# Verifying Chemical Reaction Network Implementations: A Bisimulation Approach

@article{Johnson2016VerifyingCR, title={Verifying Chemical Reaction Network Implementations: A Bisimulation Approach}, author={Robert F. Johnson and Qing Dong and Erik Winfree}, journal={Theor. Comput. Sci.}, year={2016}, volume={765}, pages={3-46} }

Efforts in programming DNA and other biological molecules have recently focused on general schemes to physically implement arbitrary Chemical Reaction Networks. Errors in some of the proposed schemes have driven a desire for formal verification methods. We show that by interpreting each implementation species as a set of formal species, the concept of weak bisimulation can be adapted to CRNs in a way that agrees with an intuitive notion of a correct implementation. We give examples of how to…

## 14 Citations

Verifying Chemical Reaction Network Implementations: A Pathway Decomposition Approach

- Computer ScienceTheor. Comput. Sci.
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It is shown how Chemical Reaction Network implementations can be built out of abstracted motifs, discussing existing implementations as well as presenting two new implementations based on 4-way strand exchange, one of which uses the new cooperative motif.

A General-Purpose CRN-to-DSD Compiler with Formal Verification, Optimization, and Simulation Capabilities

- Computer ScienceDNA
- 2017

A CRN-to-DSD compiler, Nuskell, that makes a first step in this direction and to support the wide range of translation schemes that have already been proposed in the literature, as well as potential new ones that are yet to be proposed.

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The computational complexity of deciding whether a given network is atomic according to each of these definitions is investigated and equivalence relationships between these definitions and some cases of an existing definition of atomicity due to Gnacadja are demonstrated.

A domain-level DNA strand displacement reaction enumerator allowing arbitrary non-pseudoknotted secondary structures

- BiologyJournal of the Royal Society Interface
- 2020

This work builds on prior practice to provide a new formalization of ‘domain-level’ representations of DNA strand displacement systems that has a natural connection to nucleic acid biophysics while still being suitable for formal analysis.

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

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A systematic procedure for overcoming the challenges involved in using unpurified DNA strands is developed and a model that takes synthesis errors into consideration and semi-quantitatively reproduces the experimental data is developed.

Domain-specific programming languages for computational nucleic acid systems.

- Computer Science, BiologyACS synthetic biology
- 2020

There is a continuum of practical implementation strategies for computational nucleic acid systems, which can all benefit from appropriate domain-specific languages and software design tools, and the need for specialized yet flexible tools that can be realized using domain- specific languages that compile to more general-purpose representations is emphasized.

Optimizing Tile Set Size While Preserving Proofreading with a DNA Self-assembly Compiler

- Computer ScienceDNA
- 2018

This work presents a tile set optimization technique that, through analysis of algorithmic growth equivalence, potentially sensitive error pathways, and potential lattice defects, can significantly reduce the size of tile systems while preserving proofreading behavior that is essential for obtaining low error rates.

Automated sequence-level analysis of kinetics and thermodynamics for domain-level DNA strand-displacement systems

- BiologyJournal of the Royal Society Interface
- 2018

A computational method for verifying sequence-level systems by identifying discrepancies between the domain-level and sequence- level behaviour, implemented as the Python package KinDA, will allow researchers to predict the kinetic and thermodynamic behaviour of domain- level systems after sequence assignment, as well as to detect violations of the intended behaviour.

Computing with chemical reaction networks: a tutorial

- Computer ScienceNatural Computing
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An overview of various computational models for CRNs is given and a method to implement arbitrary (abstract) CRNs in a test tube using DNA is discussed.

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