Verifying chemical reaction network implementations: A pathway decomposition approach

Shin, Seung Woo; Thachuk, Chris; Winfree, Erik

doi:10.1016/j.tcs.2017.10.011

Cited by 13 publications

(9 citation statements)

References 22 publications

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“…The mechanism of DNA strand displacement has been used to create a variety of synthetic molecular systems including circuits, motors and triggered assembly of structures 1 . Software tools have been developed for designing and analysing DNA strand displacement systems, capable of generating nucleic acid sequences from well-defined structures and molecular interactions 2 3 , calculating the thermodynamic 2 4 5 and kinetic 6 properties of designed molecules, and evaluating if the behaviours of the molecular systems agree with the higher-level designs 3 7 8 9 10 11 . There also exist a few molecular compilers that can translate abstract functions such as a logic function to DNA strand displacement implementations without requiring an understanding of the molecular level details 12 13 .…”

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confidence: 99%

Compiler-aided systematic construction of large-scale DNA strand displacement circuits using unpurified components

et al. 2017

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Biochemical circuits made of rationally designed DNA molecules are proofs of concept for embedding control within complex molecular environments. They hold promise for transforming the current technologies in chemistry, biology, medicine and material science by introducing programmable and responsive behaviour to diverse molecular systems. As the transformative power of a technology depends on its accessibility, two main challenges are an automated design process and simple experimental procedures. Here we demonstrate the use of circuit design software, combined with the use of unpurified strands and simplified experimental procedures, for creating a complex DNA strand displacement circuit that consists of 78 distinct species. We develop a systematic procedure for overcoming the challenges involved in using unpurified DNA strands. We also develop a model that takes synthesis errors into consideration and semi-quantitatively reproduces the experimental data. Our methods now enable even novice researchers to successfully design and construct complex DNA strand displacement circuits.

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confidence: 99%

Compiler-aided systematic construction of large-scale DNA strand displacement circuits using unpurified components

et al. 2017

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“…Note that an implementation of an (abstract CRN) is a CRN as well, called an implementation CRN. Verification of correctness of an implementation CRN against an abstract CRN has been studied using the notion of pathway decomposition in [60] and using the notion of bisimulation in [42]. We also remark that the notion of correctness in general depends on the computational model that is assumed.…”

Section: Implementation: Dna Strand Displacementmentioning

confidence: 99%

Computing with chemical reaction networks: a tutorial

Brijder

2019

Nat Comput

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Chemical reaction networks (CRNs) model the behavior of chemical reactions in well-mixed solutions and they can be designed to perform computations. In this tutorial we give an overview of various computational models for CRNs. Moreover, we discuss a method to implement arbitrary (abstract) CRNs in a test tube using DNA. Finally, we discuss relationships between CRNs and other models of computation.

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“…For example, we might compare the abstract description of the DNA stack machine to its actual physical implementation [42], and wonder if the properties of a stack machine are preserved. An analogous problem came up in the finite CRN case, where verification methods (based on serializability analysis [34], pathway decomposition [46], and CRN bisimulation [27]) found subtle errors in some of the proposed CRN compilation schemes. Each of those methods has advantages and disadvantages relative to the others, but all are capable of proving relevant correspondences between the behavior of physical CRN implementations and the abstract CRNs, or pointing out implementations that fail to correspond to the abstract CRNs in important ways.…”

Section: Introductionmentioning

confidence: 99%

Verifying polymer reaction networks using bisimulation

Johnson

Winfree

2020

Theoretical Computer Science

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The Chemical Reaction Network model has been proposed as a programming language for molecular programming. Methods to implement arbitrary CRNs using DNA strand displacement circuits have been investigated, as have methods to prove the correctness of those or other implementations. However, the stochastic Chemical Reaction Network model is provably not deterministically Turing-universal, that is, it is impossible to create a stochastic CRN where a given output molecule is produced if and only if an arbitrary Turing machine accepts. A DNA stack machine that can simulate arbitrary Turing machines with minimal slowdown deterministically has been proposed, but it uses unbounded polymers that cannot be modeled as a Chemical Reaction Network. We propose an extended version of a Chemical Reaction Network that models unbounded linear polymers made from a finite number of monomers. This Polymer Reaction Network model covers the DNA stack machine, as well as copy-tolerant Turing machines and some examples from biochemistry. We adapt the bisimulation method of verifying DNA implementations of Chemical Reaction Networks to our model, and use it to prove the correctness of the DNA stack machine implementation. We define a subclass of single-locus Polymer Reaction Networks and show that any member of that class can be bisimulated by a network using only four primitives, suggesting a method of DNA implementation. Finally, we prove that deciding whether an implementation is a bisimulation is 0 2 -complete, and thus undecidable in the general case, although it is tractable in many special cases of interest. We hope that the ability to model and verify implementations of Polymer Reaction Networks will aid in the rational design of molecular systems.

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Verifying chemical reaction network implementations: A pathway decomposition approach

Cited by 13 publications

References 22 publications

Compiler-aided systematic construction of large-scale DNA strand displacement circuits using unpurified components

Compiler-aided systematic construction of large-scale DNA strand displacement circuits using unpurified components

Computing with chemical reaction networks: a tutorial

Verifying polymer reaction networks using bisimulation

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