An Improved Bound for First-Fit on Posets Without Two Long Incomparable Chains

It is known that the First-Fit algorithm for partitioning a poset P into chains uses relatively few chains when P does not have two incomparable chains each of size k. In particular, if P has width w then Bosek, Krawczyk, and Szczypka (SIAM J. Discrete Math., 23(4):1992--1999, 2010) proved an upper bound of ckw^{2} on the number of chains used by First-Fit for some constant c, while Joret and Milans (Order, 28(3):455--464, 2011) gave one of ck^{2}w. In this paper we prove an upper bound of the form ckw. This is best possible up to the value of c.Comment: v3: referees' comments incorporate

Threshold-coloring and unit-cube contact representation of planar graphs

In this paper we study threshold-coloring of graphs, where the vertex colors represented by integers are used to describe any spanning subgraph of the given graph as follows. A pair of vertices with a small difference in their colors implies that the edge between them is present, while a pair of vertices with a big color difference implies that the edge is absent. Not all planar graphs are threshold-colorable, but several subclasses, such as trees, some planar grids, and planar graphs with no short cycles can always be threshold-colored. Using these results we obtain unit-cube contact representation of several subclasses of planar graphs. Variants of the threshold-coloring problem are related to well-known graph coloring and other graph-theoretic problems. Using these relations we show the NP-completeness for two of these variants, and describe a polynomial-time algorithm for another. © 2015 Elsevier B.V

Threshold-coloring and unit-cube contact representation of graphs

We study threshold coloring of graphs where the vertex colors, represented by integers, describe any spanning subgraph of the given graph as follows. Pairs of vertices with near colors imply the edge between them is present and pairs of vertices with far colors imply the edge is absent. Not all planar graphs are threshold-colorable, but several subclasses, such as trees, some planar grids, and planar graphs with no short cycles can always be threshold-colored. Using these results we obtain unit-cube contact representation of several subclasses of planar graphs. We show the NP-completeness for two variants of the threshold coloring problem and describe a polynomial-time algorithm for another. © 2013 Springer-Verlag

Design of coiled-coil protein-origami cages that self-assemble in vitro and in vivo

Polypeptides and polynucleotides are natural programmable biopolymers that can self-assemble into complex tertiary structures. We describe a system analogous to designed DNA nanostructures in which protein coiled-coil (CC) dimers serve as building blocks for modular de novo design of polyhedral protein cages that efficiently self-assemble in vitro and in vivo. We produced and characterized gt 20 single-chain protein cages in three shapes-tetrahedron, four-sided pyramid, and triangular prism-with the largest containing gt 700 amino-acid residues and measuring 11 nm in diameter. Their stability and folding kinetics were similar to those of natural proteins. Solution small-angle X-ray scattering (SAXS), electron microscopy (EM), and biophysical analysis confirmed agreement of the expressed structures with the designs. We also demonstrated self-assembly of a tetrahedral structure in bacteria, mammalian cells, and mice without evidence of inflammation. A semi-automated computational design platform and a toolbox of CC building modules are provided to enable the design of protein cages in any polyhedral shape.Supplementary material: [http://cherry.chem.bg.ac.rs/handle/123456789/3212