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.
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..
16381803
Upper and lower bounds for graph-diameter problems with application to record allocation
This paper studies three graph problems with parameters n, the number of nodes, e, the number of edges, and k, the diameter of the graph. Given any two of these three parameters, the problem is to construct a directed graph which minimizes or maximizes the third. The first problem has its origin in a recent study of record allocation in a paged computer system. It is shown how to construct graphs that are optimal for all three problems in some cases and are asymptotically optimal for other cases. The solution of the second problem answers a question raised by Berge in “The Theory of Graphs and its Application,” 1962.
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.
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.
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
21236849
Near-Optimal Solutions to a 2-Dimensional Placement Problem
We consider the problem of placing records in a 2-dimensional storage array so that expected distance between consecutive references is minimized. A simple placement heuristic which uses only relative frequency of access for different records is shown to be within an additive constant of optimal when distance is measured by the Euclidean metric. For the rectilinear and maximum metrics, we show that there is no such heuristic. For the special case in which all access probabilities are equal, however, heuristics within an additive constant of optimal do exist, and their implementation requires solution of differential equations for which we give numerical solutions.
7180182
Minimizing mean flow time with error constraint
In a new model of task systems studied by J.W.S. Liu et al. (1987) each task is logically decomposed into two subtasks, mandatory and optional. The authors discuss preemptively scheduling this kind of task system on p>or=1 identical processors so as to minimize the mean flow time. Given a task system and an error threshold K, the goal is to find a preemptive schedule such that each task is executed in the interval of its release time and deadline, the average error is no more than K, and the mean flow time of the schedule is minimized. Such a schedule is called an optimal schedule. It is shown that the problem of finding an optimal schedule is NP-hard for each p>or=1, even if all tasks have the same ready time and deadline. For a single processor, a pseudo-polynomial time algorithm and polynomial time algorithms for various special cases of the problem are given.<<ETX>>