LIPIcs, Volume 314
DNA 30, September 16-20, 2024, Baltimore, Maryland, USA
Editors: Shinnosuke Seki and Jaimie Marie Stewart
Published in: LIPIcs, Volume 314, 30th International Conference on DNA Computing and Molecular Programming (DNA 30) (2024)
30th International Conference on DNA Computing and Molecular Programming (DNA 30). Leibniz International Proceedings in Informatics (LIPIcs), Volume 314, pp. 1-124, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@Proceedings{seki_et_al:LIPIcs.DNA.30, title = {{LIPIcs, Volume 314, DNA 30, Complete Volume}}, booktitle = {30th International Conference on DNA Computing and Molecular Programming (DNA 30)}, pages = {1--124}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-344-7}, ISSN = {1868-8969}, year = {2024}, volume = {314}, editor = {Seki, Shinnosuke and Stewart, Jaimie Marie}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.30}, URN = {urn:nbn:de:0030-drops-209272}, doi = {10.4230/LIPIcs.DNA.30}, annote = {Keywords: LIPIcs, Volume 314, DNA 30, Complete Volume} }
Published in: LIPIcs, Volume 314, 30th International Conference on DNA Computing and Molecular Programming (DNA 30) (2024)
30th International Conference on DNA Computing and Molecular Programming (DNA 30). Leibniz International Proceedings in Informatics (LIPIcs), Volume 314, pp. 0:i-0:xiv, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{seki_et_al:LIPIcs.DNA.30.0, author = {Seki, Shinnosuke and Stewart, Jaimie Marie}, title = {{Front Matter, Table of Contents, Preface, Conference Organization}}, booktitle = {30th International Conference on DNA Computing and Molecular Programming (DNA 30)}, pages = {0:i--0:xiv}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-344-7}, ISSN = {1868-8969}, year = {2024}, volume = {314}, editor = {Seki, Shinnosuke and Stewart, Jaimie Marie}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.30.0}, URN = {urn:nbn:de:0030-drops-209284}, doi = {10.4230/LIPIcs.DNA.30.0}, annote = {Keywords: Front Matter, Table of Contents, Preface, Conference Organization} }
Published in: LIPIcs, Volume 314, 30th International Conference on DNA Computing and Molecular Programming (DNA 30) (2024)
Matthew R. Lakin and Sarika Kumar. Geometric Enumeration of Localized DNA Strand Displacement Reaction Networks. In 30th International Conference on DNA Computing and Molecular Programming (DNA 30). Leibniz International Proceedings in Informatics (LIPIcs), Volume 314, pp. 1:1-1:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{lakin_et_al:LIPIcs.DNA.30.1, author = {Lakin, Matthew R. and Kumar, Sarika}, title = {{Geometric Enumeration of Localized DNA Strand Displacement Reaction Networks}}, booktitle = {30th International Conference on DNA Computing and Molecular Programming (DNA 30)}, pages = {1:1--1:24}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-344-7}, ISSN = {1868-8969}, year = {2024}, volume = {314}, editor = {Seki, Shinnosuke and Stewart, Jaimie Marie}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.30.1}, URN = {urn:nbn:de:0030-drops-209294}, doi = {10.4230/LIPIcs.DNA.30.1}, annote = {Keywords: Localized circuits, reaction enumeration, DNA strand displacement, geometry, molecular computing} }
Published in: LIPIcs, Volume 314, 30th International Conference on DNA Computing and Molecular Programming (DNA 30) (2024)
Erik D. Demaine, Timothy Gomez, Elise Grizzell, Markus Hecher, Jayson Lynch, Robert Schweller, Ahmed Shalaby, and Damien Woods. Domain-Based Nucleic-Acid Minimum Free Energy: Algorithmic Hardness and Parameterized Bounds. In 30th International Conference on DNA Computing and Molecular Programming (DNA 30). Leibniz International Proceedings in Informatics (LIPIcs), Volume 314, pp. 2:1-2:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{demaine_et_al:LIPIcs.DNA.30.2, author = {Demaine, Erik D. and Gomez, Timothy and Grizzell, Elise and Hecher, Markus and Lynch, Jayson and Schweller, Robert and Shalaby, Ahmed and Woods, Damien}, title = {{Domain-Based Nucleic-Acid Minimum Free Energy: Algorithmic Hardness and Parameterized Bounds}}, booktitle = {30th International Conference on DNA Computing and Molecular Programming (DNA 30)}, pages = {2:1--2:24}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-344-7}, ISSN = {1868-8969}, year = {2024}, volume = {314}, editor = {Seki, Shinnosuke and Stewart, Jaimie Marie}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.30.2}, URN = {urn:nbn:de:0030-drops-209304}, doi = {10.4230/LIPIcs.DNA.30.2}, annote = {Keywords: Domain-based DNA designs, minimum free energy, efficient algorithms, NP-hard, P-hard, NC, fixed-parameter tractable} }
Published in: LIPIcs, Volume 314, 30th International Conference on DNA Computing and Molecular Programming (DNA 30) (2024)
Phillip Drake, Daniel Hader, and Matthew J. Patitz. Simulation of the Abstract Tile Assembly Model Using Crisscross Slats. In 30th International Conference on DNA Computing and Molecular Programming (DNA 30). Leibniz International Proceedings in Informatics (LIPIcs), Volume 314, pp. 3:1-3:25, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{drake_et_al:LIPIcs.DNA.30.3, author = {Drake, Phillip and Hader, Daniel and Patitz, Matthew J.}, title = {{Simulation of the Abstract Tile Assembly Model Using Crisscross Slats}}, booktitle = {30th International Conference on DNA Computing and Molecular Programming (DNA 30)}, pages = {3:1--3:25}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-344-7}, ISSN = {1868-8969}, year = {2024}, volume = {314}, editor = {Seki, Shinnosuke and Stewart, Jaimie Marie}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.30.3}, URN = {urn:nbn:de:0030-drops-209315}, doi = {10.4230/LIPIcs.DNA.30.3}, annote = {Keywords: DNA origami, tile-assembly, self-assembly, aTAM, kinetic modeling, computational modeling} }
Published in: LIPIcs, Volume 314, 30th International Conference on DNA Computing and Molecular Programming (DNA 30) (2024)
Antti Elonen and Pekka Orponen. Designing 3D RNA Origami Nanostructures with a Minimum Number of Kissing Loops. In 30th International Conference on DNA Computing and Molecular Programming (DNA 30). Leibniz International Proceedings in Informatics (LIPIcs), Volume 314, pp. 4:1-4:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{elonen_et_al:LIPIcs.DNA.30.4, author = {Elonen, Antti and Orponen, Pekka}, title = {{Designing 3D RNA Origami Nanostructures with a Minimum Number of Kissing Loops}}, booktitle = {30th International Conference on DNA Computing and Molecular Programming (DNA 30)}, pages = {4:1--4:12}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-344-7}, ISSN = {1868-8969}, year = {2024}, volume = {314}, editor = {Seki, Shinnosuke and Stewart, Jaimie Marie}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.30.4}, URN = {urn:nbn:de:0030-drops-209325}, doi = {10.4230/LIPIcs.DNA.30.4}, annote = {Keywords: RNA origami, wireframe nanostructures, polyhedra, kissing loops, topological graph embeddings, self-assembly} }
Published in: LIPIcs, Volume 314, 30th International Conference on DNA Computing and Molecular Programming (DNA 30) (2024)
Cameron Chalk, Salvador Buse, Krishna Shrinivas, Arvind Murugan, and Erik Winfree. Learning and Inference in a Lattice Model of Multicomponent Condensates. In 30th International Conference on DNA Computing and Molecular Programming (DNA 30). Leibniz International Proceedings in Informatics (LIPIcs), Volume 314, pp. 5:1-5:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{chalk_et_al:LIPIcs.DNA.30.5, author = {Chalk, Cameron and Buse, Salvador and Shrinivas, Krishna and Murugan, Arvind and Winfree, Erik}, title = {{Learning and Inference in a Lattice Model of Multicomponent Condensates}}, booktitle = {30th International Conference on DNA Computing and Molecular Programming (DNA 30)}, pages = {5:1--5:24}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-344-7}, ISSN = {1868-8969}, year = {2024}, volume = {314}, editor = {Seki, Shinnosuke and Stewart, Jaimie Marie}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.30.5}, URN = {urn:nbn:de:0030-drops-209330}, doi = {10.4230/LIPIcs.DNA.30.5}, annote = {Keywords: multicomponent liquid, Boltzmann machine, phase separation} }
Published in: LIPIcs, Volume 311, 35th International Conference on Concurrency Theory (CONCUR 2024)
Luc Dartois, Paul Gastin, Loïc Germerie Guizouarn, R. Govind, and Shankaranarayanan Krishna. Reversible Transducers over Infinite Words. In 35th International Conference on Concurrency Theory (CONCUR 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 311, pp. 21:1-21:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{dartois_et_al:LIPIcs.CONCUR.2024.21, author = {Dartois, Luc and Gastin, Paul and Germerie Guizouarn, Lo\"{i}c and Govind, R. and Krishna, Shankaranarayanan}, title = {{Reversible Transducers over Infinite Words}}, booktitle = {35th International Conference on Concurrency Theory (CONCUR 2024)}, pages = {21:1--21:22}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-339-3}, ISSN = {1868-8969}, year = {2024}, volume = {311}, editor = {Majumdar, Rupak and Silva, Alexandra}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CONCUR.2024.21}, URN = {urn:nbn:de:0030-drops-207932}, doi = {10.4230/LIPIcs.CONCUR.2024.21}, annote = {Keywords: Transducers, Regular functions, Reversibility, Composition, SSTs} }
Published in: LIPIcs, Volume 306, 49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024)
Alexander Rubtsov and Nikita Chudinov. Computational Model for Parsing Expression Grammars. In 49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 306, pp. 80:1-80:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{rubtsov_et_al:LIPIcs.MFCS.2024.80, author = {Rubtsov, Alexander and Chudinov, Nikita}, title = {{Computational Model for Parsing Expression Grammars}}, booktitle = {49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024)}, pages = {80:1--80:13}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-335-5}, ISSN = {1868-8969}, year = {2024}, volume = {306}, editor = {Kr\'{a}lovi\v{c}, Rastislav and Ku\v{c}era, Anton{\'\i}n}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.MFCS.2024.80}, URN = {urn:nbn:de:0030-drops-206362}, doi = {10.4230/LIPIcs.MFCS.2024.80}, annote = {Keywords: PEG, formal languages, pushdown automata, two-way pushdown automata} }
Published in: LIPIcs, Volume 248, 33rd International Symposium on Algorithms and Computation (ISAAC 2022)
Szilárd Zsolt Fazekas, Hwee Kim, Ryuichi Matsuoka, Shinnosuke Seki, and Hinano Takeuchi. On Algorithmic Self-Assembly of Squares by Co-Transcriptional Folding. In 33rd International Symposium on Algorithms and Computation (ISAAC 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 248, pp. 37:1-37:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)
@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/entities/document/10.4230/LIPIcs.ISAAC.2022.37}, 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} }
Published in: LIPIcs, Volume 219, 39th International Symposium on Theoretical Aspects of Computer Science (STACS 2022)
Daria Pchelina, Nicolas Schabanel, Shinnosuke Seki, and Guillaume Theyssier. Oritatami Systems Assemble Shapes No Less Complex Than Tile Assembly Model (ATAM). In 39th International Symposium on Theoretical Aspects of Computer Science (STACS 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 219, pp. 51:1-51:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)
@InProceedings{pchelina_et_al:LIPIcs.STACS.2022.51, author = {Pchelina, Daria and Schabanel, Nicolas and Seki, Shinnosuke and Theyssier, Guillaume}, title = {{Oritatami Systems Assemble Shapes No Less Complex Than Tile Assembly Model (ATAM)}}, booktitle = {39th International Symposium on Theoretical Aspects of Computer Science (STACS 2022)}, pages = {51:1--51:23}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-222-8}, ISSN = {1868-8969}, year = {2022}, volume = {219}, editor = {Berenbrink, Petra and Monmege, Benjamin}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.STACS.2022.51}, URN = {urn:nbn:de:0030-drops-158618}, doi = {10.4230/LIPIcs.STACS.2022.51}, annote = {Keywords: Molecular Self-assembly, Co-transcriptional folding, Intrinsic simulation, Arithmetical hierarchy of real numbers, 2D Turing machines, Computability} }
Published in: LIPIcs, Volume 123, 29th International Symposium on Algorithms and Computation (ISAAC 2018)
Cody Geary, Pierre-Étienne Meunier, Nicolas Schabanel, and Shinnosuke Seki. Proving the Turing Universality of Oritatami Co-Transcriptional Folding. In 29th International Symposium on Algorithms and Computation (ISAAC 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 123, pp. 23:1-23:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)
@InProceedings{geary_et_al:LIPIcs.ISAAC.2018.23, author = {Geary, Cody and Meunier, Pierre-\'{E}tienne and Schabanel, Nicolas and Seki, Shinnosuke}, title = {{Proving the Turing Universality of Oritatami Co-Transcriptional Folding}}, booktitle = {29th International Symposium on Algorithms and Computation (ISAAC 2018)}, pages = {23:1--23:13}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-094-1}, ISSN = {1868-8969}, year = {2018}, volume = {123}, editor = {Hsu, Wen-Lian and Lee, Der-Tsai and Liao, Chung-Shou}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ISAAC.2018.23}, URN = {urn:nbn:de:0030-drops-99715}, doi = {10.4230/LIPIcs.ISAAC.2018.23}, annote = {Keywords: Molecular computing, Turing universality, co-transcriptional folding} }
Published in: LIPIcs, Volume 58, 41st International Symposium on Mathematical Foundations of Computer Science (MFCS 2016)
Cody Geary, Pierre-Etienne Meunier, Nicolas Schabanel, and Shinnosuke Seki. Programming Biomolecules That Fold Greedily During Transcription. In 41st International Symposium on Mathematical Foundations of Computer Science (MFCS 2016). Leibniz International Proceedings in Informatics (LIPIcs), Volume 58, pp. 43:1-43:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2016)
@InProceedings{geary_et_al:LIPIcs.MFCS.2016.43, author = {Geary, Cody and Meunier, Pierre-Etienne and Schabanel, Nicolas and Seki, Shinnosuke}, title = {{Programming Biomolecules That Fold Greedily During Transcription}}, booktitle = {41st International Symposium on Mathematical Foundations of Computer Science (MFCS 2016)}, pages = {43:1--43:14}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-016-3}, ISSN = {1868-8969}, year = {2016}, volume = {58}, editor = {Faliszewski, Piotr and Muscholl, Anca and Niedermeier, Rolf}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.MFCS.2016.43}, URN = {urn:nbn:de:0030-drops-64567}, doi = {10.4230/LIPIcs.MFCS.2016.43}, annote = {Keywords: natural computing, self-assembly, molecular folding} }
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