Publications

Jack H. Lutz and Robyn R. Lutz. (2022). Reasoning As If. DNA Nanotechnology at 40 for the Next 40 Natasha Jonoska and Erik Winfree. Springer, to appear.
Robyn R. Lutz (2022). Requirements Engineering for Safety-Critical Molecular Programs. 30th IEEE International Requirements Engineering Conference (RE 2022, Melbourne, Victoria, Australia, August 15-19, 2022), pages 302-308, 2022. doi:https://doi.org/10.1109/RE54965.2022.00045
Jack H. Lutz, Neil Lutz, and Elvira Mayordomo. Extending the Reach of the Point-To-Set Principle. 39th International Symposium on Theoretical Aspects of Computer Science (STACS 2022, Marseille, France, March 15-18, 2022), volume 219, pages 1-14, 2022. doi:https://doi.org/10.4230/LIPIcs.STACS.2022.48
Titus H. Klinge, James I. Lathrop, Sonia Moreno, Hugh D. Potter, Narun K. Raman, and Matthew R. Riley. ALCH: An imperative language for chemical reaction network-controlled tile assembly. Natural Computing, pages 1-21, 2022. doi:https://doi.org/10.1007/s11047-021-09878-8
Michael C. Gerten, James I. Lathrop, Myra B. Cohen, Andrew S. Miner, and Titus H. Klinge. (2022). Inference and Test Generation Using Program Invariants in Chemical Reaction Networks. In Proceedings of the 44th International Conference on Software Engineering (ICSE 22, Pittsburgh, Pennsylvania, May 21-29, 2022), pages 1193-1205, 2022. doi:https://doi.org/10.1145/3510003.3510176
Titus H. Klinge, James I. Lathrop, Peter-Michael Osera, and Allison Rogers. (2021). Reactamole: Functional Reactive Molecular Programming. 27th International Conference on DNA Computing and Molecular Programming (DNA 27, Dagstuhl, Germany, September 12-17, 2021). volume 205, pages 1-20, 2021. doi:https://doi.org/10.4230/LIPIcs.DNA.27.10
Willem Fletcher, Titus H. Klinge, James I. Lathrop, Dawn A. Nye, and Matthew Rayman. Robust Real-Time Computing with Chemical Reaction Networks. Unconventional Computation and Natural Computation. International Conference on Unconventional Computation and Natural Computation (UCNC 2021, Espoo, Finland, October 18-22, 2021), pages 35-50, 2021. doi:https://doi.org/10.1007/978-3-030-87993-8_3
Xiang Huang, Jack H. Lutz, Elvira Mayordomo, and Donald M. Stull. Asymptotic Divergences and Strong Dichotomy. IEEE Transactions on Information Theory, volume 67, issue 10, pages 6296-6305, 2021. doi:https://doi.org/10.1109/TIT.2021.3085425
Jack H. Lutz and Elvira Mayordomo. Computing absolutely normal numbers in nearly linear time. Information and Computation, volume 281, pages 1-12, 2021. doi:https://doi.org/10.1016/j.ic.2021.104746
Ibrahim Mesecan, Michael C. Gerten, James I. Lathrop, Myra B. Cohen, and Tomas H. Caldas. (2021). CRNRepair: Automated Program Repair of Chemical Reaction Networks. In 2021 IEEE/ACM International Workshop on Genetic Improvement (GI, Madrid, Spain, May 30-31, 2021), pages 23-30, 2021. doi:https://doi.org/10.1109/GI52543.2021.00014
James I. Lathrop, Jack H. Lutz, Robyn R. Lutz, Hugh D. Potter and Matthew R. Riley. Population-Induced Phase Transitions and the Verification of Chemical Reaction Networks. In Natural Computing, pages 1-17, 2021. doi: https://doi.org/10.1007/s11047-021-09877-9
Michael C. Gerten, James I. Lathrop, Myra B. Cohen, and Titus H. Klinge. ChemTest: An automated software testing framework for an emerging paradigm. In Proceedings of the 35th IEEE/ACM International Conference on Automated Software Engineering, 2020, to appear. ACM Distinguished Paper Award.
James I. Lathrop, Jack H. Lutz, Robyn R. Lutz, Hugh D. Potter, and Matthew R. Riley. Population-ınduced phase transitions and the verification of chemical reaction networks. In Proceedings of the 26th International Conference on DNA Computing and Molecular Programming (DNA 2020, University of Oxford-virtual, Oxford, UK, September 14-17, 2020). Schloss Dagstuhl-Leibniz-Zentrum für Informatik,, 2020. Article no. 5, (17 pages).
Titus H. Klinge, James I. Lathrop, Sonia Moreno, Hugh D. Potter, Narun K. Raman, and Matthew R. Riley. ALCH: An imperative language for chemical reaction network-controlled tile assembly. In Proceedings of the 26th International Conference on DNA Computing and Molecular Programming (DNA 2020, University of Oxford-virtual, Oxford, UK, September 14-17, 2020). Schloss Dagstuhl-Leibniz-Zentrum für Informatik,, 2020. Article no. 6, (22 pages).
Titus H. Klinge, James I. Lathrop, and Jack H. Lutz. Robust biomolecular finite automata. Theoretical Computer Science, 816:114-143, 2020.
Samuel J. Ellis, Titus H. Klinge, and James I. Lathrop. Robust chemical circuits. Biosystems, 186(103983), 2019.
Xiang Huang, Jack H. Lutz, and Andrei N. Migunov. Algorithmic randomness in continuous-time markov chains. In Proceedings of the 57th Annual Allerton Conference on Communication, Control, and Computing (Allerton 2019, Monticello, IL, September 24-27, 2019), pages 615-622.
Xiang Huang, Titus H. Klinge, and James I. Lathrop. Real-time equivalence of chemical reaction networks and analog computers. In Proceedings of the 25th International Conference on DNA Computing and Molecular Programming (DNA 25, Seattle, WA, August 5-9, 2020), pages 37-53. Springer, 2020.
Jack H. Lutz, Neil Lutz, Robyn R. Lutz, and Matthew R. Riley. Robustness and games against nature in molecular programming. In Proceedings of the Forty-first International Conference on Software Engineering (ICSE 2019, Montreal, Canada, May 25-31 2019), pages 65-68.
Samuel J. Ellis, Titus H. Klinge, James I. Lathrop, Jack H. Lutz, Robyn R. Lutz, Andrew S. Miner, and Hugh D. Potter. Runtime fault detection in programmed molecular systems. In ACM Transactions on Software Engineering and Methodology, volume 28, 2019. article no. 6 (20 pages).
Xiang Huang, Titus H. Klinge, James I. Lathrop, Xiaoyuan Li, and Jack H. Lutz. Real-time computability of real numbers by chemical reaction networks. In Natural Computing, volume 18, pages 63-73, 2019.
Chase Koehler, Divita Mathur, Eric Henderson, and Robyn Lutz. Probing the Security of DNA Origami. In 2018 IEEE International Symposium on Software Reliability Engineering (ISSRE 2018) Memphis, TN, USA, Oct. 15-18, 2018, pages 138-139, 2018.
Robyn Lutz. Software Engineering for Safety in Programmed Molecular Systems (keynote abstract). In Barbara Gallina, Amund Skavhaug, and Friedemann Bitsch, editors, Proc. 37th Int’l Conference on Computer Safety, Reliability, and Security, Västerås, Sweden, Sept. 18-21, volume 11093, pages 138-139. Springer, 2018.
Jack Lutz and Robyn Lutz. Writing Requirements for Molecular Programs. In 2018 IEEE 26th International Requirements Engineering Conference (RE), Banff, Canada, Aug. 20-24, 2018, pages 512-512. IEEE,, 2018.
Xiang Huang, Jack H. Lutz, and Andrei N. Migunov. Algorithmic randomness in chemical reaction networks (abstract). Presented at CCA 2018.
Adam Case, Jack H. Lutz, and D. M. Stull. Reachability problems for continuous chemical reaction networks. In Natural Computing, volume 17(2), pages 223-230. Springer, 2018.
Samuel J. Ellis, Titus H. Klinge, and James I. Lathrop. Robust combinatorial circuits in chemical reaction networks. In TPNC 2017, pages 178-189. Springer, 2017.
Samuel J. Ellis. Devices for safety-critical molecular programmed systems. Ph.D. thesis, Iowa State University, 2017.
Samuel J. Ellis, James I. Lathrop, and Robyn R. Lutz. State logging in chemical reaction networks. In ACM NanoCom 2017. ACM, 2017. article no. 23 (6 pages)
Xiang Huang, Xiaoyuan Li, Titus H. Klinge, James I. Lathrop, and Jack H. Lutz. Real-time computability of real numbers by chemical reaction networks. In UCNC 2017, pages 29-40. Springer, 2017.
Robyn R. Lutz. Keynote: Requirements for molecular programmed nanosystems. In RE ’16, page 2. IEEE, 2016.
Robyn R. Lutz and Jack H. Lutz. Software engineering for molecular programming. In ICSE (Companion Volume), 2016, pages 888-889. ACM, 2016.
Titus H. Klinge. Robust signal restoration in chemical reaction networks. In NanoCom 2016, pages 6:1-6:6. ACM, 2016.
Titus H. Klinge. Modular and robust computation with deterministic chemical reaction networks. Ph.D. thesis, Iowa State University, 2016.
Divita Mathur and Eric R. Henderson. Programmable DNA nanosystem for molecular ınterrogation. Scientific Reports, 6:27413, 2016.
Adam Case, Jack H. Lutz, and D. M. Stull. Reachability problems for continuous chemical reaction networks. In UCNC 2016, pages 1-10. Springer, 2016.
Divita Mathur. Dynamic self-assembling DNA nanosystems: design and engineering. Ph.D. thesis, Iowa State University, 2016.
Brian Nakayama. Modeling technologies and methods for DNA origami. M.S. thesis, Iowa State University, 2016.
Thein Tun, Robyn Lutz, Brian Nakayama, Yijun Yu, Divita Mathur, and Bashar Nuseibeh. The role of environmental assumptions in failures of DNA nanosystems. In COUFLESS@ICSE 2015, pages 27-33. IEEE, 2015.
Samuel J. Ellis, Eric R. Henderson, Titus H. Klinge, James I. Lathrop, Jack H. Lutz, Robyn R. Lutz, Divita Mathur, and Andrew S. Miner. Automated requirements analysis for a molecular watchdog timer. In ASE, pages 767-778. ACM, 2014. IFIP TC2 Manfred Paul Award for Excellence in Software: Theory and Practice.
Brian Nakayama and David Bahr. Universal computation in the prisoner’s dilemma game. In UCNC, pages 293-304. Springer, 2014.
Samuel J. Ellis. Designing a molecular watchdog timer for safety critical molecular systems. M.S. thesis, Iowa State University, 2014.
Robyn R. Lutz, Jack H. Lutz, James I. Lathrop, Titus Klinge, Divita Mathur, Donald M. Stull, Taylor Bergquist, and Eric Henderson. Requirements analysis for a product family of DNA nanodevices. In RE 2012, pages 211-220. IEEE, 2012.
Robyn R. Lutz, Jack H. Lutz, James I. Lathrop, Titus Klinge, Eric Henderson, Divita Mathur, and Dalia Abo Sheasha. Engineering and verifying requirements for programmable self-assembling nanomachines. In ICSE 2012, pages 1361-1364. IEEE, 2012.
Scott M. Summers. Reducing tile complexity for the self-assembly of scaled shapes through temperature programming. Algorithmica, 63(1-2):117-136, 2012.
Jack H. Lutz and Brad Shutters. Approximate self-assembly of the Sierpinski triangle. Theory Comput. Syst., 51(3):372-400, 2012.
David Doty, Jack H. Lutz, Matthew J. Patitz, Robert T. Schweller, Scott M. Summers, and Damien Woods. The tile assembly model is ıntrinsically universal. In FOCS 2012, pages 302-310. IEEE Computer Society, 2012.
Divita Mathur and Eric R. Henderson. Complex DNA nanostructures from oligonucleotide ensembles. ACS synthetic biology, 2(4):180-185, 2012.
Steven M. Kautz and Brad Shutters. Self-assembling rulers for approximating generalized Sierpinski carpets. In COCOON 2011, volume 6842 of Lecture Notes in Computer Science, pages 284-296. Springer, 2011.
James I. Lathrop, Jack H. Lutz, Matthew J. Patitz, and Scott M. Summers. Computability and complexity in self-assembly. Theory Comput. Syst., 48(3):617-647, 2011.
Jack H. Lutz and Brad Shutters. Approximate self-assembly of the Sierpinski triangle. In CiE 2010, volume 6158 of Lecture Notes in Computer Science, pages 286-295. Springer, 2010.
Scott M. Summers. Universality in algorithmic self-assembly. Ph.D. thesis, Iowa State University, 2010.
Matthew J. Patitz. Toward a molecular programming language for algorithmic self-assembly. Ph.D. thesis, Iowa State University, 2010.
David Doty, Matthew J. Patitz, Dustin Reishus, Robert T. Schweller, and Scott M. Summers. Strong fault-tolerance for self-assembly with fuzzy temperature. In FOCS 2010, pages 417-426. IEEE Computer Society, 2010.
David Doty, Jack H. Lutz, Matthew J. Patitz, Scott M. Summers, and Damien Woods. Intrinsic universality ın self-assembly. In STACS 2010, pages 275-286. Springer, 2010.
David S. Doty. Applications of the theory of computation to nanoscale self-assembly. Ph.D. thesis, Iowa State University, 2009.
Steven M. Kautz and James I. Lathrop. Self-assembly of the discrete Sierpinski carpet and related fractals. In DNA 15, volume 5877 of Lecture Notes in Computer Science, pages 78-87. Springer, 2009.
David Doty, Jack H. Lutz, Matthew J. Patitz, Scott M. Summers, and Damien Woods. Random number selection in self-assembly. In UC 2009, volume 5715 of Lecture Notes in Computer Science, pages 143-157. Springer, 2009.
James I. Lathrop, Jack H. Lutz, and Scott M. Summers. Strict self-assembly of discrete Sierpinski triangles. Theoretical computer ſcience, 410:384-405, 2009.
David Doty. Randomized self-assembly for exact shapes. In FOCS 2009, pages 85-94. IEEE Computer Society, 2009.
David Doty and Matthew J. Patitz. A domain-specific language for programming in the tile assembly model. In DNA 15, volume 5877 of Lecture Notes in Computer Science, pages 25-34. Springer, 2009.
James I. Lathrop, Jack H. Lutz, Matthew J. Patitz, and Scott M. Summers. Computability and complexity in self-assembly. In CiE 2008, volume 5028 of Lecture Notes in Computer Science, pages 349-358. Springer, 2008.
Matthew J. Patitz and Scott M. Summers. Self-assembly of decidable sets. In UC 2008, volume 5204 of Lecture Notes in Computer Science, pages 206-219. Springer, 2008.
Matthew J. Patitz and Scott M. Summers. Self-assembly of discrete self-similar fractals. In DNA 14, volume 5347 of Lecture Notes in Computer Science, pages 156-167. Springer, 2008.
Scott M. Summers. Strict self-assembly of discrete Sierpinski triangles. M.S. thesis, Iowa State University, 2007.
James I. Lathrop, Jack H. Lutz, and Scott M. Summers. Strict self-assembly of discrete Sierpinski triangles. In CiE 2007, volume 4497 of Lecture Notes in Computer Science, pages 455-464. Springer, 2007.