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David Doty
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- affiliation: University of California Davis, CA, USA
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2020 – today
- 2024
- [c54]Austin Luchsinger
, David Doty
Brief Announcement: Optimally Encoding Information in Chemical Reaction Networks. PODC 2024: 61-64 - [c53]Kim Calabrese, David Doty:
Rate-Independent Continuous Inhibitory Chemical Reaction Networks Are Turing-Universal. UCNC 2024: 104-118 - [c52]David Doty, Ben Heckmann:
The Computational Power of Discrete Chemical Reaction Networks with Bounded Executions. DISC 2024: 20:1-20:15 - [i56]Kim Calabrese, David Doty:
Rate-independent continuous inhibitory chemical reaction networks are Turing-universal. CoRR abs/2403.07099 (2024) - [i55]David Doty, Ben Heckmann:
The computational power of discrete chemical reaction networks with bounded executions. CoRR abs/2405.08649 (2024) - 2023
- [j28]Ho-Lin Chen
Rate-independent Computation in Continuous Chemical Reaction Networks. J. ACM 70(3): 22:1-22:61 (2023) - [c51]David Doty, Hunter Fleming, Daniel Hader, Matthew J. Patitz
Accelerating Self-Assembly of Crisscross Slat Systems. DNA 2023: 7:1-7:23 - [c50]Joshua Petrack, David Soloveichik, David Doty:
Thermodynamically Driven Signal Amplification. DNA 2023: 8:1-8:22 - [c49]Austin Luchsinger, David Doty, David Soloveichik:
Optimal Information Encoding in Chemical Reaction Networks. DNA 2023: 9:1-9:16 - [e2]David Doty
2nd Symposium on Algorithmic Foundations of Dynamic Networks, SAND 2023, June 19-21, 2023, Pisa, Italy. LIPIcs 257, Schloss Dagstuhl - Leibniz-Zentrum für Informatik 2023, ISBN 978-3-95977-275-4 [contents] - [i54]Joshua Petrack, David Soloveichik, David Doty:
Thermodynamically Driven Signal Amplification. CoRR abs/2307.01550 (2023) - [i53]Austin Luchsinger, David Doty, David Soloveichik:
Optimal Information Encoding in Chemical Reaction Networks. CoRR abs/2307.01939 (2023) - [i52]David Doty, Niels Kornerup
Harvesting Brownian Motion: Zero Energy Computational Sampling. CoRR abs/2309.06957 (2023) - [i51]David H. Wolpert, Jan Korbel, Christopher Lynn, Farita Tasnim, Joshua A. Grochow, Gülce Kardes, James B. Aimone
Is stochastic thermodynamics the key to understanding the energy costs of computation? CoRR abs/2311.17166 (2023) - 2022
- [c48]David Doty
Dynamic Size Counting in Population Protocols. SAND 2022: 13:1-13:18 - [c47]David Doty
Simulating 3-Symbol Turing Machines with SIMD||DNA. SAND 2022: 14:1-14:15 - [i50]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
Programming Substrate-Independent Kinetic Barriers With Thermodynamic Binding Networks. IEEE ACM Trans. Comput. Biol. Bioinform. 18(1): 283-295 (2021) - [j24]David Doty
A survey of size counting in population protocols. Theor. Comput. Sci. 894: 91-102 (2021) - [c46]David Doty
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
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
Time-Optimal Self-Stabilizing Leader Election in Population Protocols. PODC 2021: 33-44 - [c42]David Doty, Mahsa Eftekhari
Brief Announcement: A Time and Space Optimal Stable Population Protocol Solving Exact Majority. PODC 2021: 77-80 - [i49]David Doty, Eric E. Severson:
ppsim: A software package for efficiently simulating and visualizing population protocols. CoRR abs/2105.04702 (2021) - [i48]David Doty, Mahsa Eftekhari
A survey of size counting in population protocols. CoRR abs/2105.05408 (2021) - [i47]David Doty, Aaron Ong:
Simulating 3-symbol Turing machines with SIMD||DNA. CoRR abs/2105.08559 (2021) - [i46]David Doty, Mahsa Eftekhari
A time and space optimal stable population protocol solving exact majority. CoRR abs/2106.10201 (2021) - [i45]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
scadnano: A Browser-Based, Scriptable Tool for Designing DNA Nanostructures. DNA 2020: 9:1-9:17 - [c40]Talley Amir
Message Complexity of Population Protocols. DISC 2020: 6:1-6:18 - [i44]Talley Amir, James Aspnes, David Doty, Mahsa Eftekhari H., Eric E. Severson:
Message complexity of population protocols. CoRR abs/2003.09532 (2020) - [i43]David Doty, Benjamin L. Lee, Tristan Stérin:
scadnano: A browser-based, easily scriptable tool for designing DNA nanostructures. CoRR abs/2005.11841 (2020) - [i42]David Haley, David Doty:
Computing Properties of Thermodynamic Binding Networks: An Integer Programming Approach. CoRR abs/2011.10677 (2020)
2010 – 2019
- 2019
- [j22]Damien Woods
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
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
Stable leader election in population protocols requires linear time. Distributed Comput. 31(4): 257-271 (2018) - [j20]Robert Brijder, David Doty
Democratic, existential, and consensus-based output conventions in stable computation by chemical reaction networks. Nat. Comput. 17(1): 97-108 (2018) - [j19]David Doty
Computational complexity of atomic chemical reaction networks. Nat. Comput. 17(4): 677-691 (2018) - [c37]Keenan Breik, Cameron T. Chalk, David Doty
Programming Substrate-Independent Kinetic Barriers with Thermodynamic Binding Networks. CMSB 2018: 203-219 - [c36]David Doty
Computational Complexity of Atomic Chemical Reaction Networks. SOFSEM 2018: 212-226 - [c35]David Doty, Mahsa Eftekhari
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
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
Design of Geometric Molecular Bonds. IEEE Trans. Mol. Biol. Multi Scale Commun. 3(1): 13-23 (2017) - [c34]David Doty
Thermodynamic Binding Networks. DNA 2017: 249-266 - [c33]Amanda Belleville, David Doty
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
Probability 1 computation with chemical reaction networks. Nat. Comput. 15(2): 245-261 (2016) - [c32]Robert Brijder
Robustness of Expressivity in Chemical Reaction Networks. DNA 2016: 52-66 - [c31]David Doty
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
Program Size and Temperature in Self-Assembly. Algorithmica 72(3): 884-899 (2015) - [j11]David Doty
Leaderless deterministic chemical reaction networks. Nat. Comput. 14(2): 213-223 (2015) - [c30]Ho-Lin Chen, David Doty
Pattern Overlap Implies Runaway Growth in Hierarchical Tile Systems. SoCG 2015: 360-373 - [c29]David Doty
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
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
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
Negative Interactions in Irreversible Self-assembly. Algorithmica 66(1): 153-172 (2013) - [j8]Nathaniel Bryans, Ehsan Chiniforooshan, David Doty
The Power of Nondeterminism in Self-Assembly. Theory Comput. 9: 1-29 (2013) - [c22]David Doty
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
Deterministic Function Computation with Chemical Reaction Networks. DNA 2012: 25-42 - [c20]David Doty
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
Limitations of self-assembly at temperature 1. Theor. Comput. Sci. 412(1-2): 145-158 (2011) - [c18]Ho-Lin Chen
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
Scalable, Time-Responsive, Digital, Energy-Efficient Molecular Circuits Using DNA Strand Displacement. DNA 2010: 25-36 - [c15]David Doty
Negative Interactions in Irreversible Self-assembly. DNA 2010: 37-48 - [c14]David Doty
Strong Fault-Tolerance for Self-Assembly with Fuzzy Temperature. FOCS 2010: 417-426 - [c13]David Doty
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
Constructive Dimension and Turing Degrees. Theory Comput. Syst. 45(4): 740-755 (2009) - [c12]David Doty
A Domain-Specific Language for Programming in the Tile Assembly Model. DNA 2009: 25-34 - [c11]David Doty
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
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
Finite-state dimension and real arithmetic. Inf. Comput. 205(11): 1640-1651 (2007) - [j1]David Doty
Pushdown dimension. Theor. Comput. Sci. 381(1-3): 105-123 (2007) - [c7]Laurent Bienvenu, David Doty
Constructive Dimension and Weak Truth-Table Degrees. CiE 2007: 63-72 - [c6]David Doty
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
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]David Doty, Xiaoyang Gu, Jack H. Lutz, Elvira Mayordomo, Philippe Moser:
Zeta-Dimension. CoRR abs/cs/0503052 (2005) - [i2]David Doty, Jared Nichols:
Pushdown dimension. CoRR abs/cs/0504047 (2005) - [i1]David Doty:
Every Sequence is Decompressible from a Random One. CoRR abs/cs/0511074 (2005) - 2004
- [c2]David Doty:
Nonlocal evolutionary adaptation in gridplants. IEEE Congress on Evolutionary Computation 2004: 1602-1609 - 2003
- [c1]Dan Ashlock, Dean C. Adams
Morphometric grayscale texture analysis using foot patterns. IEEE Congress on Evolutionary Computation 2003: 1575-1581
Coauthor Index
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