Dotplot: A Program for Exploring Self-Similarity in Millions of Lines of Text and Code

Abstract

An interactive program, dotplot, has been developed for browsing millions of lines of text and source code, using an approach borrowed from biology for studying homology (self-similarity) in DNA sequences. With conventional browsing tools such as a screen editor, it is difficult to identify structures that are too big to fit on the screen. In contrast, with dotplots we find that many of these structures show up as diagonals, squares, textures, and other visually recognizable features, as will be illustrated in examples selected from biology and two new application domains, text (AP news, Canadian Hansards) and source code (5ESS®). In an attempt to isolate the mechanisms that produce these features, we have synthesized similar features in dotplots of artificial sequences. We also introduce an approximation that makes the calculation of dotplots practical for use in an interactive browser.     

The stochastic interdiction median problem with disruption intensity levels

In this paper we introduce a stochastic interdiction problem for median systems in which the operational state of the system??s disrupted elements in the aftermath of the disruption is uncertain as it is based on the intensity of the disruption. We assume that a disruption disables a facility with a given probability and this probability depends on the intensity of the disruption. The objective of this problem is to identify which disruption scenario entails a maximum overall traveling distance in serving all customers. We show that the initial two stage stochastic formulation can be reformulated into a deterministic counterpart whose size is polynomial in the number of facilities and intensity levels. Then, our ensuing efforts to solve the problem efficiently focus on studying alternative deterministic formulations that allow the solution of realistic size instances of the model. We observe that the most efficient of the deterministic formulations provide great scalability with respect to variations in the input parameters and size of the instances solved. Finally, we analyze the robustness of the optimal solutions due to misestimations in the probability functions that relate disruption intensity levels with the probabilities of facility survivability.     

Applying simulated annealing to location-planning models

Simulated annealing is a computational approach that simulates an annealing schedule used in producing glass and metals. Originally developed by Metropolis et al. in 1953, it has since been applied to a number of integer programming problems, including the p-median location-allocation problem. However, previously reported results by Golden and Skiscim in 1986 were less than encouraging. This article addresses the design of a simulated-annealing approach for the p-median and maximal covering location problems. This design has produced very good solutions in modest amounts of computer time. Comparisons with an interchange heuristic demonstrate that simulated annealing has potential as a solution technique for solving location-planning problems and further research should be encouraged.     

The fate of the hydroxyalkoxy radical in the OH‐initiated oxidation of isoprene

Rate constants for several intermediate steps in the OH‐initiated oxidation of isoprene were determined using laser‐photolysis/laser‐induced fluorescence of OH radicals at total pressures between 3 and 4 Torr at 295 K. The rate constant for decomposition of the hydroxyalkoxy radical was determined to be (3.0 ± 0.5) × 10⁴ s^?1 in this pressure range, which is in fair agreement with previous work. The presence of a prompt alkoxy decomposition pathway was also investigated and found to contribute less than 10% to the total hydroxyalkoxy radical decomposition. The rate constant for the reaction of the hydroxyperoxy radical with NO was determined to be (2.5 ± 0.5) × 10^?11 cm³ molecule^?1 s^?1, which is moderately higher than previously reported. © 2002 Wiley Periodicals, Inc. Int J Chem Kinet 34: 255–261, 2002     

The Preparation of 1H-Pyrazole-5-propanoic and 1H-Pyrazole-5-butanoic Acids from Dilithiated C(α),N-Carboalkoxyhydrazones and Succinic or Glutaric Acid Anhydrides

C(α),N-Carboalkoxyhydrazones were dilithiated with excess lithium diisopropylamide, condensed with succinic or glutaric acid anhydride, and cyclized to 1H-pyrazole-5-propanoic or 1H-pyrazole-5-butanoic acids.     

Second Dissociation Constant of Bis-[(2-hydroxyethyl)amino]acetic Acid (BICINE) and pH of Its Buffer Solutions from 5 to 55 °C

The values of the second dissociation constant, K ₂, and related thermodynamic quantities of the ampholyte bis[(2-hydroxyethyl)amino]acetic acid (BICINE) have been determined at temperatures from 5 to 55 ^∘C. The pH values of six equimolal buffer solutions, and four buffer solutions having ionic strengths (I = 0.16 mol⋅kg⁻¹) similar to those in blood plasma, have been evaluated at 12 temperatures from 5 to 55 ^∘C using the Bates–Guggenheim convention. The liquid junction potentials (E _j ) between the buffer solutions of BICINE and saturated KCl solution of the calomel electrode at 25 and 37 ^∘C have been estimated by measurement with a flowing junction cell. These values of E _j have been used to ascertain the operational pH values at 25 and 37 ^∘C. The pK ₂ values at 25 and 37 ^∘C are 8.333 and 8.156, respectively. The thermodynamic quantities associated with the second acid dissociation have been calculated from the values of pK ₂ as a function of temperature. The zwitterionic buffer BICINE was shown to be useful as a pH standard in the region close to that of blood serum.     

An examination of the substitution chemistry of di-n-hexyldichlorosilane

Various nucleophiles were reacted with the substrate di-n-hexyldichlorosilane as model reactions for the substitution of two geminal Si---Cl bonds on polymer backbone repeat units. The reactants examined were chosen on the basis of steric bulk, electronic factors, and resulting stability of the product. Linear and branched alcohol nucleophiles used in conjunction with an amine proton acceptor produced disubstituted products in moderate yields, whereas bulkier reagents substituted only one silicon---chlorine bond. Due to their vastly increased nucleophilicity, alkyllithium reagents were found to have increased activity and were found to produce very high yields.