Published in: LIPIcs, Volume 347, 31st International Conference on DNA Computing and Molecular Programming (DNA 31) (2025)
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} }
Published in: LIPIcs, Volume 334, 52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025)
Ahmed Shalaby and Damien Woods. An Efficient Algorithm to Compute the Minimum Free Energy of Interacting Nucleic Acid Strands. In 52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 334, pp. 130:1-130:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)
@InProceedings{shalaby_et_al:LIPIcs.ICALP.2025.130, author = {Shalaby, Ahmed and Woods, Damien}, title = {{An Efficient Algorithm to Compute the Minimum Free Energy of Interacting Nucleic Acid Strands}}, booktitle = {52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025)}, pages = {130:1--130:20}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-372-0}, ISSN = {1868-8969}, year = {2025}, volume = {334}, editor = {Censor-Hillel, Keren and Grandoni, Fabrizio and Ouaknine, Jo\"{e}l 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.2025.130}, URN = {urn:nbn:de:0030-drops-235071}, doi = {10.4230/LIPIcs.ICALP.2025.130}, annote = {Keywords: Minimum free energy, MFE, partition function, nucleic acid, DNA, RNA, secondary structure, computational complexity, algorithm analysis and design, dynamic programming} }
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)
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.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} }