David Doty - RankMe

147 papers A* 14A 8B 22C 4Journal 87Unranked 8

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	Analog computation with transcriptional networks. CoRR David Doty, Mina Latifi, David Soloveichick
2025	J	`jnl`	Exactly simulating stochastic chemical reaction networks in sub-constant time per reaction. CoRR Joshua Petrack, David Doty
2025	A	`conf`	Robust Predicate and Function Computation in Continuous Chemical Reaction Networks. DISC Kim Calabrese, David Doty, Mina Latifi
2025	J	`jnl`	Robust predicate and function computation in continuous chemical reaction networks. CoRR Kim Calabrese, David Doty, Mina Latifi
2024	A*	`conf`	Brief Announcement: Optimally Encoding Information in Chemical Reaction Networks. PODC Austin Luchsinger, David Doty, David Soloveichik
2024	—	`conf`	Rate-Independent Continuous Inhibitory Chemical Reaction Networks Are Turing-Universal. UCNC Kim Calabrese, David Doty
2024	J	`jnl`	Rate-independent continuous inhibitory chemical reaction networks are Turing-universal. CoRR Kim Calabrese, David Doty
2024	A	`conf`	The Computational Power of Discrete Chemical Reaction Networks with Bounded Executions. DISC David Doty, Ben Heckmann
2024	J	`jnl`	The computational power of discrete chemical reaction networks with bounded executions. CoRR David Doty, Ben Heckmann
2023	—	`ed.`	2nd Symposium on Algorithmic Foundations of Dynamic Networks, SAND 2023, Pisa, Italy, June 19-21, 2023 SAND David Doty, Paul G. Spirakis
2023	B	`conf`	Accelerating Self-Assembly of Crisscross Slat Systems. DNA David Doty, Hunter Fleming, Daniel Hader, Matthew J. Patitz, Lukas A. Vaughan
2023	J	`jnl`	Harvesting Brownian Motion: Zero Energy Computational Sampling. CoRR David Doty, Niels Kornerup, Austin Luchsinger, Leo Orshansky, David Soloveichik, Damien Woods
2023	J	`jnl`	Is stochastic thermodynamics the key to understanding the energy costs of computation? CoRR 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
2023	B	`conf`	Optimal Information Encoding in Chemical Reaction Networks. DNA Austin Luchsinger, David Doty, David Soloveichik
2023	J	`jnl`	Optimal Information Encoding in Chemical Reaction Networks. CoRR Austin Luchsinger, David Doty, David Soloveichik
2023	J	`jnl`	Rate-independent Computation in Continuous Chemical Reaction Networks. J. ACM Ho-Lin Chen, David Doty, Wyatt Reeves, David Soloveichik
2023	B	`conf`	Thermodynamically Driven Signal Amplification. DNA Joshua Petrack, David Soloveichik, David Doty
2023	J	`jnl`	Thermodynamically Driven Signal Amplification. CoRR Joshua Petrack, David Soloveichik, David Doty
2022	—	`conf`	Dynamic Size Counting in Population Protocols. SAND David Doty, Mahsa Eftekhari
2022	J	`jnl`	Dynamic size counting in population protocols. CoRR David Doty, Mahsa Eftekhari
2022	—	`conf`	Simulating 3-Symbol Turing Machines with SIMD\|\|DNA. SAND David Doty, Aaron Ong
2021	J	`jnl`	A survey of size counting in population protocols. CoRR David Doty, Mahsa Eftekhari
2021	J	`jnl`	A survey of size counting in population protocols. Theor. Comput. Sci. David Doty, Mahsa Eftekhari
2021	A*	`conf`	A time and space optimal stable population protocol solving exact majority. FOCS David Doty, Mahsa Eftekhari, Leszek Gasieniec, Eric E. Severson, Przemyslaw Uznanski, Grzegorz Stachowiak
2021	J	`jnl`	A time and space optimal stable population protocol solving exact majority. CoRR David Doty, Mahsa Eftekhari, Leszek Gasieniec, Eric E. Severson, Grzegorz Stachowiak, Przemyslaw Uznanski
2021	A*	`conf`	Brief Announcement: A Time and Space Optimal Stable Population Protocol Solving Exact Majority. PODC David Doty, Mahsa Eftekhari, Leszek Gasieniec, Eric E. Severson, Grzegorz Stachowiak, Przemyslaw Uznanski
2021	J	`jnl`	Composable computation in discrete chemical reaction networks. Distributed Comput. Eric E. Severson, David Haley, David Doty
2021	B	`conf`	Computing Properties of Thermodynamic Binding Networks: An Integer Programming Approach. DNA David Haley, David Doty
2021	—	`conf`	Ppsim: A Software Package for Efficiently Simulating and Visualizing Population Protocols. CMSB David Doty, Eric E. Severson
2021	J	`jnl`	Preface. Nat. Comput. David Doty, Rudolf Freund, Natasa Jonoska, Jarkko Kari
2021	J	`jnl`	Programming Substrate-Independent Kinetic Barriers With Thermodynamic Binding Networks. IEEE ACM Trans. Comput. Biol. Bioinform. Keenan Breik, Cameron T. Chalk, David Doty, David Haley, David Soloveichik
2021	J	`jnl`	Rate-Independent Computation in Continuous Chemical Reaction Networks. CoRR Ho-Lin Chen, David Doty, David Soloveichik, Wyatt Reeves
2021	J	`jnl`	Simulating 3-symbol Turing machines with SIMD\|\|DNA. CoRR David Doty, Aaron Ong
2021	A*	`conf`	Time-Optimal Self-Stabilizing Leader Election in Population Protocols. PODC Janna Burman, Ho-Lin Chen, Hsueh-Ping Chen, David Doty, Thomas Nowak, Eric E. Severson, Chuan Xu
2021	J	`jnl`	ppsim: A software package for efficiently simulating and visualizing population protocols. CoRR David Doty, Eric E. Severson
2020	J	`jnl`	Computing Properties of Thermodynamic Binding Networks: An Integer Programming Approach. CoRR David Haley, David Doty
2020	A	`conf`	Message Complexity of Population Protocols. DISC Talley Amir, James Aspnes, David Doty, Mahsa Eftekhari, Eric E. Severson
2020	J	`jnl`	Message complexity of population protocols. CoRR Talley Amir, James Aspnes, David Doty, Mahsa Eftekhari H., Eric E. Severson
2020	J	`jnl`	Preface. Nat. Comput. David Doty, Hendrik Dietz
2020	B	`conf`	scadnano: A Browser-Based, Scriptable Tool for Designing DNA Nanostructures. DNA David Doty, Benjamin L. Lee, Tristan Stérin
2020	J	`jnl`	scadnano: A browser-based, easily scriptable tool for designing DNA nanostructures. CoRR David Doty, Benjamin L. Lee, Tristan Stérin
2019	A*	`conf`	Composable Computation in Discrete Chemical Reaction Networks. PODC Eric E. Severson, David Haley, David Doty
2019	J	`jnl`	Composable computation in discrete chemical reaction networks. CoRR Eric E. Severson, David Haley, David Doty
2019	J	`jnl`	Diverse and robust molecular algorithms using reprogrammable DNA self-assembly. Nat. Damien Woods, David Doty, Cameron Myhrvold, Joy Hui, Felix Zhou, Peng Yin, Erik Winfree
2019	A*	`conf`	Efficient Size Estimation and Impossibility of Termination in Uniform Dense Population Protocols. PODC David Doty, Mahsa Eftekhari
2019	J	`jnl`	Time-Optimal Self-Stabilizing Leader Election in Population Protocols. CoRR Janna Burman, Ho-Lin Chen, Hsueh-Ping Chen, David Doty, Thomas Nowak, Eric E. Severson, Chuan Xu
2018	A	`conf`	Brief Announcement: Exact Size Counting in Uniform Population Protocols in Nearly Logarithmic Time. DISC David Doty, Mahsa Eftekhari, Othon Michail, Paul G. Spirakis, Michail Theofilatos
2018	B	`conf`	Computational Complexity of Atomic Chemical Reaction Networks. SOFSEM David Doty, Shaopeng Zhu
2018	J	`jnl`	Computational complexity of atomic chemical reaction networks. Nat. Comput. David Doty, Shaopeng Zhu
2018	B	`ed.`	DNA Computing and Molecular Programming - 24th International Conference, DNA 2018, Jinan, China, October 8-12, 2018, Proceedings DNA David Doty, Hendrik Dietz
2018	J	`jnl`	Democratic, existential, and consensus-based output conventions in stable computation by chemical reaction networks. Nat. Comput. Robert Brijder, David Doty, David Soloveichik
2018	J	`jnl`	Efficient size estimation and impossibility of termination in uniform dense population protocols. CoRR David Doty, Mahsa Eftekhari
2018	J	`jnl`	Exact size counting in uniform population protocols in nearly logarithmic time. CoRR David Doty, Mahsa Eftekhari, Othon Michail, Paul G. Spirakis, Michail Theofilatos
2018	J	`jnl`	Hardness of computing and approximating predicates and functions with leaderless population protocols. CoRR Amanda Belleville, David Doty, David Soloveichik
2018	—	`conf`	Programming Substrate-Independent Kinetic Barriers with Thermodynamic Binding Networks. CMSB Keenan Breik, Cameron T. Chalk, David Doty, David Haley, David Soloveichik
2018	J	`jnl`	Programming Substrate-Independent Kinetic Barriers with Thermodynamic Binding Networks. CoRR Keenan Breik, Cameron T. Chalk, David Doty, David Haley, David Soloveichik
2018	J	`jnl`	Stable leader election in population protocols requires linear time. Distributed Comput. David Doty, David Soloveichik
2017	J	`jnl`	Computational Complexity of Atomic Chemical Reaction Networks. CoRR David Doty, Shaopeng Zhu
2017	J	`jnl`	Design of Geometric Molecular Bonds. IEEE Trans. Mol. Biol. Multi Scale Commun. David Doty, Andrew Winslow
2017	A*	`conf`	Hardness of Computing and Approximating Predicates and Functions with Leaderless Population Protocols. ICALP Amanda Belleville, David Doty, David Soloveichik
2017	J	`jnl`	Parallelism and Time in Hierarchical Self-Assembly. SIAM J. Comput. Ho-Lin Chen, David Doty
2017	J	`jnl`	Speed faults in computation by chemical reaction networks. Distributed Comput. Ho-Lin Chen, Rachel Cummings, David Doty, David Soloveichik
2017	B	`conf`	Thermodynamic Binding Networks. DNA David Doty, Trent A. Rogers, David Soloveichik, Chris Thachuk, Damien Woods
2017	J	`jnl`	Thermodynamic Binding Networks. CoRR David Doty, Trent A. Rogers, David Soloveichik, Chris Thachuk, Damien Woods
2016	B	`conf`	Design of geometric molecular bonds. ISIT David Doty, Andrew Winslow
2016	J	`jnl`	Design of geometric molecular bonds. CoRR David Doty, Andrew Winslow
2016	—	`ch.`	Hierarchical Self-Assembly. Encyclopedia of Algorithms David Doty
2016	J	`jnl`	Pattern overlap implies runaway growth in hierarchical tile systems. J. Comput. Geom. David Doty, Ho-Lin Chen, Ján Manuch, Arash Rafiey, Ladislav Stacho
2016	J	`jnl`	Probability 1 computation with chemical reaction networks. Nat. Comput. Rachel Cummings, David Doty, David Soloveichik
2016	J	`jnl`	Producibility in hierarchical self-assembly. Nat. Comput. David Doty
2016	—	`ch.`	Randomized Self-Assembly. Encyclopedia of Algorithms David Doty
2016	B	`conf`	Robustness of Expressivity in Chemical Reaction Networks. DNA Robert Brijder, David Doty, David Soloveichik
2016	J	`jnl`	Robustness of expressivity in chemical reaction networks. CoRR Robert Brijder, David Doty, David Soloveichik
2015	J	`jnl`	Leaderless deterministic chemical reaction networks. Nat. Comput. David Doty, Monir Hajiaghayi
2015	A*	`conf`	Pattern Overlap Implies Runaway Growth in Hierarchical Tile Systems. SoCG Ho-Lin Chen, David Doty, Ján Manuch, Arash Rafiey, Ladislav Stacho
2015	J	`jnl`	Program Size and Temperature in Self-Assembly. Algorithmica Ho-Lin Chen, David Doty, Shinnosuke Seki
2015	A	`conf`	Stable Leader Election in Population Protocols Requires Linear Time. DISC David Doty, David Soloveichik
2015	J	`jnl`	Stable leader election in population protocols requires linear time. CoRR David Doty, David Soloveichik
2014	J	`jnl`	Deterministic function computation with chemical reaction networks. Nat. Comput. Ho-Lin Chen, David Doty, David Soloveichik
2014	B	`conf`	Fast Algorithmic Self-assembly of Simple Shapes Using Random Agitation. DNA Ho-Lin Chen, David Doty, Dhiraj Holden, Chris Thachuk, Damien Woods, Chun-Tao Yang
2014	J	`jnl`	Fast algorithmic self-assembly of simple shapes using random agitation. CoRR Ho-Lin Chen, David Doty, Dhiraj Holden, Chris Thachuk, Damien Woods, Chun-Tao Yang
2014	J	`jnl`	Pattern overlap implies runaway growth in hierarchical tile systems. CoRR Ho-Lin Chen, David Doty, Ján Manuch, Arash Rafiey, Ladislav Stacho
2014	B	`conf`	Probability 1 Computation with Chemical Reaction Networks. DNA Rachel Cummings, David Doty, David Soloveichik
2014	—	`conf`	Producibility in Hierarchical Self-assembly. UCNC David Doty
2014	A	`conf`	Rate-independent computation in continuous chemical reaction networks. ITCS Ho-Lin Chen, David Doty, David Soloveichik
2014	A	`conf`	Speed Faults in Computation by Chemical Reaction Networks. DISC Ho-Lin Chen, Rachel Cummings, David Doty, David Soloveichik
2014	A*	`conf`	Timing in chemical reaction networks. SODA David Doty
2013	B	`conf`	Leaderless Deterministic Chemical Reaction Networks. DNA David Doty, Monir Hajiaghayi
2013	J	`jnl`	Leaderless deterministic chemical reaction networks CoRR David Doty, Monir Hajiaghayi
2013	J	`jnl`	Negative Interactions in Irreversible Self-assembly. Algorithmica David Doty, Lila Kari, Benoît Masson
2013	J	`jnl`	Producibility in hierarchical self-assembly CoRR David Doty
2013	J	`jnl`	The Power of Nondeterminism in Self-Assembly. Theory Comput. Nathaniel Bryans, Ehsan Chiniforooshan, David Doty, Lila Kari, Shinnosuke Seki
2013	J	`jnl`	Timing in chemical reaction networks CoRR David Doty
2012	J	`jnl`	Deterministic Function Computation with Chemical Reaction Networks CoRR Ho-Lin Chen, David Doty, David Soloveichik
2012	B	`conf`	Deterministic Function Computation with Chemical Reaction Networks. DNA Ho-Lin Chen, David Doty, David Soloveichik
2012	A*	`conf`	Parallelism and time in hierarchical self-assembly. SODA Ho-Lin Chen, David Doty
2012	A*	`conf`	The Tile Assembly Model is Intrinsically Universal. FOCS David Doty, Jack H. Lutz, Matthew J. Patitz, Robert T. Schweller, Scott M. Summers, Damien Woods
2012	J	`jnl`	Theory of algorithmic self-assembly. Commun. ACM David Doty
2011	J	`jnl`	Limitations of self-assembly at temperature 1. Theor. Comput. Sci. David Doty, Matthew J. Patitz, Scott M. Summers
2011	J	`jnl`	Parallelism and Time in Hierarchical Self-Assembly CoRR Ho-Lin Chen, David Doty
2011	B	`conf`	Program Size and Temperature in Self-Assembly. ISAAC Ho-Lin Chen, David Doty, Shinnosuke Seki
2011	A*	`conf`	The Power of Nondeterminism in Self-Assembly. SODA Nathaniel Bryans, Ehsan Chiniforooshan, David Doty, Lila Kari, Shinnosuke Seki
2011	J	`jnl`	The tile assembly model is intrinsically universal CoRR David Doty, Jack H. Lutz, Matthew J. Patitz, Robert T. Schweller, Scott M. Summers, Damien Woods
2010	J	`jnl`	An Oracle Strongly Separating Deterministic Time from Nondeterministic Time, via Kolmogorov Complexity CoRR David Doty
2010	J	`jnl`	Intrinsic Universality in Self-Assembly CoRR David Doty, Jack H. Lutz, Matthew J. Patitz, Scott M. Summers, Damien Woods
2010	A	`conf`	Intrinsic Universality in Self-Assembly. STACS David Doty, Jack H. Lutz, Matthew J. Patitz, Scott M. Summers, Damien Woods
2010	J	`jnl`	Negative Interactions in Irreversible Self-Assembly CoRR David Doty, Lila Kari, Benoît Masson
2010	B	`conf`	Negative Interactions in Irreversible Self-assembly. DNA David Doty, Lila Kari, Benoît Masson
2010	J	`jnl`	Parallelism, Program Size, Time, and Temperature in Self-Assembly CoRR Ho-Lin Chen, David Doty, Shinnosuke Seki, David Soloveichik
2010	J	`jnl`	Parallelism, Program Size, Time, and Temperature in Self-Assembly. Electron. Colloquium Comput. Complex. Ho-Lin Chen, David Doty, Shinnosuke Seki, David Soloveichik
2010	J	`jnl`	Randomized Self-Assembly for Exact Shapes. SIAM J. Comput. David Doty
2010	B	`conf`	Scalable, Time-Responsive, Digital, Energy-Efficient Molecular Circuits Using DNA Strand Displacement. DNA Ehsan Chiniforooshan, David Doty, Lila Kari, Shinnosuke Seki
2010	J	`jnl`	Scalable, Time-Responsive, Digital, Energy-Efficient Molecular Circuits using DNA Strand Displacement CoRR Ehsan Chiniforooshan, David Doty, Lila Kari, Shinnosuke Seki
2010	J	`jnl`	Strong Fault-Tolerance for Self-Assembly with Fuzzy Temperature CoRR David Doty, Matthew J. Patitz, Dustin Reishus, Robert T. Schweller, Scott M. Summers
2010	A*	`conf`	Strong Fault-Tolerance for Self-Assembly with Fuzzy Temperature. FOCS David Doty, Matthew J. Patitz, Dustin Reishus, Robert T. Schweller, Scott M. Summers
2010	J	`jnl`	The Power of Nondeterminism in Self-Assembly CoRR Nathaniel Bryans, Ehsan Chiniforooshan, David Doty, Lila Kari, Shinnosuke Seki
2010	J	`jnl`	The Power of Nondeterminism in Self-Assembly. Electron. Colloquium Comput. Complex. Nathaniel Bryans, Ehsan Chiniforooshan, David Doty, Lila Kari, Shinnosuke Seki
2009	J	`jnl`	A Domain-Specific Language for Programming in the Tile Assembly Model CoRR David Doty, Matthew J. Patitz
2009	B	`conf`	A Domain-Specific Language for Programming in the Tile Assembly Model. DNA David Doty, Matthew J. Patitz
2009	—	`—`	Applications of the theory of computation to nanoscale self-assembly. David Doty
2009	J	`jnl`	Constructive Dimension and Turing Degrees. Theory Comput. Syst. Laurent Bienvenu, David Doty, Frank Stephan
2009	J	`jnl`	Limitations of Self-Assembly at Temperature 1 CoRR David Doty, Matthew J. Patitz, Scott M. Summers
2009	B	`conf`	Limitations of Self-assembly at Temperature One. DNA David Doty, Matthew J. Patitz, Scott M. Summers
2009	C	`conf`	Random Number Selection in Self-assembly. UC David Doty, Jack H. Lutz, Matthew J. Patitz, Scott M. Summers, Damien Woods
2009	J	`jnl`	Randomized Self-Assembly for Exact Shapes CoRR David Doty
2009	A*	`conf`	Randomized Self-Assembly for Exact Shapes. FOCS David Doty
2008	J	`jnl`	Dimension Extractors and Optimal Decompression. Theory Comput. Syst. David Doty
2008	—	`conf`	Limitations of Self-Assembly at Temperature One (extended abstract) CSP David Doty, Matthew J. Patitz, Scott M. Summers
2007	J	`jnl`	Constructive Dimension and Weak Truth-Table Degrees CoRR Laurent Bienvenu, David Doty, Frank Stephan
2007	C	`conf`	Constructive Dimension and Weak Truth-Table Degrees. CiE Laurent Bienvenu, David Doty, Frank Stephan
2007	J	`jnl`	Feasible Depth CoRR David Doty, Philippe Moser
2007	C	`conf`	Feasible Depth. CiE David Doty, Philippe Moser
2007	J	`jnl`	Finite-state dimension and real arithmetic. Inf. Comput. David Doty, Jack H. Lutz, Satyadev Nandakumar
2007	J	`jnl`	Pushdown dimension. Theor. Comput. Sci. David Doty, Jared Nichols
2006	J	`jnl`	Dimension Extractors and Optimal Decompression CoRR David Doty
2006	J	`jnl`	Dimension Extractors. Electron. Colloquium Comput. Complex. David Doty
2006	C	`conf`	Every Sequence Is Decompressible from a Random One. CiE David Doty
2006	J	`jnl`	Finite-State Dimension and Lossy Decompressors CoRR David Doty, Philippe Moser
2006	J	`jnl`	Finite-State Dimension and Real Arithmetic CoRR David Doty, Jack H. Lutz, Satyadev Nandakumar
2006	—	`conf`	Finite-State Dimension and Real Arithmetic. ICALP (1) David Doty, Jack H. Lutz, Satyadev Nandakumar
2006	J	`jnl`	Finite-State Dimension and Real Arithmetic. Electron. Colloquium Comput. Complex. David Doty, Jack H. Lutz, Satyadev Nandakumar
2005	J	`jnl`	Every Sequence is Decompressible from a Random One CoRR David Doty
2005	J	`jnl`	Pushdown dimension CoRR David Doty, Jared Nichols
2005	J	`jnl`	Zeta-Dimension CoRR David Doty, Xiaoyang Gu, Jack H. Lutz, Elvira Mayordomo, Philippe Moser
2005	B	`conf`	Zeta-Dimension. MFCS David Doty, Xiaoyang Gu, Jack H. Lutz, Elvira Mayordomo, Philippe Moser
2004	B	`conf`	Nonlocal evolutionary adaptation in gridplants. IEEE Congress on Evolutionary Computation David Doty
2003	B	`conf`	Morphometric grayscale texture analysis using foot patterns. IEEE Congress on Evolutionary Computation Dan Ashlock, Dean C. Adams, David Doty