Matthew J. Patitz

• 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, to appear.
• 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 LNSA 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 here or at CoRR 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 LNSA 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

• Identifying Shapes Using Self-Assembly, Matthew J. Patitz and Scott M. Summers, to appear in Algorithmica. Special issue of invited papers from the Twenty First International Symposium on Algorithms and Computation.
• 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, to appear.
• 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

• Manufacturing From the Bottom Up: Algorithmic Self-Assembly Using Tiles, Matthew J. Patitz. Spring 2011 CSCE Seminar Series, Department of Computer Science and Computer Engineering -- University of Arkansas, March 4, 2011.
• Simulation of Self-Assembly in the Abstract Tile Assembly Model with ISU TAS, Matthew J. Patitz. Proceedings of the 6th Annual Conference of the Foundations of Nanoscience: Self-Assembled Architectures and Devices, (Snowbird, Utah, April 20-24, 2009).
• Self-Assembly of Infinite Structures, Matthew J. Patitz and Scott M. Summers. International Workshop on The Complexity of Simple Programs (CSP 2008), Turlough Neary, Damien Woods, Anthony K. Seda, and Niall Murphy (editors), (University College Cork, Ireland December 6-7, 2008) Proceedings, Cork University Press, pp 279-291.

Theses

• Toward a Molecular Programming Language for Algorithmic Self-Assembly, Matthew J. Patitz, PhD Dissertation, Iowa State University, 2010.
• An Analysis of Reconfigurable Memory Queues/Computing Units Architecture, Matthew J. Patitz, M.S. Thesis, Iowa State University, 2002.

Technical Reports

• 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. Submitted.
• Two Hands Are Better Than One (up to constant factors), Sarah Cannon, Erik D. Demaine, Martin L. Demaine, Sarah Eisenstat, Matthew J. Patitz, Robert Schweller, Scott M. Summers, Andrew Winslow.
• The tile assembly model is intrinsically universal, David Doty, Jack H. Lutz, Matthew J. Patitz, Robert T. Schweller, Scott M. Summers, and Damien Woods.