LIPIcs, Volume 276
DNA 29, September 11-15, 2023, Tohoku University, Sendai, Japan
Editors: Ho-Lin Chen and Constantine G. Evans
Published in: LIPIcs, Volume 287, 15th Innovations in Theoretical Computer Science Conference (ITCS 2024)
Erik D. Demaine, Yael Kirkpatrick, and Rebecca Lin. Graph Threading. In 15th Innovations in Theoretical Computer Science Conference (ITCS 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 287, pp. 38:1-38:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{demaine_et_al:LIPIcs.ITCS.2024.38, author = {Demaine, Erik D. and Kirkpatrick, Yael and Lin, Rebecca}, title = {{Graph Threading}}, booktitle = {15th Innovations in Theoretical Computer Science Conference (ITCS 2024)}, pages = {38:1--38:18}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-309-6}, ISSN = {1868-8969}, year = {2024}, volume = {287}, editor = {Guruswami, Venkatesan}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.ITCS.2024.38}, URN = {urn:nbn:de:0030-drops-195665}, doi = {10.4230/LIPIcs.ITCS.2024.38}, annote = {Keywords: Shortest walk, Eulerian cycle, perfect matching, beading} }
Published in: LIPIcs, Volume 276, 29th International Conference on DNA Computing and Molecular Programming (DNA 29) (2023)
29th International Conference on DNA Computing and Molecular Programming (DNA 29). Leibniz International Proceedings in Informatics (LIPIcs), Volume 276, pp. 1-230, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)
@Proceedings{chen_et_al:LIPIcs.DNA.29, title = {{LIPIcs, Volume 276, DNA 29, Complete Volume}}, booktitle = {29th International Conference on DNA Computing and Molecular Programming (DNA 29)}, pages = {1--230}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-297-6}, ISSN = {1868-8969}, year = {2023}, volume = {276}, editor = {Chen, Ho-Lin and Evans, Constantine G.}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.29}, URN = {urn:nbn:de:0030-drops-187827}, doi = {10.4230/LIPIcs.DNA.29}, annote = {Keywords: LIPIcs, Volume 276, DNA 29, Complete Volume} }
Published in: LIPIcs, Volume 276, 29th International Conference on DNA Computing and Molecular Programming (DNA 29) (2023)
29th International Conference on DNA Computing and Molecular Programming (DNA 29). Leibniz International Proceedings in Informatics (LIPIcs), Volume 276, pp. 0:i-0:xiv, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)
@InProceedings{chen_et_al:LIPIcs.DNA.29.0, author = {Chen, Ho-Lin and Evans, Constantine G.}, title = {{Front Matter, Table of Contents, Preface, Conference Organization}}, booktitle = {29th International Conference on DNA Computing and Molecular Programming (DNA 29)}, pages = {0:i--0:xiv}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-297-6}, ISSN = {1868-8969}, year = {2023}, volume = {276}, editor = {Chen, Ho-Lin and Evans, Constantine G.}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.29.0}, URN = {urn:nbn:de:0030-drops-187839}, doi = {10.4230/LIPIcs.DNA.29.0}, annote = {Keywords: Front Matter, Table of Contents, Preface, Conference Organization} }
Published in: LIPIcs, Volume 276, 29th International Conference on DNA Computing and Molecular Programming (DNA 29) (2023)
Ahmed Shalaby, Chris Thachuk, and Damien Woods. Minimum Free Energy, Partition Function and Kinetics Simulation Algorithms for a Multistranded Scaffolded DNA Computer. In 29th International Conference on DNA Computing and Molecular Programming (DNA 29). Leibniz International Proceedings in Informatics (LIPIcs), Volume 276, pp. 1:1-1:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)
@InProceedings{shalaby_et_al:LIPIcs.DNA.29.1, author = {Shalaby, Ahmed and Thachuk, Chris and Woods, Damien}, title = {{Minimum Free Energy, Partition Function and Kinetics Simulation Algorithms for a Multistranded Scaffolded DNA Computer}}, booktitle = {29th International Conference on DNA Computing and Molecular Programming (DNA 29)}, pages = {1:1--1:22}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-297-6}, ISSN = {1868-8969}, year = {2023}, volume = {276}, editor = {Chen, Ho-Lin and Evans, Constantine G.}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.29.1}, URN = {urn:nbn:de:0030-drops-187840}, doi = {10.4230/LIPIcs.DNA.29.1}, annote = {Keywords: thermodynamic computation, model of computation, molecular computing, minimum free energy, partition function, DNA computing, DNA self-assembly, DNA strand displacement, kinetics simulation} }
Published in: LIPIcs, Volume 276, 29th International Conference on DNA Computing and Molecular Programming (DNA 29) (2023)
Florent Becker and Shahrzad Heydarshahi. DNA Tile Self-Assembly for 3D-Surfaces: Towards Genus Identification. In 29th International Conference on DNA Computing and Molecular Programming (DNA 29). Leibniz International Proceedings in Informatics (LIPIcs), Volume 276, pp. 2:1-2:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)
@InProceedings{becker_et_al:LIPIcs.DNA.29.2, author = {Becker, Florent and Heydarshahi, Shahrzad}, title = {{DNA Tile Self-Assembly for 3D-Surfaces: Towards Genus Identification}}, booktitle = {29th International Conference on DNA Computing and Molecular Programming (DNA 29)}, pages = {2:1--2:21}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-297-6}, ISSN = {1868-8969}, year = {2023}, volume = {276}, editor = {Chen, Ho-Lin and Evans, Constantine G.}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.29.2}, URN = {urn:nbn:de:0030-drops-187851}, doi = {10.4230/LIPIcs.DNA.29.2}, annote = {Keywords: Tile self-assembly, DNA computing, Geometric surfaces} }
Published in: LIPIcs, Volume 276, 29th International Conference on DNA Computing and Molecular Programming (DNA 29) (2023)
Anne Condon, Yuval Emek, and Noga Harlev. On the Runtime of Chemical Reaction Networks Beyond Idealized Conditions. In 29th International Conference on DNA Computing and Molecular Programming (DNA 29). Leibniz International Proceedings in Informatics (LIPIcs), Volume 276, pp. 3:1-3:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)
@InProceedings{condon_et_al:LIPIcs.DNA.29.3, author = {Condon, Anne and Emek, Yuval and Harlev, Noga}, title = {{On the Runtime of Chemical Reaction Networks Beyond Idealized Conditions}}, booktitle = {29th International Conference on DNA Computing and Molecular Programming (DNA 29)}, pages = {3:1--3:22}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-297-6}, ISSN = {1868-8969}, year = {2023}, volume = {276}, editor = {Chen, Ho-Lin and Evans, Constantine G.}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.29.3}, URN = {urn:nbn:de:0030-drops-187861}, doi = {10.4230/LIPIcs.DNA.29.3}, annote = {Keywords: chemical reaction networks, adversarial runtime, weak fairness, predicate decidability} }
Published in: LIPIcs, Volume 276, 29th International Conference on DNA Computing and Molecular Programming (DNA 29) (2023)
Joseph Don Berleant. Rational Design of DNA Sequences with Non-Orthogonal Binding Interactions. In 29th International Conference on DNA Computing and Molecular Programming (DNA 29). Leibniz International Proceedings in Informatics (LIPIcs), Volume 276, pp. 4:1-4:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)
@InProceedings{berleant:LIPIcs.DNA.29.4, author = {Berleant, Joseph Don}, title = {{Rational Design of DNA Sequences with Non-Orthogonal Binding Interactions}}, booktitle = {29th International Conference on DNA Computing and Molecular Programming (DNA 29)}, pages = {4:1--4:22}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-297-6}, ISSN = {1868-8969}, year = {2023}, volume = {276}, editor = {Chen, Ho-Lin and Evans, Constantine G.}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.29.4}, URN = {urn:nbn:de:0030-drops-187877}, doi = {10.4230/LIPIcs.DNA.29.4}, annote = {Keywords: DNA sequence design, binding networks, promiscuous binding, non-orthogonal binding, isometric graph embeddings} }
Published in: LIPIcs, Volume 276, 29th International Conference on DNA Computing and Molecular Programming (DNA 29) (2023)
Jordan Lovrod, Boyan Beronov, Chenwei Zhang, Erik Winfree, and Anne Condon. Revisiting Hybridization Kinetics with Improved Elementary Step Simulation. In 29th International Conference on DNA Computing and Molecular Programming (DNA 29). Leibniz International Proceedings in Informatics (LIPIcs), Volume 276, pp. 5:1-5:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)
@InProceedings{lovrod_et_al:LIPIcs.DNA.29.5, author = {Lovrod, Jordan and Beronov, Boyan and Zhang, Chenwei and Winfree, Erik and Condon, Anne}, title = {{Revisiting Hybridization Kinetics with Improved Elementary Step Simulation}}, booktitle = {29th International Conference on DNA Computing and Molecular Programming (DNA 29)}, pages = {5:1--5:24}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-297-6}, ISSN = {1868-8969}, year = {2023}, volume = {276}, editor = {Chen, Ho-Lin and Evans, Constantine G.}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.29.5}, URN = {urn:nbn:de:0030-drops-187889}, doi = {10.4230/LIPIcs.DNA.29.5}, annote = {Keywords: DNA reaction kinetics, kinetic model calibration, simulation-based Bayesian inference, continuous-time Markov chains} }
Published in: LIPIcs, Volume 276, 29th International Conference on DNA Computing and Molecular Programming (DNA 29) (2023)
Hannah Amelie Earley. Reversible Bond Logic. In 29th International Conference on DNA Computing and Molecular Programming (DNA 29). Leibniz International Proceedings in Informatics (LIPIcs), Volume 276, pp. 6:1-6:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)
@InProceedings{earley:LIPIcs.DNA.29.6, author = {Earley, Hannah Amelie}, title = {{Reversible Bond Logic}}, booktitle = {29th International Conference on DNA Computing and Molecular Programming (DNA 29)}, pages = {6:1--6:23}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-297-6}, ISSN = {1868-8969}, year = {2023}, volume = {276}, editor = {Chen, Ho-Lin and Evans, Constantine G.}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.29.6}, URN = {urn:nbn:de:0030-drops-187893}, doi = {10.4230/LIPIcs.DNA.29.6}, annote = {Keywords: Molecular Programming, Reversible Computing, Structural Manipulation} }
Published in: LIPIcs, Volume 276, 29th International Conference on DNA Computing and Molecular Programming (DNA 29) (2023)
David Doty, Hunter Fleming, Daniel Hader, Matthew J. Patitz, and Lukas A. Vaughan. Accelerating Self-Assembly of Crisscross Slat Systems. In 29th International Conference on DNA Computing and Molecular Programming (DNA 29). Leibniz International Proceedings in Informatics (LIPIcs), Volume 276, pp. 7:1-7:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)
@InProceedings{doty_et_al:LIPIcs.DNA.29.7, author = {Doty, David and Fleming, Hunter and Hader, Daniel and Patitz, Matthew J. and Vaughan, Lukas A.}, title = {{Accelerating Self-Assembly of Crisscross Slat Systems}}, booktitle = {29th International Conference on DNA Computing and Molecular Programming (DNA 29)}, pages = {7:1--7:23}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-297-6}, ISSN = {1868-8969}, year = {2023}, volume = {276}, editor = {Chen, Ho-Lin and Evans, Constantine G.}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.29.7}, URN = {urn:nbn:de:0030-drops-187908}, doi = {10.4230/LIPIcs.DNA.29.7}, annote = {Keywords: DNA origami, self-assembly, kinetic modeling, computational modeling} }
Published in: LIPIcs, Volume 276, 29th International Conference on DNA Computing and Molecular Programming (DNA 29) (2023)
Joshua Petrack, David Soloveichik, and David Doty. Thermodynamically Driven Signal Amplification. In 29th International Conference on DNA Computing and Molecular Programming (DNA 29). Leibniz International Proceedings in Informatics (LIPIcs), Volume 276, pp. 8:1-8:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)
@InProceedings{petrack_et_al:LIPIcs.DNA.29.8, author = {Petrack, Joshua and Soloveichik, David and Doty, David}, title = {{Thermodynamically Driven Signal Amplification}}, booktitle = {29th International Conference on DNA Computing and Molecular Programming (DNA 29)}, pages = {8:1--8:22}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-297-6}, ISSN = {1868-8969}, year = {2023}, volume = {276}, editor = {Chen, Ho-Lin and Evans, Constantine G.}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.29.8}, URN = {urn:nbn:de:0030-drops-187917}, doi = {10.4230/LIPIcs.DNA.29.8}, annote = {Keywords: Thermodynamic binding networks, signal amplification, integer programming} }
Published in: LIPIcs, Volume 276, 29th International Conference on DNA Computing and Molecular Programming (DNA 29) (2023)
Austin Luchsinger, David Doty, and David Soloveichik. Optimal Information Encoding in Chemical Reaction Networks. In 29th International Conference on DNA Computing and Molecular Programming (DNA 29). Leibniz International Proceedings in Informatics (LIPIcs), Volume 276, pp. 9:1-9:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)
@InProceedings{luchsinger_et_al:LIPIcs.DNA.29.9, author = {Luchsinger, Austin and Doty, David and Soloveichik, David}, title = {{Optimal Information Encoding in Chemical Reaction Networks}}, booktitle = {29th International Conference on DNA Computing and Molecular Programming (DNA 29)}, pages = {9:1--9:16}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-297-6}, ISSN = {1868-8969}, year = {2023}, volume = {276}, editor = {Chen, Ho-Lin and Evans, Constantine G.}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.29.9}, URN = {urn:nbn:de:0030-drops-187920}, doi = {10.4230/LIPIcs.DNA.29.9}, annote = {Keywords: chemical reaction networks, Kolmogorov complexity, stable computation} }
Published in: LIPIcs, Volume 276, 29th International Conference on DNA Computing and Molecular Programming (DNA 29) (2023)
Robert M. Alaniz, Josh Brunner, Michael Coulombe, Erik D. Demaine, Jenny Diomidova, Timothy Gomez, Elise Grizzell, Ryan Knobel, Jayson Lynch, Andrew Rodriguez, Robert Schweller, and Tim Wylie. Complexity of Reconfiguration in Surface Chemical Reaction Networks. In 29th International Conference on DNA Computing and Molecular Programming (DNA 29). Leibniz International Proceedings in Informatics (LIPIcs), Volume 276, pp. 10:1-10:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)
@InProceedings{alaniz_et_al:LIPIcs.DNA.29.10, author = {Alaniz, Robert M. and Brunner, Josh and Coulombe, Michael and Demaine, Erik D. and Diomidova, Jenny and Gomez, Timothy and Grizzell, Elise and Knobel, Ryan and Lynch, Jayson and Rodriguez, Andrew and Schweller, Robert and Wylie, Tim}, title = {{Complexity of Reconfiguration in Surface Chemical Reaction Networks}}, booktitle = {29th International Conference on DNA Computing and Molecular Programming (DNA 29)}, pages = {10:1--10:18}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-297-6}, ISSN = {1868-8969}, year = {2023}, volume = {276}, editor = {Chen, Ho-Lin and Evans, Constantine G.}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.29.10}, URN = {urn:nbn:de:0030-drops-187936}, doi = {10.4230/LIPIcs.DNA.29.10}, annote = {Keywords: Chemical Reaction Networks, reconfiguration, hardness} }
Published in: LIPIcs, Volume 269, 28th International Conference on Types for Proofs and Programs (TYPES 2022)
Amélie Ledein, Valentin Blot, and Catherine Dubois. A Semantics of 𝕂 into Dedukti. In 28th International Conference on Types for Proofs and Programs (TYPES 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 269, pp. 12:1-12:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)
@InProceedings{ledein_et_al:LIPIcs.TYPES.2022.12, author = {Ledein, Am\'{e}lie and Blot, Valentin and Dubois, Catherine}, title = {{A Semantics of \mathbb{K} into Dedukti}}, booktitle = {28th International Conference on Types for Proofs and Programs (TYPES 2022)}, pages = {12:1--12:22}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-285-3}, ISSN = {1868-8969}, year = {2023}, volume = {269}, editor = {Kesner, Delia and P\'{e}drot, Pierre-Marie}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.TYPES.2022.12}, URN = {urn:nbn:de:0030-drops-184557}, doi = {10.4230/LIPIcs.TYPES.2022.12}, annote = {Keywords: Programming language, Semantics, Rewriting, Logical framework, Type theory} }
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