Oswin Aichholzer — Page 5

arXiv2002

Long Proteins with Unique Optimal Foldings in the H-P Model

It is widely accepted that (1) the natural or folded state of proteins is a global energy minimum, and (2) in most cases proteins fold to a unique state determined by their amino acid sequence. The H-P (hydrophobic-hydrophilic) model is a simple combinatorial model designed to answer qualitative questions about the protein folding process. In this paper we consider a problem suggested by Brian Hayes in 1998: what proteins in the two-dimensional H-P model have unique optimal (minimum energy) foldings? In particular, we prove that there are closed chains of monomers (amino acids) with this property for all (even) lengths; and that there are open monomer chains with this property for all lengths divisible by four.

cs.CG↗

arXiv2000

Flipturning polygons

A flipturn is an operation that transforms a nonconvex simple polygon into another simple polygon, by rotating a concavity 180 degrees around the midpoint of its bounding convex hull edge. Joss and Shannon proved in 1973 that a sequence of flipturns eventually transforms any simple polygon into a convex polygon. This paper describes several new results about such flipturn sequences. We show that any orthogonal polygon is convexified after at most n-5 arbitrary flipturns, or at most 5(n-4)/6 well-chosen flipturns, improving the previously best upper bound of (n-1)!/2. We also show that any simple polygon can be convexified by at most n^2-4n+1 flipturns, generalizing earlier results of Ahn et al. These bounds depend critically on how degenerate cases are handled; we carefully explore several possibilities. We describe how to maintain both a simple polygon and its convex hull in O(log^4 n) time per flipturn, using a data structure of size O(n). We show that although flipturn sequences for the same polygon can have very different lengths, the shape and position of the final convex polygon is the same for all sequences and can be computed in O(n log n) time. Finally, we demonstrate that finding the longest convexifying flipturn sequence of a simple polygon is NP-hard.

cs.CG↗