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ORCIDDamien Woods
Person information
- affiliation: National University of Ireland, Hamilton Institute, Maynooth, Ireland
- affiliation (2016 - 2018): INRIA, France
- affiliation (2009 - 2016): California Institute of Technology, Computer Science, Pasadena, CA, USA
- affiliation (2008 - 2009): University of Seville, Spain
- affiliation (2004 - 2008): University College Cork, Ireland
- affiliation (PhD 2004): Maynooth University, Department of Computer Science, Ireland
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2020 – today
- 2025
[c41]Gwendal Ducloz, Ahmed Shalaby, Damien Woods:
Algorithmic Hardness of the Partition Function for Nucleic Acid Strands. DNA 2025: 1:1-1:23- [c40]Constantine G. Evans, Angel Cervera Roldan, Trent A. Rogers, Damien Woods:
Tile Blockers as a Simple Motif to Control Self-Assembly: Kinetics and Thermodynamics. DNA 2025: 7:1-7:19 - [c39]Ahmed Shalaby, Damien Woods
:
An Efficient Algorithm to Compute the Minimum Free Energy of Interacting Nucleic Acid Strands. ICALP 2025: 130:1-130:20 - [i25]Gwendal Ducloz, Ahmed Shalaby, Damien Woods:
Algorithmic hardness of the partition function for nucleic acid strands. CoRR abs/2506.19756 (2025) - 2024
- [j18]Irina Kostitsyna, Cai Wood, Damien Woods:
Turning machines: a simple algorithmic model for molecular robotics. Nat. Comput. 23(2): 407-430 (2024) - [c38]Erik D. Demaine, Timothy Gomez, Elise Grizzell, Markus Hecher, Jayson Lynch, Robert T. Schweller, Ahmed Shalaby, Damien Woods:
Domain-Based Nucleic-Acid Minimum Free Energy: Algorithmic Hardness and Parameterized Bounds. DNA 2024: 2:1-2:24 - [c37]Tristan Stérin, Damien Woods:
Hardness of Busy Beaver Value BB(15). RP 2024: 120-137 - [i24]Ahmed Shalaby, Damien Woods:
An efficient algorithm to compute the minimum free energy of interacting nucleic acid strands. CoRR abs/2407.09676 (2024) - 2023
- [c36]Ahmed Shalaby, Chris Thachuk, Damien Woods:
Minimum Free Energy, Partition Function and Kinetics Simulation Algorithms for a Multistranded Scaffolded DNA Computer. DNA 2023: 1:1-1:22 - [i23]David Doty, Niels Kornerup, Austin Luchsinger, Leo Orshansky, David Soloveichik, Damien Woods:
Harvesting Brownian Motion: Zero Energy Computational Sampling. CoRR abs/2309.06957 (2023) - [i22]Aaron T. Becker, Sándor P. Fekete, Irina Kostitsyna, Matthew J. Patitz, Damien Woods, Ioannis Chatzigiannakis:
Algorithmic Foundations of Programmable Matter (Dagstuhl Seminar 23091). Dagstuhl Reports 13(2): 183-198 (2023) - 2021
- [c35]Matthew Cook, Tristan Stérin, Damien Woods:
Small Tile Sets That Compute While Solving Mazes. DNA 2021: 8:1-8:20 - [i21]Matthew Cook, Tristan Stérin, Damien Woods:
Small tile sets that compute while solving mazes. CoRR abs/2106.12341 (2021) - [i20]Tristan Stérin, Damien Woods:
On the hardness of knowing busy beaver values BB(15) and BB(5, 4). CoRR abs/2107.12475 (2021) - 2020
- [c34]Irina Kostitsyna, Cai Wood, Damien Woods:
Turning Machines. DNA 2020: 11:1-11:21 - [c33]Tristan Stérin, Damien Woods:
The Collatz Process Embeds a Base Conversion Algorithm. RP 2020: 131-147 - [c32]Pierre-Étienne Meunier, Damien Regnault, Damien Woods:
The program-size complexity of self-assembled paths. STOC 2020: 727-737 - [i19]Pierre-Étienne Meunier, Damien Regnault, Damien Woods:
The program-size complexity of self-assembled paths. CoRR abs/2002.04012 (2020) - [i18]Tristan Stérin, Damien Woods:
Limitations on counting in Boolean circuits and self-assembly. CoRR abs/2005.13581 (2020) - [i17]Tristan Stérin, Damien Woods:
The Collatz process embeds a base conversion algorithm. CoRR abs/2007.06979 (2020) - [i16]Irina Kostitsyna, Cai Wood, Damien Woods:
Turning machines. CoRR abs/2009.00755 (2020)
2010 – 2019
- 2019
- [j17]Damien Woods, David Doty, Cameron Myhrvold, Joy Hui, Felix Zhou, Peng Yin, Erik Winfree:
Diverse and robust molecular algorithms using reprogrammable DNA self-assembly. Nat. 567(7748): 366-372 (2019) - 2018
- [j16]Damien Woods, Yannick Rondelez:
Preface. Nat. Comput. 17(1): 1-2 (2018) - 2017
- [c31]David Doty, Trent A. Rogers, David Soloveichik, Chris Thachuk, Damien Woods:
Thermodynamic Binding Networks. DNA 2017: 249-266 - [c30]Pierre-Étienne Meunier, Damien Woods:
The non-cooperative tile assembly model is not intrinsically universal or capable of bounded Turing machine simulation. STOC 2017: 328-341 - [i15]Pierre-Étienne Meunier, Damien Woods:
The non-cooperative tile assembly model is not intrinsically universal or capable of bounded Turing machine simulation. CoRR abs/1702.00353 (2017) - [i14]David Doty, Trent A. Rogers, David Soloveichik, Chris Thachuk, Damien Woods:
Thermodynamic Binding Networks. CoRR abs/1709.07922 (2017) - 2016
- [j15]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. Algorithmica 74(2): 812-850 (2016) - [e2]Yannick Rondelez, Damien Woods:
DNA Computing and Molecular Programming - 22nd International Conference, DNA 2016, Munich, Germany, September 4-8, 2016, Proceedings. Lecture Notes in Computer Science 9818, Springer 2016, ISBN 978-3-319-43993-8 [contents] - [r3]Damien Woods:
Active Self-Assembly and Molecular Robotics with Nubots. Encyclopedia of Algorithms 2016: 13-18 - [r2]Damien Woods:
Intrinsic Universality in Self-Assembly. Encyclopedia of Algorithms 2016: 993-998 - 2015
- [j14]Damien Woods, Turlough Neary:
Yurii Rogozhin's Contributions to the Field of Small Universal Turing Machines. Fundam. Informaticae 138(1-2): 251-258 (2015) - [j13]Moya Chen, Doris Xin, Damien Woods:
Parallel computation using active self-assembly. Nat. Comput. 14(2): 225-250 (2015) - [c29]Turlough Neary, Damien Woods:
Tag Systems and the Complexity of Simple Programs. Automata 2015: 11-16 - 2014
- [j12]Niall Murphy, Damien Woods:
Uniformity is Weaker than Semi-Uniformity for Some Membrane Systems. Fundam. Informaticae 134(1-2): 129-152 (2014) - [j11]Turlough Neary, Damien Woods, Niall Murphy, Rainer Glaschick:
Wang's B machines are efficiently universal, as is Hasenjaeger's small universal electromechanical toy. J. Complex. 30(5): 634-646 (2014) - [c28]Ho-Lin Chen, David Doty, Dhiraj Holden, Chris Thachuk, Damien Woods, Chun-Tao Yang:
Fast Algorithmic Self-assembly of Simple Shapes Using Random Agitation. DNA 2014: 20-36 - [c27]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 Tile Assembly System with a Single Universal Tile. ICALP (1) 2014: 368-379 - [c26]Pierre-Etienne Meunier, Matthew J. Patitz, Scott M. Summers, Guillaume Theyssier, Andrew Winslow, Damien Woods:
Intrinsic universality in tile self-assembly requires cooperation. SODA 2014: 752-771 - [i13]Moya Chen, Doris Xin, Damien Woods:
Parallel computation using active self-assembly. CoRR abs/1405.0527 (2014) - [i12]Ho-Lin Chen, David Doty, Dhiraj Holden, Chris Thachuk, Damien Woods, Chun-Tao Yang:
Fast algorithmic self-assembly of simple shapes using random agitation. CoRR abs/1409.4828 (2014) - [i11]Niall Murphy, Damien Woods:
Uniformity is weaker than semi-uniformity for some membrane systems. CoRR abs/1412.3377 (2014) - 2013
- [c25]Moya Chen, Doris Xin, Damien Woods:
Parallel Computation Using Active Self-assembly. DNA 2013: 16-30 - [c24]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 (1) 2013: 400-412 - [c23]Damien Woods, Ho-Lin Chen, Scott Goodfriend, Nadine Dabby, Erik Winfree, Peng Yin:
Active self-assembly of algorithmic shapes and patterns in polylogarithmic time. ITCS 2013: 353-354 - [c22]Damien Woods:
Intrinsic universality and the computational power of self-assembly. MCU 2013: 16-22 - [c21]Niall Murphy, Damien Woods:
AND and/or OR: Uniform Polynomial-Size Circuits. MCU 2013: 150-166 - [i10]Damien Woods, Ho-Lin Chen, Scott Goodfriend, Nadine Dabby, Erik Winfree, Peng Yin:
Active Self-Assembly of Algorithmic Shapes and Patterns in Polylogarithmic Time. CoRR abs/1301.2626 (2013) - [i9]Turlough Neary, Damien Woods, Niall Murphy, Rainer Glaschick:
Wang's B machines are efficiently universal, as is Hasenjaeger's small universal electromechanical toy. CoRR abs/1304.0053 (2013) - [i8]Pierre-Etienne Meunier, Matthew J. Patitz, Scott M. Summers, Guillaume Theyssier, Andrew Winslow, Damien Woods:
Intrinsic universality in tile self-assembly requires cooperation. CoRR abs/1304.1679 (2013) - [i7]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. CoRR abs/1306.6710 (2013) - 2012
- [c20]David Doty, Jack H. Lutz, Matthew J. Patitz, Robert T. Schweller, Scott M. Summers, Damien Woods:
The Tile Assembly Model is Intrinsically Universal. FOCS 2012: 302-310 - [c19]Turlough Neary, Damien Woods:
The Complexity of Small Universal Turing Machines: A Survey. SOFSEM 2012: 385-405 - [i6]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. CoRR abs/1212.4756 (2012) - 2011
- [j10]Niall Murphy, Damien Woods:
The computational power of membrane systems under tight uniformity conditions. Nat. Comput. 10(1): 613-632 (2011) - [j9]Damien Woods, Turlough Neary, Anthony Karel Seda:
Preface. Theor. Comput. Sci. 412(1-2): 1 (2011) - [i5]Turlough Neary, Damien Woods:
The complexity of small universal Turing machines: a survey. CoRR abs/1110.2230 (2011) - [i4]David Doty, Jack H. Lutz, Matthew J. Patitz, Robert T. Schweller, Scott M. Summers, Damien Woods:
The tile assembly model is intrinsically universal. CoRR abs/1111.3097 (2011) - 2010
- [c18]David Doty, Jack H. Lutz, Matthew J. Patitz, Scott M. Summers, Damien Woods:
Intrinsic Universality in Self-Assembly. STACS 2010: 275-286 - [i3]David Doty, Jack H. Lutz, Matthew J. Patitz, Scott M. Summers, Damien Woods:
Intrinsic Universality in Self-Assembly. CoRR abs/1001.0208 (2010)
2000 – 2009
- 2009
- [j8]Damien Woods, Thomas J. Naughton:
Optical computing. Appl. Math. Comput. 215(4): 1417-1430 (2009) - [j7]Turlough Neary, Damien Woods:
Four Small Universal Turing Machines. Fundam. Informaticae 91(1): 123-144 (2009) - [j6]Damien Woods, Turlough Neary:
Small Semi-Weakly Universal Turing Machines. Fundam. Informaticae 91(1): 179-195 (2009) - [j5]Damien Woods, Turlough Neary:
The complexity of small universal Turing machines: A survey. Theor. Comput. Sci. 410(4-5): 443-450 (2009) - [c17]Turlough Neary, Damien Woods:
Small Weakly Universal Turing Machines. FCT 2009: 262-273 - [c16]David Doty, Jack H. Lutz, Matthew J. Patitz, Scott M. Summers, Damien Woods:
Random Number Selection in Self-assembly. UC 2009: 143-157 - [c15]Damien Woods, Niall Murphy, Mario J. Pérez-Jiménez, Agustin Riscos-Núñez:
Membrane Dissolution and Division in P. UC 2009: 262-276 - [e1]Turlough Neary, Damien Woods, Anthony Karel Seda, Niall Murphy:
Proceedings International Workshop on The Complexity of Simple Programs, CSP 2008, Cork, Ireland, 6-7th December 2008. EPTCS 1, 2009 [contents] - [r1]Thomas J. Naughton, Damien Woods:
Optical Computing. Encyclopedia of Complexity and Systems Science 2009: 6388-6407 - 2008
- [j4]Niall Murphy, Thomas J. Naughton, Damien Woods, Beverley Henley, Kieran McDermott, Elaine Duffy, Peter J. M. Van Der Burgt, Niamh Woods:
Implementations of a Model of Physical Sorting. Int. J. Unconv. Comput. 4(1): 3-12 (2008) - [j3]Damien Woods, J. Paul Gibson:
Lower bounds on the computational power of an optical model of computation. Nat. Comput. 7(1): 95-108 (2008) - [c14]Damien Woods, Thomas J. Naughton:
Parallel and Sequential Optical Computing. OSC 2008: 70-86 - [c13]Niall Murphy, Damien Woods:
A Characterisation of NL Using Membrane Systems without Charges and Dissolution. UC 2008: 164-176 - [c12]Niall Murphy, Damien Woods:
On acceptance conditions for membrane systems: characterisations of L and NL. CSP 2008: 172-184 - 2007
- [c11]Damien Woods, Turlough Neary:
The Complexity of Small Universal Turing Machines. CiE 2007: 791-799 - [c10]Turlough Neary, Damien Woods:
Four Small Universal Turing Machines. MCU 2007: 242-254 - [c9]Damien Woods, Turlough Neary:
Small Semi-weakly Universal Turing Machines. MCU 2007: 303-315 - [c8]Niall Murphy, Damien Woods:
Active Membrane Systems Without Charges and Using Only Symmetric Elementary Division Characterise P. Workshop on Membrane Computing 2007: 367-384 - [i2]Turlough Neary, Damien Woods:
Small weakly universal Turing machines. CoRR abs/0707.4489 (2007) - 2006
- [j2]Turlough Neary, Damien Woods:
Small fast universal Turing machines. Theor. Comput. Sci. 362(1-3): 171-195 (2006) - [c7]Damien Woods, Turlough Neary:
On the time complexity of 2-tag systems and small universal Turing machines. FOCS 2006: 439-448 - [c6]Turlough Neary, Damien Woods:
P-completeness of Cellular Automaton Rule 110. ICALP (1) 2006: 132-143 - [c5]Damien Woods:
Optical Computing and Computational Complexity. UC 2006: 27-40 - [i1]Damien Woods, Turlough Neary:
On the time complexity of 2-tag systems and small universal Turing machines. CoRR abs/cs/0612089 (2006) - 2005
- [j1]Damien Woods, Thomas J. Naughton:
An optical model of computation. Theor. Comput. Sci. 334(1-3): 227-258 (2005) - [c4]Damien Woods, J. Paul Gibson:
Complexity of Continuous Space Machine Operations. CiE 2005: 540-551 - [c3]Damien Woods:
Upper Bounds on the Computational Power of an Optical Model of Computation. ISAAC 2005: 777-788 - [c2]Damien Woods, J. Paul Gibson:
Lower Bounds on the Computational Power of an Optical Model of Computation. UC 2005: 237-250 - 2001
- [c1]Thomas J. Naughton, Damien Woods:
On the Computational Power of a Continuous-Space Optical Model of Computation. MCU 2001: 288-299
Coauthor Index
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