A Planarity Test via Construction Sequences

Optimal linear-time algorithms for testing the planarity of a graph are well-known for over 35 years. However, these algorithms are quite involved and recent publications still try to give simpler linear-time tests. We give a simple reduction from planarity testing to the problem of computing a certain construction of a 3-connected graph. The approach is different from previous planarity tests; as key concept, we maintain a planar embedding that is 3-connected at each point in time. The algorithm runs in linear time and computes a planar embedding if the input graph is planar and a Kuratowski-subdivision otherwise

Planarity of Streamed Graphs

In this paper we introduce a notion of planarity for graphs that are presented in a streaming fashion. A $\textit{streamed graph}$ is a stream of edges $e_1,e_2,...,e_m$ on a vertex set $V$. A streamed graph is $\omega$-$\textit{stream planar}$ with respect to a positive integer window size $\omega$ if there exists a sequence of planar topological drawings $\Gamma_i$ of the graphs $G_i=(V,\{e_j \mid i\leq j < i+\omega\})$ such that the common graph $G^{i}_\cap=G_i\cap G_{i+1}$ is drawn the same in $\Gamma_i$ and in $\Gamma_{i+1}$, for $1\leq i < m-\omega$. The $\textit{Stream Planarity}$ Problem with window size $\omega$ asks whether a given streamed graph is $\omega$-stream planar. We also consider a generalization, where there is an additional $\textit{backbone graph}$ whose edges have to be present during each time step. These problems are related to several well-studied planarity problems. We show that the $\textit{Stream Planarity}$ Problem is NP-complete even when the window size is a constant and that the variant with a backbone graph is NP-complete for all $\omega \ge 2$. On the positive side, we provide $O(n+\omega{}m)$-time algorithms for (i) the case $\omega = 1$ and (ii) all values of $\omega$ provided the backbone graph consists of one $2$-connected component plus isolated vertices and no stream edge connects two isolated vertices. Our results improve on the Hanani-Tutte-style $O((nm)^3)$-time algorithm proposed by Schaefer [GD'14] for $\omega=1$.Comment: 21 pages, 9 figures, extended version of "Planarity of Streamed Graphs" (9th International Conference on Algorithms and Complexity, 2015

Homologous Pairing between Long DNA Double Helices

Molecular recognition between two double stranded (ds) DNA with homologous sequences may not seem compatible with the B-DNA structure because the sequence information is hidden when it is used for joining the two strands. Nevertheless, it has to be invoked to account for various biological data. Using quantum chemistry, molecular mechanics, and hints from recent genetics experiments I show here that direct recognition between homologous dsDNA is possible through formation of short quadruplexes due to direct complementary hydrogen bonding of major groove surfaces in parallel alignment. The constraints imposed by the predicted structures of the recognition units determine the mechanism of complexation between long dsDNA. This mechanism and concomitant predictions agree with available experimental data and shed light upon the sequence effects and the possible involvement of topoisomerase II in the recognition.Comment: 10 pages, 7 figures, Includes Supplemental Material. To appear in Phys. Rev. Let