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ORCIDDavid Doty
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- affiliation: University of California Davis, CA, USA
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2020 – today
- 2022
[c48]David Doty, Mahsa Eftekhari:
Dynamic Size Counting in Population Protocols. SAND 2022: 13:1-13:18- [c47]David Doty, Aaron Ong:
Simulating 3-Symbol Turing Machines with SIMD||DNA. SAND 2022: 14:1-14:15 - [i51]David Doty, Mahsa Eftekhari:
Dynamic size counting in population protocols. CoRR abs/2202.12864 (2022) - 2021
- [j27]Eric E. Severson, David Haley, David Doty
:
Composable computation in discrete chemical reaction networks. Distributed Comput. 34(6): 437-461 (2021) - [j26]David Doty, Rudolf Freund, Natasa Jonoska, Jarkko Kari:
Preface. Nat. Comput. 20(4): 637-638 (2021) - [j25]Keenan Breik, Cameron T. Chalk, David Doty, David Haley, David Soloveichik:
Programming Substrate-Independent Kinetic Barriers With Thermodynamic Binding Networks. IEEE ACM Trans. Comput. Biol. Bioinform. 18(1): 283-295 (2021) - [j24]David Doty, Mahsa Eftekhari:
A survey of size counting in population protocols. Theor. Comput. Sci. 894: 91-102 (2021) - [c46]David Doty, Eric E. Severson:
Ppsim: A Software Package for Efficiently Simulating and Visualizing Population Protocols. CMSB 2021: 245-253 - [c45]David Haley, David Doty:
Computing Properties of Thermodynamic Binding Networks: An Integer Programming Approach. DNA 2021: 2:1-2:16 - [c44]David Doty, Mahsa Eftekhari, Leszek Gasieniec, Eric E. Severson, Przemyslaw Uznanski, Grzegorz Stachowiak:
A time and space optimal stable population protocol solving exact majority. FOCS 2021: 1044-1055 - [c43]Janna Burman, Ho-Lin Chen, Hsueh-Ping Chen, David Doty, Thomas Nowak, Eric E. Severson, Chuan Xu:
Time-Optimal Self-Stabilizing Leader Election in Population Protocols. PODC 2021: 33-44 - [c42]David Doty, Mahsa Eftekhari, Leszek Gasieniec, Eric E. Severson, Grzegorz Stachowiak, Przemyslaw Uznanski:
Brief Announcement: A Time and Space Optimal Stable Population Protocol Solving Exact Majority. PODC 2021: 77-80 - [i50]David Doty, Eric E. Severson:
ppsim: A software package for efficiently simulating and visualizing population protocols. CoRR abs/2105.04702 (2021) - [i49]David Doty, Mahsa Eftekhari:
A survey of size counting in population protocols. CoRR abs/2105.05408 (2021) - [i48]David Doty, Aaron Ong:
Simulating 3-symbol Turing machines with SIMD||DNA. CoRR abs/2105.08559 (2021) - [i47]David Doty, Mahsa Eftekhari, Leszek Gasieniec, Eric E. Severson, Grzegorz Stachowiak, Przemyslaw Uznanski:
A time and space optimal stable population protocol solving exact majority. CoRR abs/2106.10201 (2021) - [i46]Ho-Lin Chen, David Doty, David Soloveichik, Wyatt Reeves:
Rate-Independent Computation in Continuous Chemical Reaction Networks. CoRR abs/2107.13681 (2021) - 2020
- [j23]David Doty, Hendrik Dietz:
Preface. Nat. Comput. 19(2): 321-322 (2020) - [c41]David Doty, Benjamin L. Lee, Tristan Stérin:
scadnano: A Browser-Based, Scriptable Tool for Designing DNA Nanostructures. DNA 2020: 9:1-9:17 - [c40]Talley Amir, James Aspnes, David Doty, Mahsa Eftekhari, Eric E. Severson:
Message Complexity of Population Protocols. DISC 2020: 6:1-6:18 - [i45]Talley Amir, James Aspnes, David Doty, Mahsa Eftekhari H., Eric E. Severson:
Message complexity of population protocols. CoRR abs/2003.09532 (2020) - [i44]David Doty, Benjamin L. Lee, Tristan Stérin:
scadnano: A browser-based, easily scriptable tool for designing DNA nanostructures. CoRR abs/2005.11841 (2020) - [i43]David Haley, David Doty:
Computing Properties of Thermodynamic Binding Networks: An Integer Programming Approach. CoRR abs/2011.10677 (2020) - [i42]David Doty, Mahsa Eftekhari, Eric E. Severson:
A stable majority population protocol using logarithmic time and states. CoRR abs/2012.15800 (2020)
2010 – 2019
- 2019
- [j22]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) - [c39]Eric E. Severson, David Haley, David Doty:
Composable Computation in Discrete Chemical Reaction Networks. PODC 2019: 14-23 - [c38]David Doty, Mahsa Eftekhari:
Efficient Size Estimation and Impossibility of Termination in Uniform Dense Population Protocols. PODC 2019: 34-42 - [i41]Eric E. Severson, David Haley, David Doty:
Composable computation in discrete chemical reaction networks. CoRR abs/1903.02637 (2019) - [i40]Janna Burman, Ho-Lin Chen, Hsueh-Ping Chen, David Doty, Thomas Nowak, Eric E. Severson, Chuan Xu:
Time-Optimal Self-Stabilizing Leader Election in Population Protocols. CoRR abs/1907.06068 (2019) - 2018
- [j21]David Doty, David Soloveichik:
Stable leader election in population protocols requires linear time. Distributed Comput. 31(4): 257-271 (2018) - [j20]Robert Brijder, David Doty, David Soloveichik:
Democratic, existential, and consensus-based output conventions in stable computation by chemical reaction networks. Nat. Comput. 17(1): 97-108 (2018) - [j19]David Doty, Shaopeng Zhu:
Computational complexity of atomic chemical reaction networks. Nat. Comput. 17(4): 677-691 (2018) - [c37]Keenan Breik, Cameron T. Chalk, David Doty, David Haley, David Soloveichik:
Programming Substrate-Independent Kinetic Barriers with Thermodynamic Binding Networks. CMSB 2018: 203-219 - [c36]David Doty, Shaopeng Zhu:
Computational Complexity of Atomic Chemical Reaction Networks. SOFSEM 2018: 212-226 - [c35]David Doty, Mahsa Eftekhari, Othon Michail, Paul G. Spirakis, Michail Theofilatos:
Brief Announcement: Exact Size Counting in Uniform Population Protocols in Nearly Logarithmic Time. DISC 2018: 46:1-46:3 - [e1]David Doty, Hendrik Dietz:
DNA Computing and Molecular Programming - 24th International Conference, DNA 24, Jinan, China, October 8-12, 2018, Proceedings. Lecture Notes in Computer Science 11145, Springer 2018, ISBN 978-3-030-00029-5 [contents] - [i39]David Doty, Mahsa Eftekhari, Othon Michail, Paul G. Spirakis, Michail Theofilatos:
Exact size counting in uniform population protocols in nearly logarithmic time. CoRR abs/1805.04832 (2018) - [i38]David Doty, Mahsa Eftekhari:
Efficient size estimation and impossibility of termination in uniform dense population protocols. CoRR abs/1808.08913 (2018) - [i37]Keenan Breik, Cameron T. Chalk, David Doty, David Haley, David Soloveichik:
Programming Substrate-Independent Kinetic Barriers with Thermodynamic Binding Networks. CoRR abs/1810.12889 (2018) - [i36]Amanda Belleville, David Doty, David Soloveichik:
Hardness of computing and approximating predicates and functions with leaderless population protocols. CoRR abs/1811.01235 (2018) - 2017
- [j18]Ho-Lin Chen, Rachel Cummings, David Doty, David Soloveichik:
Speed faults in computation by chemical reaction networks. Distributed Comput. 30(5): 373-390 (2017) - [j17]Ho-Lin Chen, David Doty:
Parallelism and Time in Hierarchical Self-Assembly. SIAM J. Comput. 46(2): 661-709 (2017) - [j16]David Doty, Andrew Winslow:
Design of Geometric Molecular Bonds. IEEE Trans. Mol. Biol. Multi Scale Commun. 3(1): 13-23 (2017) - [c34]David Doty, Trent A. Rogers, David Soloveichik, Chris Thachuk, Damien Woods:
Thermodynamic Binding Networks. DNA 2017: 249-266 - [c33]Amanda Belleville, David Doty, David Soloveichik:
Hardness of Computing and Approximating Predicates and Functions with Leaderless Population Protocols. ICALP 2017: 141:1-141:14 - [i35]David Doty, Shaopeng Zhu:
Computational Complexity of Atomic Chemical Reaction Networks. CoRR abs/1702.05704 (2017) - [i34]David Doty, Trent A. Rogers, David Soloveichik, Chris Thachuk, Damien Woods:
Thermodynamic Binding Networks. CoRR abs/1709.07922 (2017) - 2016
- [j15]David Doty, Ho-Lin Chen, Ján Manuch, Arash Rafiey, Ladislav Stacho:
Pattern overlap implies runaway growth in hierarchical tile systems. J. Comput. Geom. 7(2): 3-18 (2016) - [j14]David Doty:
Producibility in hierarchical self-assembly. Nat. Comput. 15(1): 41-49 (2016) - [j13]Rachel Cummings, David Doty, David Soloveichik:
Probability 1 computation with chemical reaction networks. Nat. Comput. 15(2): 245-261 (2016) - [c32]Robert Brijder, David Doty, David Soloveichik:
Robustness of Expressivity in Chemical Reaction Networks. DNA 2016: 52-66 - [c31]David Doty, Andrew Winslow:
Design of geometric molecular bonds. ISIT 2016: 1789-1793 - [r2]David Doty:
Hierarchical Self-Assembly. Encyclopedia of Algorithms 2016: 903-909 - [r1]David Doty:
Randomized Self-Assembly. Encyclopedia of Algorithms 2016: 1759-1767 - [i33]David Doty, Andrew Winslow:
Design of geometric molecular bonds. CoRR abs/1602.01600 (2016) - [i32]Robert Brijder, David Doty, David Soloveichik:
Robustness of expressivity in chemical reaction networks. CoRR abs/1604.03687 (2016) - 2015
- [j12]Ho-Lin Chen, David Doty, Shinnosuke Seki:
Program Size and Temperature in Self-Assembly. Algorithmica 72(3): 884-899 (2015) - [j11]David Doty, Monir Hajiaghayi:
Leaderless deterministic chemical reaction networks. Nat. Comput. 14(2): 213-223 (2015) - [c30]Ho-Lin Chen, David Doty, Ján Manuch, Arash Rafiey, Ladislav Stacho:
Pattern Overlap Implies Runaway Growth in Hierarchical Tile Systems. SoCG 2015: 360-373 - [c29]David Doty, David Soloveichik:
Stable Leader Election in Population Protocols Requires Linear Time. DISC 2015: 602-616 - [i31]David Doty, David Soloveichik:
Stable leader election in population protocols requires linear time. CoRR abs/1502.04246 (2015) - 2014
- [j10]Ho-Lin Chen, David Doty, David Soloveichik:
Deterministic function computation with chemical reaction networks. Nat. Comput. 13(4): 517-534 (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]Rachel Cummings, David Doty, David Soloveichik:
Probability 1 Computation with Chemical Reaction Networks. DNA 2014: 37-52 - [c26]Ho-Lin Chen, David Doty, David Soloveichik:
Rate-independent computation in continuous chemical reaction networks. ITCS 2014: 313-326 - [c25]David Doty:
Timing in chemical reaction networks. SODA 2014: 772-784 - [c24]David Doty:
Producibility in Hierarchical Self-assembly. UCNC 2014: 142-154 - [c23]Ho-Lin Chen, Rachel Cummings, David Doty, David Soloveichik:
Speed Faults in Computation by Chemical Reaction Networks. DISC 2014: 16-30 - [i30]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) - [i29]Ho-Lin Chen, David Doty, Ján Manuch, Arash Rafiey, Ladislav Stacho:
Pattern overlap implies runaway growth in hierarchical tile systems. CoRR abs/1411.6672 (2014) - 2013
- [j9]David Doty, Lila Kari, Benoît Masson:
Negative Interactions in Irreversible Self-assembly. Algorithmica 66(1): 153-172 (2013) - [j8]Nathaniel Bryans, Ehsan Chiniforooshan, David Doty, Lila Kari, Shinnosuke Seki:
The Power of Nondeterminism in Self-Assembly. Theory Comput. 9: 1-29 (2013) - [c22]David Doty, Monir Hajiaghayi:
Leaderless Deterministic Chemical Reaction Networks. DNA 2013: 46-60 - [i28]David Doty:
Timing in chemical reaction networks. CoRR abs/1304.0872 (2013) - [i27]David Doty, Monir Hajiaghayi:
Leaderless deterministic chemical reaction networks. CoRR abs/1304.4519 (2013) - [i26]David Doty:
Producibility in hierarchical self-assembly. CoRR abs/1304.7804 (2013) - 2012
- [j7]David Doty:
Theory of algorithmic self-assembly. Commun. ACM 55(12): 78-88 (2012) - [c21]Ho-Lin Chen, David Doty, David Soloveichik:
Deterministic Function Computation with Chemical Reaction Networks. DNA 2012: 25-42 - [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]Ho-Lin Chen, David Doty:
Parallelism and time in hierarchical self-assembly. SODA 2012: 1163-1182 - [i25]Ho-Lin Chen, David Doty, David Soloveichik:
Deterministic Function Computation with Chemical Reaction Networks. CoRR abs/1204.4176 (2012) - 2011
- [j6]David Doty, Matthew J. Patitz, Scott M. Summers:
Limitations of self-assembly at temperature 1. Theor. Comput. Sci. 412(1-2): 145-158 (2011) - [c18]Ho-Lin Chen, David Doty, Shinnosuke Seki:
Program Size and Temperature in Self-Assembly. ISAAC 2011: 445-453 - [c17]Nathaniel Bryans, Ehsan Chiniforooshan, David Doty, Lila Kari, Shinnosuke Seki:
The Power of Nondeterminism in Self-Assembly. SODA 2011: 590-602 - [i24]Ho-Lin Chen, David Doty:
Parallelism and Time in Hierarchical Self-Assembly. CoRR abs/1104.5226 (2011) - [i23]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
- [j5]David Doty:
Randomized Self-Assembly for Exact Shapes. SIAM J. Comput. 39(8): 3521-3552 (2010) - [c16]Ehsan Chiniforooshan, David Doty, Lila Kari, Shinnosuke Seki:
Scalable, Time-Responsive, Digital, Energy-Efficient Molecular Circuits Using DNA Strand Displacement. DNA 2010: 25-36 - [c15]David Doty, Lila Kari, Benoît Masson:
Negative Interactions in Irreversible Self-assembly. DNA 2010: 37-48 - [c14]David Doty, Matthew J. Patitz, Dustin Reishus, Robert T. Schweller, Scott M. Summers:
Strong Fault-Tolerance for Self-Assembly with Fuzzy Temperature. FOCS 2010: 417-426 - [c13]David Doty, Jack H. Lutz, Matthew J. Patitz, Scott M. Summers, Damien Woods:
Intrinsic Universality in Self-Assembly. STACS 2010: 275-286 - [i22]David Doty, Jack H. Lutz, Matthew J. Patitz, Scott M. Summers, Damien Woods:
Intrinsic Universality in Self-Assembly. CoRR abs/1001.0208 (2010) - [i21]David Doty, Lila Kari, Benoît Masson:
Negative Interactions in Irreversible Self-Assembly. CoRR abs/1002.2746 (2010) - [i20]Ehsan Chiniforooshan, David Doty, Lila Kari, Shinnosuke Seki:
Scalable, Time-Responsive, Digital, Energy-Efficient Molecular Circuits using DNA Strand Displacement. CoRR abs/1003.3275 (2010) - [i19]David Doty, Matthew J. Patitz, Dustin Reishus, Robert T. Schweller, Scott M. Summers:
Strong Fault-Tolerance for Self-Assembly with Fuzzy Temperature. CoRR abs/1004.0995 (2010) - [i18]David Doty:
An Oracle Strongly Separating Deterministic Time from Nondeterministic Time, via Kolmogorov Complexity. CoRR abs/1004.3993 (2010) - [i17]Nathaniel Bryans, Ehsan Chiniforooshan, David Doty, Lila Kari, Shinnosuke Seki:
The Power of Nondeterminism in Self-Assembly. CoRR abs/1006.2897 (2010) - [i16]Ho-Lin Chen, David Doty, Shinnosuke Seki, David Soloveichik:
Parallelism, Program Size, Time, and Temperature in Self-Assembly. CoRR abs/1011.3493 (2010) - [i15]Nathaniel Bryans, Ehsan Chiniforooshan, David Doty, Lila Kari, Shinnosuke Seki:
The Power of Nondeterminism in Self-Assembly. Electron. Colloquium Comput. Complex. TR10 (2010) - [i14]Ho-Lin Chen, David Doty, Shinnosuke Seki, David Soloveichik:
Parallelism, Program Size, Time, and Temperature in Self-Assembly. Electron. Colloquium Comput. Complex. TR10 (2010)
2000 – 2009
- 2009
- [j4]Laurent Bienvenu, David Doty, Frank Stephan:
Constructive Dimension and Turing Degrees. Theory Comput. Syst. 45(4): 740-755 (2009) - [c12]David Doty, Matthew J. Patitz:
A Domain-Specific Language for Programming in the Tile Assembly Model. DNA 2009: 25-34 - [c11]David Doty, Matthew J. Patitz, Scott M. Summers:
Limitations of Self-assembly at Temperature One. DNA 2009: 35-44 - [c10]David Doty:
Randomized Self-Assembly for Exact Shapes. FOCS 2009: 85-94 - [c9]David Doty, Jack H. Lutz, Matthew J. Patitz, Scott M. Summers, Damien Woods:
Random Number Selection in Self-assembly. UC 2009: 143-157 - [i13]David Doty:
Randomized Self-Assembly for Exact Shapes. CoRR abs/0901.1849 (2009) - [i12]David Doty, Matthew J. Patitz:
A Domain-Specific Language for Programming in the Tile Assembly Model. CoRR abs/0903.0889 (2009) - [i11]David Doty, Matthew J. Patitz, Scott M. Summers:
Limitations of Self-Assembly at Temperature 1. CoRR abs/0903.1857 (2009) - 2008
- [j3]David Doty:
Dimension Extractors and Optimal Decompression. Theory Comput. Syst. 43(3-4): 425-463 (2008) - [c8]David Doty, Matthew J. Patitz, Scott M. Summers:
Limitations of Self-Assembly at Temperature One (extended abstract). CSP 2008: 67-69 - 2007
- [j2]David Doty, Jack H. Lutz, Satyadev Nandakumar:
Finite-state dimension and real arithmetic. Inf. Comput. 205(11): 1640-1651 (2007) - [j1]David Doty, Jared Nichols:
Pushdown dimension. Theor. Comput. Sci. 381(1-3): 105-123 (2007) - [c7]Laurent Bienvenu, David Doty, Frank Stephan:
Constructive Dimension and Weak Truth-Table Degrees. CiE 2007: 63-72 - [c6]David Doty, Philippe Moser:
Feasible Depth. CiE 2007: 228-237 - [i10]Laurent Bienvenu, David Doty, Frank Stephan:
Constructive Dimension and Weak Truth-Table Degrees. CoRR abs/cs/0701089 (2007) - [i9]David Doty, Philippe Moser:
Feasible Depth. CoRR abs/cs/0701123 (2007) - 2006
- [c5]David Doty:
Every Sequence Is Decompressible from a Random One. CiE 2006: 153-162 - [c4]David Doty, Jack H. Lutz, Satyadev Nandakumar:
Finite-State Dimension and Real Arithmetic. ICALP (1) 2006: 537-547 - [i8]David Doty, Jack H. Lutz, Satyadev Nandakumar:
Finite-State Dimension and Real Arithmetic. CoRR abs/cs/0602032 (2006) - [i7]David Doty:
Dimension Extractors and Optimal Decompression. CoRR abs/cs/0606078 (2006) - [i6]David Doty, Philippe Moser:
Finite-State Dimension and Lossy Decompressors. CoRR abs/cs/0609096 (2006) - [i5]David Doty:
Dimension Extractors. Electron. Colloquium Comput. Complex. TR06 (2006) - [i4]David Doty, Jack H. Lutz, Satyadev Nandakumar:
Finite-State Dimension and Real Arithmetic. Electron. Colloquium Comput. Complex. TR06 (2006) - 2005
- [c3]David Doty, Xiaoyang Gu, Jack H. Lutz, Elvira Mayordomo, Philippe Moser:
Zeta-Dimension. MFCS 2005: 283-294 - [i3]