LIPIcs, Volume 174
DNA 26, September 14-17, 2020, Oxford, UK (Virtual Conference)
Editors: Cody Geary and Matthew J. Patitz
Published in: Dagstuhl Reports, Volume 13, Issue 2 (2023)
Aaron Becker, Sándor Fekete, Irina Kostitsyna, Matthew J. Patitz, Damien Woods, and Ioannis Chatzigiannakis. Algorithmic Foundations of Programmable Matter (Dagstuhl Seminar 23091). In Dagstuhl Reports, Volume 13, Issue 2, pp. 183-198, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2023)
@Article{becker_et_al:DagRep.13.2.183, author = {Becker, Aaron and Fekete, S\'{a}ndor and Kostitsyna, Irina and Patitz, Matthew J. and Woods, Damien and Chatzigiannakis, Ioannis}, title = {{Algorithmic Foundations of Programmable Matter (Dagstuhl Seminar 23091)}}, pages = {183--198}, journal = {Dagstuhl Reports}, ISSN = {2192-5283}, year = {2023}, volume = {13}, number = {2}, editor = {Becker, Aaron and Fekete, S\'{a}ndor and Kostitsyna, Irina and Patitz, Matthew J. and Woods, Damien and Chatzigiannakis, Ioannis}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/DagRep.13.2.183}, URN = {urn:nbn:de:0030-drops-191848}, doi = {10.4230/DagRep.13.2.183}, annote = {Keywords: computational geometry, distributed algorithms, DNA computing, programmable matter, swarm robotics} }
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.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 261, 50th International Colloquium on Automata, Languages, and Programming (ICALP 2023)
Daniel Hader and Matthew J. Patitz. The Impacts of Dimensionality, Diffusion, and Directedness on Intrinsic Cross-Model Simulation in Tile-Based Self-Assembly. In 50th International Colloquium on Automata, Languages, and Programming (ICALP 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 261, pp. 71:1-71:19, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2023)
@InProceedings{hader_et_al:LIPIcs.ICALP.2023.71, author = {Hader, Daniel and Patitz, Matthew J.}, title = {{The Impacts of Dimensionality, Diffusion, and Directedness on Intrinsic Cross-Model Simulation in Tile-Based Self-Assembly}}, booktitle = {50th International Colloquium on Automata, Languages, and Programming (ICALP 2023)}, pages = {71:1--71:19}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-278-5}, ISSN = {1868-8969}, year = {2023}, volume = {261}, editor = {Etessami, Kousha and Feige, Uriel and Puppis, Gabriele}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICALP.2023.71}, URN = {urn:nbn:de:0030-drops-181238}, doi = {10.4230/LIPIcs.ICALP.2023.71}, annote = {Keywords: Tile-Assembly, Tiles, aTAM, Intrinsic Simulation, Simulation} }
Published in: LIPIcs, Volume 238, 28th International Conference on DNA Computing and Molecular Programming (DNA 28) (2022)
Andrew Alseth, Daniel Hader, and Matthew J. Patitz. Universal Shape Replication via Self-Assembly with Signal-Passing Tiles (Extended Abstract). In 28th International Conference on DNA Computing and Molecular Programming (DNA 28). Leibniz International Proceedings in Informatics (LIPIcs), Volume 238, pp. 2:1-2:24, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2022)
@InProceedings{alseth_et_al:LIPIcs.DNA.28.2, author = {Alseth, Andrew and Hader, Daniel and Patitz, Matthew J.}, title = {{Universal Shape Replication via Self-Assembly with Signal-Passing Tiles}}, booktitle = {28th International Conference on DNA Computing and Molecular Programming (DNA 28)}, pages = {2:1--2:24}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-253-2}, ISSN = {1868-8969}, year = {2022}, volume = {238}, editor = {Ouldridge, Thomas E. and Wickham, Shelley F. J.}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.28.2}, URN = {urn:nbn:de:0030-drops-167876}, doi = {10.4230/LIPIcs.DNA.28.2}, annote = {Keywords: Algorithmic self-assembly, Tile Assembly Model, shape replication} }
Published in: LIPIcs, Volume 205, 27th International Conference on DNA Computing and Molecular Programming (DNA 27) (2021)
Andrew Alseth, Daniel Hader, and Matthew J. Patitz. Self-Replication via Tile Self-Assembly (Extended Abstract). In 27th International Conference on DNA Computing and Molecular Programming (DNA 27). Leibniz International Proceedings in Informatics (LIPIcs), Volume 205, pp. 3:1-3:22, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2021)
@InProceedings{alseth_et_al:LIPIcs.DNA.27.3, author = {Alseth, Andrew and Hader, Daniel and Patitz, Matthew J.}, title = {{Self-Replication via Tile Self-Assembly (Extended Abstract)}}, booktitle = {27th International Conference on DNA Computing and Molecular Programming (DNA 27)}, pages = {3:1--3:22}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-205-1}, ISSN = {1868-8969}, year = {2021}, volume = {205}, editor = {Lakin, Matthew R. and \v{S}ulc, Petr}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.27.3}, URN = {urn:nbn:de:0030-drops-146707}, doi = {10.4230/LIPIcs.DNA.27.3}, annote = {Keywords: Algorithmic self-assembly, tile assembly model, self-replication} }
Published in: LIPIcs, Volume 174, 26th International Conference on DNA Computing and Molecular Programming (DNA 26) (2020)
Cody Geary and Matthew J. Patitz. LIPIcs, Volume 174, DNA 26, Complete Volume. In 26th International Conference on DNA Computing and Molecular Programming (DNA 26). Leibniz International Proceedings in Informatics (LIPIcs), Volume 174, pp. 1-230, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2020)
@Proceedings{geary_et_al:LIPIcs.DNA.2020, title = {{LIPIcs, Volume 174, DNA 26, Complete Volume}}, booktitle = {26th International Conference on DNA Computing and Molecular Programming (DNA 26)}, pages = {1--230}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-163-4}, ISSN = {1868-8969}, year = {2020}, volume = {174}, editor = {Geary, Cody and Patitz, Matthew J.}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.2020}, URN = {urn:nbn:de:0030-drops-129529}, doi = {10.4230/LIPIcs.DNA.2020}, annote = {Keywords: LIPIcs, Volume 174, DNA 26, Complete Volume} }
Published in: LIPIcs, Volume 174, 26th International Conference on DNA Computing and Molecular Programming (DNA 26) (2020)
Cody Geary and Matthew J. Patitz. Front Matter, Table of Contents, Preface, Conference Organization. In 26th International Conference on DNA Computing and Molecular Programming (DNA 26). Leibniz International Proceedings in Informatics (LIPIcs), Volume 174, pp. 0:i-0:xiv, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2020)
@InProceedings{geary_et_al:LIPIcs.DNA.2020.0, author = {Geary, Cody and Patitz, Matthew J.}, title = {{Front Matter, Table of Contents, Preface, Conference Organization}}, booktitle = {26th International Conference on DNA Computing and Molecular Programming (DNA 26)}, pages = {0:i--0:xiv}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-163-4}, ISSN = {1868-8969}, year = {2020}, volume = {174}, editor = {Geary, Cody and Patitz, Matthew J.}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.2020.0}, URN = {urn:nbn:de:0030-drops-129533}, doi = {10.4230/LIPIcs.DNA.2020.0}, annote = {Keywords: Front Matter, Table of Contents, Preface, Conference Organization} }
Published in: LIPIcs, Volume 174, 26th International Conference on DNA Computing and Molecular Programming (DNA 26) (2020)
Abdulmelik Mohammed, Nataša Jonoska, and Masahico Saito. The Topology of Scaffold Routings on Non-Spherical Mesh Wireframes. In 26th International Conference on DNA Computing and Molecular Programming (DNA 26). Leibniz International Proceedings in Informatics (LIPIcs), Volume 174, pp. 1:1-1:17, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2020)
@InProceedings{mohammed_et_al:LIPIcs.DNA.2020.1, author = {Mohammed, Abdulmelik and Jonoska, Nata\v{s}a and Saito, Masahico}, title = {{The Topology of Scaffold Routings on Non-Spherical Mesh Wireframes}}, booktitle = {26th International Conference on DNA Computing and Molecular Programming (DNA 26)}, pages = {1:1--1:17}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-163-4}, ISSN = {1868-8969}, year = {2020}, volume = {174}, editor = {Geary, Cody and Patitz, Matthew J.}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.2020.1}, URN = {urn:nbn:de:0030-drops-129540}, doi = {10.4230/LIPIcs.DNA.2020.1}, annote = {Keywords: DNA origami, Scaffold routing, Graphs, Surfaces, Knots, Eulerian circuits} }
Published in: LIPIcs, Volume 174, 26th International Conference on DNA Computing and Molecular Programming (DNA 26) (2020)
Robert F. Johnson and Lulu Qian. Simplifying Chemical Reaction Network Implementations with Two-Stranded DNA Building Blocks. In 26th International Conference on DNA Computing and Molecular Programming (DNA 26). Leibniz International Proceedings in Informatics (LIPIcs), Volume 174, pp. 2:1-2:14, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2020)
@InProceedings{johnson_et_al:LIPIcs.DNA.2020.2, author = {Johnson, Robert F. and Qian, Lulu}, title = {{Simplifying Chemical Reaction Network Implementations with Two-Stranded DNA Building Blocks}}, booktitle = {26th International Conference on DNA Computing and Molecular Programming (DNA 26)}, pages = {2:1--2:14}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-163-4}, ISSN = {1868-8969}, year = {2020}, volume = {174}, editor = {Geary, Cody and Patitz, Matthew J.}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.2020.2}, URN = {urn:nbn:de:0030-drops-129557}, doi = {10.4230/LIPIcs.DNA.2020.2}, annote = {Keywords: Molecular programming, DNA computing, Chemical Reaction Networks, DNA strand displacement} }
Published in: LIPIcs, Volume 174, 26th International Conference on DNA Computing and Molecular Programming (DNA 26) (2020)
Hooman Hashemi, Ben Chugg, and Anne Condon. Composable Computation in Leaderless, Discrete Chemical Reaction Networks. In 26th International Conference on DNA Computing and Molecular Programming (DNA 26). Leibniz International Proceedings in Informatics (LIPIcs), Volume 174, pp. 3:1-3:18, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2020)
@InProceedings{hashemi_et_al:LIPIcs.DNA.2020.3, author = {Hashemi, Hooman and Chugg, Ben and Condon, Anne}, title = {{Composable Computation in Leaderless, Discrete Chemical Reaction Networks}}, booktitle = {26th International Conference on DNA Computing and Molecular Programming (DNA 26)}, pages = {3:1--3:18}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-163-4}, ISSN = {1868-8969}, year = {2020}, volume = {174}, editor = {Geary, Cody and Patitz, Matthew J.}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.2020.3}, URN = {urn:nbn:de:0030-drops-129560}, doi = {10.4230/LIPIcs.DNA.2020.3}, annote = {Keywords: Chemical Reaction Networks, Stable Function Computation, Output-Oblivious, Output-Monotonic} }
Published in: LIPIcs, Volume 174, 26th International Conference on DNA Computing and Molecular Programming (DNA 26) (2020)
Marko Vasic, David Soloveichik, and Sarfraz Khurshid. CRNs Exposed: A Method for the Systematic Exploration of Chemical Reaction Networks. In 26th International Conference on DNA Computing and Molecular Programming (DNA 26). Leibniz International Proceedings in Informatics (LIPIcs), Volume 174, pp. 4:1-4:25, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2020)
@InProceedings{vasic_et_al:LIPIcs.DNA.2020.4, author = {Vasic, Marko and Soloveichik, David and Khurshid, Sarfraz}, title = {{CRNs Exposed: A Method for the Systematic Exploration of Chemical Reaction Networks}}, booktitle = {26th International Conference on DNA Computing and Molecular Programming (DNA 26)}, pages = {4:1--4:25}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-163-4}, ISSN = {1868-8969}, year = {2020}, volume = {174}, editor = {Geary, Cody and Patitz, Matthew J.}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.2020.4}, URN = {urn:nbn:de:0030-drops-129574}, doi = {10.4230/LIPIcs.DNA.2020.4}, annote = {Keywords: molecular programming, formal methods} }
Published in: LIPIcs, Volume 174, 26th International Conference on DNA Computing and Molecular Programming (DNA 26) (2020)
James I. Lathrop, Jack H. Lutz, Robyn R. Lutz, Hugh D. Potter, and Matthew R. Riley. Population-Induced Phase Transitions and the Verification of Chemical Reaction Networks. In 26th International Conference on DNA Computing and Molecular Programming (DNA 26). Leibniz International Proceedings in Informatics (LIPIcs), Volume 174, pp. 5:1-5:17, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2020)
@InProceedings{lathrop_et_al:LIPIcs.DNA.2020.5, author = {Lathrop, James I. and Lutz, Jack H. and Lutz, Robyn R. and Potter, Hugh D. and Riley, Matthew R.}, title = {{Population-Induced Phase Transitions and the Verification of Chemical Reaction Networks}}, booktitle = {26th International Conference on DNA Computing and Molecular Programming (DNA 26)}, pages = {5:1--5:17}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-163-4}, ISSN = {1868-8969}, year = {2020}, volume = {174}, editor = {Geary, Cody and Patitz, Matthew J.}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.2020.5}, URN = {urn:nbn:de:0030-drops-129583}, doi = {10.4230/LIPIcs.DNA.2020.5}, annote = {Keywords: chemical reaction networks, molecular programming, phase transitions, population protocols, verification} }
Published in: LIPIcs, Volume 174, 26th International Conference on DNA Computing and Molecular Programming (DNA 26) (2020)
Titus H. Klinge, James I. Lathrop, Sonia Moreno, Hugh D. Potter, Narun K. Raman, and Matthew R. Riley. ALCH: An Imperative Language for Chemical Reaction Network-Controlled Tile Assembly. In 26th International Conference on DNA Computing and Molecular Programming (DNA 26). Leibniz International Proceedings in Informatics (LIPIcs), Volume 174, pp. 6:1-6:22, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2020)
@InProceedings{klinge_et_al:LIPIcs.DNA.2020.6, author = {Klinge, Titus H. and Lathrop, James I. and Moreno, Sonia and Potter, Hugh D. and Raman, Narun K. and Riley, Matthew R.}, title = {{ALCH: An Imperative Language for Chemical Reaction Network-Controlled Tile Assembly}}, booktitle = {26th International Conference on DNA Computing and Molecular Programming (DNA 26)}, pages = {6:1--6:22}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-163-4}, ISSN = {1868-8969}, year = {2020}, volume = {174}, editor = {Geary, Cody and Patitz, Matthew J.}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.2020.6}, URN = {urn:nbn:de:0030-drops-129592}, doi = {10.4230/LIPIcs.DNA.2020.6}, annote = {Keywords: Tile assembly, Chemical reaction network, Sierpinski triangle} }
Published in: LIPIcs, Volume 174, 26th International Conference on DNA Computing and Molecular Programming (DNA 26) (2020)
Antti Lankinen, Ismael Mullor Ruiz, and Thomas E. Ouldridge. Implementing Non-Equilibrium Networks with Active Circuits of Duplex Catalysts. In 26th International Conference on DNA Computing and Molecular Programming (DNA 26). Leibniz International Proceedings in Informatics (LIPIcs), Volume 174, pp. 7:1-7:25, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2020)
@InProceedings{lankinen_et_al:LIPIcs.DNA.2020.7, author = {Lankinen, Antti and Mullor Ruiz, Ismael and Ouldridge, Thomas E.}, title = {{Implementing Non-Equilibrium Networks with Active Circuits of Duplex Catalysts}}, booktitle = {26th International Conference on DNA Computing and Molecular Programming (DNA 26)}, pages = {7:1--7:25}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-163-4}, ISSN = {1868-8969}, year = {2020}, volume = {174}, editor = {Geary, Cody and Patitz, Matthew J.}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.2020.7}, URN = {urn:nbn:de:0030-drops-129602}, doi = {10.4230/LIPIcs.DNA.2020.7}, annote = {Keywords: DNA strand displacement, Catalysis, Information-processing networks} }
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