Caltech
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caltech.eduPublications by topic:
Small universal Turing machines
Optical computing
Computational complexity and biological computing
Algorithmic self-assembly: Active self-assembly
Algorithmic self-assembly: Intrinsic universality
Joy Hui. SURF 2013, Harvard College (co-mentored with Erik Winfree)
Dhiraj Holden. SURF 2013, Caltech (co-mentored with Erik Winfree)
Moya Chen. SURF 2012, EE, Caltech (co-mentored with Erik Winfree)
Pierre-Etienne Meunier. Summer 2013. (co-hosted with Erik Winfree)
Turlough Neary. PhD, graduated 2008, NUI Maynooth CS (co-supervised with Paul Gibson)
Niall Murphy. PhD, graduated 2010, NUI Maynooth CS (co-supervised with Tom Naughton)
Doris Xin. Senior Thesis 2012, CS, Caltech (co-mentored with Erik Winfree)
Felix Zhou. SURF 2012, University of Cambridge, UK (co-mentored with Erik Winfree, David Doty)
Zibo Chen. SURF, BIOMOD 2011, National University of Singapore (co-mentored with Erik Winfree, Lulu Qian, Niranjan Srinivas)
Shayan Doroudi. SURF, BIOMOD 2011, Caltech (co-mentored with Erik Winfree, Lulu Qian, Niranjan Srinivas)
Greg Izatt. SURF, BIOMOD 2011, Caltech (co-mentored with Erik Winfree, Lulu Qian, Niranjan Srinivas)
Yae Lim Lee. SURF, BIOMOD 2011. Caltech EE (co-mentored with Erik Winfree, Lulu Qian, Niranjan Srinivas)
Sarah Wittman. SURF, BIOMOD 2011 (co-mentored with Erik Winfree, Lulu Qian, Niranjan Srinivas)
Turlough Neary. Final year thesis, BSc. NUI Maynooth CS
Conferences I've been involved with as a PC member or invited speaker: MCU 2013, DNA19, UCNC 2013, DNA18 (tutorial), OSC 2012, Automata 2011, DNA17 (co-chair), LATA 2011, PC 2011, TCS 2010, UC 2010, OSC 2010, DCM 2009, OSC '09, CRPC '09, UC '08, PC '08, OSC '08, MCU '07, UC '07, LNPC '07, MFCSIT '06, UC '06 (workshop). I was one of the co-chairs of Complexity of Simple Programs 2008, the proceedings of which are here, and a follow-on journal special issue is availiable here (TCS, vol 142, issue 1-2).
I attended the BIOMOD 2011 Jamboree, and co-mentored the Caltech BIOMOD team, see the other teams here.
I previously worked in the Research Group on Natural Computing at the University of Seville and the Cork Complex Systems Lab (CCSL) in University college Cork. Before that I was at the Boole Centre For Research in Informatics and the School of Mathematics. I did my PhD at the Department of Computer Science at NUI Maynooth.
Small universal Turing machines & other simple universal systems
T. Neary, D. Woods, N. Murphy, R. Glaschick. Wang's B machines are efficiently universal, as is Hasenjaeger's small universal electromechanical toy. arXiv:1304.0053 [cs.CC]
Earlier version: R. Glaschick, T. Neary, D. Woods, N. Murphy: Hasenjaeger's electromechanical small universal Turing machine is time efficient. Turing in Context II. Oct 10-12, 2012. Abstract, page 22. Brussels, Belgium.
T. Neary, D. Woods "The complexity of small universal Turing machines: A survey".
SOFSEM 2012: 38th Intl. Conf. on Current Trends in Theory and Practice of Computer Science. Špindlerův Mlýn, Czech Republic. January, 2012. Springer LNCS 7147:385-405. [arxiv]
Older version: D. Woods, T. Neary, "The complexity of small universal Turing machines: A survey". Theoretical Computer Science 410(4-5):443-450, 2009. (Invited) [pdf]
Even older version: D. Woods, T. Neary, "The complexity of small universal Turing machines", CiE 2007: Conference of Computability in Europe, Siena, Italy, June 2007. Springer LNCS vol. 4497. S. Barry Cooper, Benedikt Löwe, and Andrea Sorbi (editors).
T. Neary, D. Woods. Small weakly universal Turing machines.
Conference version: FCT 2009 - 17th International Symposium on Fundamentals of Computation Theory, Wrocław, Poland. Springer LNCS, vol. 5699: 262-273. M. Kutylowski, M. Gebala, W. Charatonik (editors). [pdf]
arXiv version: [arxiv] [cs.CC] July 2007
D. Woods, T. Neary. "Small semi-weakly universal Turing machines".
Journal version: Fundamenta Informaticae. 91:179-195 (2009). (Special issue. Incorrect page numbers in pdf) [pdf]
Conference version: Machines, Computations, and Universality (MCU) 2007, Orléans, France. Springer LNCS, vol. 4664:303-315. J. Durand-Lose, M. Margenstern (editors). [pdf]
T. Neary, D. Woods. "Four small universal Turing machines".
Journal version: Fundamenta Informaticae. 91:123-144 (2009). (Special issue. Incorrect page numbers in pdf) [pdf]
Conference version: Machines, Computations, and Universality (MCU) 2007, Orléans, France. Springer LNCS, vol. 4664:242-254 J. Durand-Lose, M. Margenstern (editors). [pdf]
D. Woods, T. Neary, "On the time complexity of 2-tag systems and small universal Turing machines", FOCS - 2006, 47th Annual IEEE Symposium on Foundations of Computer Science, IEEE, 2006, Berkeley, California. pp 439-446. [pdf]
T. Neary, D. Woods, "P-completeness of cellular automaton Rule 110", ICALP 2006 - International Colloquium on Automata Languages and Programming, Venice, Italy. Springer LNCS vol. 4051, part 1, pp 132-143. [pdf] [.ps]
D. Woods, T. Neary. "Remarks on the computational complexity of small universal Turing machines". MFCSIT 2006. Cork, Ireland. pp 334-338. [pdf]
T. Neary, D. Woods, "Small fast universal Turing machines," Theoretical Computer Science, 362(1-3): 171-195, 11 October 2006. [pdf]
Optical computing
D. Woods, T. J. Naughton, "Optical computing: Photonic neural networks". Nature Physics, News and Views. 8(4):257-259, April 2012. [pdf]
D. Woods, T. J. Naughton, "Optical Computing"
Journal version: Applied Mathematics and Computation, 215(4): 1417-1430, October 2009. (Special issue on Physics and Computation) [pdf]
Conference version: Workshop on Physics and Computation, Vienna, August, 2008. Pre-proceedings published as CDMTCS Research Report 327 (July 2008). Invited. [pdf]
D. Woods, T. J. Naughton, "Parallel and sequential optical computing," International Workshop on Optical Supercomputing. Vienna, August 2008. Springer LNCS vol 5172, pp 70-86. [pdf]
T. J. Naughton, D. Woods, "Optical Computing," In R. Meyer ed., Encyclopedia of Complexity and System Science, Springer. 2009 (Invited survey chapter).
D. Woods, "Optical computing and computational complexity", UC'06 - Fifth International Conference on Unconventional Computation, York, UK 2006, Springer LNCS, vol 4135 , pp 27-40 [pdf] [.ps], (invited.)
D. Woods, "Upper bounds on the computational power of an optical model of computation", ISAAC 2005 - The 16th Annual International Symposium on Algorithms and Computation, Sanya, Hainan, China, December 2005. Springer LNCS, vol 3827, pp 777-788. [pdf] [.ps]
D. Woods, J. P. Gibson, "Lower bounds on the computational power of an optical model of computation"
Journal version: Natural Computing, 7(1): 95-108. March 2008. Springer. [pdf]
Conference version: UC'05 - Fourth International Conference on Unconventional Computation, Sevilla, October 2005. Springer LNCS vol 3699, pp 237-250. [pdf] [.ps]
D. Woods, J. P. Gibson, "Complexity of continuous space machine operations", CiE'05 - Computability in Europe 2005: New Computational Paradigms, Amsterdam, June 2005, S. B. Cooper, B. Löwe, and L. Torenvliet, Eds. Springer LNCS vol. 3526, pp 540-551. [pdf] [.ps]
D. Woods, T. J. Naughton, "An optical model of computation," Theoretical Computer Science, 334(1-3): 227-258, April 2005. [pdf]
T. J. Naughton, D. Woods, "On the computational power of a continuous-space optical model of computation", MCU 2001 - Third International Conference on Machines, Computations and Universality 2001, Maurice Margenstern and Yurii Rogozhin, Eds., Chisinau, Moldova, May 2001. Springer LNCS vol. 2055, pp. 288-299. [pdf] [.ps]
Computational complexity and biological computing
N. Murphy, D. Woods. "AND and/or OR: Uniform Polynomial-Size Circuits".
Machines, Computations and Universality. Accepted.
[arxiv] [cs.CC] Dec 2012
N. Murphy, D. Woods. "Uniformity conditions in natural computing", DNA 16 - The 16th International Conference on DNA Computing and Molecular Programming. Hong Kong, China, June 14-17, Preproceedings, 2010, pp. 109--120. (Niall got the Best Student Paper award!).
D. Woods, N. Murphy, M.J. Pérez-Jiménez, A. Riscos-Núñez. Membrane dissolution and division in P. UC'09 - Eighth International Conference on Unconventional Computation, Ponta Delgada (Azores), Portugal. Springer LNCS, vol 5715 , pp 268-282 [pdf]
N. Murphy, D. Woods. Uniformity: Uncovering the Frontier of Parallelism, Proceedings of the 10th Workshop on Membrane Computing, Curtea de Argeş, Romania, 2009. Pages 556-560. [pdf] (A short survey highlighting some of our work.)
M.J. Pérez-Jiménez, A. Riscos-Núñez, A. Romero-Jiménez, D. Woods. Complexity: Membrane division, membrane creation. In Gh. Paun, G. Rozenberg, A. Salomaa (eds.) The Oxford Handbook of Membrane Computing, Oxford University Press, 2009, Chapter 12, pp. 302-336.
N. Murphy, D. Woods. "On acceptance conditions for membrane systems: characterisations of L and NL", The Complexity of Simple Programs, Cork, Ireland, 6-7 december, 2008. Cork University Press, pp 225-242. [pdf]
N. Murphy, D. Woods. "The computational power of membrane systems under tight uniformity conditions" (Invited journal version) Natural Computing, 10(1): 613-631, 2011. [pdf]
Conference version: N. Murphy, D. Woods. "A characterisation of NL using membrane systems without charges and dissolution", UC'08 - Seventh International Conference on Unconventional Computation, Vienna, 2008. Springer LNCS, vol 5204 , pp 164-176 [pdf]
N. Murphy, D. Woods. "Active membrane systems without charges and using only symmetric elementary division characterise P", Proceedings of the 8th Workshop on Membrane Computing, 2007, Thessaloniki, Greece. Springer LNCS vol. 4860, pp 367-384. [pdf]
N. Murphy, T. J. Naughton, D. Woods, B. Henley, K. McDermott, E. Duffy, P. J. M. van der Burgt, N. Woods "Implementations of a model of physical sorting". International Journal of Unconventional Computing, 4(1), pp 3-12, 2008. [pdf]
Conference version: Pre-proceedings of the workshop From Utopian to Genuine Unconventional Computers (part of UC'06), York, UK. Luniver Press, pp 79-99. [pdf]
N. Murphy, D. Woods, T. J. Naughton. "Bio-Computation using Holliday junctions". MFCSIT 2006. Cork, Ireland. pp 317-320. [pdf] [.ps]
D. Woods, A. Trenaman, "Simultaneous satisfaction of hard and soft timetable constraints for a university department using evolutionary timetabling", Proceedings of Artificial Intelligence & Cognitive Science 1999, Cork, Ireland, September 1999, pp 1-7. [.ps]
Algorithmic self-assembly: Active self-assembly
Moya Chen, Doris Xin, Damien Woods. Parallel computation using active self-assembly. DNA19. The 19th International Conference on DNA Computing and Molecular Programming. 2013. Accepted.
D. Woods, H.L. Chen, S. Goodfriend, N. Dabby, E. Winfree, P. Yin.
Active Self-Assembly of Algorithmic Shapes and Patterns in Polylogarithmic Time.
ITCS 2013: Innovations in Theoretical Computer Science. Berkeley, California, pages 353-354, January 10-12, 2013. Full paper: [pdf], [arxiv], [blurbification]. ACM 2-page extended abstract: [ACM].
Algorithmic self-assembly: Intrinsic universality
[α] = Alphabetical author order
[α] Erik D. Demaine, Matthew J. Patitz, Trent A. Rogers, Robert T. Schweller, Scott M. Summers, Damien Woods.
The two-handed tile assembly model is not intrinsically universal. ICALP 2013.
[α] Pierre-Étienne Meunier, Matthew J. Patitz, Scott M. Summers, Guillaume Theyssier, Andrew Winslow, Damien Woods.
Intrinsic universality in tile self-assembly requires cooperation. [pdf] [arxiv]
[α] Erik D. Demaine, Martin L. Demaine, Sándor P. Fekete, Matthew J. Patitz, Robert T. Schweller, Andrew Winslow, Damien Woods.
One Tile to Rule Them All: Simulating Any Turing Machine, Tile Assembly System, or Tiling System with a Single Puzzle Piece, [arxiv] [cs.CC] Dec 2012
[α] D.S. Doty, J.H. Lutz, M.J. Patitz, R.T. Schweller, S.M. Summers, D.Woods.
The tile assembly model is intrinsically universal. FOCS 2012: The 53rd Annual Symposium on Foundations of Computer Science. Oct 20-23. IEEE. pp 302-310. [arxiv] [blurbification]
[α] D.S. Doty, J.H. Lutz, M.J. Patitz, S.M. Summers, D.Woods.
Intrinsic Universality in Self-Assembly. STACS 2010 - Proceedings of the 27th International Symposium on Theoretical Aspects of Computer Science, (Nancy, France, March 4-6, 2010). [pdf]
[α] D.S. Doty, J.H. Lutz, M.J. Patitz, S.M. Summers, D.Woods.
Random number selection in self-assembly. UC'09 - Eighth International Conference on Unconventional Computation, Ponta Delgada (Azores), Portugal. Springer LNCS, vol 5715 , pp 143-157. [pdf]
PhD thesis
D. Woods, "Computational Complexity of an optical model of computation" PhD Thesis, NUI Maynooth, 2005.
Technical reports, short conference abstracts, etc.
N. Murphy, D. Woods. "The Computational Complexity of Uniformity and Semi-uniformity in Membrane Systems", Unrefereed report in the 7th Brainstorming Week on Membrane Computing, 2009. [pdf] Newer version appeared at DNA16, 2010.
N. Murphy, D. Woods. "A characterisation of NL using membrane systems without charges and dissolution", Technical Report NUIM-CS-TR-2008-01, Jan 2008, Department of Computer Science, National University of Ireland Maynooth, Ireland. [pdf]
N. Murphy, D. Woods, T.J. Naughton, "Stable Sorting Using Special-Purpose Physical Devices", BCRI Preprint 06/2006, May 2006, Boole Centre for Research in Informatics, University College Cork, Ireland. [pdf] [.ps]
T. Neary, D. Woods, "P-completeness of cellular automaton Rule 110", BCRI Preprint 04/2006, April 2006, Boole Centre for Research in Informatics, University College Cork, Ireland. [pdf] [.ps]
T. Neary, D. Woods, "A small fast universal Turing machine" Technical Report NUIM-CS-TR-2005-12, CS Dept., NUI Maynooth, 2005. [pdf] [.ps]
T. Neary, D. Woods, "Small fast universal Turing machines" Technical Report NUIM-CS-TR-2005-11, CS Dept., NUI Maynooth, 2005. [pdf] [.ps]
N. Murphy, D. Woods, T. J. Naughton, "On the computational power of photosynthesis," Technical Report NUIM-CS-TR-2005-03, CS Dept., NUI Maynooth, July 2005. [pdf]
D. Woods, "Computational complexity of an optical model of computation," (Invited.) International workshop on computations on the continuum. Lisbon, Portugal, June 27-28, 2005.
T. Neary, D. Woods, "Simulating Turing machines using switching map systems" Technical Report NUIM-CS-TR-2003-11, NUI Maynooth, December 2003. [pdf] [.ps]
D. Woods, T. J. Naughton, J. P. Gibson, "Continuous-space model of computation," (Invited.) American Mathematical Society - Spring Western Section Meeting #987, Special Session on Beyond Classical Boundaries of Computability, M. Burgin, P. Wegner, Eds., San Francisco, California, 3-4 May 2003. Reprinted in Abstracts of Papers Presented to the American Mathematical Society, vol. 24, no. 3, p. 484, September 2003.
A. Delaney, T. J. Naughton, D.Woods, "Towards a minimal computational power operating system." In British Colloquium for Theoretical Computer Science, number 19, Leicester, UK, April 2003. [.ps] [.pdf]
D. Woods, T. J. Naughton, "Analog recurrent neural network simulation and
(log2 n) unordered search with an optically inspired model of computation" Technical Report NUIM-CS-TR-2003-04, NUI Maynooth, March 2003. [pdf] [.ps]D. Woods, T. J. Naughton, J. Paul Gibson, "Analog recurrent neural network simulation,
(log2 n) unordered search, and bitonic sort with an optically-inspired model of computation" Technical Report NUIM-CS-TR-2001-06, NUI Maynooth, October 2001. (This report is a preliminary version of NUIM-CS-TR-2003-04 above.) [pdf]T. J. Naughton, D. Woods, "On the computational power of a continuous-space optical model of computation" Technical Report NUIM-CS-TR-2001-01, NUI Maynooth, January 2001. [pdf]
PhD Supervision
Niall Murphy. Uniformity conditions for membrane systems: uncovering complexity below P. PhD awarded: 2010. Examiners: Petr Sosík, Philippe Moser. Co-supervised by Tom Naughton.
Turlough Neary. Small universal Turing machines. PhD awarded: 2008. Examiners: Maurice Margenstern, James Power. Co-supervised by Paul Gibson
Some links: Carrick Castles, A course on cybernetics.