Refereed Conference Papers

(Note that following standard convention for publications in theoretical Computer Science, my co-authors and I are listed on all publications in strictly alphabetical order, with no special positions for lead author, second author, etc.)

  • Universal Simulation of Directed Systems in the abstract Tile Assembly Model Requires Undirectedness, Jacob Hendricks, Matthew J. Patitz, Trent A. Rogers. Proceedings of the 57th Annual IEEE Symposium on Foundations of Computer Science (FOCS 2016), (October 9-11, 2016, New Brunswick, New Jersey), pp. 800-809.
  • Hierarchical Self-Assembly of Fractals with Signal-Passing Tiles (extended abstract), Jacob Hendricks, Meagan Olsen, Matthew J. Patitz, Trent A. Rogers, and Hadley Thomas. Proceedings of the 22nd International Conference on DNA Computing and Molecular Programming (DNA 22), (September 4-8, 2016, Ludwig-Maximilians-Universität, Munich, Germany), pp. 82-97.
  • Resiliency to Multiple Nucleation in Temperature-1 Self-Assembly, Matthew J. Patitz, Trent A. Rogers, Robert T. Schweller, Scott M. Summers, Andrew Winslow. Proceedings of the 22nd International Conference on DNA Computing and Molecular Programming (DNA 22), (September 4-8, 2016, Ludwig-Maximilians-Universität, Munich, Germany), pp. 98-113.
  • Computing in continuous space with self-assembling polygonal tiles, Oscar Gilbert, Jacob Hendricks, Matthew J. Patitz, Trent A. Rogers. Proceedings of the ACM-SIAM Symposium on Discrete Algorithms (SODA 2016), (Arlington, VA, USA, January 10-12, 2016), pp. 937-956.
  • The Simulation Powers and Limitations of Higher Temperature Hierarchical Self-Assembly Systems, Jacob Hendricks, Matthew J. Patitz, Trent A. Rogers. Proceedings of the 7th International Conference on Machines, Computations and Universality (MCU'15), (9-11 September, 2015, Eastern Mediterranean University, Famagusta, North Cyprus), pp. 149-163. Best Paper Award
  • Reflections on Tiles (in Self-Assembly), Jacob Hendricks, Matthew J. Patitz, Trent A. Rogers. Proceedings of the 21st International Conference on DNA Computing and Molecular Programming (DNA 21), (August 17-21, 2015, Harvard University, Cambridge, MA, USA.), pp. 55-70.
  • Binary pattern tile set synthesis is NP-hard, Lila Kari, Steffen Kopecki, Pierre-Étienne Meunier, Matthew J. Patitz, Shinnosuke Seki. Proceedings of the 42nd International Colloquium on Automata, Languages, and Programming (ICALP 2015), (6-10 July 2015, Kyoto, Japan), LNCS Vol. 9134, pp. 1022-1034.
  • Replication of arbitrary hole-free shapes via self-assembly with signal-passing tiles (extended abstract), Jacob Hendricks, Matthew J. Patitz, Trent A. Rogers. Proceeding of the 14th International Conference on Unconventional Computation and Natural Computation (UCNC 2015), (University of Auckland, New Zealand, 31 August – 4 September, 2015), pp. 202-214.
  • Universal Computation with Arbitrary Polyomino Tiles in Non-Cooperative Self-Assembly, Sándor P. Fekete, Jacob Hendricks, Matthew J. Patitz, Trent A. Rogers, Robert T. Schweller. Proceedings of the ACM-SIAM Symposium on Discrete Algorithms (SODA 2015), (San Diego, CA, USA, January 4-6, 2015), pp. 148-167.
  • Doubles and Negatives are Positive (in Self-Assembly), Jacob Hendricks, Matthew J. Patitz, Trent A. Rogers. Proceeding of the 13th International Conference on Unconventional Computation and Natural Computation (UCNC 2014), (University of Western Ontario, London, Ontario, Canada, July 14-18, 2014), pp. 190-202.
  • One Tile to Rule Them All: Simulating Any Tile Assembly System with a Single Universal Tile, Erik D. Demaine, Martin L. Demaine, Sándor P. Fekete, Matthew J. Patitz, Robert T. Schweller, Andrew Winslow, and Damien Woods. Proceedings of the 41st International Colloquium on Automata, Languages, and Programming (ICALP 2014), (IT University of Copenhagen, Denmark, July 8-11, 2014), pp. 368-379.
  • The Power of Duples (in Self-Assembly): It's Not So Hip To Be Square, Jacob Hendricks, Matthew J. Patitz, Trent A. Rogers, Scott M. Summers. Proceedings of the 20th International Computing and Combinatorics Conference (COCOON 2014), (Atlanta, GA, USA, August 4-6, 2014), pp. 215-226.
  • Intrinsic universality in tile self-assembly requires cooperation, Pierre-Étienne Meunier, Matthew J. Patitz, Scott M. Summers, Guillaume Theyssier, Andrew Winslow, Damien Woods. Proceedings of the ACM-SIAM Symposium on Discrete Algorithms (SODA 2014), (Portland, OR, USA, January 5-7, 2014), pp. 752-771.
  • Tile Assembly Simulator: A Software Package for Tile-Based Algorithmic Self-Assembly, Tyler Fochtman and Matthew Patitz. Proceedings of the Seventh IEEE International Conference on Self-Adaptive and Self-Organizing Systems Workshops (SASOW), Philadelphia, PA, USA, September 9-13, 2013. IEEE Computer Society Press, pp. 27-28.
  • On the Equivalence of Cellular Automata and the Tile Assembly Model, Jacob Hendricks and Matthew J. Patitz. Proceedings of Machines, Computations and Universality (MCU 2013), (University of Zürich, Switzerland, September 9-12, 2013), pp. 167-189.
  • Signal Transmission Across Tile Assemblies: 3D Static Tiles Simulate Active Self-Assembly by 2D Signal-Passing Tiles, Jacob Hendricks, Jennifer E. Padilla, Matthew J. Patitz, and Trent A. Rogers. Proceedings of the 19th International Conference on DNA Computing and Molecular Programming (DNA 19), (Arizona State University, Tempe, AZ, USA, September 22-27, 2013), Lecture Notes in Computer Science, Volume 8141, 2013, pp 90-104.
  • The two-handed tile assembly model is not intrinsically universal, Erik D. Demaine, Matthew J. Patitz, Trent A. Rogers, Robert T. Schweller, Scott M. Summers, and Damien Woods, Proceedings of the Fortieth International Colloquium on Automata, Languages and Programming (ICALP 2013), (Riga, Latvia, July 8-12, 2013), Lecture Notes in Computer Science, Volume 7965, 2013, pp 400-412.
  • Asynchronous Signal Passing for Tile Self-Assembly: Fuel Efficient Computation and Efficient Assembly of Shapes, Jennifer E. Padilla, Matthew J. Patitz, Raul Pena, Robert T. Schweller, Nadrian C. Seeman, Robert Sheline, Scott M. Summers, Xingsi Zhong. Proceedings of Unconventional Computation & Natural Computation 2013 (UCNC 2013), (Università degli Studi di Milano-Bicocca, Milano, Italy on 1–5 July 2013), Lecture Notes in Computer Science, Volume 7956, 2013, pp 174-185.
  • Two Hands Are Better Than One (up to constant factors): Self-Assembly In The 2HAM vs. aTAM  (arXiv version here), Sarah Cannon, Erik D. Demaine, Martin L. Demaine, Sarah Eisenstat, Matthew J. Patitz, Robert Schweller, Scott M. Summers, Andrew Winslow. Proceedings of the Thirtieth International Symposium on Theoretical Aspects of Computer Science (STACS 2013), (Kiel, Germany, February 27-March 2, 2013), pp. 172--184.
  • The tile assembly model is intrinsically universal, David Doty, Jack H. Lutz, Matthew J. Patitz, Robert T. Schweller, Scott M. Summers, and Damien Woods. Proceedings of the 53rd Annual IEEE Symposium on Foundations of Computer Science (FOCS 2012), New Brunswick, New Jersey, October 20-23, 2012, pp.302-310.
  • Self-Assembly with Geometric Tiles, Bin Fu, Matthew J. Patitz, Robert T. Schweller, and Bobby Sheline. Proceedings of the 39th International Colloquium on Automata, Languages and Programming (ICALP 2012), University of Warwick, UK, July 9-13 2012, pp 714-725.
  • Exact Shapes and Turing Universality at Temperature 1 with a Single Negative Glue, Matthew J. Patitz, Robert T. Schweller, and Scott M. Summers. Proceedings of the Seventeenth International Conference on DNA Computing and Molecular Programming (DNA 17), (California Institute of Technology, Pasadena, California, September 19-23, 2011), Lecture Notes in Computer Science, volume 6937, Springer-Verlag, 2011, pp. 175--189.
  • Self-Assembly of Arbitrary Shapes Using RNAse Enzymes: Meeting the Kolmogorov Bound with Small Scale Factor (extended abstract), Erik D. Demaine, Matthew J. Patitz, Robert T. Schweller, Scott M. Summers. Proceedings of the Twenty Eighth International Symposium on Theoretical Aspects of Computer Science (STACS 2011), (Dortmund, Germany, March 10-12, 2011), volume 9 of Leibniz International Proceedings in Informatics (LIPIcs), pp 201--212.
  • Identifying Shapes Using Self-Assembly (extended abstract), Matthew J. Patitz and Scott M. Summers, Proceedings of the Twenty First International Symposium on Algorithms and Computation (ISAAC 2010), (Jeju Island, Korea, December 15-17 2010), Part II, Lecture Notes in Computer Science, volume 6507, Springer-Verlag, 2010, pp. 458-469.
  • Strong Fault-Tolerance for Self-Assembly with Fuzzy Temperature, David Doty, Matthew J. Patitz, Dustin Reishus, Robert T. Schweller, and Scott M. Summers. Proceedings of the 51st Annual IEEE Symposium on Foundations of Computer Science (FOCS 2010), (Las Vegas, Nevada, USA, October 23-26, 2010), pp. 417-426.
  • Intrinsic Universality in Self-Assembly, David Doty, Jack H. Lutz, Matthew J. Patitz, Scott M. Summers, and Damien Woods. Proceedings of the 27th International Symposium on Theoretical Aspects of Computer Science (STACS 2010), (Nancy, France, March 4-6, 2010), pp. 275-286.
  • Random Number Selection in Self-Assembly, David Doty, Jack H. Lutz, Matthew J. Patitz, Scott M. Summers, and Damien Woods. Proceedings of the Eighth International Conference on Unconventional Computation (UC 2009), (Ponta Delgada, Portugal, September 7-11, 2009), Proceedings, Lecture Notes in Computer Science, volume 5715, Springer-Verlag, 2009, pp. 143-157.
  • A Domain-Specific Language for Programming in the Tile Assembly Model, David Doty and Matthew J. Patitz. Proceedings of The Fifteenth International Meeting on DNA Computing and Molecular Programming (DNA 15), (Fayetteville, Arkansas, USA, June 8-11, 2009). Proceedings, Lecture Notes in Computer Science, volume 5877, Springer-Verlag, 2009, pp.25-34.
  • Limitations of Self-Assembly at Temperature 1, David Doty, Matthew J. Patitz, and Scott M. Summers. Proceedings of The Fifteenth International Meeting on DNA Computing and Molecular Programming (DNA 15), (Fayetteville, Arkansas, USA, June 8-11, 2009). Proceedings, Lecture Notes in Computer Science, volume 5877, Springer-Verlag, 2009, pp. 35-44.
  • Self-Assembly of Decidable Sets (extended abstract), Matthew J. Patitz and Scott M. Summers. Proceedings of the Seventh International Conference on Unconventional Computation (Vienna, Austria, August 25-28, 2008), Proceedings, Lecture Notes in Computer Science, volume 5204, Springer-Verlag, 2008, pp. 206-219.
    • For software that programmatically generates tile sets which weakly self-assemble the canonical two-dimensional representation of decidable languages and their complements, see the DeciderTiler on the Software page
  • Self-Assembly of Discrete Self-Similar Fractals (extended abstract), Matthew J. Patitz and Scott M. Summers. Proceedings of the Fourteenth International Meeting on DNA Computing (Prague, Czech Republic, June 2-6, 2008), Proceedings, Lecture Notes in Computer Science, volume 5347, Springer-Verlag, 2009, pp. 156-167. An expanded version which includes proofs can be found in the "Journal Papers" section here.
    • For supplementary information including software that programmatically generates tile sets for fibered fractal assemblies (along with the source code) and images, please see the FiberedFractalTiler on the Software page
  • Computability and Complexity in Self-Assembly, James I. Lathrop, Jack H. Lutz, Matthew J. Patitz, and Scott M. Summers. Logic and Theory of Algorithms: Proceedings of the Fourth Conference on Computability in Europe (Athens, Greece, June 15-20, 2008), pp. 349-358.

Journal Papers

  • Binary pattern tile set synthesis is NP-hard, Lila Kari, Steffen Kopecki, Pierre-Étienne Meunier, Matthew J. Patitz, Shinnosuke Seki. Algorithmica, 2016, pp. 1-46. DOI: 10.1007/s00453-016-0154-7.
  • The Simulation Powers and Limitations of Higher Temperature Hierarchical Self-Assembly Systems, Jacob Hendricks, Matthew J. Patitz, Trent A. Rogers. Fundam. Inform. 155(1-2): 131-162 (2017)
  • Reflections on tiles (in self-assembly), Jacob Hendricks, Matthew J. Patitz, Trent A. Rogers. Natural Computing, 16(2): 295-316 (2017).
  • The two-handed tile assembly model is not intrinsically universal, Erik D. Demaine, Matthew J. Patitz, Trent A. Rogers, Robert T. Schweller, Scott M. Summers, and Damien Woods, Algorithmica, February 2016, Volume 74, Issue 2, pp 812-850.
  • Self-Assembly of Fractals, Matthew J. Patitz. Encyclopedia of Algorithms, Springer, January 2015.
  • The power of duples (in self-assembly): It's not so hip to be square, Jacob Hendricks, Matthew J. Patitz, Trent A. Rogers, Scott M. Summers. Theoretical Computer Science (TCS), special issue of invited papers from the 20th International Computing and Combinatorics Conference (COCOON 2014), DOI: 10.1016/j.tcs.2015.12.008.
  • Doubles and Negatives are Positive (in Self-Assembly), Jacob Hendricks, Matthew J. Patitz, Trent A. Rogers. Special issue of invited papers from 13th International Conference on Unconventional Computation and Natural Computation (UCNC 2014), Natural Computing, 15(1), pp 69-85. (arxiv version here)
  • Signal transmission across tile assemblies: 3D static tiles simulate active self-assembly by 2D signal-passing tiles, Tyler Fochtman, Jacob Hendricks, Jennifer E. Padilla, Matthew J. Patitz, Trent A. Rogers. Natural Computing, June 2014, pp. 1-14.
  • Asynchronous Signal Passing for Tile Self-Assembly: Fuel Efficient Computation and Efficient Assembly of Shapes, Jennifer E. Padilla, Matthew J. Patitz, Robert T. Schweller, Nadrian C. Seeman, Scott M. Summers, Xingsi Zhong. International Journal of Foundations of Computer Science, Volume 25, Number 4 (June 2014), pp. 459-488.
  • An Introduction to Tile-Based Self-Assembly and a Survey of Recent Results, Matthew J. Patitz, Natural Computing, Volume 13, Issue 2 (2014), pp. 195-224.
  • Identifying Shapes Using Self-Assembly, Matthew J. Patitz and Scott M. Summers, Algorithmica, special issue of invited papers from the Twenty First International Symposium on Algorithms and Computation, 2012, Volume 64, Number 3, pp. 481-510.
  • Self-Assembly of Infinite Structures: A Survey, Matthew J. Patitz and Scott M. Summers. Theoretical Computer Science, special issue of invited papers from the International Workshop on The Complexity of Simple Programs (CSP 2008), Volume 412, pp. 159-165.
  • Limitations of Self-Assembly at Temperature 1, David Doty, Matthew J. Patitz, and Scott M. Summers. Theoretical Computer Science, special issue of invited papers from the International Workshop on The Complexity of Simple Programs (CSP 2008), Volume 412, pp. 145-158.
  • Self-Assembly of Decidable Sets, Matthew J. Patitz and Scott M. Summers. Natural Computing, special issue of invited papers from Unconventional Computation 2008, 2011, Volume 10, Number 2, pp. 853-877.
  • Self-Assembly of Discrete Self-Similar Fractals, Matthew J. Patitz, and Scott M. Summers. Natural Computing, Volume 9, Number 1, pp. 135-172, 2010.
  • Computability and Complexity in Self-Assembly, James I. Lathrop, Jack H. Lutz, Matthew J. Patitz, and Scott M. Summers. Theory of Computing Systems, 48:617--647, 2011. Special issue of invited papers from Computability in Europe 2008.

Invited Talks

Theses

Technical Reports