight services with different costs and transit times are available between the two cities. An optimal solution would have to specify the route as well as the waiting times of the freight at each city so that the overall cost is minimum. A dynamic programming approach is used to compute the shortest path from the origin node to the destination node. Three cases are considered for the waiting times and an algorithm is suggested for each of those cases. This problem is obviously an NP-Complete problem as it is more difficult to solve than a problem with constant transit times and arc costs such as the previous problem which is NP-Complete. Some definitions: Waiting time w(x i) at a vertex x i is a nonnegative integer with an upper bound U x >= 0. Let P be a path from vertex x 1 to x r. The departure time T(x i) at a vertex x i can be expressed as below: T(x 1) = w(x 1) The departure time for all other vertices on the path can be expressed recursively as : The time of path P is defined as T(x r) where x r is the final node on the path..
38611039
Vertex Ranking of Asteroidal Triple-Free Graphs
We present an efficient algorithm for computing the vertex ranking number of an asteroidal triple-free graph. Its running time is bounded by a polynomial in the number of vertices and the number of minimal separators of the input graph.
46500499
Minimum Fill-in on Circle and Circular-Arc Graphs
We present two algorithms solving the minimum fill-in problem on circle graphs and on circular-arc graphs in timeO(n3).
6074974
Vertex Ranking of Asteroidal Triple-Free Graphs
We present an efficient algorithm for computing the vertex ranking number of an asteroidal triple-free graph. Its running time is bounded by a polynomial in the number of vertices and the number of minimal separators of the input graph.
43443657
A note on visibility graphs
Abstract Given a set S = {s1, s2,…, sn} of vertical line segments, s1, sj see each other if there is a horizontal line segment which intersects them, but does not intersect any other line segment between them. A visibility graph G of vertices {v1, v2,…, vn} is put into a one-to-one correspondence with S, such that si corresponds to v1, and edge {vi, vj} exists in G iff si, sj see each other. We prove that any visibility graph G is ipo-triangular, that is, it can be transformed into a planar multigraph with all triangular finite faces, by successive duplications of existing edges of G. Conversely we prove that any ipo-triangular graph is a visibility graph for some set S.
8508688
New algorithms for the rectilinear Steiner tree problem
An approach to constructing the rectilinear Steiner tree (RST) of a given set of points in the plane, starting from a minimum spanning tree (MST), is discussed. The main idea in this approach is to find layouts for the edges of the MST that maximize the overlaps between the layouts, thus minimizing the cost (i.e. wire length) of the resulting rectilinear Steiner tree. Two algorithms for constructing rectilinear Steiner trees from MSTs, which are optimal under the conditions that the layout of each edge of the MST is an L shape or any staircase, respectively, are described. The first algorithm has linear time complexity and the second algorithm has a higher polynomial time complexity. Steiner trees produced by the second algorithm have a property called stability, which allows the rerouting of any segment of the tree, while maintaining the cost of the tree, and without causing overlaps with the rest of the tree. Stability is a desirable property in VLSI global routing applications. >
12009161
Dynamic Placement of Records in Linear Storage
This paper considers allocation of space in a hnear storage medium when space must be allocated dynamically as customers arrive A heuristic is proposed for this problem and for a simple model of the resultmg reference sequence, we show that the average distance between consecutive references is asymptotically 7n/30, where n is the size of the storage For optimal static placement where one waits for all arrivals before any space allocation, the average distance is shown to be asymptotically 7n/30 For random placement, the average distance is asymptotically n/3 Thus, the heuristic is asymptotically optimal in a strong sense For reasonable values of n, we demonstrate that the heuristic is nearly as good as optimal static placement and much better than random placement
47450428
An Algorithm to Compact a VLSI Symbolic Layout with Mixed Constraints
A popular algorithm to compact VLSI symbolic layout is to use a graph algorithm similar to finding the "longest path" in a network. The algorithm assumes that the spacing constraints on the mask elements are of the lower bound type. However, to enable the user to have close control over the compaction result, a desired symbolic layout system should allow the user to add either the equality or the upper bound constraints on selected pairs of mask elements as well. This paper proposes an algorithm which uses a graph-theoretic approach to solve efficiently the compaction problem with mixed constraints.
7582792
Relative contributions of desolvation, inter- and intramolecular interactions to binding affinity in protein kinase systems
In several previous studies, we performed sensitivity analysis to gauge the relative importance of different atomic partial charges in determining protein-ligand binding. In this work, we gain further insights by decomposing these results into three contributions: desolvation, intramolecular interactions, and intermolecular interactions, again based on a Poisson continuum electrostatics model. Three protein kinase-inhibitor systems have been analyzed: CDK2-deschloroflavopiridol, PKA-PKI, and LCK-PP2. Although our results point out the importance of specific intermolecular interactions to the binding affinity, they also reveal the remarkable contributions from the solvent-mediated intramolecular interactions in some cases. Thus, it is necessary to look beyond analyzing protein-ligand interactions to understand protein-ligand recognition or to gain insights into designing ligands and proteins. In analyzing the contributions of the three components to the overall binding free energy, the PKA-PKI system with a much larger ligand was found to behave differently from the other two systems with smaller ligands. In the former case, the intermolecular interactions are very favorable, and together with the favorable solvent-mediated intramolecular interactions, they overcome the large desolvation penalties to give a favorable electrostatics contribution to the overall binding affinity. On the other hand, the other two systems with smaller ligands only present modest intermolecular interactions and they are not or are only barely sufficient to overcome the desolvation penalty even with the aid of the favorable intramolecular contributions. As a result, the binding affinity of these two systems do not or only barely benefit from electrostatics contributions.
10692185
Optimal and Near-Optimal Scheduling Algorithms for Batched Processing in Linear Storage
In this paper, we consider the accessing of batched requests in a linear storage medium. The batch size is assumed fixed and the access probabilities of individual records known. For a given arrangement of records in the storage, we consider the problem of read/write head scheduling to minimize the expected access time for a batch measured in terms of the distance traveled by the head. In the first part of the paper, several simple algorithms are proposed, analyzed and compared. The effect of different record arrangements is also discussed. In the second part of the paper, a family of algorithms called B-optimal rules are described. When B is $\infty $, an $\infty $-optimal rule is indeed optimal in the sense of minimizing expected distance traveled by the head per batch when accessing an arbitrarily large number of batches. A procedure to calculate an $\infty $-optimal rule for any given record arrangement is described, which is based on the idea of “discrete dynamic programming”.