ArticleJournal of the Royal Society, Interface2012
Design and analysis of DNA strand displacement devices using probabilistic model checking.
Article in Journal of the Royal Society, Interface, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Verifiable biology.Journal of the Royal Society, Interface · 2023Review
- Analytical design of multi-threshold and high fan-in DNA-based logical sensors to profile the pattern of MS microRNAs.Biomedical engineering letters · 2021Article
- Chemical reaction network designs for asynchronous logic circuits.Natural computing · 2018Article
- Compiler-aided systematic construction of large-scale DNA strand displacement circuits using unpurified components.Nature communications · 2017Article
- A strand graph semantics for DNA-based computation.Theoretical computer science · 2016Article
- Modular verification of chemical reaction network encodings via serializability analysis.Theoretical computer science · 2016Article
- Gener: a minimal programming module for chemical controllers based on DNA strand displacement.Bioinformatics (Oxford, England) · 2015Article
- Synthesizing Configurable Biochemical Implementation of Linear Systems from Their Transfer Function Specifications.PloS one · 2015Article
- A Novel Computational Method to Reduce Leaky Reaction in DNA Strand Displacement.Journal of analytical methods in chemistry · 2015Article
- Design of a biochemical circuit motif for learning linear functions.Journal of the Royal Society, Interface · 2014Article
- Computer-assisted design for scaling up systems based on DNA reaction networks.Journal of the Royal Society, Interface · 2014Article
- Biophysically inspired rational design of structured chimeric substrates for DNAzyme cascade engineering.PloS one · 2014Article
- DNA computing: Molecules reach consensus.Nature nanotechnology · 2013Article
- Scaling down DNA circuits with competitive neural networks.Journal of the Royal Society, Interface · 2013Article
- Synthetic in vitro circuits.Current opinion in chemical biology · 2012Review
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Designing correct, robust DNA devices is difficult because of the many possibilities for unwanted interference between molecules in the system. DNA strand displacement has been proposed as a design paradigm for DNA devices, and the DNA strand displacement (DSD) programming language has been developed as a means of formally programming and analysing these devices to check for unwanted interference. We demonstrate, for the first time, the use of probabilistic verification techniques to analyse the correctness, reliability and performance of DNA devices during the design phase. We use the probabilistic model checker prism, in combination with the DSD language, to design and debug DNA strand displacement components and to investigate their kinetics. We show how our techniques can be used to identify design flaws and to evaluate the merits of contrasting design decisions, even on devices comprising relatively few inputs. We then demonstrate the use of these components to construct a DNA strand displacement device for approximate majority voting. Finally, we discuss some of the challenges and possible directions for applying these methods to more complex designs.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.