Prof Damien Woods

Biography
Research Interests
Research Projects
Project | Role | Funding Body / Program | Description | Start Date | End Date | Award (€) | |
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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-24 | 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 | |
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Constantine Evans | Molecular Computing | Post Doctorate | European Research Council / ERC | |
Trent Rogers | Molecular Computing | Post Doctorate | Science Foundation Ireland | |
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 | |
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2022 | 'Turning machines: a simple algorithmic model for molecular robotics'
Irnia Kostitsyna, Cai Wood, Damien Woods (2022) 'Turning machines: a simple algorithmic model for molecular robotics'. Natural Computing, [DOI] [Details] |
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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] |
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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] |
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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] |
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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] |
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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] |
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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] |
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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] |
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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] |
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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] |
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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] |
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2009 | 'Optical computing'
Woods, D;Naughton, TJ (2009) 'Optical computing'. Applied Mathematics and Computation, 215 :1417-1430 [DOI] [full-text] [Details] |
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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] |
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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] |
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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] |
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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] |
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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] |
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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] |
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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 | |
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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 [full-text] [Details] |
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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] [full-text] [Details] |
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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] |
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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 [full-text] [Details] |
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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] |
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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] |
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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 [full-text] [Details] |
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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 [full-text] [Details] |
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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 [full-text] [Details] |
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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 [full-text] [Details] |
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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 [full-text] [Details] |
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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 [full-text] [Details] |
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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 [full-text] [Details] |
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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 [full-text] [Details] |
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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 [full-text] [Details] |
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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 [full-text] [Details] |
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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] |
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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] |
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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 [full-text] [Details] |
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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 [full-text] [Details] |
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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 [full-text] [Details] |
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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 [full-text] [Details] |
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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 [full-text] [Details] |
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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 [full-text] [Details] |
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2008 | Optical computing
D. Woods, T. J. Naughton. (2008) Optical computing Proceedings of the first Workshop on Physics and Computation Vienna, , pp.307-330 [full-text] [Details] |
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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 [full-text] [Details] |
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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] [full-text] [Details] |
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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 [full-text] [Details] |
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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 [full-text] [Details] |
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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 [full-text] [Details] |
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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 [full-text] [Details] |
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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 [full-text] [Details] |
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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 [full-text] [Details] |
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2006 | Optical computing and computational complexity
Woods, Damien (2006) Optical computing and computational complexity International Conference on Unconventional Computation , pp.27-40 [full-text] [Details] |
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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 [full-text] [Details] |
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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 [full-text] [Details] |
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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 [full-text] [Details] |
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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 [full-text] [Details] |
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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 [full-text] [Details] |
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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 | |
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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] |
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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] |
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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] |
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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] |
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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 | |
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2017 | 'Intrinsic Universality in Self-Assembly'
Woods, Damien (2017) 'Intrinsic Universality in Self-Assembly' In: Encyclopedia of Algorithms, 2nd Ed. Berlin Heidelberg: Springer. [Details] |
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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] |
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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] |
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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] |
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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] |