Design and analysis of DNA strand displacement devices using probabilistic model checking

Lakin, Matthew R.; Parker, David; Cardelli, Luca; Kwiatkowska, Marta; Phillips, Andrew

doi:10.1098/rsif.2011.0800

Cited by 72 publications

(58 citation statements)

References 37 publications

(78 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…These constraints are necessary conditions for the existence of a set of biochemically realizable reactions that react according to the dynamics y = p(y). Note however that we shall not discuss here the choice of their possible implementations by particular biochemical devices, such as DNA polymers [40], DNA double strands [33] or enzymatic reactions [19,37] as this is beyond the scope of this paper.…”

Section: Definitionmentioning

confidence: 99%

Strong Turing Completeness of Continuous Chemical Reaction Networks and Compilation of Mixed Analog-Digital Programs

Fages

Guludec

Bournez

et al. 2017

Lecture Notes in Computer Science

101

View full text Add to dashboard Cite

Abstract. When seeking to understand how computation is carried out in the cell to maintain itself in its environment, process signals and make decisions, the continuous nature of protein interaction processes forces us to consider also analog computation models and mixed analog-digital computation programs. However, recent results in the theory of analog computability and complexity establish fundamental links with classical programming. In this paper, we derive from these results the strong (uniform computability) Turing completeness of chemical reaction networks over a finite set of molecular species under the differential semantics, solving a long standing open problem. Furthermore we derive from the proof a compiler of mathematical functions into elementary chemical reactions. We illustrate the reaction code generated by our compiler on trigonometric functions, and on various sigmoid functions which can serve as markers of presence or absence for implementing program control instructions in the cell and imperative programs. Then we start comparing our compiler-generated circuits to the natural circuit of the MAPK signaling network, which plays the role of an analog-digital converter in the cell with a Hill type sigmoid input/output functions.

show abstract

Section: Definitionmentioning

confidence: 99%

Strong Turing Completeness of Continuous Chemical Reaction Networks and Compilation of Mixed Analog-Digital Programs

Fages

Guludec

Bournez

et al. 2017

Lecture Notes in Computer Science

101

View full text Add to dashboard Cite

show abstract

“…Quantitative modelling and verification technology has already been applied to DNA computing devices [42], where it was able to automatically discover and diagnose a design error. These methods are applicable to molecular sensing devices at the nanoscale.…”

Section: Further Advancesmentioning

confidence: 99%

Advances in Quantitative Verification for Ubiquitous Computing

Kwiatkowska

2013

Theoretical Aspects of Computing – ICTAC 2013

Self Cite

View full text Add to dashboard Cite

Abstract. Ubiquitous computing, where computers 'disappear' and instead sensor-enabled and software-controlled devices assist us in everyday tasks, has become an established trend. To ensure the safety and reliability of software embedded in these devices, rigorous model-based design methodologies are called for. Quantitative verification, a powerful technique for analysing system models against quantitative properties such as "the probability of a data packet being delivered within 1ms to a nearby Bluetooth device is at least 0.98", has proved useful by detecting and correcting flaws in a number of ubiquitous computing applications. In this paper, we focus on three key aspects of ubiquitous computing: autonomous behaviour, constrained resources and adaptiveness. We summarise recent advances of quantitative verification in relation to these aspects, illustrating each with a case study analysed using the probabilistic model checker PRISM. The paper concludes with an outline of future challenges that remain in this area.

show abstract

“…The feasibility of this sort of unintended interaction has been shown experimentally and in formal verification of composed DNA gates [17]. Crosstalk is recognized as a potentially significant threat to successful self-assembly.…”

Section: E Requirements Evolutionmentioning

confidence: 99%

“…The most relevant work is that of Lakin, Parker, Cardelli, Kwiatkowska and Phillips. They have recently used the DSD strand displacement specification language and the probabilistic model checker PRISM to verify properties on simple DNA reaction gates and then composed them into a larger DNA system that implements the approximate majority protocol [17]. Our work differs from theirs in focusing on the identification, analysis and verification of requirements rather than, as they do, on design.…”

Section: Related Workmentioning

confidence: 99%

“…Most DNA nanohnology experiments are already so complex that their initial designs require nontrivial computations with software tools such as caDNAno [14] or the DSD programming language [15]. Probabilistic model checking has also been used to make preliminary analyses of experimental designs [16], [17]. These design-stage computations, much faster and cheaper than the experiments themselves, are essential to the predictability, and hence the productivity, of DNA nanotechnology.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Requirements analysis for a product family of DNA nanodevices

Lutz

Lathrop

et al. 2012

2012 20th IEEE International Requirements Engineering Conference (RE)

View full text Add to dashboard Cite

Abstract-DNA nanotechnology uses the information processing capabilities of nucleic acids to design self-assembling, programmable structures and devices at the nanoscale. Devices developed to date have been programmed to implement logic circuits and neural networks, capture or release specific molecules, and traverse molecular tracks and mazes.Here we investigate the use of requirements engineering methods to make DNA nanotechnology more productive, predictable, and safe. We use goal-oriented requirements modeling to identify, specify, and analyze a product family of DNA nanodevices, and we use PRISM model checking to verify both common properties across the family and properties that are specific to individual products. Challenges to doing requirements engineering in this domain include the errorprone nature of nanodevices carrying out their tasks in the probabilistic world of chemical kinetics, the fact that roughly a nanomole (a 1 followed by 14 0s) of devices are typically deployed at once, and the difficulty of specifying and achieving modularity in a realm where devices have many opportunities to interfere with each other. Nevertheless, our results show that requirements engineering is useful in DNA nanotechnology and that leveraging the similarities among nanodevices in the product family improves the modeling and analysis by supporting reuse.

show abstract

Design and analysis of DNA strand displacement devices using probabilistic model checking

Cited by 72 publications

References 37 publications

Strong Turing Completeness of Continuous Chemical Reaction Networks and Compilation of Mixed Analog-Digital Programs

Strong Turing Completeness of Continuous Chemical Reaction Networks and Compilation of Mixed Analog-Digital Programs

Advances in Quantitative Verification for Ubiquitous Computing

Requirements analysis for a product family of DNA nanodevices

Contact Info

Product

Resources

About