Cache-Oblivious Planar Shortest Paths

2005 ◽  
pp. 563-575 ◽  
Author(s):  
Hema Jampala ◽  
Norbert Zeh
Keyword(s):  
Shortest Paths ◽  
Cache Oblivious

scholarly journals Cache-Oblivious Data Structures and Algorithms for Undirected Breadth-First Search and Shortest Paths

2004 ◽  
Vol 11 (2) ◽  
Author(s):  
Gerth Stølting Brodal ◽  
Rolf Fagerberg ◽  
Ulrich Meyer ◽  
Norbert Zeh
Keyword(s):  
Data Structures ◽  
Shortest Paths ◽  
Block Size ◽  
Priority Queue ◽  
Breadth First Search ◽  
Undirected Graphs ◽  
Performance Gap ◽  
Negative Edge ◽  
Data Structures And Algorithms ◽  
Cache Oblivious

We present improved cache-oblivious data structures and algorithms for breadth-first search (BFS) on undirected graphs and the single-source shortest path (SSSP) problem on undirected graphs with non-negative edge weights. For the SSSP problem, our result closes the performance gap between the currently best <em>cache-aware</em> algorithm and the <em>cache-oblivious</em> counterpart. Our cache-oblivious SSSP-algorithm takes nearly full advantage of block transfers for <em>dense</em> graphs. The algorithm relies on a new data structure, called <em>bucket heap</em>, which is the first cache-oblivious priority queue to efficiently support a weak D<small>ECREASE</small>K<small>EY</small> operation. For the BFS problem, we reduce the number of I/Os for <em>sparse</em> graphs by a factor of nearly sqrt{B}, where B is the cache-block size, nearly closing the performance gap between the currently best <em>cache-aware</em> and <em>cache-oblivious</em> algorithms.

eMap: A Web Application for Identifying and Visualizing Electron or Hole Hopping Pathways in Proteins

2019 ◽  
Author(s):  
Ruslan N. Tazhigulov ◽  
James R. Gayvert ◽  
Melissa Wei ◽  
Ksenia B. Bravaya
Keyword(s):  
Web Application ◽  
Shortest Paths ◽  
Coarse Grained ◽  
Decay Parameter ◽  
Electron Hole ◽  
Web Based ◽  
Aromatic Amino Acid Residue ◽  
Pathways Model ◽  
Visualization Tools ◽  
Effective Decay

<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>

Computer algorithms

2018 ◽  
Author(s):  
Mark Newman
Keyword(s):  
Data Structures ◽  
Analysis Of Algorithms ◽  
Shortest Paths ◽  
Minimum Cut ◽  
Network Data ◽  
Computer Algorithms ◽  
Breadth First Search ◽  
Augmenting Path ◽  
Basic Concepts ◽  
Maximum Flows

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.

scholarly journals Lower bounds for computing geometric spanners and approximate shortest paths

2001 ◽  
Vol 110 (2-3) ◽  
pp. 151-167 ◽  
Author(s):  
Danny Z. Chen ◽  
Gautam Das ◽  
Michiel Smid
Keyword(s):  
Lower Bounds ◽  
Shortest Paths ◽  
Geometric Spanners

Shortest Paths on Cubes

2021 ◽  
Vol 52 (2) ◽  
pp. 121-132
Author(s):  
Richard Goldstone ◽  
Rachel Roca ◽  
Robert Suzzi Valli
Keyword(s):  
Shortest Paths
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