| Diverse and robust molecular algorithms using reprogrammable DNA self-assembly D Woods, D Doty, C Myhrvold, J Hui, F Zhou, P Yin, E Winfree Nature 567 (7748), 366-372, 2019 | 263 | 2019 |
| Theory of algorithmic self-assembly D Doty Communications of the ACM 55 (12), 78-88, 2012 | 155 | 2012 |
| Deterministic function computation with chemical reaction networks HL Chen, D Doty, D Soloveichik Natural computing 13, 517-534, 2014 | 151 | 2014 |
| The tile assembly model is intrinsically universal D Doty, JH Lutz, MJ Patitz, RT Schweller, SM Summers, D Woods FOCS 2012, 2012 | 121 | 2012 |
| Stable leader election in population protocols requires linear time D Doty, D Soloveichik Distributed Computing 31 (4), 257–271, 2018 | 114 | 2018 |
| Limitations of self-assembly at temperature 1 D Doty, MJ Patitz, SM Summers Theoretical Computer Science 412 (1-2), 145-158, 2011 | 90* | 2011 |
| Timing in chemical reaction networks D Doty Proceedings of the twenty-fifth annual ACM-SIAM symposium on Discrete …, 2014 | 84 | 2014 |
| Randomized self-assembly for exact shapes D Doty SIAM Journal on Computing 39 (8), 3521-3552, 2010 | 70 | 2010 |
| Parallelism and time in hierarchical self-assembly HL Chen, D Doty SIAM Journal on Computing 46 (2), 661-709, 2017 | 59* | 2017 |
| Speed faults in computation by chemical reaction networks HL Chen, R Cummings, D Doty, D Soloveichik Distributed Computing 30 (5), 373-390, 2017 | 56 | 2017 |
| Rate-independent computation in continuous chemical reaction networks HL Chen, D Doty, D Soloveichik Proceedings of the 5th conference on Innovations in theoretical computer …, 2014 | 54 | 2014 |
| Strong fault-tolerance for self-assembly with fuzzy temperature D Doty, MJ Patitz, D Reishus, RT Schweller, SM Summers 2010 IEEE 51st Annual Symposium on Foundations of Computer Science, 417-426, 2010 | 48 | 2010 |
| Negative interactions in irreversible self-assembly D Doty, L Kari, B Masson Algorithmica 66 (1), 153-172, 2013 | 47 | 2013 |
| Probability 1 computation with chemical reaction networks R Cummings, D Doty, D Soloveichik Natural Computing 15, 245-261, 2016 | 44 | 2016 |
| Intrinsic universality in self-assembly D Doty, JH Lutz, MJ Patitz, SM Summers, D Woods 27th International Symposium on Theoretical Aspects of Computer Science …, 2010 | 42 | 2010 |
| Leaderless deterministic chemical reaction networks D Doty, M Hajiaghayi Natural Computing 14, 213-223, 2015 | 41 | 2015 |
| The power of nondeterminism in self-assembly N Bryans, E Chiniforooshan, D Doty, L Kari, S Seki Theory of Computing 9 (1), 1-29, 2013 | 38 | 2013 |
| Scalable, time-responsive, digital, energy-efficient molecular circuits using DNA strand displacement E Chiniforooshan, D Doty, L Kari, S Seki DNA Computing and Molecular Programming: 16th International Conference, DNA …, 2011 | 38 | 2011 |
| Zeta-Dimension: (Preliminary Version) D Doty, X Gu, JH Lutz, E Mayordomo, P Moser Mathematical Foundations of Computer Science 2005: 30th International …, 2005 | 35 | 2005 |
| scadnano: A browser-based, scriptable tool for designing DNA nanostructures D Doty, BL Lee, T Stérin 26th International Conference on DNA Computing and Molecular Programming …, 2020 | 32 | 2020 |
| Constructive dimension and Turing degrees L Bienvenu, D Doty, F Stephan Theory of Computing Systems 45 (4), 740-755, 2009 | 31* | 2009 |
| Hardness of computing and approximating predicates and functions with leaderless population protocols A Belleville, D Doty, D Soloveichik 44th International Colloquium on Automata, Languages, and Programming (ICALP …, 2017 | 30 | 2017 |
| Time-optimal self-stabilizing leader election in population protocols J Burman, HL Chen, HP Chen, D Doty, T Nowak, E Severson, C Xu Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing …, 2021 | 26* | 2021 |
| Dimension extractors and optimal decompression D Doty Theory of Computing Systems 43 (3), 425-463, 2008 | 26* | 2008 |
| Efficient size estimation and impossibility of termination in uniform dense population protocols D Doty, M Eftekhari Proceedings of the 2019 ACM Symposium on Principles of Distributed Computing …, 2019 | 25 | 2019 |
| A time and space optimal stable population protocol solving exact majority D Doty, M Eftekhari, L Gasieniec, E Severson, G Stachowiak, P Uznanski 62nd Annual IEEE Symposium on Foundations of Computer Science, 2021 | 22* | 2021 |
| Feasible depth D Doty, P Moser Computation and Logic in the Real World: Third Conference on Computability …, 2007 | 22 | 2007 |
| Brief announcement: Exact size counting in uniform population protocols in nearly logarithmic time D Doty, M Eftekhari, O Michail, PG Spirakis, M Theofilatos Leibniz International Proceedings in Informatics, LIPIcs 121, 46, 2018 | 20* | 2018 |
| Fast algorithmic self-assembly of simple shapes using random agitation HL Chen, D Doty, D Holden, C Thachuk, D Woods, CT Yang DNA Computing and Molecular Programming: 20th International Conference, DNA …, 2014 | 20 | 2014 |
| Thermodynamic binding networks D Doty, TA Rogers, D Soloveichik, C Thachuk, D Woods International Conference on DNA Computing and Molecular Programming, 249-266, 2017 | 19 | 2017 |
| Producibility in hierarchical self-assembly D Doty Natural Computing, 15(1):41-49, 2016 15 (1), 41-49, 2016 | 18 | 2016 |
| Composable computation in discrete chemical reaction networks EE Severson, D Haley, D Doty Proceedings of the 2019 ACM Symposium on Principles of Distributed Computing …, 2019 | 17 | 2019 |
| A domain-specific language for programming in the tile assembly model D Doty, MJ Patitz International Workshop on DNA-Based Computers, 25-34, 2009 | 17 | 2009 |
| Program size and temperature in self-assembly HL Chen, D Doty, S Seki Algorithmica 72 (3), 884-899, 2015., 2015 | 16* | 2015 |
| Random number selection in self-assembly D Doty, JH Lutz, MJ Patitz, SM Summers, D Woods Unconventional Computation: 8th International Conference, UC 2009, Ponta …, 2009 | 16 | 2009 |
| Finite-state dimension and real arithmetic D Doty, JH Lutz, S Nandakumar Information and Computation 205 (11), 1640-1651, 2007 | 16 | 2007 |
| Nonlocal evolutionary adaptation in gridplants D Doty Proceedings of the 2004 Congress on Evolutionary Computation (IEEE Cat. No …, 2004 | 13 | 2004 |
| Message complexity of population protocols T Amir, J Aspnes, D Doty, M Eftekhari, E Severson arXiv preprint arXiv:2003.09532, 2020 | 10 | 2020 |
| Finite-state dimension and lossy decompressors D Doty, P Moser arXiv preprint cs/0609096, 2006 | 10 | 2006 |
| Programming substrate-independent kinetic barriers with thermodynamic binding networks K Breik, C Chalk, D Doty, D Haley, D Soloveichik IEEE/ACM transactions on computational biology and bioinformatics 18 (1 …, 2019 | 9 | 2019 |
| Pattern overlap implies runaway growth in hierarchical tile systems HL Chen, D Doty, J Maňuch, A Rafiey, L Stacho Journal of Computational Geometry 7 (2), 3-18, 2016 | 9 | 2016 |
| Pushdown dimension D Doty, J Nichols Theoretical Computer Science 381 (1-3), 105-123, 2007 | 8 | 2007 |
| Computational complexity of atomic chemical reaction networks D Doty, S Zhu Natural Computing 17 (4), 677-691, 2018 | 7 | 2018 |
| Democratic, existential, and consensus-based output conventions in stable computation by chemical reaction networks R Brijder, D Doty, D Soloveichik Natural Computing 17, 97-108, 2018 | 7* | 2018 |
| Design of geometric molecular bonds D Doty, A Winslow IEEE Transactions on Molecular, Biological and Multi-Scale Communications 3 …, 2017 | 7 | 2017 |
| Morphometric grayscale texture analysis using foot patterns D Ashlock, DC Adams, D Doty The 2003 Congress on Evolutionary Computation, 2003. CEC'03. 3, 1575-1581, 2003 | 5 | 2003 |
| A survey of size counting in population protocols D Doty, M Eftekhari Theoretical Computer Science 894, 91-102, 2021 | 4 | 2021 |
| ppsim: A software package for efficiently simulating and visualizing population protocols D Doty, E Severson Computational Methods in Systems Biology: 19th International Conference …, 2021 | 4 | 2021 |
| Designing ordered nucleic acid self-assembly processes R Schulman, D Doty Current Opinion in Structural Biology 31, 57-63, 2015 | 4 | 2015 |
| Rate-independent computation in continuous chemical reaction networks HL Chen, D Doty, W Reeves, D Soloveichik Journal of the ACM 70 (3), 1-61, 2023 | 3 | 2023 |
| Computing properties of thermodynamic binding networks: An integer programming approach D Haley, D Doty arXiv preprint arXiv:2011.10677, 2020 | 3 | 2020 |
| Accelerating Self-Assembly of Crisscross Slat Systems D Doty, H Fleming, D Hader, MJ Patitz, LA Vaughan 29th International Conference on DNA Computing and Molecular Programming …, 2023 | 2 | 2023 |
| Simulating 3-symbol Turing machines with SIMD|| DNA D Doty, A Ong arXiv preprint arXiv:2105.08559, 2021 | 2 | 2021 |
| Genetic algorithm-based simulation of electric power markets D Doty | 2 | 2002 |
| Is stochastic thermodynamics the key to understanding the energy costs of computation? D Wolpert, J Korbel, C Lynn, F Tasnim, J Grochow, G Kardeş, J Aimone, ... arXiv preprint arXiv:2311.17166, 2023 | 1 | 2023 |
| Dynamic size counting in population protocols D Doty, M Eftekhari arXiv preprint arXiv:2202.12864, 2022 | 1 | 2022 |
| Applications of the theory of computation to nanoscale self-assembly DS Doty Iowa State University, 2009 | 1 | 2009 |
| Rate-independent continuous inhibitory chemical reaction networks are Turing-universal K Calabrese, D Doty arXiv preprint arXiv:2403.07099, 2024 | | 2024 |
| Harvesting Brownian Motion: Zero Energy Computational Sampling D Doty, N Kornerup, A Luchsinger, L Orshansky, D Soloveichik, D Woods arXiv preprint arXiv:2309.06957, 2023 | | 2023 |
| Optimal Information Encoding in Chemical Reaction Networks A Luchsinger, D Doty, D Soloveichik arXiv preprint arXiv:2307.01939, 2023 | | 2023 |
| Thermodynamically Driven Signal Amplification J Petrack, D Soloveichik, D Doty arXiv preprint arXiv:2307.01550, 2023 | | 2023 |
| Proceedings of the 2nd Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2023) D Doty, P Spirakis Schloss Dagstuhl–Leibniz-Zentrum für Informatik, 2023 | | 2023 |
| 2nd Symposium on Algorithmic Foundations of Dynamic Networks D Doty, P Spirakis | | 2023 |
| Proceedings of the 29th International Conference on DNA Computing and Molecular Programming (DNA 29) J Petrack, D Soloveichik, D Doty Schloss Dagstuhl–Leibniz-Zentrum für Informatik, 2023 | | 2023 |
| LIPIcs, Volume 257, SAND 2023, Complete Volume D Doty, P Spirakis 2nd Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2023), 2023 | | 2023 |
| Lecture Notes for ECS 289A: Theory of Molecular Computation D Doty | | 2020 |
| Randomized Self-Assembly D Doty Encyclopedia of Algorithms, 1759-1767, 2016 | | 2016 |
| Hierarchical Self-Assembly D Doty Encyclopedia of Algorithms, 903-909, 2016 | | 2016 |
| An Oracle Strongly Separating Deterministic Time from Nondeterministic Time, via Kolmogorov Complexity D Doty arXiv preprint arXiv:1004.3993, 2010 | | 2010 |
| Theory of Algorithmic Self-Assembly The challenge of programming molecules to manipulate themselves. D Doty | | |
| Diverse and robust molecular algorithms using reprogrammable DNA self-assembly–Supplementary Information B: DNA sequences– D Woods, D Doty, C Myhrvold, J Hui, F Zhou, P Yin, E Winfree | | |
| Rate-Independent Computation in Continuous Chemical Reaction Networks D Doty, D Soloveichik, HL Chen, W Reeves 2024 Joint Mathematics Meetings (JMM 2024), 0 | | |
| Counting with Thermodynamic Binding Networks D Haley, D Doty Catalyst 11, 14, 0 | | |
David SoloveichikUniversity of Texas at AustinVerified email at utexas.edu
