David Doty

Orcid: 0000-0002-3922-172X

Affiliations:
  • University of California Davis, CA, USA


According to our database1, David Doty authored at least 73 papers between 2003 and 2023.

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Bibliography

2023
Rate-independent Computation in Continuous Chemical Reaction Networks.
J. ACM, June, 2023

Is stochastic thermodynamics the key to understanding the energy costs of computation?
CoRR, 2023

Harvesting Brownian Motion: Zero Energy Computational Sampling.
CoRR, 2023

Thermodynamically Driven Signal Amplification.
Proceedings of the 29th International Conference on DNA Computing and Molecular Programming, 2023

Optimal Information Encoding in Chemical Reaction Networks.
Proceedings of the 29th International Conference on DNA Computing and Molecular Programming, 2023

Accelerating Self-Assembly of Crisscross Slat Systems.
Proceedings of the 29th International Conference on DNA Computing and Molecular Programming, 2023

2022
Simulating 3-Symbol Turing Machines with SIMD||DNA.
Proceedings of the 1st Symposium on Algorithmic Foundations of Dynamic Networks, 2022

Dynamic Size Counting in Population Protocols.
Proceedings of the 1st Symposium on Algorithmic Foundations of Dynamic Networks, 2022

2021
A survey of size counting in population protocols.
Theor. Comput. Sci., 2021

Programming Substrate-Independent Kinetic Barriers With Thermodynamic Binding Networks.
IEEE ACM Trans. Comput. Biol. Bioinform., 2021

Preface.
Nat. Comput., 2021

Composable computation in discrete chemical reaction networks.
Distributed Comput., 2021

Brief Announcement: A Time and Space Optimal Stable Population Protocol Solving Exact Majority.
Proceedings of the PODC '21: ACM Symposium on Principles of Distributed Computing, 2021

Time-Optimal Self-Stabilizing Leader Election in Population Protocols.
Proceedings of the PODC '21: ACM Symposium on Principles of Distributed Computing, 2021

A time and space optimal stable population protocol solving exact majority.
Proceedings of the 62nd IEEE Annual Symposium on Foundations of Computer Science, 2021

Computing Properties of Thermodynamic Binding Networks: An Integer Programming Approach.
Proceedings of the 27th International Conference on DNA Computing and Molecular Programming, 2021

Ppsim: A Software Package for Efficiently Simulating and Visualizing Population Protocols.
Proceedings of the Computational Methods in Systems Biology, 2021

2020
Preface.
Nat. Comput., 2020

scadnano: A browser-based, easily scriptable tool for designing DNA nanostructures.
CoRR, 2020

Message Complexity of Population Protocols.
Proceedings of the 34th International Symposium on Distributed Computing, 2020

scadnano: A Browser-Based, Scriptable Tool for Designing DNA Nanostructures.
Proceedings of the 26th International Conference on DNA Computing and Molecular Programming, 2020

2019
Diverse and robust molecular algorithms using reprogrammable DNA self-assembly.
Nat., 2019

Time-Optimal Self-Stabilizing Leader Election in Population Protocols.
CoRR, 2019

Efficient Size Estimation and Impossibility of Termination in Uniform Dense Population Protocols.
Proceedings of the 2019 ACM Symposium on Principles of Distributed Computing, 2019

2018
Computational complexity of atomic chemical reaction networks.
Nat. Comput., 2018

Democratic, existential, and consensus-based output conventions in stable computation by chemical reaction networks.
Nat. Comput., 2018

Stable leader election in population protocols requires linear time.
Distributed Comput., 2018

Exact size counting in uniform population protocols in nearly logarithmic time.
CoRR, 2018

Brief Announcement: Exact Size Counting in Uniform Population Protocols in Nearly Logarithmic Time.
Proceedings of the 32nd International Symposium on Distributed Computing, 2018

2017
Design of Geometric Molecular Bonds.
IEEE Trans. Mol. Biol. Multi Scale Commun., 2017

Parallelism and Time in Hierarchical Self-Assembly.
SIAM J. Comput., 2017

Speed faults in computation by chemical reaction networks.
Distributed Comput., 2017

Hardness of Computing and Approximating Predicates and Functions with Leaderless Population Protocols.
Proceedings of the 44th International Colloquium on Automata, Languages, and Programming, 2017

Thermodynamic Binding Networks.
Proceedings of the DNA Computing and Molecular Programming - 23rd International Conference, 2017

2016
Randomized Self-Assembly.
Encyclopedia of Algorithms, 2016

Hierarchical Self-Assembly.
Encyclopedia of Algorithms, 2016

Producibility in hierarchical self-assembly.
Nat. Comput., 2016

Probability 1 computation with chemical reaction networks.
Nat. Comput., 2016

Pattern overlap implies runaway growth in hierarchical tile systems.
J. Comput. Geom., 2016

Robustness of Expressivity in Chemical Reaction Networks.
Proceedings of the DNA Computing and Molecular Programming - 22nd International Conference, 2016

2015
Leaderless deterministic chemical reaction networks.
Nat. Comput., 2015

Program Size and Temperature in Self-Assembly.
Algorithmica, 2015

2014
Deterministic function computation with chemical reaction networks.
Nat. Comput., 2014

Timing in chemical reaction networks.
Proceedings of the Twenty-Fifth Annual ACM-SIAM Symposium on Discrete Algorithms, 2014

Rate-independent computation in continuous chemical reaction networks.
Proceedings of the Innovations in Theoretical Computer Science, 2014

Fast Algorithmic Self-assembly of Simple Shapes Using Random Agitation.
Proceedings of the DNA Computing and Molecular Programming - 20th International Conference, 2014

2013
The Power of Nondeterminism in Self-Assembly.
Theory Comput., 2013

Negative Interactions in Irreversible Self-assembly.
Algorithmica, 2013

2012
Theory of algorithmic self-assembly.
Commun. ACM, 2012

The Tile Assembly Model is Intrinsically Universal.
Proceedings of the 53rd Annual IEEE Symposium on Foundations of Computer Science, 2012

2011
Limitations of self-assembly at temperature 1.
Theor. Comput. Sci., 2011

2010
Randomized Self-Assembly for Exact Shapes.
SIAM J. Comput., 2010

Parallelism, Program Size, Time, and Temperature in Self-Assembly.
Electron. Colloquium Comput. Complex., 2010

An Oracle Strongly Separating Deterministic Time from Nondeterministic Time, via Kolmogorov Complexity
CoRR, 2010

Intrinsic Universality in Self-Assembly.
Proceedings of the 27th International Symposium on Theoretical Aspects of Computer Science, 2010

Strong Fault-Tolerance for Self-Assembly with Fuzzy Temperature.
Proceedings of the 51th Annual IEEE Symposium on Foundations of Computer Science, 2010

Scalable, Time-Responsive, Digital, Energy-Efficient Molecular Circuits Using DNA Strand Displacement.
Proceedings of the DNA Computing and Molecular Programming - 16th International Conference, 2010

2009
Constructive Dimension and Turing Degrees.
Theory Comput. Syst., 2009

Random Number Selection in Self-assembly.
Proceedings of the Unconventional Computation, 8th International Conference, 2009

Limitations of Self-assembly at Temperature One.
Proceedings of the DNA Computing and Molecular Programming, 15th International Conference, 2009

A Domain-Specific Language for Programming in the Tile Assembly Model.
Proceedings of the DNA Computing and Molecular Programming, 15th International Conference, 2009

2008
Dimension Extractors and Optimal Decompression.
Theory Comput. Syst., 2008

Limitations of Self-Assembly at Temperature One (extended abstract)
Proceedings of the Proceedings International Workshop on The Complexity of Simple Programs, 2008

2007
Pushdown dimension.
Theor. Comput. Sci., 2007

Feasible Depth.
Proceedings of the Computation and Logic in the Real World, 2007

Constructive Dimension and Weak Truth-Table Degrees.
Proceedings of the Computation and Logic in the Real World, 2007

2006
Finite-State Dimension and Real Arithmetic.
Electron. Colloquium Comput. Complex., 2006

Dimension Extractors.
Electron. Colloquium Comput. Complex., 2006

Finite-State Dimension and Lossy Decompressors
CoRR, 2006

Every Sequence Is Decompressible from a Random One.
Proceedings of the Logical Approaches to Computational Barriers, 2006

2005
Zeta-Dimension.
Proceedings of the Mathematical Foundations of Computer Science 2005, 2005

2004
Nonlocal evolutionary adaptation in gridplants.
Proceedings of the IEEE Congress on Evolutionary Computation, 2004

2003
Morphometric grayscale texture analysis using foot patterns.
Proceedings of the IEEE Congress on Evolutionary Computation, 2003


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