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Multi-Directional Width-Bounded Geometric Separator and Protein Folding

By Bin Fu, Sorinel A. Oprisan and Lizhe Xu

Abstract

We introduce the concept of multi-directional width-bounded geometric separators and obtain an improved separator for grid graphs. This yields an improved exact algorithm for the protein folding problem in the HP-model. For a grid graph G with n grid points P, there exists a separator A ⊆ P such that A has at most 1.02074 √ n points, and G −A has two disconnected subgraphs each with at most 2 n nodes. This improves the previous 3 upper bound of 1.129 √ n 10. We also derive a 0.7555 √ n lower bound for such a separator in grid graphs

Topics: Geometric Separator, Grid Graph, Protein Folding
Year: 2007
OAI identifier: oai:CiteSeerX.psu:10.1.1.188.8103
Provided by: CiteSeerX
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