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 [Formula: see text] points, and G − A has two disconnected subgraphs each with at most [Formula: see text] nodes. This improves the previous upper bound of [Formula: see text]. We also derive a [Formula: see text] lower bound for such a separator in grid graphs.
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