Prof Damien Woods
Biography
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  01DEC21  30NOV25  604266  
Active DNA: Computationally Active DNA Nanostructures  PI  EU Horizon 2020 / ERC Consolidator Grant  01NOV18  31OCT24  2349603  
SFI ERC support award  PI  Science Foundation Ireland /  31OCT18  31OCT23  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  ActiveDNA  Post Doctorate  European Research Council / ERC  
Abeer Eshra  ActiveDNA  Post Doctorate  European Research Council / ERC  
Tristan Lancelot Dylan Cosmo Sterin  ActiveDNA  Postgraduate student  European Research Council / ERC  
Cai Alan Wood  ActiveDNA  Postgraduate student  European Research Council / ERC 
Peer Reviewed Journals
Year  Publication  

2019  'Diverse and robust molecular algorithms using reprogrammable DNA selfassembly'
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 selfassembly'. Nature, 567 :366372 [DOI] [fulltext] [Details] 

2017  'A cargosorting DNA robot'
Thubagere, Li, Johnson, Chen, Doroudi, Lee, Izatt, Wittman, Srinivas, Woods, Winfree, Qian (2017) 'A cargosorting DNA robot'. Science, 357 (6356) [DOI] [fulltext] [Details] 

2016  'The twohanded 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 twohanded tile assembly model is not intrinsically universal'. Algorithmica, 74 (2):812850 [fulltext] [Details] 

2015  'Intrinsic universality and the computational power of selfassembly'
Woods, Damien (2015) 'Intrinsic universality and the computational power of selfassembly'. Philosophical transactions of the royal society, 373 (2046) [fulltext] [Details] 

2015  'Parallel Computation Using Active Selfassembly'
Chen, Moya and Xin, Doris and Woods, Damien (2015) 'Parallel Computation Using Active Selfassembly'. Natural Computing, 14 (2):225250 [fulltext] [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 (12):251258 [fulltext] [Details] 

2014  'Uniformity is weaker than semiuniformity for some membrane systems'
Murphy, Niall and Woods, Damien (2014) 'Uniformity is weaker than semiuniformity for some membrane systems'. Fundamenta Informaticae, 134 (12):129152 [fulltext] [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):634646 [fulltext] [Details] 

2012  'Optical Computing: Photonic neural networks'
Woods, D;Naughton, TJ (2012) 'Optical Computing: Photonic neural networks'. Nature Physics, 8 :257259 [DOI] [fulltext] [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 :613632 [DOI] [fulltext] [Details] 

2009  'Optical computing'
Woods, D;Naughton, TJ (2009) 'Optical computing'. Applied Mathematics and Computation, 215 :14171430 [DOI] [fulltext] [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 (45):443450 [fulltext] [Details] 

2009  'Small semiweakly universal Turing machines'
Woods, Damien and Neary, Turlough (2009) 'Small semiweakly universal Turing machines'. Fundamenta Informaticae, 91 (1):179195 [fulltext] [Details] 

2009  'Four small universal Turing machines'
Neary, Turlough and Woods, Damien (2009) 'Four small universal Turing machines'. Fundamenta Informaticae, 91 (1):123144 [fulltext] [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):95108 [fulltext] [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 :312 [fulltext] [Details] 

2006  'Small fast universal Turing machines'
Neary, T;Woods, D (2006) 'Small fast universal Turing machines'. Theoretical Computer Science, 362 :171195 [DOI] [fulltext] [Details] 

2005  'An optical model of computation'
Woods, D;Naughton, TJ (2005) 'An optical model of computation'. Theoretical Computer Science, 334 :227258 [DOI] [fulltext] [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.120 [fulltext] [Details] 

2020  The programsize complexity of selfassembled paths
PierreÉtienne Meunier, Damien Regnault, Damien Woods (2020) The programsize complexity of selfassembled paths STOC 2020: Proceedings of the 52nd Annual ACM SIGACT Symposium on Theory of Computing Seattle, , 22JUN20  26JUN20 , pp.727737 [DOI] [fulltext] [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.121 [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.131147 [fulltext] [Details] 

2017  The noncooperative tile assembly model is not intrinsically universal or capable of bounded Turing machine simulation
PierreÉtienne Meunier, Damien Woods (2017) The noncooperative 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.328341 [fulltext] [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.249266 [fulltext] [Details] 

2014  Intrinsic universality in tile selfassembly requires cooperation
Meunier, PierreEtienne and Patitz, Matthew J and Summers, Scott M and Theyssier, Guillaume and Winslow, Andrew and Woods, Damien (2014) Intrinsic universality in tile selfassembly requires cooperation SODA: Proceedings of the twentyfifth annual ACMSIAM symposium on Discrete algorithms , pp.752771 [fulltext] [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.368379 [fulltext] [Details] 

2014  Fast algorithmic selfassembly of simple shapes using random agitation
Chen, HoLin and Doty, David and Holden, Dhiraj and Thachuk, Chris and Woods, Damien and Yang, ChunTao (2014) Fast algorithmic selfassembly of simple shapes using random agitation DNA20: The 20th International Conference on DNA Computing and Molecular Programming , pp.2036 [fulltext] [Details] 

2013  The TwoHanded 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 TwoHanded Tile Assembly Model Is Not Intrinsically Universal ICALP: International Colloquium on Automata, Languages, and Programming , pp.400412 [fulltext] [Details] 

2013  Parallel Computation Using Active Selfassembly⋆
Chen, Moya and Xin, Doris and Woods, Damien (2013) Parallel Computation Using Active Selfassembly⋆ DNA19: The 19th International Conference on DNA Computing and Molecular Programming , pp.1630 [fulltext] [Details] 

2013  Active selfassembly of algorithmic shapes and patterns in polylogarithmic time
Woods, Damien and Chen, HoLin and Goodfriend, Scott and Dabby, Nadine and Winfree, Erik and Yin, Peng (2013) Active selfassembly of algorithmic shapes and patterns in polylogarithmic time ITCS: Proceedings of the 4th conference on Innovations in Theoretical Computer Science , pp.353354 [fulltext] [Details] 

2013  AND and/or OR: Uniform PolynomialSize Circuits
N. Murphy, D. Woods. (2013) AND and/or OR: Uniform PolynomialSize Circuits MCU: Machines, Computations and Universality Zürich, Switzerland. Electronic Proceedings in Theoretical Computer Science, vol 128, , pp.150166 [fulltext] [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.302310 [fulltext] [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 [fulltext] [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.385405 [fulltext] [Details] 

2010  Intrinsic universality in selfassembly
Doty, David and Lutz, Jack H and Patitz, Matthew J and Summers, Scott M and Woods, Damien (2010) Intrinsic universality in selfassembly STACS: The 27th International Symposium on Theoretical Aspects of Computer Science , pp.275286 [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.107120 [Details] 

2009  Random number selection in selfassembly
Doty, David and Lutz, Jack H and Patitz, Matthew J and Summers, Scott M and Woods, Damien (2009) Random number selection in selfassembly International Conference on Unconventional Computation , pp.143157 [fulltext] [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.262273 [fulltext] [Details] 

2009  Membrane dissolution and division in P
Woods, Damien and Murphy, Niall and PérezJiménez, Mario J and RiscosNúñez, Agustín (2009) Membrane dissolution and division in P International Conference on Unconventional Computation , pp.262276 [fulltext] [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.15 [fulltext] [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.7086 [fulltext] [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.164176 [fulltext] [Details] 

2008  Optical computing
D. Woods, T. J. Naughton. (2008) Optical computing Proceedings of the first Workshop on Physics and Computation Vienna, , pp.307330 [fulltext] [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.367384 [fulltext] [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.791798 [DOI] [fulltext] [Details] 

2007  Small semiweakly universal Turing machines
Woods, Damien; Neary, Turlough (2007) Small semiweakly universal Turing machines MCU: 5th International Conference on Machines, Computations and Universality , pp.303315 [fulltext] [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.242254 [fulltext] [Details] 

2006  On the time complexity of 2tag systems and small universal Turing machines
Neary, T and Woods, Damien (2006) On the time complexity of 2tag systems and small universal Turing machines FOCS: Proceedings of the 47th Annual IEEE Symposium on Foundations of Computer Science , pp.439446 [fulltext] [Details] 

2006  Pcompleteness of cellular automaton Rule 110
Neary, Turlough and Woods, Damien (2006) Pcompleteness of cellular automaton Rule 110 ICALP: International Colloquium on Automata, Languages, and Programming , pp.132143 [fulltext] [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.7999 [fulltext] [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.334338 [fulltext] [Details] 

2006  Optical computing and computational complexity
Woods, Damien (2006) Optical computing and computational complexity International Conference on Unconventional Computation , pp.2740 [fulltext] [Details] 

2006  Biocomputation using Holliday junctions
N. Murphy, D. Woods, T.J. Naughton (2006) Biocomputation using Holliday junctions MFCSIT: Fourth Irish Conference on the Mathematical Foundations of Computer Science and Information Technology Cork, Ireland, , pp.317320 [fulltext] [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.777788 [fulltext] [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.237250 [fulltext] [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.540551 [fulltext] [Details] 

2001  On the computational power of a continuousspace optical model of computation
Naughton, Thomas J and Woods, Damien (2001) On the computational power of a continuousspace optical model of computation MCU: International Conference on Machines, Computations, and Universality , pp.288299 [fulltext] [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.17 [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 SelfAssembly'
Woods, Damien (2017) 'Intrinsic Universality in SelfAssembly' In: Encyclopedia of Algorithms, 2nd Ed. Berlin Heidelberg: Springer. [Details] 

2017  'Active selfassembly and molecular robotics with nubots'
Woods, Damien (2017) 'Active selfassembly 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  'Complexitymembrane division, membrane creation'
PérezJiménez, Mario J and RiscosNúñez, Agustín and RomeroJiménez, A and Woods, Damien (2009) 'Complexitymembrane division, membrane creation' In: Handbook of Membrane Computing. Oxford: Oxford University Press. [Details] 