Computing with chemical reaction networks: a tutorial
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Modes of computation (nondeterministic, parallel, interactive, probabilistic, etc.) (68Q10) Models and methods for concurrent and distributed computing (process algebras, bisimulation, transition nets, etc.) (68Q85) Biologically inspired models of computation (DNA computing, membrane computing, etc.) (68Q07)
Abstract: 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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Cites work
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- A general-purpose CRN-to-DSD compiler with formal verification, optimization, and simulation capabilities
- An Algorithm for the General Petri Net Reachability Problem
- Chemical mechanism structure and the coincidence of the stoichiometric and kinetie subspaces
- Chemical reaction network designs for asynchronous logic circuits
- Computation in networks of passively mobile finite-state sensors
- Computation with finite stochastic chemical reaction networks
- Deterministic function computation with chemical reaction networks
- Dominance and deficiency for Petri nets and chemical reaction networks
- Fast computation by population protocols with a leader
- Leaderless Deterministic Chemical Reaction Networks
- Lectures on Petri nets. 1: Basic models. Advances in Petri nets
- Mathematical Theory of the Differential Analyzer
- Minimal output unstable configurations in chemical reaction networks and deciders
- On the reachability problem for 5-dimensional vector addition systems
- Parallel and scalable computation and spatial dynamics with DNA-based chemical reaction networks on a surface
- Parallel program schemata
- Polynomial differential equations compute all real computable functions on computable compact intervals
- Probability 1 computation with chemical reaction networks
- Programming discrete distributions with chemical reaction networks
- Rate-independent computation in continuous chemical reaction networks
- Recursive unsolvability of Post's problem of Tag und other topics in theory of Turing machines
- Semigroups, Presburger formulas, and languages
- Speed faults in computation by chemical reaction networks
- Stochastic approach to chemical kinetics
- Strong Turing completeness of continuous chemical reaction networks and compilation of mixed analog-digital programs
- The computational power of population protocols
- Thermodynamic Analysis of Interacting Nucleic Acid Strands
- Verifying chemical reaction network implementations: a bisimulation approach
- Verifying chemical reaction network implementations: a pathway decomposition approach
- Verifying polymer reaction networks using bisimulation
Cited in
(6)- Facilitation in reaction systems
- Reactamole: functional reactive molecular programming
- Molecular computing for Markov chains
- Molecular device design based on chemical reaction networks: state feedback controller, static pre-filter, addition gate control system and full-dimensional state observer
- Rate-independent computation in continuous chemical reaction networks
- Simplifying Chemical Reaction Network Implementations with Two-Stranded DNA Building Blocks
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