A divide and conquer approach to shortest paths in planar layered digraphs

Author(s):  
S. Sairam ◽  
R. Tamassia ◽  
J.S. Vitter
2019 ◽  
Author(s):  
Ruslan N. Tazhigulov ◽  
James R. Gayvert ◽  
Melissa Wei ◽  
Ksenia B. Bravaya

<p>eMap is a web-based platform for identifying and visualizing electron or hole transfer pathways in proteins based on their crystal structures. The underlying model can be viewed as a coarse-grained version of the Pathways model, where each tunneling step between hopping sites represented by electron transfer active (ETA) moieties is described with one effective decay parameter that describes protein-mediated tunneling. ETA moieties include aromatic amino acid residue side chains and aromatic fragments of cofactors that are automatically detected, and, in addition, electron/hole residing sites that can be specified by the users. The software searches for the shortest paths connecting the user-specified electron/hole source to either all surface-exposed ETA residues or to the user-specified target. The identified pathways are ranked based on their length. The pathways are visualized in 2D as a graph, in which each node represents an ETA site, and in 3D using available protein visualization tools. Here, we present the capability and user interface of eMap 1.0, which is available at https://emap.bu.edu.</p>


2011 ◽  
Vol 36 (12) ◽  
pp. 1697-1705 ◽  
Author(s):  
Rong-Chuan SUN ◽  
Shu-Gen MA ◽  
Bin LI ◽  
Ming-Hui WANG ◽  
Yue-Chao WANG
Keyword(s):  

2014 ◽  
Vol 12 (2) ◽  
pp. 124-130 ◽  
Author(s):  
Cosme Santiesteban-Toca ◽  
Gerardo Casanola-Martin ◽  
Jesus Aguilar-Ruiz

Author(s):  
Mark Newman

This chapter introduces some of the fundamental concepts of numerical network calculations. The chapter starts with a discussion of basic concepts of computational complexity and data structures for storing network data, then progresses to the description and analysis of algorithms for a range of network calculations: breadth-first search and its use for calculating shortest paths, shortest distances, components, closeness, and betweenness; Dijkstra's algorithm for shortest paths and distances on weighted networks; and the augmenting path algorithm for calculating maximum flows, minimum cut sets, and independent paths in networks.


Author(s):  
Anany Levitin ◽  
Maria Levitin

While many think of algorithms as specific to computer science, at its core algorithmic thinking is defined by the use of analytical logic to solve problems. This logic extends far beyond the realm of computer science and into the wide and entertaining world of puzzles. In Algorithmic Puzzles, Anany and Maria Levitin use many classic brainteasers as well as newer examples from job interviews with major corporations to show readers how to apply analytical thinking to solve puzzles requiring well-defined procedures. The book's unique collection of puzzles is supplemented with carefully developed tutorials on algorithm design strategies and analysis techniques intended to walk the reader step-by-step through the various approaches to algorithmic problem solving. Mastery of these strategies--exhaustive search, backtracking, and divide-and-conquer, among others--will aid the reader in solving not only the puzzles contained in this book, but also others encountered in interviews, puzzle collections, and throughout everyday life. Each of the 150 puzzles contains hints and solutions, along with commentary on the puzzle's origins and solution methods. The only book of its kind, Algorithmic Puzzles houses puzzles for all skill levels. Readers with only middle school mathematics will develop their algorithmic problem-solving skills through puzzles at the elementary level, while seasoned puzzle solvers will enjoy the challenge of thinking through more difficult puzzles.


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