David Doty

ORCID

Publication Activity (10 Years)

Years Active: 2003-2024
Publications (10 Years): 66

Top Venues

Publications

Kim Calabrese, David Doty
Rate-independent continuous inhibitory chemical reaction networks are Turing-universal. CoRR (2024)
David Doty, Ben Heckmann
The computational power of discrete chemical reaction networks with bounded executions. CoRR (2024)
Kim Calabrese, David Doty
Rate-Independent Continuous Inhibitory Chemical Reaction Networks Are Turing-Universal. UCNC (2024)
Austin Luchsinger, David Doty, David Soloveichik
Brief Announcement: Optimally Encoding Information in Chemical Reaction Networks. PODC (2024)
Austin Luchsinger, David Doty, David Soloveichik
Optimal Information Encoding in Chemical Reaction Networks. DNA (2023)
David H. Wolpert, Jan Korbel, Christopher Lynn, Farita Tasnim, Joshua A. Grochow, Gülce Kardes, James B. Aimone, Vijay Balasubramanian, Eric De Giuli, David Doty, Nahuel Freitas, Matteo Marsili, Thomas E. Ouldridge, Andréa W. Richa, Paul M. Riechers, Édgar Roldán, Brenda M. Rubenstein, Zoltán Toroczkai, Joseph A. Paradiso
Is stochastic thermodynamics the key to understanding the energy costs of computation? CoRR (2023)
David Doty, Hunter Fleming, Daniel Hader, Matthew J. Patitz, Lukas A. Vaughan
Accelerating Self-Assembly of Crisscross Slat Systems. DNA (2023)
Ho-Lin Chen, David Doty, Wyatt Reeves, David Soloveichik
Rate-independent Computation in Continuous Chemical Reaction Networks. J. ACM 70 (3) (2023)
Austin Luchsinger, David Doty, David Soloveichik
Optimal Information Encoding in Chemical Reaction Networks. CoRR (2023)
David Doty, Niels Kornerup, Austin Luchsinger, Leo Orshansky, David Soloveichik, Damien Woods
Harvesting Brownian Motion: Zero Energy Computational Sampling. CoRR (2023)
Joshua Petrack, David Soloveichik, David Doty
Thermodynamically Driven Signal Amplification. CoRR (2023)
Joshua Petrack, David Soloveichik, David Doty
Thermodynamically Driven Signal Amplification. DNA (2023)
David Doty, Aaron Ong
Simulating 3-Symbol Turing Machines with SIMD||DNA. SAND (2022)
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 (2022)
David Doty, Mahsa Eftekhari
Dynamic Size Counting in Population Protocols. SAND (2022)
David Doty, Mahsa Eftekhari
Dynamic size counting in population protocols. CoRR (2022)
David Doty, Mahsa Eftekhari
A survey of size counting in population protocols. CoRR (2021)
Ho-Lin Chen, David Doty, David Soloveichik, Wyatt Reeves
Rate-Independent Computation in Continuous Chemical Reaction Networks. CoRR (2021)
David Doty, Mahsa Eftekhari
A survey of size counting in population protocols. Theor. Comput. Sci. 894 (2021)
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)
David Doty, Eric E. Severson
ppsim: A software package for efficiently simulating and visualizing population protocols. CoRR (2021)
David Doty, Rudolf Freund, Natasa Jonoska, Jarkko Kari
Preface. Nat. Comput. 20 (4) (2021)
Eric E. Severson, David Haley, David Doty
Composable computation in discrete chemical reaction networks. Distributed Comput. 34 (6) (2021)
David Doty, Aaron Ong
Simulating 3-symbol Turing machines with SIMD||DNA. CoRR (2021)
David Doty, Eric E. Severson
Ppsim: A Software Package for Efficiently Simulating and Visualizing Population Protocols. CMSB (2021)
David Haley, David Doty
Computing Properties of Thermodynamic Binding Networks: An Integer Programming Approach. DNA (2021)
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 (2021)
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)
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)
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) (2021)
David Doty, Hendrik Dietz
Preface. Nat. Comput. 19 (2) (2020)
David Doty, Benjamin L. Lee, Tristan Stérin
scadnano: A Browser-Based, Scriptable Tool for Designing DNA Nanostructures. DNA (2020)
David Haley, David Doty
Computing Properties of Thermodynamic Binding Networks: An Integer Programming Approach. CoRR (2020)
Talley Amir, James Aspnes, David Doty, Mahsa Eftekhari, Eric E. Severson
Message Complexity of Population Protocols. DISC (2020)
David Doty, Mahsa Eftekhari, Eric E. Severson
A stable majority population protocol using logarithmic time and states. CoRR (2020)
Talley Amir, James Aspnes, David Doty, Mahsa Eftekhari H., Eric E. Severson
Message complexity of population protocols. CoRR (2020)
David Doty, Benjamin L. Lee, Tristan Stérin
scadnano: A browser-based, easily scriptable tool for designing DNA nanostructures. CoRR (2020)
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) (2019)
David Doty, Mahsa Eftekhari
Efficient Size Estimation and Impossibility of Termination in Uniform Dense Population Protocols. PODC (2019)
Eric E. Severson, David Haley, David Doty
Composable Computation in Discrete Chemical Reaction Networks. PODC (2019)
Eric E. Severson, David Haley, David Doty
Composable computation in discrete chemical reaction networks. CoRR (2019)
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 (2019)
David Doty, Mahsa Eftekhari, Othon Michail, Paul G. Spirakis, Michail Theofilatos
Exact size counting in uniform population protocols in nearly logarithmic time. CoRR (2018)
Robert Brijder, David Doty, David Soloveichik
Democratic, existential, and consensus-based output conventions in stable computation by chemical reaction networks. Nat. Comput. 17 (1) (2018)
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)
David Doty, Shaopeng Zhu
Computational Complexity of Atomic Chemical Reaction Networks. SOFSEM (2018)
Keenan Breik, Cameron T. Chalk, David Doty, David Haley, David Soloveichik
Programming Substrate-Independent Kinetic Barriers with Thermodynamic Binding Networks. CoRR (2018)
David Doty, Mahsa Eftekhari
Efficient size estimation and impossibility of termination in uniform dense population protocols. CoRR (2018)
Amanda Belleville, David Doty, David Soloveichik
Hardness of computing and approximating predicates and functions with leaderless population protocols. CoRR (2018)
David Doty, Shaopeng Zhu
Computational complexity of atomic chemical reaction networks. Nat. Comput. 17 (4) (2018)
David Doty, David Soloveichik
Stable leader election in population protocols requires linear time. Distributed Comput. 31 (4) (2018)
Keenan Breik, Cameron T. Chalk, David Doty, David Haley, David Soloveichik
Programming Substrate-Independent Kinetic Barriers with Thermodynamic Binding Networks. CMSB (2018)
Ho-Lin Chen, David Doty
Parallelism and Time in Hierarchical Self-Assembly. SIAM J. Comput. 46 (2) (2017)
David Doty, Shaopeng Zhu
Computational Complexity of Atomic Chemical Reaction Networks. CoRR (2017)
David Doty, Andrew Winslow
Design of Geometric Molecular Bonds. IEEE Trans. Mol. Biol. Multi Scale Commun. 3 (1) (2017)
Amanda Belleville, David Doty, David Soloveichik
Hardness of Computing and Approximating Predicates and Functions with Leaderless Population Protocols. ICALP (2017)
David Doty, Trent A. Rogers, David Soloveichik, Chris Thachuk, Damien Woods
Thermodynamic Binding Networks. CoRR (2017)
David Doty, Trent A. Rogers, David Soloveichik, Chris Thachuk, Damien Woods
Thermodynamic Binding Networks. DNA (2017)
Ho-Lin Chen, Rachel Cummings, David Doty, David Soloveichik
Speed faults in computation by chemical reaction networks. Distributed Comput. 30 (5) (2017)
David Doty, Andrew Winslow
Design of geometric molecular bonds. CoRR (2016)
Rachel Cummings, David Doty, David Soloveichik
Probability 1 computation with chemical reaction networks. Nat. Comput. 15 (2) (2016)
David Doty
Producibility in hierarchical self-assembly. Nat. Comput. 15 (1) (2016)
David Doty, Andrew Winslow
Design of geometric molecular bonds. ISIT (2016)
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) (2016)
Robert Brijder, David Doty, David Soloveichik
Robustness of Expressivity in Chemical Reaction Networks. DNA (2016)
Robert Brijder, David Doty, David Soloveichik
Robustness of expressivity in chemical reaction networks. CoRR (2016)
David Doty, David Soloveichik
Stable leader election in population protocols requires linear time. CoRR (2015)
David Doty, Monir Hajiaghayi
Leaderless deterministic chemical reaction networks. Nat. Comput. 14 (2) (2015)
Ho-Lin Chen, David Doty, Shinnosuke Seki
Program Size and Temperature in Self-Assembly. Algorithmica 72 (3) (2015)
Ho-Lin Chen, David Doty, Ján Manuch, Arash Rafiey, Ladislav Stacho
Pattern Overlap Implies Runaway Growth in Hierarchical Tile Systems. SoCG (2015)
David Doty, David Soloveichik
Stable Leader Election in Population Protocols Requires Linear Time. DISC (2015)
Ho-Lin Chen, Rachel Cummings, David Doty, David Soloveichik
Speed Faults in Computation by Chemical Reaction Networks. DISC (2014)
Ho-Lin Chen, David Doty, Ján Manuch, Arash Rafiey, Ladislav Stacho
Pattern overlap implies runaway growth in hierarchical tile systems. CoRR (2014)
Ho-Lin Chen, David Doty, David Soloveichik
Deterministic function computation with chemical reaction networks. Nat. Comput. 13 (4) (2014)
Rachel Cummings, David Doty, David Soloveichik
Probability 1 Computation with Chemical Reaction Networks. DNA (2014)
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)
David Doty
Producibility in Hierarchical Self-assembly. UCNC (2014)
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 (2014)
Ho-Lin Chen, David Doty, David Soloveichik
Rate-independent computation in continuous chemical reaction networks. ITCS (2014)
David Doty
Timing in chemical reaction networks. SODA (2014)
David Doty, Monir Hajiaghayi
Leaderless deterministic chemical reaction networks CoRR (2013)
Nathaniel Bryans, Ehsan Chiniforooshan, David Doty, Lila Kari, Shinnosuke Seki
The Power of Nondeterminism in Self-Assembly. Theory Comput. 9 (2013)
David Doty
Producibility in hierarchical self-assembly CoRR (2013)
David Doty, Lila Kari, Benoît Masson
Negative Interactions in Irreversible Self-assembly. Algorithmica 66 (1) (2013)
David Doty
Timing in chemical reaction networks CoRR (2013)
David Doty, Monir Hajiaghayi
Leaderless Deterministic Chemical Reaction Networks. DNA (2013)
David Doty
Theory of algorithmic self-assembly. Commun. ACM 55 (12) (2012)
Ho-Lin Chen, David Doty, David Soloveichik
Deterministic Function Computation with Chemical Reaction Networks. DNA (2012)
Ho-Lin Chen, David Doty
Parallelism and time in hierarchical self-assembly. SODA (2012)
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)
Ho-Lin Chen, David Doty, David Soloveichik
Deterministic Function Computation with Chemical Reaction Networks CoRR (2012)
Ho-Lin Chen, David Doty, Shinnosuke Seki
Program Size and Temperature in Self-Assembly. ISAAC (2011)
David Doty, Jack H. Lutz, Matthew J. Patitz, Robert T. Schweller, Scott M. Summers, Damien Woods
The tile assembly model is intrinsically universal CoRR (2011)
Nathaniel Bryans, Ehsan Chiniforooshan, David Doty, Lila Kari, Shinnosuke Seki
The Power of Nondeterminism in Self-Assembly. SODA (2011)
Ho-Lin Chen, David Doty
Parallelism and Time in Hierarchical Self-Assembly CoRR (2011)
David Doty, Matthew J. Patitz, Scott M. Summers
Limitations of self-assembly at temperature 1. Theor. Comput. Sci. 412 (1-2) (2011)
David Doty, Jack H. Lutz, Matthew J. Patitz, Scott M. Summers, Damien Woods
Intrinsic Universality in Self-Assembly. STACS (2010)
David Doty
An Oracle Strongly Separating Deterministic Time from Nondeterministic Time, via Kolmogorov Complexity CoRR (2010)
Nathaniel Bryans, Ehsan Chiniforooshan, David Doty, Lila Kari, Shinnosuke Seki
The Power of Nondeterminism in Self-Assembly. Electron. Colloquium Comput. Complex. 17 (2010)
Ehsan Chiniforooshan, David Doty, Lila Kari, Shinnosuke Seki
Scalable, Time-Responsive, Digital, Energy-Efficient Molecular Circuits using DNA Strand Displacement CoRR (2010)

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Publication Activity (10 Years)

Top Topics

Top Venues

David Doty