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)
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 261, 50th International Colloquium on Automata, Languages, and Programming (ICALP 2023)
Paul Beame and Niels Kornerup. Cumulative Memory Lower Bounds for Randomized and Quantum Computation. In 50th International Colloquium on Automata, Languages, and Programming (ICALP 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 261, pp. 17:1-17:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)
@InProceedings{beame_et_al:LIPIcs.ICALP.2023.17, author = {Beame, Paul and Kornerup, Niels}, title = {{Cumulative Memory Lower Bounds for Randomized and Quantum Computation}}, booktitle = {50th International Colloquium on Automata, Languages, and Programming (ICALP 2023)}, pages = {17:1--17:20}, 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-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.ICALP.2023.17}, URN = {urn:nbn:de:0030-drops-180694}, doi = {10.4230/LIPIcs.ICALP.2023.17}, annote = {Keywords: Cumulative memory complexity, time-space tradeoffs, branching programs, quantum lower bounds} }
Published in: LIPIcs, Volume 221, 1st Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2022)
David Doty and Aaron Ong. Simulating 3-Symbol Turing Machines with SIMD||DNA. In 1st Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 221, pp. 14:1-14:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)
@InProceedings{doty_et_al:LIPIcs.SAND.2022.14, author = {Doty, David and Ong, Aaron}, title = {{Simulating 3-Symbol Turing Machines with SIMD||DNA}}, booktitle = {1st Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2022)}, pages = {14:1--14:15}, 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-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.SAND.2022.14}, URN = {urn:nbn:de:0030-drops-159568}, doi = {10.4230/LIPIcs.SAND.2022.14}, annote = {Keywords: DNA storage, strand displacement, parallel computation} }
Published in: LIPIcs, Volume 205, 27th International Conference on DNA Computing and Molecular Programming (DNA 27) (2021)
Keenan Breik, Austin Luchsinger, and David Soloveichik. Molecular Machines from Topological Linkages. In 27th International Conference on DNA Computing and Molecular Programming (DNA 27). Leibniz International Proceedings in Informatics (LIPIcs), Volume 205, pp. 7:1-7:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)
@InProceedings{breik_et_al:LIPIcs.DNA.27.7, author = {Breik, Keenan and Luchsinger, Austin and Soloveichik, David}, title = {{Molecular Machines from Topological Linkages}}, booktitle = {27th International Conference on DNA Computing and Molecular Programming (DNA 27)}, pages = {7:1--7:20}, 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-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.27.7}, URN = {urn:nbn:de:0030-drops-146749}, doi = {10.4230/LIPIcs.DNA.27.7}, annote = {Keywords: chemical computation, mechanical computation, bioengineering, models of biochemistry, molecular machines, mechanical linkages, generic rigidity} }
Published in: LIPIcs, Volume 205, 27th International Conference on DNA Computing and Molecular Programming (DNA 27) (2021)
Tonglin Chen, Arnav Solanki, and Marc Riedel. Parallel Pairwise Operations on Data Stored in DNA: Sorting, Shifting, and Searching. In 27th International Conference on DNA Computing and Molecular Programming (DNA 27). Leibniz International Proceedings in Informatics (LIPIcs), Volume 205, pp. 11:1-11:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)
@InProceedings{chen_et_al:LIPIcs.DNA.27.11, author = {Chen, Tonglin and Solanki, Arnav and Riedel, Marc}, title = {{Parallel Pairwise Operations on Data Stored in DNA: Sorting, Shifting, and Searching}}, booktitle = {27th International Conference on DNA Computing and Molecular Programming (DNA 27)}, pages = {11:1--11:21}, 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-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.27.11}, URN = {urn:nbn:de:0030-drops-146780}, doi = {10.4230/LIPIcs.DNA.27.11}, annote = {Keywords: Molecular Computing, DNA Computing, DNA Storage, Parallel Computing, Strand Displacement} }
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-dev.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 80, 44th International Colloquium on Automata, Languages, and Programming (ICALP 2017)
Amanda Belleville, David Doty, and David Soloveichik. Hardness of Computing and Approximating Predicates and Functions with Leaderless Population Protocols. In 44th International Colloquium on Automata, Languages, and Programming (ICALP 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 80, pp. 141:1-141:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2017)
@InProceedings{belleville_et_al:LIPIcs.ICALP.2017.141, author = {Belleville, Amanda and Doty, David and Soloveichik, David}, title = {{Hardness of Computing and Approximating Predicates and Functions with Leaderless Population Protocols}}, booktitle = {44th International Colloquium on Automata, Languages, and Programming (ICALP 2017)}, pages = {141:1--141:14}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-041-5}, ISSN = {1868-8969}, year = {2017}, volume = {80}, editor = {Chatzigiannakis, Ioannis and Indyk, Piotr and Kuhn, Fabian and Muscholl, Anca}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.ICALP.2017.141}, URN = {urn:nbn:de:0030-drops-75044}, doi = {10.4230/LIPIcs.ICALP.2017.141}, annote = {Keywords: population protocol, time lower bound, stable computation} }
Published in: LIPIcs, Volume 5, 27th International Symposium on Theoretical Aspects of Computer Science (2010)
David Doty, Jack H. Lutz, Matthew J. Patitz, Scott M. Summers, and Damien Woods. Intrinsic Universality in Self-Assembly. In 27th International Symposium on Theoretical Aspects of Computer Science. Leibniz International Proceedings in Informatics (LIPIcs), Volume 5, pp. 275-286, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2010)
@InProceedings{doty_et_al:LIPIcs.STACS.2010.2461, author = {Doty, David and Lutz, Jack H. and Patitz, Matthew J. and Summers, Scott M. and Woods, Damien}, title = {{Intrinsic Universality in Self-Assembly}}, booktitle = {27th International Symposium on Theoretical Aspects of Computer Science}, pages = {275--286}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-939897-16-3}, ISSN = {1868-8969}, year = {2010}, volume = {5}, editor = {Marion, Jean-Yves and Schwentick, Thomas}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.STACS.2010.2461}, URN = {urn:nbn:de:0030-drops-24619}, doi = {10.4230/LIPIcs.STACS.2010.2461}, annote = {Keywords: Biological computing, Molecular computation, intrinsic universality, self-assembly} }
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