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

Badelt, Stefan; Shin, Seung Woo; Johnson, Robert F.; Dong, Qing; Thachuk, Chris; Winfree, Erik

doi:10.1007/978-3-319-66799-7_15

Cited by 30 publications

(34 citation statements)

References 19 publications

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“…We have designed and verified our MWT at the CRN level of abstraction, but it is useful to estimate the feasibility of actually implementing our design in DNA. For this purpose we used the compiler reported in a very recent paper by Badelt et al [6]. Using this compiler and its encoding of the translation scheme of Chen et al [14], we compiled the CRN for a small MWT and oscillator into DNA strands.…”

Section: Mapping To Moleculesmentioning

confidence: 99%

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Runtime Fault Detection in Programmed Molecular Systems

Ellis

Klinge

Lathrop

et al. 2019

ACM Trans. Softw. Eng. Methodol.

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Watchdog timers are devices that are commonly used to monitor the health of safety-critical hardware and software systems. Their primary function is to raise an alarm if the monitored systems fail to emit periodic "heartbeats" that signal their well-being. In this paper we design and verify a molecular watchdog timer for monitoring the health of programmed molecular nanosystems. This raises new challenges because our molecular watchdog timer and the system that it monitors both operate in the probabilistic environment of chemical kinetics, where many failures are certain to occur and it is especially hard to detect the absence of a signal.Our molecular watchdog timer is the result of an incremental design process that uses goal-oriented requirements engineering, simulation, stochastic analysis, and software verification tools. We demonstrate the molecular watchdog's functionality by having it monitor a molecular oscillator. Both the molecular watchdog timer and the oscillator are implemented as chemical reaction networks, which are the current programming language of choice for many molecular programming applications.

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Section: Mapping To Moleculesmentioning

confidence: 99%

“…In addition to alarming, our MWT can trigger the recovery of a monitored system. 6. Our MWT is automatically reusable rather than having to be discarded after a single failure.…”

Section: Introductionmentioning

confidence: 99%

Runtime Fault Detection in Programmed Molecular Systems

Ellis

Klinge

Lathrop

et al. 2019

ACM Trans. Softw. Eng. Methodol.

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“…Decoupling reactions from chemical implementations introduces a higher level of abstraction, where CRNs become a high-level programming language. Using a (semi-)automated method, arbitrary abstract CRNs can then be compiled to chemical implementations [62,23,7].…”

Section: Introductionmentioning

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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“…A stack of tools is emerging to help automate the design process. We can now compile abstract reaction networks to a set of DNA oligonucleotides that will implement the dynamics of the network in solution [12]. We can computationally simulate the dynamics of these oligonucleotide molecular systems [13] to allow debugging prior to experimental implementation.…”

Section: Introductionmentioning

confidence: 99%

A Reaction Network Scheme Which Implements Inference and Learning for Hidden Markov Models

Singh

Wiuf

Behera

et al. 2019

Lecture Notes in Computer Science

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With a view towards molecular communication systems and molecular multi-agent systems, we propose the Chemical Baum-Welch Algorithm, a novel reaction network scheme that learns parameters for Hidden Markov Models (HMMs). Each reaction in our scheme changes only one molecule of one species to one molecule of another. The reverse change is also accessible but via a different set of enzymes, in a design reminiscent of futile cycles in biochemical pathways. We show that every fixed point of the Baum-Welch algorithm for HMMs is a fixed point of our reaction network scheme, and every positive fixed point of our scheme is a fixed point of the Baum-Welch algorithm. We prove that the "Expectation" step and the "Maximization" step of our reaction network separately converge exponentially fast. We simulate mass-action kinetics for our network on an example sequence, and show that it learns the same parameters for the HMM as the Baum-Welch algorithm.

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

Cited by 30 publications

References 19 publications

Runtime Fault Detection in Programmed Molecular Systems

Runtime Fault Detection in Programmed Molecular Systems

Computing with chemical reaction networks: a tutorial

A Reaction Network Scheme Which Implements Inference and Learning for Hidden Markov Models

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