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DOI: 10.4230/LIPIcs.ISAAC.2022.37
URN: urn:nbn:de:0030-drops-173228
URL: https://drops.dagstuhl.de/opus/volltexte/2022/17322/
Fazekas, Szilárd Zsolt ; Kim, Hwee ; Matsuoka, Ryuichi ; Seki, Shinnosuke ; Takeuchi, Hinano
On Algorithmic Self-Assembly of Squares by Co-Transcriptional Folding
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Abstract
Algorithms play a primary role in programming an orchestrated self-assembly of shapes into molecules. In this paper, we study the algorithmic self-assembly of squares by RNA co-transcriptional folding in its oritatami model. We formalize the square self-assembly problem in oritatami and propose a universal oritatami transcript made of 939 types of abstract molecules (beads) and of period 1294 that folds deterministically and co-transcriptionally at delay 3 and maximum arity into the n × n square modulo horizontal and vertical scaling factors for all sufficiently large n’s after building a Θ(log n) width "ruler" that measures n upon the seed of size Θ(log n) on which n is encoded in binary.
BibTeX - Entry
@InProceedings{fazekas_et_al:LIPIcs.ISAAC.2022.37,
author = {Fazekas, Szil\'{a}rd Zsolt and Kim, Hwee and Matsuoka, Ryuichi and Seki, Shinnosuke and Takeuchi, Hinano},
title = {{On Algorithmic Self-Assembly of Squares by Co-Transcriptional Folding}},
booktitle = {33rd International Symposium on Algorithms and Computation (ISAAC 2022)},
pages = {37:1--37:15},
series = {Leibniz International Proceedings in Informatics (LIPIcs)},
ISBN = {978-3-95977-258-7},
ISSN = {1868-8969},
year = {2022},
volume = {248},
editor = {Bae, Sang Won and Park, Heejin},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/opus/volltexte/2022/17322},
URN = {urn:nbn:de:0030-drops-173228},
doi = {10.4230/LIPIcs.ISAAC.2022.37},
annote = {Keywords: Algorithmic molecular self-assembly, Co-transcriptional folding, Oritatami system, Self-assembly of squares}
}
| Keywords: | Algorithmic molecular self-assembly, Co-transcriptional folding, Oritatami system, Self-assembly of squares | |
| Seminar: | 33rd International Symposium on Algorithms and Computation (ISAAC 2022) | |
| Issue date: | 2022 | |
| Date of publication: | 14.12.2022 | |
| Supplementary Material: | Software (Source Code): https://github.com/rmatsuoka/oritatami_square archived at: https://archive.softwareheritage.org/swh:1:dir:016668d43c79b95a11aa013450ee472c2c7569cf |
