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Author: | Mohammed, Abdulmelik |
Title: | Combinatorial algorithms for the design of nanoscale systems |
Publication type: | Master's thesis |
Publication year: | 2014 |
Pages: | 72 Language: eng |
Department/School: | Perustieteiden korkeakoulu |
Main subject: | Tietojenkäsittelyteoria (T-79) |
Supervisor: | Orponen, Pekka |
Instructor: | Czeizler, Eugen |
Electronic version URL: | http://urn.fi/URN:NBN:fi:aalto-201507013655 |
OEVS: | Electronic archive copy is available via Aalto Thesis Database.
Instructions Reading digital theses in the closed network of the Aalto University Harald Herlin Learning CentreIn the closed network of Learning Centre you can read digital and digitized theses not available in the open network. The Learning Centre contact details and opening hours: https://learningcentre.aalto.fi/en/harald-herlin-learning-centre/ You can read theses on the Learning Centre customer computers, which are available on all floors.
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Location: | P1 Ark Aalto | Archive |
Keywords: | DNA nanotechnology DNA origami polyhedra graphs combinatorial algorithms |
Abstract (eng): | Over the past 30 years, DNA, with its exquisitely specific Watson-Crick base pairing rules, has found a novel use as a nanoscale construction material in DNA nanotechnology. DNA origami is a popular recent technique in DNA nanotechnology for the design and synthesis of DNA nanoscale shapes and patterns. DNA origami operates by the folding of a single long strand of DNA called a scaffold with the help of numerous shorter strands of DNA called staples. Recently, DNA origami design for polyhedral beam-frameworks has been proposed where a scaffold strand is conceptually routed over the beams of a polyhedron so that complementary strands potentially fold the scaffold to the framework in a solution. In this work, we modelled the problem of finding a scaffold routing path for polyhedral frameworks in graph-theoretic terms whereby the routing path was found to coincide with a specific type of Eulerian trail, called an A-trail, on the polyhedral skeleton. We studied the complexity of deciding whether an A-trail exists with an emphasis on rigid triangular frameworks or equivalently on plane triangulations. While the decision problem was found to be NP-complete in general, we learned that Eulerian triangulations always have A-trails if a long standing conjecture by Barnette on the Hamiltonicity of bipartite cubic polyhedral graphs holds. Given the general NP-completeness result, we developed a backtracking search algorithm for finding A-trails. To improve the backtrack search; we introduced an enumeration heuristic, tuned in particular to Eulerian triangulations, to schedule the nodes in the search tree. The algorithm, guided by the heuristic, efficiently found A-trails for a family of Eulerian triangulations as well as a family of braced grid graphs. Furthermore, we implemented a software package, BScOR (Beam Scaffolded-Origami Routing), which generates an A-trail, or equivalently a scaffold routing path, given a three-dimensional object description in a Polygon File Format. |
ED: | 2014-03-03 |
INSSI record number: 48706
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