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Thermodynamic Binding Networks

Abstract : 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 thermodynamic equilibrium--is often incompatible with the desired computation. Basic physical chemistry implicates this inconsistency as a source of unavoidable error. Can the thermodynamic equilibrium be made consistent with the desired computational pathway? In order to formally study this question, we introduce a new model of molecular computing in which computation is driven by the thermodynamic driving forces of enthalpy and entropy. To ensure greatest generality we do not assume that there are any constraints imposed by geometry and treat monomers as unstructured collections of binding sites. In this model we design Boolean AND/OR formulas, as well as a self-assembling binary counter, where the thermodynamically favored states are exactly the desired final output configurations. Though inspired by DNA nanotechnology, the model is sufficiently general to apply to a wide variety of chemical systems.
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Contributor : Damien Woods Connect in order to contact the contributor
Submitted on : Wednesday, December 13, 2017 - 2:14:45 AM
Last modification on : Wednesday, June 8, 2022 - 12:50:06 PM

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Damien Woods, David Doty, Trent A. Rogers, David Soloveichik, Chris Thachuk. Thermodynamic Binding Networks. DNA 2017 - The 23rd International Conference on DNA Computing and Molecular Programming, Sep 2017, Austin, United States. pp.249-266, ⟨10.1007/978-3-319-66799-7_16⟩. ⟨hal-01662285⟩



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