TAPDANCE: Publications

Publications

Hardness of Busy Beaver Value BB(15)
Tristan Stérin, Damien Woods
International Conference on Reachability Problems
Springer Nature Switzerland, LNCS 15050:120--137, 2024 [Proceedings], [arXiv], [bib], [blog post], [browser-based simulator], [simulator source code]
An efficient algorithm to compute the minimum free energy of interacting nucleic acid strands
Ahmed Shalaby, Damien Woods
2024 [arXiv], [bib]
Minimum free energy, partition function and kinetics simulation algorithms for a multistranded scaffolded DNA computer
Erik D. Demaine, Timothy Gomez, Elise Grizzell, Markus Hecher, Jayson Lynch, Robert Schweller, Ahmed Shalaby, Damien Woods
DNA30: The 30th International Conference on DNA Computing and Molecular Programming
Schloss Dagstuhl—Leibniz-Zentrum für Informatik LIPIcs:To appear, 2024 [proceedings],
[Open Access full paper to appear], [bib]
Pattern recognition in the nucleation kinetics of non-equilibrium self-assembly
Constantine Glen Evans, Jackson O’Brien, Erik Winfree, Arvind Murugan
Nature
625:500-507, 2024 [Nature]

Harvesting Brownian Motion: Zero Energy Computational Sampling
David Doty, Niels Kornerup, Austin Luchsinger, Leo Orshansky, David Soloveichik, Damien Woods
2023 [arXiv]
Six Tiles: From Collatz Sequences to Algorithmic DNA Origami
Tristan Stérin
PhD thesis. Maynooth University. 2023
Minimum free energy, partition function and kinetics simulation algorithms for a multistranded scaffolded DNA computer
Ahmed Shalaby, Chris Thachuk, Damien Woods
DNA29: The 29th International Conference on DNA Computing and Molecular Programming
Schloss Dagstuhl—Leibniz-Zentrum für Informatik LIPIcs:1:1--1:22, 2023 [proceedings],
[Open Access full paper], [bib]

Turning machines: a simple algorithmic model for molecular robotics
Irina Kostitsyna, Cai Wood, Damien Woods
Natural Computing Springer 2022 (Open Access published on 22/2/22)
[Open Access full paper], [arXiv], [bib], [blog post],

On the hardness of knowing busy beaver values BB(15) and BB(5,4)
Tristan Stérin, Damien Woods
Preprint. 2021 [arXiv], [browser-based simulator], [simulator source code], [bib], [blog post]
Small tile sets that compute while solving mazes
Matthew Cook, Tristan Stérin, Damien Woods
DNA27: The 27th International Conference on DNA Computing and Molecular Programming
Schloss Dagstuhl—Leibniz-Zentrum für Informatik, LIPIcs 205:8:1--8:20, 2021 [Proceedings], [arXiv], [bib], [blog post]

Diverse and robust molecular algorithms using reprogrammable DNA self-assembly
Damien Woods, David Doty, Cameron Myhrvold, Joy Hui, Felix Zhou, Peng Yin, Erik Winfree
Nature
567:366—372, 2019 (Woods & Doty joint lead co-authors). [pdf], [Nature version], [video presentation], [bib],
Suppl Info A (theory, design, results), Suppl Info B (DNA sequences), Suppl Info C (sample images), DNA sequence design code, Data and analysis code (to reproduce our findings, and discover your own), Raw data (AFM images in Bruker file format)
Media: The Irish Times, Chemistry World, PhysicsWorld, Wired, IEEE Spectrum, Silicon Republic, Europa Press (in Spanish), Nature Asia, The California Aggie.
Live interviews: Futureproof on Newstalk radio, Short video interview, The Wider View on Northern Sound.
Press releases: Maynooth University, Inria (in French), Caltech, UC Davis.
An art exhibition with some quirky visitors. Erik's blurbification.
Non-cooperatively assembling large structures
Pierre-Étienne Meunier, Damien Regnault
DNA25: The 25th International Conference on DNA Computing and Molecular Programming
Springer LNCS 11648:120—139, 2019 [arxiv], [paper]

Proving the Turing Universality of Oritatami Co-Transcriptional Folding
Cody Geary, Pierre-Étienne Meunier, Nicolas Schabanel, Shinnosuke Seki
ISAAC: The 29th International Symposium on Algorithms and Computation
LIPIcs:23:1—23:13, 2018 [arxiv], [LIPIcs]

A cargo-sorting DNA robot
Anupama J. Thubagere, Wei Li, Robert F. Johnson, Zibo Chen, Shayan Doroudi, Yae Lim Lee, Gregory Izatt, Sarah Wittman, Niranjan Srinivas, Damien Woods, Erik Winfree, Lulu Qian
Science
357 (6356, eaan6558) 2017 [paper], [Supplementary Material]
Science perspective 357(6356):1095-1096, by John Reif
Thermodynamic Binding Networks
David Doty, Trent Rogers, David Soloveichik, Chris Thachuk, Damien Woods
DNA23: The 23rd International Conference on DNA Computing and Molecular Programming
Springer LNCS 10467:249—266, 2017 [arxiv], [pdf]
Binary Pattern Tileset Synthesis is NP-hard
Lila Kari, Steffen Kopecki, Pierre-Étienne Meunier, Matthew J. Patitz, Shinnosuke Seki
Algorithmica
78:1—46, 2017 [arxiv]
The non-cooperative tile assembly model is not intrinsically universal or capable of bounded Turing machine simulation
Pierre-Étienne Meunier, Damien Woods
STOC 2017: Proceedings of the 49th Annual ACM SIGACT Symposium on Theory of Computing
ACM:328—341, 2017 [arxiv], [bib]

Damien's pre-2017 papers.