Multi-directional width-bounded geometric separator and protein folding

Authors:
Bin Fu;Sorinel A Oprisan;Lizhe Xu
Affiliations:
,Dept. of Computer Science, University of New Orleans, LA;Dept. of Psychology, University of New Orleans, LA;,Dept. of Computer Science, University of New Orleans, LA
Venue:
ISAAC'05 Proceedings of the 16th international conference on Algorithms and Computation
Year:
2005

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Abstract

We introduce the concept of multi-directional width-bounded geometric separator and get improved separator for the grid graph, which improves 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 less than or equal to 1.02074$\sqrt{n}$ points, and G–A has two disconnected subgraphs with less than or equal to ${2 \over 3}n$ nodes on each of them. We also derive 0.7555$\sqrt{n}$ lower bound for such a separator on grid graph. The previous upper bound record for the grid graph $2 \over 3$-separator is 1.129$\sqrt{n}$ [6].