NodeTrix Planarity Testing with Small Clusters

We study the NodeTrix planarity testing problem for flat clustered graphs when the maximum size of each cluster is bounded by a constant $k$. We consider both the case when the sides of the matrices to which the edges are incident are fixed and the case when they can be chosen arbitrarily. We show that NodeTrix planarity testing with fixed sides can be solved in $O(k^{3k+\frac{3}{2}} \cdot n)$ time for every flat clustered graph that can be reduced to a partial 2-tree by collapsing its clusters into single vertices. In the general case, NodeTrix planarity testing with fixed sides can be solved in $O(n)$ time for $k = 2$, but it is NP-complete for any $k > 2$. NodeTrix planarity testing remains NP-complete also in the free sides model when $k > 4$.Comment: Appears in the Proceedings of the 25th International Symposium on Graph Drawing and Network Visualization (GD 2017

On building 4-critical plane and projective plane multiwheels from odd wheels

We build unbounded classes of plane and projective plane multiwheels that are 4-critical that are received summing odd wheels as edge sums modulo two. These classes can be considered as ascending from single common graph that can be received as edge sum modulo two of the octahedron graph O and the minimal wheel W3. All graphs of these classes belong to 2n-2-edges-class of graphs, among which are those that quadrangulate projective plane, i.e., graphs from Gr\"otzsch class, received applying Mycielski's Construction to odd cycle.Comment: 10 page

Tangle analysis of difference topology experiments: applications to a Mu protein-DNA complex

We develop topological methods for analyzing difference topology experiments involving 3-string tangles. Difference topology is a novel technique used to unveil the structure of stable protein-DNA complexes involving two or more DNA segments. We analyze such experiments for the Mu protein-DNA complex. We characterize the solutions to the corresponding tangle equations by certain knotted graphs. By investigating planarity conditions on these graphs we show that there is a unique biologically relevant solution. That is, we show there is a unique rational tangle solution, which is also the unique solution with small crossing number.Comment: 60 pages, 74 figure

A tight Erd\H{o}s-P\'osa function for wheel minors

Let $W_t$ denote the wheel on $t+1$ vertices. We prove that for every integer $t \geq 3$ there is a constant $c=c(t)$ such that for every integer $k\geq 1$ and every graph $G$, either $G$ has $k$ vertex-disjoint subgraphs each containing $W_t$ as minor, or there is a subset $X$ of at most $c k \log k$ vertices such that $G-X$ has no $W_t$ minor. This is best possible, up to the value of $c$. We conjecture that the result remains true more generally if we replace $W_t$ with any fixed planar graph $H$.Comment: 15 pages, 1 figur