A DNA approach to the Road-Coloring Problem

The Road-Coloring Problem in graph theory can be stated as follows: Is any irreducible aperiodic directed graph with constant outdegree 2 road-colorable? In other words, does such a graph have a synchronizing instruction? That is to say: can we label (or color) the two outgoing edges at each vertex, one with “b” or blue color and the other with “r” or red color, in such a manner that there will be an instruction in the form of a finite sequence in “b”s and “r”s (example: rrbrbbbr) such that this instruction will lead each vertex to the same “target” vertex? This thesis is concerned with writing a DNA algorithm which can be followed in the laboratory to produce an explicit solution of a given Road-Coloring problem. This kind of DNA approach was first introduced by Adleman to find an effective method of finding the solution of a given Hamiltonian Path Problem. The Road-Coloring Problem, though introduced over 30 years ago in 1977 by Adler, Goodwyn, and Weiss was only recently solved by Trahtman. But his solution does not give explicitly the synchronizing instruction

Dagstuhl Reports : Volume 1, Issue 2, February 2011

Online Privacy: Towards Informational Self-Determination on the Internet (Dagstuhl Perspectives Workshop 11061) : Simone Fischer-Hübner, Chris Hoofnagle, Kai Rannenberg, Michael Waidner, Ioannis Krontiris and Michael Marhöfer Self-Repairing Programs (Dagstuhl Seminar 11062) : Mauro Pezzé, Martin C. Rinard, Westley Weimer and Andreas Zeller Theory and Applications of Graph Searching Problems (Dagstuhl Seminar 11071) : Fedor V. Fomin, Pierre Fraigniaud, Stephan Kreutzer and Dimitrios M. Thilikos Combinatorial and Algorithmic Aspects of Sequence Processing (Dagstuhl Seminar 11081) : Maxime Crochemore, Lila Kari, Mehryar Mohri and Dirk Nowotka Packing and Scheduling Algorithms for Information and Communication Services (Dagstuhl Seminar 11091) Klaus Jansen, Claire Mathieu, Hadas Shachnai and Neal E. Youn

The Topology of Scaffold Routings on Non-Spherical Mesh Wireframes

The routing of a DNA-origami scaffold strand is often modelled as an Eulerian circuit of an Eulerian graph in combinatorial models of DNA origami design. The knot type of the scaffold strand dictates the feasibility of an Eulerian circuit to be used as the scaffold route in the design. Motivated by the topology of scaffold routings in 3D DNA origami, we investigate the knottedness of Eulerian circuits on surface-embedded graphs. We show that certain graph embeddings, checkerboard colorable, always admit unknotted Eulerian circuits. On the other hand, we prove that if a graph admits an embedding in a torus that is not checkerboard colorable, then it can be re-embedded so that all its non-intersecting Eulerian circuits are knotted. For surfaces of genus greater than one, we present an infinite family of checkerboard-colorable graph embeddings where there exist knotted Eulerian circuits

09061 Abstracts Collection -- Combinatorial Scientific Computing

From 01.02.2009 to 06.02.2009, the Dagstuhl Seminar 09061 ``Combinatorial Scientific Computing \u27\u27 was held in Schloss Dagstuhl -- Leibniz Center for Informatics. During the seminar, several participants presented their current research, and ongoing work and open problems were discussed. Abstracts of the presentations given during the seminar as well as abstracts of seminar results and ideas are put together in this paper. The first section describes the seminar topics and goals in general. Links to extended abstracts or full papers are provided, if available