Algorithmic Pot Generation: Algorithms for the Flexible-Tile Model of DNA Self-Assembly

Recent advancements in microbiology have motivated the study of the production of nanostructures with applications such as biomedical computing and molecular robotics. One way to construct these structures is to construct branched DNA molecules that bond to each other at complementary cohesive ends....

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Bibliographic Details
Main Authors Ashworth, Jacob, Grossmann, Luca, Navarro, Fausto, Almodovar, Leyda, Harsy, Amanda, Johnson, Cory, Sorrells, Jessica
Format Journal Article
LanguageEnglish
Published 31.07.2024
Subjects
Mathematics - Combinatorics
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DOI10.48550/arxiv.2408.00192

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Summary:Recent advancements in microbiology have motivated the study of the production of nanostructures with applications such as biomedical computing and molecular robotics. One way to construct these structures is to construct branched DNA molecules that bond to each other at complementary cohesive ends. One practical question is: given a target nanostructure, what is the optimal set of DNA molecules that assemble such a structure? We use a flexible-tile graph theoretic model to develop several algorithmic approaches, including a integer programming approach. These approaches take a target undirected graph as an input and output an optimal collection of component building blocks to construct the desired structure.
DOI:10.48550/arxiv.2408.00192