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].
This research is supported by Louisiana Board of Regents fund under contract number LEQSF(2004-07)-RD-A-35.
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Fu, B., Oprisan, S.A., Xu, L. (2005). Multi-directional Width-Bounded Geometric Separator and Protein Folding. In: Deng, X., Du, DZ. (eds) Algorithms and Computation. ISAAC 2005. Lecture Notes in Computer Science, vol 3827. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11602613_99
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DOI: https://doi.org/10.1007/11602613_99
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