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 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.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 257, 2nd Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2023)
Robert M. Alaniz, David Caballero, Timothy Gomez, Elise Grizzell, Andrew Rodriguez, Robert Schweller, and Tim Wylie. Covert Computation in the Abstract Tile-Assembly Model. In 2nd Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 257, pp. 12:1-12:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)
@InProceedings{alaniz_et_al:LIPIcs.SAND.2023.12, author = {Alaniz, Robert M. and Caballero, David and Gomez, Timothy and Grizzell, Elise and Rodriguez, Andrew and Schweller, Robert and Wylie, Tim}, title = {{Covert Computation in the Abstract Tile-Assembly Model}}, booktitle = {2nd Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2023)}, pages = {12:1--12:17}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-275-4}, ISSN = {1868-8969}, year = {2023}, volume = {257}, editor = {Doty, David and Spirakis, Paul}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SAND.2023.12}, URN = {urn:nbn:de:0030-drops-179482}, doi = {10.4230/LIPIcs.SAND.2023.12}, annote = {Keywords: self-assembly, covert computation, atam} }
Published in: LIPIcs, Volume 229, 49th International Colloquium on Automata, Languages, and Programming (ICALP 2022)
David Caballero, Timothy Gomez, Robert Schweller, and Tim Wylie. Unique Assembly Verification in Two-Handed Self-Assembly. In 49th International Colloquium on Automata, Languages, and Programming (ICALP 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 229, pp. 34:1-34:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)
@InProceedings{caballero_et_al:LIPIcs.ICALP.2022.34, author = {Caballero, David and Gomez, Timothy and Schweller, Robert and Wylie, Tim}, title = {{Unique Assembly Verification in Two-Handed Self-Assembly}}, booktitle = {49th International Colloquium on Automata, Languages, and Programming (ICALP 2022)}, pages = {34:1--34:21}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-235-8}, ISSN = {1868-8969}, year = {2022}, volume = {229}, editor = {Boja\'{n}czyk, Miko{\l}aj and Merelli, Emanuela and Woodruff, David P.}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICALP.2022.34}, URN = {urn:nbn:de:0030-drops-163751}, doi = {10.4230/LIPIcs.ICALP.2022.34}, annote = {Keywords: self-assembly, unique assembly verification, 2-handed assembly model} }
Published in: LIPIcs, Volume 221, 1st Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2022)
Robert M. Alaniz, David Caballero, Sonya C. Cirlos, Timothy Gomez, Elise Grizzell, Andrew Rodriguez, Robert Schweller, Armando Tenorio, and Tim Wylie. Building Squares with Optimal State Complexity in Restricted Active Self-Assembly. In 1st Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 221, pp. 6:1-6:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)
@InProceedings{alaniz_et_al:LIPIcs.SAND.2022.6, author = {Alaniz, Robert M. and Caballero, David and Cirlos, Sonya C. and Gomez, Timothy and Grizzell, Elise and Rodriguez, Andrew and Schweller, Robert and Tenorio, Armando and Wylie, Tim}, title = {{Building Squares with Optimal State Complexity in Restricted Active Self-Assembly}}, booktitle = {1st Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2022)}, pages = {6:1--6:18}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-224-2}, ISSN = {1868-8969}, year = {2022}, volume = {221}, editor = {Aspnes, James and Michail, Othon}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SAND.2022.6}, URN = {urn:nbn:de:0030-drops-159482}, doi = {10.4230/LIPIcs.SAND.2022.6}, annote = {Keywords: Active Self-Assembly, State Complexity, Tile Automata} }
Published in: LIPIcs, Volume 221, 1st Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2022)
David Caballero, Timothy Gomez, Robert Schweller, and Tim Wylie. Complexity of Verification in Self-Assembly with Prebuilt Assemblies. In 1st Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 221, pp. 8:1-8:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)
@InProceedings{caballero_et_al:LIPIcs.SAND.2022.8, author = {Caballero, David and Gomez, Timothy and Schweller, Robert and Wylie, Tim}, title = {{Complexity of Verification in Self-Assembly with Prebuilt Assemblies}}, booktitle = {1st Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2022)}, pages = {8:1--8:15}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-224-2}, ISSN = {1868-8969}, year = {2022}, volume = {221}, editor = {Aspnes, James and Michail, Othon}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SAND.2022.8}, URN = {urn:nbn:de:0030-drops-159503}, doi = {10.4230/LIPIcs.SAND.2022.8}, annote = {Keywords: 2-handed assembly, verification, prebuilt} }
Published in: LIPIcs, Volume 204, 29th Annual European Symposium on Algorithms (ESA 2021)
David Caballero, Timothy Gomez, Robert Schweller, and Tim Wylie. Covert Computation in Staged Self-Assembly: Verification Is PSPACE-Complete. In 29th Annual European Symposium on Algorithms (ESA 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 204, pp. 23:1-23:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)
@InProceedings{caballero_et_al:LIPIcs.ESA.2021.23, author = {Caballero, David and Gomez, Timothy and Schweller, Robert and Wylie, Tim}, title = {{Covert Computation in Staged Self-Assembly: Verification Is PSPACE-Complete}}, booktitle = {29th Annual European Symposium on Algorithms (ESA 2021)}, pages = {23:1--23:18}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-204-4}, ISSN = {1868-8969}, year = {2021}, volume = {204}, editor = {Mutzel, Petra and Pagh, Rasmus and Herman, Grzegorz}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ESA.2021.23}, URN = {urn:nbn:de:0030-drops-146047}, doi = {10.4230/LIPIcs.ESA.2021.23}, annote = {Keywords: self-assembly, covert computation, staged self-assembly, assembly verification} }
Published in: LIPIcs, Volume 181, 31st International Symposium on Algorithms and Computation (ISAAC 2020)
Angel A. Cantu, Austin Luchsinger, Robert Schweller, and Tim Wylie. Signal Passing Self-Assembly Simulates Tile Automata. In 31st International Symposium on Algorithms and Computation (ISAAC 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 181, pp. 53:1-53:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)
@InProceedings{cantu_et_al:LIPIcs.ISAAC.2020.53, author = {Cantu, Angel A. and Luchsinger, Austin and Schweller, Robert and Wylie, Tim}, title = {{Signal Passing Self-Assembly Simulates Tile Automata}}, booktitle = {31st International Symposium on Algorithms and Computation (ISAAC 2020)}, pages = {53:1--53:17}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-173-3}, ISSN = {1868-8969}, year = {2020}, volume = {181}, editor = {Cao, Yixin and Cheng, Siu-Wing and Li, Minming}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ISAAC.2020.53}, URN = {urn:nbn:de:0030-drops-133978}, doi = {10.4230/LIPIcs.ISAAC.2020.53}, annote = {Keywords: self-assembly, signal-passing tile assembly model, tile automata, cellular automata, simulation} }
Published in: LIPIcs, Volume 174, 26th International Conference on DNA Computing and Molecular Programming (DNA 26) (2020)
David Caballero, Timothy Gomez, Robert Schweller, and Tim Wylie. Verification and Computation in Restricted Tile Automata. In 26th International Conference on DNA Computing and Molecular Programming (DNA 26). Leibniz International Proceedings in Informatics (LIPIcs), Volume 174, pp. 10:1-10:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)
@InProceedings{caballero_et_al:LIPIcs.DNA.2020.10, author = {Caballero, David and Gomez, Timothy and Schweller, Robert and Wylie, Tim}, title = {{Verification and Computation in Restricted Tile Automata}}, booktitle = {26th International Conference on DNA Computing and Molecular Programming (DNA 26)}, pages = {10:1--10:18}, 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.2020.10}, URN = {urn:nbn:de:0030-drops-129635}, doi = {10.4230/LIPIcs.DNA.2020.10}, annote = {Keywords: Tile Automata, Turing Machines, Unique Assembly Verification} }
Published in: LIPIcs, Volume 132, 46th International Colloquium on Automata, Languages, and Programming (ICALP 2019)
Angel A. Cantu, Austin Luchsinger, Robert Schweller, and Tim Wylie. Covert Computation in Self-Assembled Circuits. In 46th International Colloquium on Automata, Languages, and Programming (ICALP 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 132, pp. 31:1-31:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)
@InProceedings{cantu_et_al:LIPIcs.ICALP.2019.31, author = {Cantu, Angel A. and Luchsinger, Austin and Schweller, Robert and Wylie, Tim}, title = {{Covert Computation in Self-Assembled Circuits}}, booktitle = {46th International Colloquium on Automata, Languages, and Programming (ICALP 2019)}, pages = {31:1--31:14}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-109-2}, ISSN = {1868-8969}, year = {2019}, volume = {132}, editor = {Baier, Christel and Chatzigiannakis, Ioannis and Flocchini, Paola and Leonardi, Stefano}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICALP.2019.31}, URN = {urn:nbn:de:0030-drops-106075}, doi = {10.4230/LIPIcs.ICALP.2019.31}, annote = {Keywords: self-assembly, covert circuits} }
Published in: LIPIcs, Volume 112, 26th Annual European Symposium on Algorithms (ESA 2018)
Cameron Chalk, Austin Luchsinger, Robert Schweller, and Tim Wylie. Self-Assembly of Any Shape with Constant Tile Types using High Temperature. In 26th Annual European Symposium on Algorithms (ESA 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 112, pp. 14:1-14:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)
@InProceedings{chalk_et_al:LIPIcs.ESA.2018.14, author = {Chalk, Cameron and Luchsinger, Austin and Schweller, Robert and Wylie, Tim}, title = {{Self-Assembly of Any Shape with Constant Tile Types using High Temperature}}, booktitle = {26th Annual European Symposium on Algorithms (ESA 2018)}, pages = {14:1--14:14}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-081-1}, ISSN = {1868-8969}, year = {2018}, volume = {112}, editor = {Azar, Yossi and Bast, Hannah and Herman, Grzegorz}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ESA.2018.14}, URN = {urn:nbn:de:0030-drops-94773}, doi = {10.4230/LIPIcs.ESA.2018.14}, annote = {Keywords: self-assembly, molecular computing, tiling, tile, shapes} }
Published in: LIPIcs, Volume 57, 24th Annual European Symposium on Algorithms (ESA 2016)
Cameron Chalk, Eric Martinez, Robert Schweller, Luis Vega, Andrew Winslow, and Tim Wylie. Optimal Staged Self-Assembly of General Shapes. In 24th Annual European Symposium on Algorithms (ESA 2016). Leibniz International Proceedings in Informatics (LIPIcs), Volume 57, pp. 26:1-26:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2016)
@InProceedings{chalk_et_al:LIPIcs.ESA.2016.26, author = {Chalk, Cameron and Martinez, Eric and Schweller, Robert and Vega, Luis and Winslow, Andrew and Wylie, Tim}, title = {{Optimal Staged Self-Assembly of General Shapes}}, booktitle = {24th Annual European Symposium on Algorithms (ESA 2016)}, pages = {26:1--26:17}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-015-6}, ISSN = {1868-8969}, year = {2016}, volume = {57}, editor = {Sankowski, Piotr and Zaroliagis, Christos}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ESA.2016.26}, URN = {urn:nbn:de:0030-drops-63776}, doi = {10.4230/LIPIcs.ESA.2016.26}, annote = {Keywords: Tile self-assembly, 2HAM, aTAM, DNA computing, biocomputing} }
Published in: LIPIcs, Volume 20, 30th International Symposium on Theoretical Aspects of Computer Science (STACS 2013)
Sarah Cannon, Erik D. Demaine, Martin L. Demaine, Sarah Eisenstat, Matthew J. Patitz, Robert T. Schweller, Scott M Summers, and Andrew Winslow. Two Hands Are Better Than One (up to constant factors): Self-Assembly In The 2HAM vs. aTAM. In 30th International Symposium on Theoretical Aspects of Computer Science (STACS 2013). Leibniz International Proceedings in Informatics (LIPIcs), Volume 20, pp. 172-184, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2013)
@InProceedings{cannon_et_al:LIPIcs.STACS.2013.172, author = {Cannon, Sarah and Demaine, Erik D. and Demaine, Martin L. and Eisenstat, Sarah and Patitz, Matthew J. and Schweller, Robert T. and Summers, Scott M and Winslow, Andrew}, title = {{Two Hands Are Better Than One (up to constant factors): Self-Assembly In The 2HAM vs. aTAM}}, booktitle = {30th International Symposium on Theoretical Aspects of Computer Science (STACS 2013)}, pages = {172--184}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-939897-50-7}, ISSN = {1868-8969}, year = {2013}, volume = {20}, editor = {Portier, Natacha and Wilke, Thomas}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.STACS.2013.172}, URN = {urn:nbn:de:0030-drops-39321}, doi = {10.4230/LIPIcs.STACS.2013.172}, annote = {Keywords: abstract tile assembly model, hierarchical tile assembly model, two-handed tile assembly model, algorithmic self-assembly, DNA computing, biocomputing} }
Published in: LIPIcs, Volume 9, 28th International Symposium on Theoretical Aspects of Computer Science (STACS 2011)
Erik D. Demaine, Matthew J. Patitz, Robert T. Schweller, and Scott M. Summers. Self-Assembly of Arbitrary Shapes Using RNAse Enzymes: Meeting the Kolmogorov Bound with Small Scale Factor (Extended Abstract). In 28th International Symposium on Theoretical Aspects of Computer Science (STACS 2011). Leibniz International Proceedings in Informatics (LIPIcs), Volume 9, pp. 201-212, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2011)
@InProceedings{demaine_et_al:LIPIcs.STACS.2011.201, author = {Demaine, Erik D. and Patitz, Matthew J. and Schweller, Robert T. and Summers, Scott M.}, title = {{Self-Assembly of Arbitrary Shapes Using RNAse Enzymes: Meeting the Kolmogorov Bound with Small Scale Factor}}, booktitle = {28th International Symposium on Theoretical Aspects of Computer Science (STACS 2011)}, pages = {201--212}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-939897-25-5}, ISSN = {1868-8969}, year = {2011}, volume = {9}, editor = {Schwentick, Thomas and D\"{u}rr, Christoph}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.STACS.2011.201}, URN = {urn:nbn:de:0030-drops-30118}, doi = {10.4230/LIPIcs.STACS.2011.201}, annote = {Keywords: Biomolecular computation, RNAse enzyme self-assembly, algorithmic self-assembly, Komogorov complexity} }
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