Molecular system for an exponentially fast growing programmable synthetic polymer
- Creators
- Dabby, Nadine
- Barr, Alan
- Chen, Ho-Lin
Abstract
In this paper, we demonstrate a molecular system for the first active self-assembly linear DNA polymer that exhibits programmable molecular exponential growth in real time, also the first to implement "internal" parallel insertion that does not rely on adding successive layers to "external" edges for growth. Approaches like this can produce enhanced exponential growth behavior that is less limited by volume and external surface interference, for an early step toward efficiently building two and three dimensional shapes in logarithmic time. We experimentally demonstrate the division of these polymers via the addition of a single DNA complex that competes with the insertion mechanism and results in the exponential growth of a population of polymers per unit time. In the supplementary material, we note that an "extension" beyond conventional Turing machine theory is needed to theoretically analyze exponential growth itself in programmable physical systems. Sequential physical Turing Machines that run a roughly constant number of Turing steps per unit time cannot achieve an exponential growth of structure per time. In contrast, the "active" self-assembly model in this paper, computationally equivalent to a Push-Down Automaton, is exponentially fast when implemented in molecules, but is taxonomically less powerful than a Turing machine. In this sense, a physical Push-Down Automaton can be more powerful than a sequential physical Turing Machine, even though the Turing Machine can compute any computable function. A need for an "extended" computational/physical theory arises, described in the supplementary material section S1.
Additional Information
© The Author(s) 2023. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The authors would like to thank Richard Murray, Niles Pierce and Erik Winfree for the use of their labs. We would also like to thank Bernard Yurke, Damien Woods, Deborah Fygenson, Paul Rothemund, Harry Choi and Niles Pierce for additional discussions and suggestions in regard to this work. Nadine Dabby was supported by a NSF Graduate Research Fellowship and the Molecular Programming Project under NSF grant 0832824. Ho-Lin Chen was supported by Molecular Programming Project under NSF grant 0832824 and MOST (Taiwan) grant 101-2218-E-002-007- and 110-2223-E-002-006-MY3. Data availability: All data generated or analysed during this study are included in this published article and its supplementary information files. Contributions: N.D. and H.-L.C. proposed the molecular system. N.D. performed the experiments. A.B. proposed to add the connection to physical computation into the paper. N.D. wrote the main manuscript text. All authors reviewed and revised the main manuscript text. The authors declare no competing interests.Attached Files
Published - s41598-023-35720-5.pdf
Supplemental Material - 41598_2023_35720_MOESM1_ESM.pdf
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Additional details
- PMCID
- PMC10338630
- Eprint ID
- 122480
- Resolver ID
- CaltechAUTHORS:20230725-857238000.53
- NSF Graduate Research Fellowship
- NSF
- CCF-0832824
- Ministry of Science and Technology (Taipei)
- 101-2218-E-002-007-MY3
- Ministry of Science and Technology (Taipei)
- 110-2223-E-002-006-MY3
- Created
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2023-08-11Created from EPrint's datestamp field
- Updated
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2023-08-14Created from EPrint's last_modified field