Complexity of Interlocking Polyominoes

Polyominoes are a subset of polygons which can be constructed from integer-length squares fused at their edges. A system of polygons P is interlocked if no subset of the polygons in P can be removed arbitrarily far away from the rest. It is already known that polyominoes with four or fewer squares cannot interlock. It is also known that determining the interlockedness of polyominoes with an arbitrary number of squares is PSPACE hard. Here, we prove that a system of polyominoes with five or fewer squares cannot interlock, and that determining interlockedness of a system of polyominoes including hexominoes (polyominoes with six squares) or larger polyominoes is PSPACE hard.Comment: 18 pages, 15 figure

Configurations of Rank-40r Extremal Even Unimodular Lattices (r=1,2,3)

We show that if L is an extremal even unimodular lattice of rank 40r with r=1,2,3 then L is generated by its vectors of norms 4r and 4r+2. Our result is an extension of Ozeki's result for the case r=1.Comment: 5 pages. To appear, Journal de Theorie des Nombres de Bordeau

Flat Foldings of Plane Graphs with Prescribed Angles and Edge Lengths

When can a plane graph with prescribed edge lengths and prescribed angles (from among $\{0,180^\circ, 360^\circ$\}) be folded flat to lie in an infinitesimally thin line, without crossings? This problem generalizes the classic theory of single-vertex flat origami with prescribed mountain-valley assignment, which corresponds to the case of a cycle graph. We characterize such flat-foldable plane graphs by two obviously necessary but also sufficient conditions, proving a conjecture made in 2001: the angles at each vertex should sum to $360^\circ$, and every face of the graph must itself be flat foldable. This characterization leads to a linear-time algorithm for testing flat foldability of plane graphs with prescribed edge lengths and angles, and a polynomial-time algorithm for counting the number of distinct folded states.Comment: 21 pages, 10 figure

Development of prokaryotic cell-free systems for synthetic biology

Prokaryotic cell-free systems are currently heavily used for the production of protein that can be otherwise challenging to produce in cells. However, historically cell-free systems were used to explore natural phenomena before the advent of genetic modification and transformation technology. Recently, synthetic biology has seen a resurgence of this historical use of cell-free systems as a prototyping tool of synthetic and natural genetic circuits. For these cell-free systems to be effective prototyping tools, an understanding of cell-free system mechanics must be established that is not purely protein-expression driven. Here we discuss the development of E. coli-based cell-free systems, with an emphasis on documenting published extract and energy preparation methods into a uniform format. We also discuss additional considerations when applying cell-free systems to synthetic biology

Conflict-Free Coloring of Planar Graphs

A conflict-free k-coloring of a graph assigns one of k different colors to some of the vertices such that, for every vertex v, there is a color that is assigned to exactly one vertex among v and v's neighbors. Such colorings have applications in wireless networking, robotics, and geometry, and are well-studied in graph theory. Here we study the natural problem of the conflict-free chromatic number chi_CF(G) (the smallest k for which conflict-free k-colorings exist). We provide results both for closed neighborhoods N[v], for which a vertex v is a member of its neighborhood, and for open neighborhoods N(v), for which vertex v is not a member of its neighborhood. For closed neighborhoods, we prove the conflict-free variant of the famous Hadwiger Conjecture: If an arbitrary graph G does not contain K_{k+1} as a minor, then chi_CF(G) <= k. For planar graphs, we obtain a tight worst-case bound: three colors are sometimes necessary and always sufficient. We also give a complete characterization of the computational complexity of conflict-free coloring. Deciding whether chi_CF(G)<= 1 is NP-complete for planar graphs G, but polynomial for outerplanar graphs. Furthermore, deciding whether chi_CF(G)<= 2 is NP-complete for planar graphs G, but always true for outerplanar graphs. For the bicriteria problem of minimizing the number of colored vertices subject to a given bound k on the number of colors, we give a full algorithmic characterization in terms of complexity and approximation for outerplanar and planar graphs. For open neighborhoods, we show that every planar bipartite graph has a conflict-free coloring with at most four colors; on the other hand, we prove that for k in {1,2,3}, it is NP-complete to decide whether a planar bipartite graph has a conflict-free k-coloring. Moreover, we establish that any general} planar graph has a conflict-free coloring with at most eight colors.Comment: 30 pages, 17 figures; full version (to appear in SIAM Journal on Discrete Mathematics) of extended abstract that appears in Proceeedings of the Twenty-Eighth Annual ACM-SIAM Symposium on Discrete Algorithms (SODA 2017), pp. 1951-196

Who witnesses The Witness? Finding witnesses in The Witness is hard and sometimes impossible

We analyze the computational complexity of the many types of pencil-and-paper-style puzzles featured in the 2016 puzzle video game The Witness. In all puzzles, the goal is to draw a simple path in a rectangular grid graph from a start vertex to a destination vertex. The different puzzle types place different constraints on the path: preventing some edges from being visited (broken edges); forcing some edges or vertices to be visited (hexagons); forcing some cells to have certain numbers of incident path edges (triangles); or forcing the regions formed by the path to be partially monochromatic (squares), have exactly two special cells (stars), or be singly covered by given shapes (polyominoes) and/or negatively counting shapes (antipolyominoes). We show that any one of these clue types (except the first) is enough to make path finding NP-complete ("witnesses exist but are hard to find"), even for rectangular boards. Furthermore, we show that a final clue type (antibody), which necessarily "cancels" the effect of another clue in the same region, makes path finding $\Sigma_2$-complete ("witnesses do not exist"), even with a single antibody (combined with many anti/polyominoes), and the problem gets no harder with many antibodies. On the positive side, we give a polynomial-time algorithm for monomino clues, by reducing to hexagon clues on the boundary of the puzzle, even in the presence of broken edges, and solving "subset Hamiltonian path" for terminals on the boundary of an embedded planar graph in polynomial time.Comment: 72 pages, 59 figures. Revised proof of Lemma 3.5. A short version of this paper appeared at the 9th International Conference on Fun with Algorithms (FUN 2018

Rigid Origami Vertices: Conditions and Forcing Sets

We develop an intrinsic necessary and sufficient condition for single-vertex origami crease patterns to be able to fold rigidly. We classify such patterns in the case where the creases are pre-assigned to be mountains and valleys as well as in the unassigned case. We also illustrate the utility of this result by applying it to the new concept of minimal forcing sets for rigid origami models, which are the smallest collection of creases that, when folded, will force all the other creases to fold in a prescribed way