Article

Cook, Matthew and Sterin, Tristan and Woods, Damien (2021) Small tile sets that compute while solving mazes. 27th International Conference on DNA Computing and Molecular Programming (DNA 27). pp. 1-18.

Sterin, Tristan and Woods, Damien (2020) The Collatz Process Embeds a Base Conversion Algorithm. Lecture Notes in Computer Science. pp. 131-147. ISSN 0302-9743

Meunier, Pierre-Étienne and Regnault, Damien and Woods, Damien (2020) The program-size complexity of self-assembled paths. STOC 2020: Proceedings of the 52nd Annual ACM SIGACT Symposium on Theory of Computing. pp. 727-737.

Woods, Damien and Doty, David and Myhrvold, Cameron and Hui, Joy and Zhou, Felix and Yin, Peng and Winfree, Erik (2019) Diverse and robust molecular algorithms using reprogrammable DNA self-assembly. Nature, 567. pp. 366-372. ISSN 0028-0836

Thubagere, Anupama J. and Liu, Wei and Johnson, Robert F. and Chen, Zibo and Doroudi, Shayan and Lee, Yae Lim and Izatt, Gregory and Wittman, Sarah and Srinivas, Niranjan and Woods, Damien and Winfree, Erik and Qian, Lulu (2017) A cargo-sorting DNA robot. Science, 357 (6356). eaan6558. ISSN 0036-8075

Demaine, Erik D. and Patitz, Mathhew J. and Rogers, Trent A. and Schweller, Robert and Summers, Scott M. and Woods, Damien (2016) The two-handed tile assembly model is not intrinsically universal. Algorithmica, 74 (2). pp. 812-850. ISSN 1432-0541

Woods, Damien (2015) Intrinsic universality and the computational power of self-assembly. Philosophical Transactions of the Royal Society A, 373 (2046). ISSN 0264-3820

Chen, Moya and Xin, Doris and Woods, Damien (2015) Parallel computation using active self-assembly. Natural Computing, 14 (2). pp. 225-250. ISSN 1572-9796

Woods, Damien and Neary, Turlough (2015) Yurii Rogozhin’s Contributions to the Field of Small Universal Turing Machines. Fundamenta Informaticae, 137. pp. 1-9. ISSN 0169-2968

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). pp. 634-646. ISSN 0885-064X

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. Lecture Notes in Computer Science. pp. 20-36. ISSN 0302-9743

Demaine, Erik D. and Demaine, Martin L. and Sandor, Fekete P and Patitz, Mathhew J. and Schweller, Robert and Winslow, Andrew and Woods, Damien (2014) One tile to rule them all: Simulating any tile assembly system with a single universal tile. Lecture Notes in Computer Science. pp. 368-379. ISSN 0302-9743

Murphy, Niall and Woods, Damien (2014) Uniformity is weaker than semi-uniformity for some membrane systems. Fundamenta Informaticae, 134 (1-2). pp. 129-152. ISSN 1875-8681

Murphy, Niall and Woods, Damien (2013) AND and/or OR: Uniform Polynomial-Size Circuits. Electronic Proceedings in Theoretical Computer Science, 128. pp. 150-166. ISSN 2075-2180

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.

Meunier, Pierre-Etienne and Patitz, Matthew J. and Summers, Scott M. and Theyssier, Guillaume and Winslow, Andrew and Woods, Damien (2013) Intrinsic universality in tile self-assembly requires cooperation. SODA '14: Proceedings of the twenty-fifth annual ACM-SIAM symposium on Discrete algorithms. pp. 752-771.

Woods, Damien and Naughton, Thomas J. (2012) Optical computing: Photonic neural networks. Nature Physics, 8 (4). pp. 257-259. ISSN 1745-2473

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. 2012 IEEE 53rd Annual Symposium on Foundations of Computer Science. pp. 302-310. ISSN 0272-5428

Murphy, Niall and Woods, Damien (2011) The computational power of membrane systems under tight uniformity conditions. Natural Computing, 10 (1). pp. 613-632. ISSN 1572-9796

Woods, Damien and Naughton, Thomas J. (2009) Optical computing. Applied Mathematics and Computation, 215 (4). pp. 1417-1430. ISSN 0096-3003

Woods, Damien and Neary, Turlough (2009) The complexity of small universal Turing machines: A survey. Theoretical Computer Science, 410 (4-5). pp. 443-450. ISSN 0304-3975

Neary, Turlough and Woods, Damien (2009) Four Small Universal Turing Machines. Fundamenta Informaticae, 91 (1). pp. 123-144. ISSN 0169-2968

Woods, Damien and Neary, Turlough (2009) Small Semi-Weakly Universal Turing Machines. Fundamenta Informaticae, 91 (1). pp. 179-195. ISSN 0169-2968

Woods, Damien and Gibson, J. Paul (2008) Lower bounds on the computational power of an optical model of computation. Natural Computing, 7 (1). pp. 95-108. ISSN 1567-7818

Murphy, Niall and Woods, Damien (2008) A characterisation of NL using membrane systems without charges and dissolution. Technical Report NUIM-CS-TR-2008-01, National University of Ireland Maynooth. pp. 1-12.

Woods, Damien and Naughton, Thomas J. (2008) Parallel and sequential optical computing. Lecture Notes in Computer Science, 5172. pp. 70-86. ISSN 0302-9743

Murphy, Niall and Naughton, Thomas J. and Woods, Damien and Henley, Beverley and McDermott, Kieran and Duffy, Elaine and van der Burgt, Peter J.M. and Woods, Niamh (2007) Implementations of a model of physical sorting. International Journal of Unconventional Computing, 4 (1). pp. 3-12. ISSN 1548-7199

Neary, Turlough and Woods, Damien (2006) Small fast universal Turing machines. Theoretical Computer Science, 362. pp. 171-195. ISSN 0304-3975

Neary, Turlough and Woods, Damien (2006) P-completeness of Cellular Automaton Rule 110. Lecture Notes in Computer Science, 4051. pp. 132-143. ISSN 0302-9743

Woods, Damien and Naughton, Thomas J. (2005) An optical model of computation. Theoretical Computer Science, 334. pp. 227-258.

Book Section

Doty, David and Rogers, Trent A. and Soloveichik, David and Thachuk, Chris and Woods, Damien (2017) Thermodynamic Binding Networks. In: DNA Computing and Molecular Programming. DNA 2017. Lecture Notes in Computer Science (10467). Springer, Cham, Switzerland, pp. 249-266. ISBN 978-3-319-66799-7

Woods, Damien and Murphy, Niall and Pérez-Jiménez, Mario J. and Riscos-Núñez, Agustín (2009) Membrane dissolution and division in P. In: Unconventional Computation, Proceedings of the 8th International Conference, UC 2009, Ponta Delgada, Portugal. Springer, Berlin, pp. 262-276. ISBN 9783642037443

Doty, David and Lutz, Jack H. and Patitz, Mathhew J. and Summers, Scott M. and Woods, Damien (2009) Random number selection in self-assembly. In: Unconventional Computation. Springer, pp. 143-157. ISBN 3-642-03744-5

Neary, Turlough and Woods, Damien (2009) Small weakly universal Turing machines. In: Fundamentals of Computation Theory. Springer Verlag, pp. 267-273. ISBN 3-642-03408-X

Woods, Damien and Naughton, Thomas J. (2008) Optical Computing. In: CDMTCS Research Report Series. Centre for Discrete Mathematics and Theoretical Computer Science, pp. 307-330.

Murphy, Niall and Woods, Damien (2007) Active membrane systems without charges and using only symmetric elementary division characterise P. In: Membrane Computing. International Workshop WMC9. Springer Berlin / Heidelberg, pp. 367-384. ISBN 978-3540958840

Woods, Damien and Neary, Turlough (2006) On the time complexity of 2-tag systems and small universal Turing machines. In: 2006 47th Annual IEEE Symposium on Foundations of Computer Science (FOCS'06). IEEE, pp. 439-448. ISBN 0-7695-2720-5

Woods, Damien (2006) Optical computing and computational complexity. In: Unconventional Computation. Springer, pp. 27-40. ISBN 3-540-38593-2

Woods, Damien and Gibson, Paul (2005) Complexity of continuous space machine operations. In: New Computational Paradigms. Springer, pp. 540-555.

Woods, Damien (2005) Upper bounds on the computational power of an optical model of computation. In: Algorithms and Computation. Springer, pp. 777-788. ISBN 3-540-30935-7

Naughton, Thomas J. and Woods, Damien (2001) On the Computational Power of a Continuous-Space Optical Model of Computation. In: MCU 2001: Machines, Computations, and Universality. Lecture Notes in Computer Science book series (LNCS) (2055). Springer, pp. 288-299. ISBN 3540421211

Conference or Workshop Item

Meunier, Pierre-Etienne and Woods, Damien (2017) The non-cooperative tile assembly model is not intrinsically universal or capable of bounded Turing machine simulation. In: STOC 2017 49th Annual ACM SIGACT Symposium on Theory of Computing, 19-23 June 2017, Montreal, Canada.

Glaschick, Rainer and Neary, Turlough and Woods, Damien and Murphy, Niall (2012) Hasenjaeger's electromechanical small universal Turing machine is time efficient. In: Turing in Context II, October, 2012.

Murphy, Niall and Woods, Damien (2009) The Computational Complexity of Uniformity and Semi-uniformity in Membrane Systems. In: Seventh Brainstorming Week on Membrane Computing, 2 – 6 February 2009, Seville. (Unpublished)

Murphy, Niall and Woods, Damien (2009) Uniformity: Uncovering the Frontier of Parallelism. In: 10th Workshop on Membrane Computing, 24-27 August 2009, Curtea de Argeş, Romania. (Unpublished)

Murphy, Niall and Woods, Damien and Naughton, Thomas J. (2006) Bio-Computation using Holliday junctions. In: Information-MFCSIT'06 : Fourth International Conference on Information, Information'06, and the Fourth Irish Conference on the Mathematical Foundations of Computer Science and Information Technology'06, August 1-5, 2016, University College Cork. (Unpublished)

Woods, Damien and Neary, Turlough (2006) Remarks on the computational complexity of small universal Turing machines. In: Proceedings Of The Fourth International Conference On Information And The Fourth Irish Conference On The Mathematical Foundations Of Computer Science And Information Technology Mfcsit, 2006.