Modelling, simulating and verifying Turing-powerful strand displacement systems

DOI10.1007/978-3-642-23638-9_12MaRDI QIDQ3092338zbMATH OpenOpenAlexFDO

Authors Matthew R. Lakin, Andrew Phillips

Publication date 16 September 2011

Published in Lecture Notes in Computer Science (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1007/978-3-642-23638-9_12

Mathematics Subject Classification ID

Modes of computation (nondeterministic, parallel, interactive, probabilistic, etc.) (68Q10) Specification and verification (program logics, model checking, etc.) (68Q60) Protein sequences, DNA sequences (92D20)

Recommendations

• Functional analysis of large-scale DNA strand displacement circuits
• Space and energy efficient computation with DNA strand displacement systems
• Implementation of Turing machine using DNA strand displacement
• Two-domain DNA strand displacement
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Cites work

• Computation with finite stochastic chemical reaction networks
• Efficient Turing-universal computation with DNA polymers
• On Computable Numbers, with an Application to the Entscheidungsproblem
• Turing universality of the biochemical ground form

Cited in

(19)

• Performance limits and trade-offs in entropy-driven biochemical computers
• Implementation of Turing machine using DNA strand displacement
• Verifying polymer reaction networks using bisimulation
• Formal semantics and verification of network-based biocomputation circuits
• SIMD||DNA: single instruction, multiple data computation with DNA strand displacement cascades
• An RNA-based theory of natural universal computation
• In vitro implementation of a stack data structure based on DNA strand displacement
• Time complexity of computation and construction in the chemical reaction network-controlled tile assembly model
• Modular verification of chemical reaction network encodings via serializability analysis
• A strand graph semantics for DNA-based computation
• Leakless DNA strand displacement systems
• Efficient Turing-universal computation with DNA polymers
• Toehold DNA languages are regular (extended abstract)
• Stochastic simulation of multiple process calculi for biology
• Two-domain DNA strand displacement
• Two-domain DNA strand displacement
• Modular verification of DNA strand displacement networks via serializability analysis
• Functional analysis of large-scale DNA strand displacement circuits
• Space and energy efficient computation with DNA strand displacement systems

Describes a project that uses

Uses Software

• PRISM

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