haku: @keyword DNA nanotechnology / yhteensä: 6
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Tekijä: | Mohammed, Abdulmelik |
Työn nimi: | Combinatorial algorithms for the design of nanoscale systems |
Julkaisutyyppi: | Diplomityö |
Julkaisuvuosi: | 2014 |
Sivut: | 72 Kieli: eng |
Koulu/Laitos/Osasto: | Perustieteiden korkeakoulu |
Oppiaine: | Tietojenkäsittelyteoria (T-79) |
Valvoja: | Orponen, Pekka |
Ohjaaja: | Czeizler, Eugen |
Elektroninen julkaisu: | http://urn.fi/URN:NBN:fi:aalto-201507013655 |
OEVS: | Sähköinen arkistokappale on luettavissa Aalto Thesis Databasen kautta.
Ohje Digitaalisten opinnäytteiden lukeminen Aalto-yliopiston Harald Herlin -oppimiskeskuksen suljetussa verkossaOppimiskeskuksen suljetussa verkossa voi lukea sellaisia digitaalisia ja digitoituja opinnäytteitä, joille ei ole saatu julkaisulupaa avoimessa verkossa. Oppimiskeskuksen yhteystiedot ja aukioloajat: https://learningcentre.aalto.fi/fi/harald-herlin-oppimiskeskus/ Opinnäytteitä voi lukea Oppimiskeskuksen asiakaskoneilla, joita löytyy kaikista kerroksista.
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Sijainti: | P1 Ark Aalto | Arkisto |
Avainsanat: | DNA nanotechnology DNA origami polyhedra graphs combinatorial algorithms |
Tiivistelmä (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 tietueen numero: 48706
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