ترغب بنشر مسار تعليمي؟ اضغط هنا

Edge-outer graph embedding and the complexity of the DNA reporter strand problem

64   0   0.0 ( 0 )
 نشر من قبل Joanna Ellis-Monaghan
 تاريخ النشر 2017
  مجال البحث
والبحث باللغة English




اسأل ChatGPT حول البحث

In 2009, Jonoska, Seeman and Wu showed that every graph admits a route for a DNA reporter strand, that is, a closed walk covering every edge either once or twice, in opposite directions if twice, and passing through each vertex in a particular way. This corresponds to showing that every graph has an emph{edge-outer embedding}, that is, an orientable embedding with some face that is incident with every edge. In the motivating application, the objective is such a closed walk of minimum length. Here we give a short algorithmic proof of the original existence result, and also prove that finding a shortest length solution is NP-hard, even for $3$-connected cubic ($3$-regular) planar graphs. Independent of the motivating application, this problem opens a new direction in the study of graph embeddings, and we suggest new problems emerging from it.

قيم البحث

اقرأ أيضاً

Building a structure using self-assembly of DNA molecules by origami folding requires finding a route for the scaffolding strand through the desired structure. When the target structure is a 1-complex (or the geometric realization of a graph), an opt imal route corresponds to an Eulerian circuit through the graph with minimum turning cost. By showing that it leads to a solution to the 3-SAT problem, we prove that the general problem of finding an optimal route for a scaffolding strand for such structures is NP-hard. We then show that the problem may readily be transformed into a Traveling Salesman Problem (TSP), so that machinery that has been developed for the TSP may be applied to find optimal routes for the scaffolding strand in a DNA origami self-assembly process. We give results for a few special cases, showing for example that the problem remains intractable for graphs with maximum degree 8, but is polynomial time for 4-regular plane graphs if the circuit is restricted to following faces. We conclude with some implications of these results for related problems, such as biomolecular computing and mill routing problems.
We propose a class of two person perfect information games based on weighted graphs. One of these games can be described in terms of a round pizza which is cut radially into pieces of varying size. The two players alternately take pieces subject to t he following rule: Once the first piece has been chosen, all subsequent selections must be adjacent to the hole left by the previously taken pieces. Each player tries to get as much pizza as possible. The original pizza problem was to settle the conjecture that Player One can always get at least half of the pizza. The conjecture turned out to be false. Our main result is a complete solution of a somewhat simpler class of games, concatenations of stacks and two-ended stacks, and we provide a linear time algorithm for this. The algorithm and its output can be described without reference to games. It produces a certain kind of partition of a given finite sequence of real numbers. The conditions on the partition involve alternating sums of various segments of the given sequence. We do not know whether these partitions have applications outside of game theory. The algorithm leads to a quadratic time algorithm which gives the value and an optimal initial move for pizza games. We also provide some general theory concerning the semigroup of equivalence classes of graph games.
Let $G$ be a graph such that each edge has its list of available colors, and assume that each list is a subset of the common set consisting of $k$ colors. Suppose that we are given two list edge-colorings $f_0$ and $f_r$ of $G$, and asked whether the re exists a sequence of list edge-colorings of $G$ between $f_0$ and $f_r$ such that each list edge-coloring can be obtained from the previous one by changing a color assignment of exactly one edge. This problem is known to be PSPACE-complete for every integer $k ge 6$ and planar graphs of maximum degree three, but any complexity hardness was unknown for the non-list variant. In this paper, we first improve the known result by proving that, for every integer $k ge 4$, the problem remains PSPACE-complete even if an input graph is planar, bounded bandwidth, and of maximum degree three. We then give the first complexity hardness result for the non-list variant: for every integer $k ge 5$, we prove that the non-list variant is PSPACE-complete even if an input graph is planar, of bandwidth linear in $k$, and of maximum degree $k$.
Let $X=(V,E)$ be a finite simple connected graph with $n$ vertices and $m$ edges. A configuration is an assignment of one of two colors, black or white, to each edge of $X.$ A move applied to a configuration is to select a black edge $epsilonin E$ an d change the colors of all adjacent edges of $epsilon.$ Given an initial configuration and a final configuration, try to find a sequence of moves that transforms the initial configuration into the final configuration. This is the edge-flipping puzzle on $X,$ and it corresponds to a group action. This group is called the edge-flipping group $mathbf{W}_E(X)$ of $X.$ This paper shows that if $X$ has at least three vertices, $mathbf{W}_E(X)$ is isomorphic to a semidirect product of $(mathbb{Z}/2mathbb{Z})^k$ and the symmetric group $S_n$ of degree $n,$ where $k=(n-1)(m-n+1)$ if $n$ is odd, $k=(n-2)(m-n+1)$ if $n$ is even, and $mathbb{Z}$ is the additive group of integers.
We propose novel chemical reaction networks to translate levels of concentration into unique DNA strand species, which we call concentration translators. Our design of the concentration translators is based on combination of two chemical reaction net works, consensus network and conversion network with any number of chemical species. We give geometric analysis of the proposed CRNs from the viewpoint of nonlinear dynamical systems and show that the CRNs can actually operate as translator. Our concentration translators exploit DNA strand displacement (DSD) reaction, which is known for a universal reaction that can implement arbitrary chemical reaction networks. We demonstrate two specific types of concentration translators (translator A and B) with different switching behavior and biochemical cost and compared their characteristics computationally. The proposed concentration translators have an advantage of being able to readout the concentration of targeted nucleic acid strand without any fluorescence-based techniques. These characteristics can be tailored according to requirements from applications, including dynamic range, sensitivity and implementation cost.
التعليقات
جاري جلب التعليقات جاري جلب التعليقات
سجل دخول لتتمكن من متابعة معايير البحث التي قمت باختيارها
mircosoft-partner

هل ترغب بارسال اشعارات عن اخر التحديثات في شمرا-اكاديميا