## Prof Damien Woods

### Biography

### Research Interests

### Research Projects

### Peer Reviewed Journal

Year | Publication | |
---|---|---|

2022 |
Irnia Kostitsyna, Cai Wood, Damien Woods (2022) 'Turning machines: a simple algorithmic model for molecular robotics'. Natural Computing, . [Link] [DOI] | |

2019 |
Damien Woods and David Doty and Cameron Myhrvold and Joy Hui and Felix Zhou and Peng Yin and Erik Winfree (2019) 'Diverse and robust molecular algorithms using reprogrammable DNA self-assembly'. Nature, 567 :366-372. [DOI] [Full-Text] | |

2017 |
Thubagere, Li, Johnson, Chen, Doroudi, Lee, Izatt, Wittman, Srinivas, Woods, Winfree, Qian (2017) 'A cargo-sorting DNA robot'. Science, 357 (6356). [DOI] [Full-Text] | |

2016 |
Demaine, Erik D and Patitz, Matthew J and Rogers, Trent A and Schweller, Robert T and Summers, Scott M and Woods, Damien (2016) 'The two-handed tile assembly model is not intrinsically universal'. 74 (2):812-850. [Full-Text] | |

2015 |
Woods, Damien (2015) 'Intrinsic universality and the computational power of self-assembly'. 373 (2046). [Full-Text] | |

2015 |
Chen, Moya and Xin, Doris and Woods, Damien (2015) 'Parallel Computation Using Active Self-assembly'. Natural Computing, 14 (2):225-250. [Full-Text] | |

2015 |
Woods, Damien and Neary, Turlough (2015) 'Yurii Rogozhin's Contributions to the Field of Small Universal Turing Machines'. 138 (1-2):251-258. [Full-Text] | |

2014 |
Murphy, Niall and Woods, Damien (2014) 'Uniformity is weaker than semi-uniformity for some membrane systems'. 134 (1-2):129-152. [Full-Text] | |

2014 |
Neary, Turlough and Woods, Damien and Murphy, Niall and Glaschick, Rainer (2014) 'Wang’s B machines are efficiently universal, as is Hasenjaeger’s small universal electromechanical toy'. 30 (5):634-646. [Full-Text] | |

2012 |
Woods, D; Naughton, TJ (2012) 'Optical Computing: Photonic neural networks'. Nature Physics, 8 :257-259. [DOI] [Full-Text] | |

2011 |
Murphy, N; Woods, D (2011) 'The computational power of membrane systems under tight uniformity conditions'. Natural Computing, 10 :613-632. [DOI] [Full-Text] | |

2009 |
Woods, D; Naughton, TJ (2009) 'Optical computing'. Applied Mathematics and Computation, 215 :1417-1430. [DOI] [Full-Text] | |

2009 |
Woods, Damien and Neary, Turlough (2009) 'The complexity of small universal Turing machines: A survey'. 410 (4-5):443-450. [Full-Text] | |

2009 |
Woods, Damien and Neary, Turlough (2009) 'Small semi-weakly universal Turing machines'. 91 (1):179-195. [Full-Text] | |

2009 |
Neary, Turlough and Woods, Damien (2009) 'Four small universal Turing machines'. 91 (1):123-144. [Full-Text] | |

2008 |
Woods, Damien and Gibson, J Paul (2008) 'Lower bounds on the computational power of an optical model of computation'. 7 (1):95-108. [Full-Text] | |

2008 |
Murphy, N.; Naughton, T. J.; Woods, D.; Henley, B.; McDermott, K.; Duffy, E.; van der Burgt, P. J. M. ; Woods, N. (2008) 'Implementations of a model of physical sorting'. International Journal of Unconventional Computing, 4 :3-12. [Full-Text] | |

2006 |
Neary, T; Woods, D (2006) 'Small fast universal Turing machines'. Theoretical Computer Science, 362 :171-195. [DOI] [Full-Text] | |

2005 |
Woods, D; Naughton, TJ (2005) 'An optical model of computation'. Theoretical Computer Science, 334 :227-258. [DOI] [Full-Text] |

### Conference Publication

Year | Publication | |
---|---|---|

2023 |
Shalaby, A.; Thachuk, C.; Woods, D. (2023) Leibniz International Proceedings in Informatics, LIPIcs [Link] [DOI] Minimum Free Energy, Partition Function and Kinetics Simulation Algorithms for a Multistranded Scaffolded DNA Computer | |

2021 |
Matthew Cook, Tristan Stérin, Damien Woods (2021) 27th International Conference on DNA Computing and Molecular Programming (DNA 27) . In: Matthew Lakin and Petr Sulc eds. Oxford, UK, [Link] [Full-Text]Small tile sets that compute while solving mazes | |

2020 |
Pierre-Étienne Meunier, Damien Regnault, Damien Woods (2020) STOC 2020: Proceedings of the 52nd Annual ACM SIGACT Symposium on Theory of Computing Seattle, 22/06/2020- 26/06/2020 [Link] https://doi.org/10.1145/3357713.3384263 [Full-Text]The program-size complexity of self-assembled paths | |

2020 |
Irina Kostitsyna, Cai Wood, Damien Woods (2020) 26th International Conference on DNA Computing and Molecular Programming (DNA 26) . In: Cody Geary and Matthew J. Patitz eds. Oxford, UK, [Link] Turning Machines | |

2020 |
Tristan Stérin and Damien Woods (2020) The 14th International Conference on Reachability Problems . In: Igor Potapov and Sylvain Schmitz eds. [Full-Text]The Collatz process embeds a base conversion algorithm | |

2017 |
Pierre-Étienne Meunier, Damien Woods (2017) STOC: Proceedings of the 49th Annual ACM SIGACT Symposium on Theory of Computing [Link] [Full-Text]The non-cooperative tile assembly model is not intrinsically universal or capable of bounded Turing machine simulation | |

2017 |
Doty, David and Rogers, Trent A and Soloveichik, David and Thachuk, Chris and Woods, Damien (2017) The 23rd International Conference on DNA Computing and Molecular Programming [Full-Text]Thermodynamic binding networks | |

2014 |
Meunier, Pierre-Etienne and Patitz, Matthew J and Summers, Scott M and Theyssier, Guillaume and Winslow, Andrew and Woods, Damien (2014) SODA: Proceedings of the twenty-fifth annual ACM-SIAM symposium on Discrete algorithms [Full-Text]Intrinsic universality in tile self-assembly requires cooperation | |

2014 |
Demaine, Erik D and Demaine, Martin L and Fekete, S\'andor P and Patitz, Matthew J and Schweller, Robert T and Winslow, Andrew and Woods, Damien (2014) ICALP: International Colloquium on Automata, Languages, and Programming [Full-Text]One tile to rule them all: Simulating any tile assembly system with a single universal tile | |

2014 |
Chen, Ho-Lin and Doty, David and Holden, Dhiraj and Thachuk, Chris and Woods, Damien and Yang, Chun-Tao (2014) DNA20: The 20th International Conference on DNA Computing and Molecular Programming [Full-Text]Fast algorithmic self-assembly of simple shapes using random agitation | |

2013 |
Demaine, Erik D and Patitz, Matthew J and Rogers, Trent A and Schweller, Robert T and Summers, Scott M and Woods, Damien (2013) ICALP: International Colloquium on Automata, Languages, and Programming [Full-Text]The Two-Handed Tile Assembly Model Is Not Intrinsically Universal | |

2013 |
Chen, Moya and Xin, Doris and Woods, Damien (2013) DNA19: The 19th International Conference on DNA Computing and Molecular Programming [Full-Text]Parallel Computation Using Active Self-assembly⋆ | |

2013 |
Woods, Damien and Chen, Ho-Lin and Goodfriend, Scott and Dabby, Nadine and Winfree, Erik and Yin, Peng (2013) ITCS: Proceedings of the 4th conference on Innovations in Theoretical Computer Science [Full-Text]Active self-assembly of algorithmic shapes and patterns in polylogarithmic time | |

2013 |
N. Murphy, D. Woods. (2013) MCU: Machines, Computations and Universality Zürich, Switzerland. Electronic Proceedings in Theoretical Computer Science, vol 128, [Full-Text]AND and/or OR: Uniform Polynomial-Size Circuits | |

2012 |
Doty, David and Lutz, Jack H and Patitz, Matthew J and Schweller, Robert T and Summers, Scott M and Woods, Damien (2012) FOCS: 53rd Annual Symposium on Foundations of Computer Sciences [Full-Text]The tile assembly model is intrinsically universal | |

2012 |
R. Glaschick, T. Neary, D. Woods, N. Murphy: (2012) Turing in Context II [Full-Text]Hasenjaeger's electromechanical small universal Turing machine is time efficient | |

2012 |
T. Neary, D. Woods (2012) SOFSEM 38th International Conference on Current Trends in Theory and Practice of Computer Science . In: Springer LNCS 7147 eds. Špindlerův Mlýn, Czech Republic, [Full-Text]The complexity of small universal Turing machines: A survey | |

2010 |
Doty, David and Lutz, Jack H and Patitz, Matthew J and Summers, Scott M and Woods, Damien (2010) STACS: The 27th International Symposium on Theoretical Aspects of Computer Science Intrinsic universality in self-assembly | |

2010 |
Murphy N., Woods D (2010) DNA16: The 16th International Conference on DNA Computing and Molecular Programming, preproceedings Best student paper award, Uniformity conditions in natural computing | |

2009 |
Doty, David and Lutz, Jack H and Patitz, Matthew J and Summers, Scott M and Woods, Damien (2009) International Conference on Unconventional Computation [Full-Text]Random number selection in self-assembly | |

2009 |
Neary, Turlough and Woods, Damien (2009) FCT: Proceedings of the 17th international conference on Fundamentals of computation theory [Full-Text]Small weakly universal Turing machines | |

2009 |
Woods, Damien and Murphy, Niall and Pérez-Jiménez, Mario J and Riscos-Núñez, Agustín (2009) International Conference on Unconventional Computation [Full-Text]Membrane dissolution and division in P | |

2009 |
Murphy, Niall and Woods, Damien (2009) Membrane computing 10th international workshop; revised selected and invited papers [Full-Text]Uniformity: uncovering the frontier of parallelism | |

2008 |
Woods, Damien and Naughton, Thomas J (2008) International Workshop on Optical Supercomputing [Full-Text]Parallel and sequential optical computing | |

2008 |
Murphy, Niall; Woods, Damien (2008) International Conference on Unconventional Computation [Full-Text]A characterisation of NL using membrane systems without charges and dissolution | |

2008 |
D. Woods, T. J. Naughton. (2008) Proceedings of the first Workshop on Physics and Computation Vienna, [Full-Text]Optical computing | |

2007 |
Murphy, Niall and Woods, Damien (2007) International Workshop on Membrane Computing [Full-Text]Active membrane systems without charges and using only symmetric elementary division characterise P | |

2007 |
Woods D.; Neary T. (2007) CiE: Computability in Europe [DOI] [Full-Text]The complexity of small universal Turing machines | |

2007 |
Woods, Damien; Neary, Turlough (2007) MCU: 5th International Conference on Machines, Computations and Universality [Full-Text]Small semi-weakly universal Turing machines | |

2007 |
Neary, Turlough; Woods, Damien (2007) MCU: 5th International Conference on Machines, Computations and Universality [Full-Text]Four small universal Turing machines | |

2006 |
Neary, T and Woods, Damien (2006) FOCS: Proceedings of the 47th Annual IEEE Symposium on Foundations of Computer Science [Full-Text]On the time complexity of 2-tag systems and small universal Turing machines | |

2006 |
Neary, Turlough and Woods, Damien (2006) ICALP: International Colloquium on Automata, Languages, and Programming [Full-Text]P-completeness of cellular automaton Rule 110 | |

2006 |
N. Murphy, T.J. Naughton, D. Woods, B. Henley, K. McDermott, E. Duffy, P.J.M. van~der Burgt, N. Woods (2006) From Utopian to Genuine Unconventional Computers [Full-Text]Implementations of a model of physical sorting | |

2006 |
Woods, Damien and Neary, Turlough (2006) MFCSIT: Fourth Irish Conference on the Mathematical Foundations of Computer Science and Information Technology [Full-Text]Remarks on the computational complexity of small universal Turing machines | |

2006 |
Woods, Damien (2006) International Conference on Unconventional Computation [Full-Text]Optical computing and computational complexity | |

2006 |
N. Murphy, D. Woods, T.J. Naughton (2006) MFCSIT: Fourth Irish Conference on the Mathematical Foundations of Computer Science and Information Technology Cork, Ireland, [Full-Text]Bio-computation using Holliday junctions | |

2005 |
Woods, Damien (2005) ISAAC: International Symposium on Algorithms and Computation [Full-Text]Upper bounds on the computational power of an optical model of computation | |

2005 |
Woods, Damien; Gibson J Paul (2005) 4th International Conference on Unconventional Computation Seville, Spain, [Full-Text]Lower bounds on the computational power of an optical model of computation | |

2005 |
Woods, Damien; Gibson, J Paul (2005) CiE: Computability in Europe 2005: New Computational Paradigms [Full-Text]Complexity of continuous space machine operations | |

2001 |
Naughton, Thomas J and Woods, Damien (2001) MCU: International Conference on Machines, Computations, and Universality [Full-Text]On the computational power of a continuous-space optical model of computation | |

1999 |
Woods, Damien and Trenaman, Adrian (1999) Artificial Intelligence and Cognitive Science Cork, Ireland, Simultaneous satisfaction of hard and soft timetable constraints for a university department using evolutionary timetabling |

### Edited Book

### Book Chapter

Year | Publication | |
---|---|---|

2017 |
Woods, Damien (2017) 'Intrinsic Universality in Self-Assembly' In: Encyclopedia of Algorithms, 2nd Ed. Berlin Heidelberg : Springer. | |

2017 |
Woods, Damien (2017) 'Active self-assembly and molecular robotics with nubots' In: Encyclopedia of Algorithms, 2nd Ed. Berlin Heidelberg : Springer. | |

2015 |
Turlough Neary., Damien Woods (2015) 'Maurice Margenstern's contributions to the field of small universal Turing machines' In: Automata, Computation, Universality. Berlin Heidelberg : Springer. | |

2015 |
T.J. Naughton and D. Woods (2015) 'Optical Computing' In: Encyclopedia of Complexity and Systems Science. Berlin : Springer Berlin Heidelberg. [DOI] | |

2009 |
Pérez-Jiménez, Mario J and Riscos-Núñez, Agustín and Romero-Jiménez, A and Woods, Damien (2009) 'Complexity-membrane division, membrane creation' In: Handbook of Membrane Computing. Oxford : Oxford University Press. |

### Conference Contribution

Certain data included herein are derived from the © Web of Science (2023) of Clarivate. All rights reserved.