31st International Conference on DNA Computing and Molecular Programming (DNA 31). Leibniz International Proceedings in Informatics (LIPIcs), Volume 347, pp. 1-254, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)
@Proceedings{schaeffer_et_al:LIPIcs.DNA.31, title = {{LIPIcs, Volume 347, DNA 31, Complete Volume}}, booktitle = {31st International Conference on DNA Computing and Molecular Programming (DNA 31)}, pages = {1--254}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-399-7}, ISSN = {1868-8969}, year = {2025}, volume = {347}, editor = {Schaeffer, Josie and Zhang, Fei}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.31}, URN = {urn:nbn:de:0030-drops-244444}, doi = {10.4230/LIPIcs.DNA.31}, annote = {Keywords: LIPIcs, Volume 347, DNA 31, Complete Volume} }
31st International Conference on DNA Computing and Molecular Programming (DNA 31). Leibniz International Proceedings in Informatics (LIPIcs), Volume 347, pp. 0:i-0:xviii, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)
@InProceedings{schaeffer_et_al:LIPIcs.DNA.31.0, author = {Schaeffer, Josie and Zhang, Fei}, title = {{Front Matter, Table of Contents, Preface, Conference Organization}}, booktitle = {31st International Conference on DNA Computing and Molecular Programming (DNA 31)}, pages = {0:i--0:xviii}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-399-7}, ISSN = {1868-8969}, year = {2025}, volume = {347}, editor = {Schaeffer, Josie and Zhang, Fei}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.31.0}, URN = {urn:nbn:de:0030-drops-244397}, doi = {10.4230/LIPIcs.DNA.31.0}, annote = {Keywords: Front Matter, Table of Contents, Preface, Conference Organization} }
Gwendal Ducloz, Ahmed Shalaby, and Damien Woods. Algorithmic Hardness of the Partition Function for Nucleic Acid Strands. In 31st International Conference on DNA Computing and Molecular Programming (DNA 31). Leibniz International Proceedings in Informatics (LIPIcs), Volume 347, pp. 1:1-1:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)
@InProceedings{ducloz_et_al:LIPIcs.DNA.31.1, author = {Ducloz, Gwendal and Shalaby, Ahmed and Woods, Damien}, title = {{Algorithmic Hardness of the Partition Function for Nucleic Acid Strands}}, booktitle = {31st International Conference on DNA Computing and Molecular Programming (DNA 31)}, pages = {1:1--1:23}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-399-7}, ISSN = {1868-8969}, year = {2025}, volume = {347}, editor = {Schaeffer, Josie and Zhang, Fei}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.31.1}, URN = {urn:nbn:de:0030-drops-238504}, doi = {10.4230/LIPIcs.DNA.31.1}, annote = {Keywords: Partition function, minimum free energy, nucleic acid, DNA, RNA, secondary structure, computational complexity, #P-hardness} }
Hope Amber Johnson and Anne Condon. A Coupled Reconfiguration Mechanism That Enables Powerful, Pseudoknot-Robust DNA Strand Displacement Devices with 2-Stranded Inputs. In 31st International Conference on DNA Computing and Molecular Programming (DNA 31). Leibniz International Proceedings in Informatics (LIPIcs), Volume 347, pp. 2:1-2:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)
@InProceedings{johnson_et_al:LIPIcs.DNA.31.2, author = {Johnson, Hope Amber and Condon, Anne}, title = {{A Coupled Reconfiguration Mechanism That Enables Powerful, Pseudoknot-Robust DNA Strand Displacement Devices with 2-Stranded Inputs}}, booktitle = {31st International Conference on DNA Computing and Molecular Programming (DNA 31)}, pages = {2:1--2:23}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-399-7}, ISSN = {1868-8969}, year = {2025}, volume = {347}, editor = {Schaeffer, Josie and Zhang, Fei}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.31.2}, URN = {urn:nbn:de:0030-drops-238514}, doi = {10.4230/LIPIcs.DNA.31.2}, annote = {Keywords: Molecular programming, DNA strand displacement, Chemical Reaction Networks} }
Bin Fu, Timothy Gomez, Ryan Knobel, Austin Luchsinger, Aiden Massie, Marco Rodriguez, Adrian Salinas, Robert Schweller, and Tim Wylie. Reachability in Deletion-Only Chemical Reaction Networks. In 31st International Conference on DNA Computing and Molecular Programming (DNA 31). Leibniz International Proceedings in Informatics (LIPIcs), Volume 347, pp. 3:1-3:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)
@InProceedings{fu_et_al:LIPIcs.DNA.31.3, author = {Fu, Bin and Gomez, Timothy and Knobel, Ryan and Luchsinger, Austin and Massie, Aiden and Rodriguez, Marco and Salinas, Adrian and Schweller, Robert and Wylie, Tim}, title = {{Reachability in Deletion-Only Chemical Reaction Networks}}, booktitle = {31st International Conference on DNA Computing and Molecular Programming (DNA 31)}, pages = {3:1--3:21}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-399-7}, ISSN = {1868-8969}, year = {2025}, volume = {347}, editor = {Schaeffer, Josie and Zhang, Fei}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.31.3}, URN = {urn:nbn:de:0030-drops-238521}, doi = {10.4230/LIPIcs.DNA.31.3}, annote = {Keywords: CRN, Chemical Reaction Network, Reachability, Void Reactions} }
Inhoo Lee, Salvador Buse, and Erik Winfree. Differentiable Programming of Indexed Chemical Reaction Networks and Reaction-Diffusion Systems. In 31st International Conference on DNA Computing and Molecular Programming (DNA 31). Leibniz International Proceedings in Informatics (LIPIcs), Volume 347, pp. 4:1-4:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)
@InProceedings{lee_et_al:LIPIcs.DNA.31.4, author = {Lee, Inhoo and Buse, Salvador and Winfree, Erik}, title = {{Differentiable Programming of Indexed Chemical Reaction Networks and Reaction-Diffusion Systems}}, booktitle = {31st International Conference on DNA Computing and Molecular Programming (DNA 31)}, pages = {4:1--4:23}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-399-7}, ISSN = {1868-8969}, year = {2025}, volume = {347}, editor = {Schaeffer, Josie and Zhang, Fei}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.31.4}, URN = {urn:nbn:de:0030-drops-238534}, doi = {10.4230/LIPIcs.DNA.31.4}, annote = {Keywords: Differentiable Programming, Chemical Reaction Networks, Reaction-Diffusion Systems} }
Da-Jung Cho, Szilárd Zsolt Fazekas, Shinnosuke Seki, and Max Wiedenhöft. Programmable Co‑Transcriptional Splicing: Realizing Regular Languages via Hairpin Deletion. In 31st International Conference on DNA Computing and Molecular Programming (DNA 31). Leibniz International Proceedings in Informatics (LIPIcs), Volume 347, pp. 5:1-5:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)
@InProceedings{cho_et_al:LIPIcs.DNA.31.5, author = {Cho, Da-Jung and Fazekas, Szil\'{a}rd Zsolt and Seki, Shinnosuke and Wiedenh\"{o}ft, Max}, title = {{Programmable Co‑Transcriptional Splicing: Realizing Regular Languages via Hairpin Deletion}}, booktitle = {31st International Conference on DNA Computing and Molecular Programming (DNA 31)}, pages = {5:1--5:22}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-399-7}, ISSN = {1868-8969}, year = {2025}, volume = {347}, editor = {Schaeffer, Josie and Zhang, Fei}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.31.5}, URN = {urn:nbn:de:0030-drops-238548}, doi = {10.4230/LIPIcs.DNA.31.5}, annote = {Keywords: RNA Transcription, Co-Transcriptional Splicing, Finite Automata Simulation, NFA Minimization} }
Pekka Orponen, Shinnosuke Seki, and Antti Elonen. Secondary Structure Design for Cotranscriptional 3D RNA Origami Wireframes. In 31st International Conference on DNA Computing and Molecular Programming (DNA 31). Leibniz International Proceedings in Informatics (LIPIcs), Volume 347, pp. 6:1-6:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)
@InProceedings{orponen_et_al:LIPIcs.DNA.31.6, author = {Orponen, Pekka and Seki, Shinnosuke and Elonen, Antti}, title = {{Secondary Structure Design for Cotranscriptional 3D RNA Origami Wireframes}}, booktitle = {31st International Conference on DNA Computing and Molecular Programming (DNA 31)}, pages = {6:1--6:18}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-399-7}, ISSN = {1868-8969}, year = {2025}, volume = {347}, editor = {Schaeffer, Josie and Zhang, Fei}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.31.6}, URN = {urn:nbn:de:0030-drops-238558}, doi = {10.4230/LIPIcs.DNA.31.6}, annote = {Keywords: RNA origami, wireframe nanostructures, cotranscriptional folding, secondary structure, kissing loops, algorithms, self-assembly} }
Constantine G. Evans, Angel Cervera Roldan, Trent Rogers, and Damien Woods. Tile Blockers as a Simple Motif to Control Self-Assembly: Kinetics and Thermodynamics. In 31st International Conference on DNA Computing and Molecular Programming (DNA 31). Leibniz International Proceedings in Informatics (LIPIcs), Volume 347, pp. 7:1-7:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)
@InProceedings{evans_et_al:LIPIcs.DNA.31.7, author = {Evans, Constantine G. and Cervera Roldan, Angel and Rogers, Trent and Woods, Damien}, title = {{Tile Blockers as a Simple Motif to Control Self-Assembly: Kinetics and Thermodynamics}}, booktitle = {31st International Conference on DNA Computing and Molecular Programming (DNA 31)}, pages = {7:1--7:19}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-399-7}, ISSN = {1868-8969}, year = {2025}, volume = {347}, editor = {Schaeffer, Josie and Zhang, Fei}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.31.7}, URN = {urn:nbn:de:0030-drops-238564}, doi = {10.4230/LIPIcs.DNA.31.7}, annote = {Keywords: Self-assembly, kinetic model, kinetic simulation, thermodynamic prediction} }
Matthew J. Patitz and Trent A. Rogers. An Axiomatic Study of Leveraging Blockers to Self-Assemble Arbitrary Shapes via Temperature Programming. In 31st International Conference on DNA Computing and Molecular Programming (DNA 31). Leibniz International Proceedings in Informatics (LIPIcs), Volume 347, pp. 8:1-8:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)
@InProceedings{patitz_et_al:LIPIcs.DNA.31.8, author = {Patitz, Matthew J. and Rogers, Trent A.}, title = {{An Axiomatic Study of Leveraging Blockers to Self-Assemble Arbitrary Shapes via Temperature Programming}}, booktitle = {31st International Conference on DNA Computing and Molecular Programming (DNA 31)}, pages = {8:1--8:20}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-399-7}, ISSN = {1868-8969}, year = {2025}, volume = {347}, editor = {Schaeffer, Josie and Zhang, Fei}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.31.8}, URN = {urn:nbn:de:0030-drops-238574}, doi = {10.4230/LIPIcs.DNA.31.8}, annote = {Keywords: DNA tiles, self-assembly, temperature programming} }
Florent Becker, Phillip Drake, Matthew J. Patitz, and Trent A. Rogers. Synchronous Versus Asynchronous Tile-Based Self-Assembly. In 31st International Conference on DNA Computing and Molecular Programming (DNA 31). Leibniz International Proceedings in Informatics (LIPIcs), Volume 347, pp. 9:1-9:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)
@InProceedings{becker_et_al:LIPIcs.DNA.31.9, author = {Becker, Florent and Drake, Phillip and Patitz, Matthew J. and Rogers, Trent A.}, title = {{Synchronous Versus Asynchronous Tile-Based Self-Assembly}}, booktitle = {31st International Conference on DNA Computing and Molecular Programming (DNA 31)}, pages = {9:1--9:21}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-399-7}, ISSN = {1868-8969}, year = {2025}, volume = {347}, editor = {Schaeffer, Josie and Zhang, Fei}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.31.9}, URN = {urn:nbn:de:0030-drops-238580}, doi = {10.4230/LIPIcs.DNA.31.9}, annote = {Keywords: self-assembly, noncooperative self-assembly, models of computation, tile assembly systems} }
Hamidreza Akef, Minki Hhan, and David Soloveichik. Computing and Bounding Equilibrium Concentrations in Athermic Chemical Systems. In 31st International Conference on DNA Computing and Molecular Programming (DNA 31). Leibniz International Proceedings in Informatics (LIPIcs), Volume 347, pp. 10:1-10:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)
@InProceedings{akef_et_al:LIPIcs.DNA.31.10, author = {Akef, Hamidreza and Hhan, Minki and Soloveichik, David}, title = {{Computing and Bounding Equilibrium Concentrations in Athermic Chemical Systems}}, booktitle = {31st International Conference on DNA Computing and Molecular Programming (DNA 31)}, pages = {10:1--10:19}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-399-7}, ISSN = {1868-8969}, year = {2025}, volume = {347}, editor = {Schaeffer, Josie and Zhang, Fei}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.31.10}, URN = {urn:nbn:de:0030-drops-238595}, doi = {10.4230/LIPIcs.DNA.31.10}, annote = {Keywords: Equilibrium concentrations, Thermodynamic Binding Networks, Monomer-polymer model, Detailed balance} }
Zoë Evelyn Mōhalakealoha Derauf and Chris Thachuk. Leakless Polymerase-Dependent Strand Displacement Systems. In 31st International Conference on DNA Computing and Molecular Programming (DNA 31). Leibniz International Proceedings in Informatics (LIPIcs), Volume 347, pp. 11:1-11:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)
@InProceedings{derauf_et_al:LIPIcs.DNA.31.11, author = {Derauf, Zo\"{e} Evelyn M\={o}halakealoha and Thachuk, Chris}, title = {{Leakless Polymerase-Dependent Strand Displacement Systems}}, booktitle = {31st International Conference on DNA Computing and Molecular Programming (DNA 31)}, pages = {11:1--11:19}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-399-7}, ISSN = {1868-8969}, year = {2025}, volume = {347}, editor = {Schaeffer, Josie and Zhang, Fei}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.31.11}, URN = {urn:nbn:de:0030-drops-238608}, doi = {10.4230/LIPIcs.DNA.31.11}, annote = {Keywords: DNA strand displacement, strand-displacing polymerases, molecular computation, energy barriers, kinetics} }
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