Prof Damien Woods

    Computer Science, Hamilton Institute

    Eolas Building
    3rd
    343
    (01) 708 6788

    Biography

    Research group website: https://dna.hamilton.ie

    Research Interests




    Research Projects

    Title Role Description Start date End date Amount
    DISCO: DNA Infrastructure for Storage and COmputation - EIC Pathfinder Challenge grant PI Throughout evolution, Biology has found an almost-perfect molecule to pass information down through the millennia. Whether for a simple bacterium or the largest whale, DNA achieves high information density while permitting cellular machinery rapid random-access retrieval to decode everything from a single protein to the development of an entire human brain. Humanity's rapidly-growing data storage and computing needs make it is tempting to exploit optimised biological molecules and processes, but biology is messy, poorly-understood and much more specialised for life than it is for our needs -- we propose to use DNA for storage together with a rationally designed, well-characterised and robust molecular computing architecture. The DISCO project will address the challenge of engineering a programmable and robust DNA storage and computing platform. DISCO combines powerful molecular-algorithmic ideas from DNA computing with notions of thermodynamic stability from DNA nanostructures, to provide an expressive and robust system design. The project proposes the use of long DNA scaffold strands, upon which hundreds of smaller strands bind to store data, which can be later read, erased, rewritten and computed upon. DISCO begins with the aim of trialling a small, but thoroughly characterised and modelled prototype, that facilitates storage and computation on 10 bits. Then, DISCO will scale-up the system to hundreds of bits by leveraging recent technological advances to enable high-throughput techniques at both the experimental and data-readout stages. Finally, DISCO will be extended to two-dimensional DNA origami structures, each carrying about a hundred bits, but with millions of structures in the same test tube, exhibiting DNA storage and computation in a distributed system at a massively parallel scale. 01/10/2023 30/09/2028 3993665
    Active DNA: Computationally Active DNA Nanostructures - ERC Consolidator Grant PI During the 20th century computer technology evolved from bulky, slow, special purpose mechanical engines to the now ubiquitous silicon chips and software that are one of the pinnacles of human ingenuity. The goal of the field of molecular programming is to take the next leap and build a new generation of matter-based computers using DNA, RNA and proteins. This will be accomplished by computer scientists, physicists and chemists designing molecules to execute ``wet'' nanoscale programs in test tubes. The workflow includes proposing theoretical models, mathematically proving their computational properties, physical modelling and implementation in the wet-lab. The past decade has seen remarkable progress at building static 2D and 3D DNA nanostructures. However, unlike biological macromolecules and complexes that are built via specified self-assembly pathways, that execute robotic-like movements, and that undergo evolution, the activity of human-engineered nanostructures is severely limited. We will need sophisticated algorithmic ideas to build structures that rival active living systems. Active-DNA, aims to address this challenge by achieving a number of objectives on computation, DNA-based self-assembly and molecular robotics. Active-DNA research work will range from defining models and proving theorems that characterise the computational and expressive capabilities of such active programmable materials to experimental work implementing active DNA nanostructures in the wet-lab. 01/11/2018 31/10/2024 2349603
    Active DNA tiles for programmable nucleation of robust DNA nanostructures PI 01/12/2021 30/11/2025 604266
    SFI ERC support award PI 31/10/2018 31/10/2023 656500

    Post Doctoral Fellows / Research Team

    Researcher Name Project Funding Body
    Constantine Evans Molecular Computing
    Abeer Eshra Active-DNA
    Tristan Lancelot Dylan Cosmo Sterin Active-DNA
    Cai Alan Wood Active-DNA
    Ahmed Shalaby SFI FFP: Active DNA tiles for programmable nucleation of robust DNA nanostructures

    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] [Full-Text]
    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
    2024 Stérin, T.; Woods, D. (2024) Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) Hardness of Busy Beaver Value BB(15) [Link] [DOI]
    2024 Demaine, E.D.; Gomez, T.; Grizzell, E.; Hecher, M.; Lynch, J.; Schweller, R.; Shalaby, A.; Woods, D. (2024) Leibniz International Proceedings in Informatics, LIPIcs Domain-Based Nucleic-Acid Minimum Free Energy: Algorithmic Hardness and Parameterized Bounds [Link] [DOI]
    2023 Shalaby, A.; Thachuk, C.; Woods, D. (2023) Leibniz International Proceedings in Informatics, LIPIcs Minimum Free Energy, Partition Function and Kinetics Simulation Algorithms for a Multistranded Scaffolded DNA Computer [Link] [DOI]
    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. Small tile sets that compute while solving mazes Oxford, UK, [Link] [Full-Text]
    2020 Pierre-Étienne Meunier, Damien Regnault, Damien Woods (2020) STOC 2020: Proceedings of the 52nd Annual ACM SIGACT Symposium on Theory of Computing The program-size complexity of self-assembled paths Seattle, 22/06/2020- 26/06/2020 [Link] https://doi.org/10.1145/3357713.3384263 [Full-Text]
    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. Turning Machines Oxford, UK, [Link]
    2020 Tristan Stérin and Damien Woods (2020) The 14th International Conference on Reachability Problems . In: Igor Potapov and Sylvain Schmitz eds. The Collatz process embeds a base conversion algorithm [Full-Text]
    2017 Pierre-Étienne Meunier, Damien Woods (2017) STOC: Proceedings of the 49th Annual ACM SIGACT Symposium on Theory of Computing The non-cooperative tile assembly model is not intrinsically universal or capable of bounded Turing machine simulation [Link] [Full-Text]
    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 Thermodynamic binding networks [Full-Text]
    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 Intrinsic universality in tile self-assembly requires cooperation [Full-Text]
    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 One tile to rule them all: Simulating any tile assembly system with a single universal tile [Full-Text]
    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 Fast algorithmic self-assembly of simple shapes using random agitation [Full-Text]
    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 The Two-Handed Tile Assembly Model Is Not Intrinsically Universal [Full-Text]
    2013 Chen, Moya and Xin, Doris and Woods, Damien (2013) DNA19: The 19th International Conference on DNA Computing and Molecular Programming Parallel Computation Using Active Self-assembly⋆ [Full-Text]
    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 Active self-assembly of algorithmic shapes and patterns in polylogarithmic time [Full-Text]
    2013 N. Murphy, D. Woods. (2013) MCU: Machines, Computations and Universality AND and/or OR: Uniform Polynomial-Size Circuits Zürich, Switzerland. Electronic Proceedings in Theoretical Computer Science, vol 128, [Full-Text]
    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 The tile assembly model is intrinsically universal [Full-Text]
    2012 R. Glaschick, T. Neary, D. Woods, N. Murphy: (2012) Turing in Context II Hasenjaeger's electromechanical small universal Turing machine is time efficient [Full-Text]
    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. The complexity of small universal Turing machines: A survey Špindlerův Mlýn, Czech Republic, [Full-Text]
    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 Uniformity conditions in natural computing Best student paper award,
    2009 Doty, David and Lutz, Jack H and Patitz, Matthew J and Summers, Scott M and Woods, Damien (2009) International Conference on Unconventional Computation Random number selection in self-assembly [Full-Text]
    2009 Neary, Turlough and Woods, Damien (2009) FCT: Proceedings of the 17th international conference on Fundamentals of computation theory Small weakly universal Turing machines [Full-Text]
    2009 Woods, Damien and Murphy, Niall and Pérez-Jiménez, Mario J and Riscos-Núñez, Agustín (2009) International Conference on Unconventional Computation Membrane dissolution and division in P [Full-Text]
    2009 Murphy, Niall and Woods, Damien (2009) Membrane computing 10th international workshop; revised selected and invited papers Uniformity: uncovering the frontier of parallelism [Full-Text]
    2008 Woods, Damien and Naughton, Thomas J (2008) International Workshop on Optical Supercomputing Parallel and sequential optical computing [Full-Text]
    2008 Murphy, Niall; Woods, Damien (2008) International Conference on Unconventional Computation A characterisation of NL using membrane systems without charges and dissolution [Full-Text]
    2008 D. Woods, T. J. Naughton. (2008) Proceedings of the first Workshop on Physics and Computation Optical computing Vienna, [Full-Text]
    2007 Murphy, Niall and Woods, Damien (2007) International Workshop on Membrane Computing Active membrane systems without charges and using only symmetric elementary division characterise P [Full-Text]
    2007 Woods D.; Neary T. (2007) CiE: Computability in Europe The complexity of small universal Turing machines [DOI] [Full-Text]
    2007 Woods, Damien; Neary, Turlough (2007) MCU: 5th International Conference on Machines, Computations and Universality Small semi-weakly universal Turing machines [Full-Text]
    2007 Neary, Turlough; Woods, Damien (2007) MCU: 5th International Conference on Machines, Computations and Universality Four small universal Turing machines [Full-Text]
    2006 Neary, T and Woods, Damien (2006) FOCS: Proceedings of the 47th Annual IEEE Symposium on Foundations of Computer Science On the time complexity of 2-tag systems and small universal Turing machines [Full-Text]
    2006 Neary, Turlough and Woods, Damien (2006) ICALP: International Colloquium on Automata, Languages, and Programming P-completeness of cellular automaton Rule 110 [Full-Text]
    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 Implementations of a model of physical sorting [Full-Text]
    2006 Woods, Damien and Neary, Turlough (2006) MFCSIT: Fourth Irish Conference on the Mathematical Foundations of Computer Science and Information Technology Remarks on the computational complexity of small universal Turing machines [Full-Text]
    2006 Woods, Damien (2006) International Conference on Unconventional Computation Optical computing and computational complexity [Full-Text]
    2006 N. Murphy, D. Woods, T.J. Naughton (2006) MFCSIT: Fourth Irish Conference on the Mathematical Foundations of Computer Science and Information Technology Bio-computation using Holliday junctions Cork, Ireland, [Full-Text]
    2005 Woods, Damien (2005) ISAAC: International Symposium on Algorithms and Computation Upper bounds on the computational power of an optical model of computation [Full-Text]
    2005 Woods, Damien; Gibson J Paul (2005) 4th International Conference on Unconventional Computation Lower bounds on the computational power of an optical model of computation Seville, Spain, [Full-Text]
    2005 Woods, Damien; Gibson, J Paul (2005) CiE: Computability in Europe 2005: New Computational Paradigms Complexity of continuous space machine operations [Full-Text]
    2001 Naughton, Thomas J and Woods, Damien (2001) MCU: International Conference on Machines, Computations, and Universality On the computational power of a continuous-space optical model of computation [Full-Text]
    1999 Woods, Damien and Trenaman, Adrian (1999) Artificial Intelligence and Cognitive Science Simultaneous satisfaction of hard and soft timetable constraints for a university department using evolutionary timetabling Cork, Ireland,

    Edited Book

    Year Publication
    2018 Damien Woods and Yannick Rondelez (Ed.). (2018) Journal of Natural Computing: Special issue on DNA Computing and Molecular Programming. Berlin Heidelberg: Springer,
    2016 Damien Woods and Yannick Rondelez (Ed.). (2016) Conference Proceedings: DNA Computing and Molecular Programming, 22nd International Conference. Berlin Heidelberg: Springer, LNCS,
    2011 D. Woods, T. Neary, A.K. Seda (Ed.). (2011) Journal of Theoretical Computer Science, Special Issue on the Complexity of Simple Programs. Berlin Heidelberg: Springer,
    2008 (2008) Proceedings of the International Workshop on The Complexity of Simple Programs. Electronic Proceedings in Theoretical Computer Science (EPTCS),
    2006 (2006) Proceedings of the 4th International Conference on Information, and Proceedings of the 4th Irish Conference on Mathematical Foundations of Computer Science and Information Technology. University College Cork Press note=Cork, Ireland,

    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

    Year Publication
    2022 Constantine G. Evans, David Doty, Damien Woods (2022) 28th International Conference on DNA Computing and Molecular Programming Growth dynamics: Precisely controlled self-assembly order of DNA tile nanostructures Albuquerque, New Mexico, .
    2022 Trent Rogers, Constantine Evans, Damien Woods (2022) 28th International Conference on DNA Computing and Molecular Programming Covered DNA core tiles for robust tuning of spurious nucleation Albuquerque, New Mexico, .

    Other Publication

    Year Publication
    2019 Woods, D.; Doty, D.; Myhrvold, C.; Hui, J.; Zhou, F.; Yin, P.; Winfree, E. (2019) Author Correction: Diverse and robust molecular algorithms using reprogrammable DNA self-assembly (Nature, (2019), 567, 7748, (366-372), 10.1038/s41586-019-1014-9). [Link] [DOI]
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