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

      Project Role Funding Body / Program Description Start Date End Date Award (€)
    Active DNA tiles for programmable nucleation of robust DNA nanostructures PI Science Foundation Ireland / Frontiers for the Future PROJECT 01-DEC-21 30-NOV-25 604266
    Active DNA: Computationally Active DNA Nanostructures PI EU Horizon 2020 / ERC Consolidator Grant 01-NOV-18 31-OCT-23 2349603
    SFI ERC support award PI Science Foundation Ireland / 31-OCT-18 31-OCT-23 656500

    Post Doctoral Fellows/Research Team

      Researcher Name Project Role Funding Body
    Constantine Evans Molecular Computing Post Doctorate European Research Council / ERC
    Trent Rogers Molecular Computing Post Doctorate European Research Council / ERC
    Ismael Mullor Ruiz Active-DNA Post Doctorate European Research Council / ERC
    Abeer Eshra Active-DNA Post Doctorate European Research Council / ERC
    Tristan Lancelot Dylan Cosmo Sterin Active-DNA Postgraduate student European Research Council / ERC
    Cai Alan Wood Active-DNA Postgraduate student European Research Council / ERC

    Peer Reviewed Journals

      Year Publication
    2019 'Diverse and robust molecular algorithms using reprogrammable DNA self-assembly'
    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] [Details]
    2017 'A cargo-sorting DNA robot'
    Thubagere, Li, Johnson, Chen, Doroudi, Lee, Izatt, Wittman, Srinivas, Woods, Winfree, Qian (2017) 'A cargo-sorting DNA robot'. Science, 357 (6356) [DOI] [full-text] [Details]
    2016 'The two-handed tile assembly model is not intrinsically universal'
    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'. Algorithmica, 74 (2):812-850 [full-text] [Details]
    2015 'Intrinsic universality and the computational power of self-assembly'
    Woods, Damien (2015) 'Intrinsic universality and the computational power of self-assembly'. Philosophical transactions of the royal society, 373 (2046) [full-text] [Details]
    2015 'Parallel Computation Using Active Self-assembly'
    Chen, Moya and Xin, Doris and Woods, Damien (2015) 'Parallel Computation Using Active Self-assembly'. Natural Computing, 14 (2):225-250 [full-text] [Details]
    2015 'Yurii Rogozhin's Contributions to the Field of Small Universal Turing Machines'
    Woods, Damien and Neary, Turlough (2015) 'Yurii Rogozhin's Contributions to the Field of Small Universal Turing Machines'. Fundamenta Informaticae, 138 (1-2):251-258 [full-text] [Details]
    2014 'Uniformity is weaker than semi-uniformity for some membrane systems'
    Murphy, Niall and Woods, Damien (2014) 'Uniformity is weaker than semi-uniformity for some membrane systems'. Fundamenta Informaticae, 134 (1-2):129-152 [full-text] [Details]
    2014 'Wang’s B machines are efficiently universal, as is Hasenjaeger’s small universal electromechanical toy'
    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'. Journal of Complexity, 30 (5):634-646 [full-text] [Details]
    2012 'Optical Computing: Photonic neural networks'
    Woods, D;Naughton, TJ (2012) 'Optical Computing: Photonic neural networks'. Nature Physics, 8 :257-259 [DOI] [full-text] [Details]
    2011 'The computational power of membrane systems under tight uniformity conditions'
    Murphy, N;Woods, D (2011) 'The computational power of membrane systems under tight uniformity conditions'. Natural Computing, 10 :613-632 [DOI] [full-text] [Details]
    2009 'Optical computing'
    Woods, D;Naughton, TJ (2009) 'Optical computing'. Applied Mathematics and Computation, 215 :1417-1430 [DOI] [full-text] [Details]
    2009 'The complexity of small universal Turing machines: A survey'
    Woods, Damien and Neary, Turlough (2009) 'The complexity of small universal Turing machines: A survey'. Theoretical Computer Science, 410 (4-5):443-450 [full-text] [Details]
    2009 'Small semi-weakly universal Turing machines'
    Woods, Damien and Neary, Turlough (2009) 'Small semi-weakly universal Turing machines'. Fundamenta Informaticae, 91 (1):179-195 [full-text] [Details]
    2009 'Four small universal Turing machines'
    Neary, Turlough and Woods, Damien (2009) 'Four small universal Turing machines'. Fundamenta Informaticae, 91 (1):123-144 [full-text] [Details]
    2008 'Lower bounds on the computational power of an optical model of computation'
    Woods, Damien and Gibson, J Paul (2008) 'Lower bounds on the computational power of an optical model of computation'. Natural Computing, 7 (1):95-108 [full-text] [Details]
    2008 'Implementations of a model of physical sorting'
    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] [Details]
    2006 'Small fast universal Turing machines'
    Neary, T;Woods, D (2006) 'Small fast universal Turing machines'. Theoretical Computer Science, 362 :171-195 [DOI] [full-text] [Details]
    2005 'An optical model of computation'
    Woods, D;Naughton, TJ (2005) 'An optical model of computation'. Theoretical Computer Science, 334 :227-258 [DOI] [full-text] [Details]

    Conference Publications

      Year Publication
    2021 Small tile sets that compute while solving mazes
    Matthew Cook, Tristan Stérin, Damien Woods (2021) Small tile sets that compute while solving mazes . In: Matthew Lakin and Petr Sulc eds. 27th International Conference on DNA Computing and Molecular Programming (DNA 27) Oxford, UK, , pp.1-20 [Details]
    2020 The program-size complexity of self-assembled paths
    Pierre-Étienne Meunier, Damien Regnault, Damien Woods (2020) The program-size complexity of self-assembled paths STOC 2020: Proceedings of the 52nd Annual ACM SIGACT Symposium on Theory of Computing Seattle, , 22-JUN-20 - 26-JUN-20 , pp.727-737 [DOI] [Details]
    2020 Turning Machines
    Irina Kostitsyna, Cai Wood, Damien Woods (2020) Turning Machines . In: Cody Geary and Matthew J. Patitz eds. 26th International Conference on DNA Computing and Molecular Programming (DNA 26) Oxford, UK, , pp.1-21 [Details]
    2020 The Collatz process embeds a base conversion algorithm
    Tristan Stérin and Damien Woods (2020) The Collatz process embeds a base conversion algorithm . In: Igor Potapov and Sylvain Schmitz eds. The 14th International Conference on Reachability Problems , pp.131-147 [Details]
    2017 The non-cooperative tile assembly model is not intrinsically universal or capable of bounded Turing machine simulation
    Pierre-Étienne Meunier, Damien Woods (2017) The non-cooperative tile assembly model is not intrinsically universal or capable of bounded Turing machine simulation STOC: Proceedings of the 49th Annual ACM SIGACT Symposium on Theory of Computing , pp.328-341 [full-text] [Details]
    2017 Thermodynamic binding networks
    Doty, David and Rogers, Trent A and Soloveichik, David and Thachuk, Chris and Woods, Damien (2017) Thermodynamic binding networks The 23rd International Conference on DNA Computing and Molecular Programming , pp.249-266 [full-text] [Details]
    2014 Intrinsic universality in tile self-assembly requires cooperation
    Meunier, Pierre-Etienne and Patitz, Matthew J and Summers, Scott M and Theyssier, Guillaume and Winslow, Andrew and Woods, Damien (2014) Intrinsic universality in tile self-assembly requires cooperation SODA: Proceedings of the twenty-fifth annual ACM-SIAM symposium on Discrete algorithms , pp.752-771 [Details]
    2014 One tile to rule them all: Simulating any tile assembly system with a single universal tile
    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) One tile to rule them all: Simulating any tile assembly system with a single universal tile ICALP: International Colloquium on Automata, Languages, and Programming , pp.368-379 [Details]
    2014 Fast algorithmic self-assembly of simple shapes using random agitation
    Chen, Ho-Lin and Doty, David and Holden, Dhiraj and Thachuk, Chris and Woods, Damien and Yang, Chun-Tao (2014) Fast algorithmic self-assembly of simple shapes using random agitation DNA20: The 20th International Conference on DNA Computing and Molecular Programming , pp.20-36 [Details]
    2013 The Two-Handed Tile Assembly Model Is Not Intrinsically Universal
    Demaine, Erik D and Patitz, Matthew J and Rogers, Trent A and Schweller, Robert T and Summers, Scott M and Woods, Damien (2013) The Two-Handed Tile Assembly Model Is Not Intrinsically Universal ICALP: International Colloquium on Automata, Languages, and Programming , pp.400-412 [Details]
    2013 Parallel Computation Using Active Self-assembly⋆
    Chen, Moya and Xin, Doris and Woods, Damien (2013) Parallel Computation Using Active Self-assembly⋆ DNA19: The 19th International Conference on DNA Computing and Molecular Programming , pp.16-30 [Details]
    2013 Active self-assembly of algorithmic shapes and patterns in polylogarithmic time
    Woods, Damien and Chen, Ho-Lin and Goodfriend, Scott and Dabby, Nadine and Winfree, Erik and Yin, Peng (2013) Active self-assembly of algorithmic shapes and patterns in polylogarithmic time ITCS: Proceedings of the 4th conference on Innovations in Theoretical Computer Science , pp.353-354 [Details]
    2013 AND and/or OR: Uniform Polynomial-Size Circuits
    N. Murphy, D. Woods. (2013) AND and/or OR: Uniform Polynomial-Size Circuits MCU: Machines, Computations and Universality Zürich, Switzerland. Electronic Proceedings in Theoretical Computer Science, vol 128, , pp.150-166 [Details]
    2012 The tile assembly model is intrinsically universal
    Doty, David and Lutz, Jack H and Patitz, Matthew J and Schweller, Robert T and Summers, Scott M and Woods, Damien (2012) The tile assembly model is intrinsically universal FOCS: 53rd Annual Symposium on Foundations of Computer Sciences , pp.302-310 [Details]
    2012 Hasenjaeger's electromechanical small universal Turing machine is time efficient
    R. Glaschick, T. Neary, D. Woods, N. Murphy: (2012) Hasenjaeger's electromechanical small universal Turing machine is time efficient Turing in Context II [Details]
    2012 The complexity of small universal Turing machines: A survey
    T. Neary, D. Woods (2012) The complexity of small universal Turing machines: A survey . In: Springer LNCS 7147 eds. SOFSEM 38th International Conference on Current Trends in Theory and Practice of Computer Science Špindlerův Mlýn, Czech Republic, , pp.385-405 [Details]
    2010 Intrinsic universality in self-assembly
    Doty, David and Lutz, Jack H and Patitz, Matthew J and Summers, Scott M and Woods, Damien (2010) Intrinsic universality in self-assembly STACS: The 27th International Symposium on Theoretical Aspects of Computer Science , pp.275-286 [Details]
    2010 Uniformity conditions in natural computing
    Murphy N., Woods D (2010) Uniformity conditions in natural computing DNA16: The 16th International Conference on DNA Computing and Molecular Programming, preproceedings Best student paper award, , pp.107-120 [Details]
    2009 Random number selection in self-assembly
    Doty, David and Lutz, Jack H and Patitz, Matthew J and Summers, Scott M and Woods, Damien (2009) Random number selection in self-assembly International Conference on Unconventional Computation , pp.143-157 [Details]
    2009 Small weakly universal Turing machines
    Neary, Turlough and Woods, Damien (2009) Small weakly universal Turing machines FCT: Proceedings of the 17th international conference on Fundamentals of computation theory , pp.262-273 [Details]
    2009 Membrane dissolution and division in P
    Woods, Damien and Murphy, Niall and Pérez-Jiménez, Mario J and Riscos-Núñez, Agustín (2009) Membrane dissolution and division in P International Conference on Unconventional Computation , pp.262-276 [Details]
    2009 Uniformity: uncovering the frontier of parallelism
    Murphy, Niall and Woods, Damien (2009) Uniformity: uncovering the frontier of parallelism Membrane computing 10th international workshop; revised selected and invited papers , pp.1-5 [Details]
    2008 Parallel and sequential optical computing
    Woods, Damien and Naughton, Thomas J (2008) Parallel and sequential optical computing International Workshop on Optical Supercomputing , pp.70-86 [Details]
    2008 A characterisation of NL using membrane systems without charges and dissolution
    Murphy, Niall; Woods, Damien (2008) A characterisation of NL using membrane systems without charges and dissolution International Conference on Unconventional Computation , pp.164-176 [Details]
    2008 Optical computing
    D. Woods, T. J. Naughton. (2008) Optical computing Proceedings of the first Workshop on Physics and Computation Vienna, , pp.307-330 [Details]
    2007 Active membrane systems without charges and using only symmetric elementary division characterise P
    Murphy, Niall and Woods, Damien (2007) Active membrane systems without charges and using only symmetric elementary division characterise P International Workshop on Membrane Computing , pp.367-384 [Details]
    2007 The complexity of small universal Turing machines
    Woods D.;Neary T. (2007) The complexity of small universal Turing machines CiE: Computability in Europe , pp.791-798 [DOI] [Details]
    2007 Small semi-weakly universal Turing machines
    Woods, Damien; Neary, Turlough (2007) Small semi-weakly universal Turing machines MCU: 5th International Conference on Machines, Computations and Universality , pp.303-315 [Details]
    2007 Four small universal Turing machines
    Neary, Turlough; Woods, Damien (2007) Four small universal Turing machines MCU: 5th International Conference on Machines, Computations and Universality , pp.242-254 [Details]
    2006 On the time complexity of 2-tag systems and small universal Turing machines
    Neary, T and Woods, Damien (2006) On the time complexity of 2-tag systems and small universal Turing machines FOCS: Proceedings of the 47th Annual IEEE Symposium on Foundations of Computer Science , pp.439-446 [Details]
    2006 P-completeness of cellular automaton Rule 110
    Neary, Turlough and Woods, Damien (2006) P-completeness of cellular automaton Rule 110 ICALP: International Colloquium on Automata, Languages, and Programming , pp.132-143 [Details]
    2006 Implementations of a model of physical sorting
    N. Murphy, T.J. Naughton, D. Woods, B. Henley, K. McDermott, E. Duffy, P.J.M. van~der Burgt, N. Woods (2006) Implementations of a model of physical sorting From Utopian to Genuine Unconventional Computers , pp.79-99 [Details]
    2006 Remarks on the computational complexity of small universal Turing machines
    Woods, Damien and Neary, Turlough (2006) Remarks on the computational complexity of small universal Turing machines MFCSIT: Fourth Irish Conference on the Mathematical Foundations of Computer Science and Information Technology , pp.334-338 [Details]
    2006 Optical computing and computational complexity
    Woods, Damien (2006) Optical computing and computational complexity International Conference on Unconventional Computation , pp.27-40 [Details]
    2006 Bio-computation using Holliday junctions
    N. Murphy, D. Woods, T.J. Naughton (2006) Bio-computation using Holliday junctions MFCSIT: Fourth Irish Conference on the Mathematical Foundations of Computer Science and Information Technology Cork, Ireland, , pp.317-320 [Details]
    2005 Upper bounds on the computational power of an optical model of computation
    Woods, Damien (2005) Upper bounds on the computational power of an optical model of computation ISAAC: International Symposium on Algorithms and Computation , pp.777-788 [Details]
    2005 Lower bounds on the computational power of an optical model of computation
    Woods, Damien; Gibson J Paul (2005) Lower bounds on the computational power of an optical model of computation 4th International Conference on Unconventional Computation Seville, Spain, , pp.237-250 [Details]
    2005 Complexity of continuous space machine operations
    Woods, Damien; Gibson, J Paul (2005) Complexity of continuous space machine operations CiE: Computability in Europe 2005: New Computational Paradigms , pp.540-551 [Details]
    2001 On the computational power of a continuous-space optical model of computation
    Naughton, Thomas J and Woods, Damien (2001) On the computational power of a continuous-space optical model of computation MCU: International Conference on Machines, Computations, and Universality , pp.288-299 [Details]
    1999 Simultaneous satisfaction of hard and soft timetable constraints for a university department using evolutionary timetabling
    Woods, Damien and Trenaman, Adrian (1999) Simultaneous satisfaction of hard and soft timetable constraints for a university department using evolutionary timetabling Artificial Intelligence and Cognitive Science Cork, Ireland, , pp.1-7 [Details]

    Edited Books

      Year Publication
    2018 Journal of Natural Computing: Special issue on DNA Computing and Molecular Programming
    Damien Woods and Yannick Rondelez (Ed.). (2018) Journal of Natural Computing: Special issue on DNA Computing and Molecular Programming Berlin Heidelberg: Springer. [Details]
    2016 Conference Proceedings: DNA Computing and Molecular Programming, 22nd International Conference
    Damien Woods and Yannick Rondelez (Ed.). (2016) Conference Proceedings: DNA Computing and Molecular Programming, 22nd International Conference Berlin Heidelberg: Springer, LNCS. [Details]
    2011 Journal of Theoretical Computer Science, Special Issue on the Complexity of Simple Programs
    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. [Details]
    2008 Proceedings of the International Workshop on The Complexity of Simple Programs
    (2008) Proceedings of the International Workshop on The Complexity of Simple Programs Electronic Proceedings in Theoretical Computer Science (EPTCS). [Details]
    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
    (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. [Details]

    Book Chapters

      Year Publication
    2017 'Intrinsic Universality in Self-Assembly'
    Woods, Damien (2017) 'Intrinsic Universality in Self-Assembly' In: Encyclopedia of Algorithms, 2nd Ed. Berlin Heidelberg: Springer. [Details]
    2017 'Active self-assembly and molecular robotics with nubots'
    Woods, Damien (2017) 'Active self-assembly and molecular robotics with nubots' In: Encyclopedia of Algorithms, 2nd Ed. Berlin Heidelberg: Springer. [Details]
    2015 'Maurice Margenstern's contributions to the field of small universal Turing machines'
    Turlough Neary., Damien Woods (2015) 'Maurice Margenstern's contributions to the field of small universal Turing machines' In: Automata, Computation, Universality. Berlin Heidelberg: Springer. [Details]
    2015 'Optical Computing'
    T.J. Naughton and D. Woods (2015) 'Optical Computing' In: Robert A. Meyers (eds). Encyclopedia of Complexity and Systems Science. Berlin: Springer Berlin Heidelberg. [DOI] [Details]
    2009 'Complexity-membrane division, membrane creation'
    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. [Details]