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  1. No Access

    Article

    CRN++: Molecular programming language

    Synthetic biology is a rapidly emerging research area, with expected wide-ranging impact in biology, nanofabrication, and medicine. A key technical challenge lies in embedding computation in molecular contexts...

    Marko Vasić, David Soloveichik, Sarfraz Khurshid in Natural Computing (2020)

  2. Article

    Open Access

    DNA punch cards for storing data on native DNA sequences via enzymatic nicking

    Synthetic DNA-based data storage systems have received significant attention due to the promise of ultrahigh storage density and long-term stability. However, all known platforms suffer from high cost, read-wr...

    S. Kasra Tabatabaei, Boya Wang, Nagendra Bala Murali Athreya… in Nature Communications (2020)

    Download PDF (1003 KB) View Article

  3. No Access

    Chapter and Conference Paper

    SIMD||DNA: Single Instruction, Multiple Data Computation with DNA Strand Displacement Cascades

    Typical DNA storage schemes do not allow in-m...

    Boya Wang, Cameron Chalk, David Soloveichik in DNA Computing and Molecular Programming (2019)

  4. No Access

    Article

    Stable leader election in population protocols requires linear time

    A population protocol stably elects a leader if, for all n, starting from an initial configuration with n agents each in an identical state, with probability 1 it reaches a configuration

    David Doty, David Soloveichik in Distributed Computing (2018)

  5. No Access

    Article

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

    We show that some natural output conventions for error-free computation in chemical reaction networks (CRN) lead to a common level of computational expressivity. Our main results are that the standard consensu...

    Robert Brijder, David Doty, David Soloveichik in Natural Computing (2018)

  6. No Access

    Chapter and Conference Paper

    Composable Rate-Independent Computation in Continuous Chemical Reaction Networks

    Biological regulatory networks depend upon chemical interactions to process information. Engineering such molecular computing systems is a major challenge for synthetic biology and related fields. The chemical...

    Cameron Chalk, Niels Kornerup, Wyatt Reeves… in Computational Methods in Systems Biology (2018)

  7. No Access

    Chapter and Conference Paper

    Programming Substrate-Independent Kinetic Barriers with Thermodynamic Binding Networks

    Engineering molecular systems that exhibit complex behavior requires the design of kinetic barriers. For example, an effective catalytic pathway must have a large barrier when the catalyst is absent. While pro...

    Keenan Breik, Cameron Chalk, David Doty… in Computational Methods in Systems Biology (2018)

  8. No Access

    Chapter and Conference Paper

    CRN++: Molecular Programming Language

    Synthetic biology is a rapidly emerging research area, with expected wide-ranging impact in biology, nanofabrication, and medicine. A key technical challenge lies in embedding computation in molecular contexts...

    Marko Vasic, David Soloveichik, Sarfraz Khurshid in DNA Computing and Molecular Programming (2018)

  9. No Access

    Article

    Speed faults in computation by chemical reaction networks

    Chemical reaction networks (CRNs) formally model chemistry in a well-mixed solution. Assuming a fixed molecular population size and bimolecular reactions, CRNs are formally equivalent to population protocols, ...

    Ho-Lin Chen, Rachel Cummings, David Doty, David Soloveichik in Distributed Computing (2017)

  10. No Access

    Chapter and Conference Paper

    Robust Detection in Leak-Prone Population Protocols

    In contrast to electronic computation, chemical computation is noisy and susceptible to a variety of sources of error, which has prevented the construction of robust complex systems. To be effective, chemical ...

    Dan Alistarh, Bartłomiej Dudek, Adrian Kosowski… in DNA Computing and Molecular Programming (2017)

  11. No Access

    Chapter and Conference Paper

    The Design Space of Strand Displacement Cascades with Toehold-Size Clamps

    DNA strand displacement cascades have proven to be a uniquely flexible and programmable primitive for constructing molecular logic circuits, smart structures and devices, and for systems with complex autonomou...

    Boya Wang, Chris Thachuk, Andrew D. Ellington… in DNA Computing and Molecular Programming (2017)

  12. No Access

    Chapter and Conference Paper

    Thermodynamic Binding Networks

    Strand displacement and tile assembly systems are designed to follow prescribed kinetic rules (i.e., exhibit a specific time-evolution). However, the expected behavior in the limit of infinite time—known as th...

    David Doty, Trent A. Rogers, David Soloveichik… in DNA Computing and Molecular Programming (2017)

  13. No Access

    Article

    Probability 1 computation with chemical reaction networks

    The computational power of stochastic chemical reaction networks (CRNs) varies significantly with the output convention and whether or not error is permitted. Focusing on probability 1 computation, we demonstr...

    Rachel Cummings, David Doty, David Soloveichik in Natural Computing (2016)

  14. No Access

    Chapter and Conference Paper

    Robustness of Expressivity in Chemical Reaction Networks

    We show that some natural output conventions for error-free computation in chemical reaction networks (CRN) lead to a common level of computational expressivity. Our main results are that the standard definiti...

    Robert Brijder, David Doty, David Soloveichik in DNA Computing and Molecular Programming (2016)

  15. Article

    Preface

    David Soloveichik, Bernard Yurke in Natural Computing (2015)

    Download PDF (288 KB) View Article

  16. No Access

    Chapter and Conference Paper

    Leakless DNA Strand Displacement Systems

    While current experimental demonstrations have been limited to small computational tasks, DNA strand displacement systems (DSD systems) [25] hold promise for sophisticated information processing within chemical o...

    Chris Thachuk, Erik Winfree, David Soloveichik in DNA Computing and Molecular Programming (2015)

  17. No Access

    Chapter and Conference Paper

    Stable Leader Election in Population Protocols Requires Linear Time

    A population protocol stably elects a leader if, for all n, starting from an initial configuration with n agents each in an identical state, with probability 1 it reaches a configuration y that is correct (exactl...

    David Doty, David Soloveichik in Distributed Computing (2015)

  18. No Access

    Article

    Deterministic function computation with chemical reaction networks

    Chemical reaction networks (CRNs) formally model chemistry in a well-mixed solution. CRNs are widely used to describe information processing occurring in natural cellular regulatory networks, and with upcoming...

    Ho-Lin Chen, David Doty, David Soloveichik in Natural Computing (2014)

  19. No Access

    Chapter and Conference Paper

    Probability 1 Computation with Chemical Reaction Networks

    The computational power of stochastic chemical reaction networks (CRNs) varies significantly with the output convention and whether or not error is permitted. Focusing on probability 1 computation, we demonstr...

    Rachel Cummings, David Doty, David Soloveichik in DNA Computing and Molecular Programming (2014)

  20. No Access

    Chapter and Conference Paper

    Speed Faults in Computation by Chemical Reaction Networks

    Chemical reaction networks (CRNs) formally model chemistry in a well-mixed solution. Assuming a fixed molecular population size and bimolecular reactions, CRNs are formally equivalent to population protocols, ...

    Ho-Lin Chen, Rachel Cummings, David Doty, David Soloveichik in Distributed Computing (2014)

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