Model-Based Design and Control of Distributed DNA-Based Systems by Petri Nets

NANO ◽  
2016 ◽  
Vol 11 (01) ◽  
pp. 1650003
Author(s):  
Rizki Mardian ◽  
Kosuke Sekiyama
Keyword(s):  
Petri Nets ◽  
Design Strategy ◽  
Multi Agent Systems ◽  
Individual Level ◽  
Dna Strand Displacement ◽  
In Silico Simulation ◽  
Dna Strand ◽  
High Level ◽  
Silicon Based ◽  
And Control

Coordination is an important aspect in developing distributed systems. While in silicon-based agents, i.e., mechanical robotics, designing individual-level behavior that may emerge into one global function is a typical approach to such systems, in DNA-based agents, programming of each individual’s behavior still remains a challenge, as they are based on chemical reactions. These reactions occur immediately after all reactants have been mixed into a solution, which introduces challenges in logical control. In this work, we report a design strategy for coordinated event-driven DNA-based systems by using a Petri Nets model. First, computational primitives based on DNA strand displacement reaction are introduced. Second, their molecular implementation is abstracted by Petri Nets for high-level design. Third, as our main contribution, we propose the model of interacting multi-agent systems based on DNA-only reactions. We verify our design via in silico simulation and show initial experiments of Petri Nets operators. From the obtained results, we argue that our design strategy is feasible for coordinating interaction of distributed DNA-based systems.

scholarly journals A domain-level DNA strand displacement reaction enumerator allowing arbitrary non-pseudoknotted secondary structures

2020 ◽  
Vol 17 (167) ◽  
pp. 20190866 ◽  
Author(s):  
Stefan Badelt ◽  
Casey Grun ◽  
Karthik V. Sarma ◽  
Brian Wolfe ◽  
Seung Woo Shin ◽  
...  
Keyword(s):  
Dna Nanotechnology ◽  
Biophysical Model ◽  
Kinetic Properties ◽  
Strand Displacement ◽  
Natural Connection ◽  
Dna Strand Displacement ◽  
Wide Range ◽  
Dna Strand ◽  
High Level ◽  
Domain Level

Information technologies enable programmers and engineers to design and synthesize systems of startling complexity that nonetheless behave as intended. This mastery of complexity is made possible by a hierarchy of formal abstractions that span from high-level programming languages down to low-level implementation specifications, with rigorous connections between the levels. DNA nanotechnology presents us with a new molecular information technology whose potential has not yet been fully unlocked in this way. Developing an effective hierarchy of abstractions may be critical for increasing the complexity of programmable DNA systems. Here, we build on prior practice to provide a new formalization of ‘domain-level’ representations of DNA strand displacement systems that has a natural connection to nucleic acid biophysics while still being suitable for formal analysis. Enumeration of unimolecular and bimolecular reactions provides a semantics for programmable molecular interactions, with kinetics given by an approximate biophysical model. Reaction condensation provides a tractable simplification of the detailed reactions that respects overall kinetic properties. The applicability and accuracy of the model is evaluated across a wide range of engineered DNA strand displacement systems. Thus, our work can serve as an interface between lower-level DNA models that operate at the nucleotide sequence level, and high-level chemical reaction network models that operate at the level of interactions between abstract species.

scholarly journals Logical Inference by DNA Strand Algebra

2016 ◽  
Vol 12 (01) ◽  
pp. 29-44
Author(s):  
Kumar S. Ray ◽  
Mandrita Mondal
Keyword(s):  
Expert System ◽  
Paradigm Shift ◽  
Dna Computing ◽  
Modus Ponens ◽  
Logical Inference ◽  
Inference Mechanism ◽  
Dna Strand Displacement ◽  
Draw Conclusion ◽  
Dna Strand ◽  
Silicon Based

Based on the concept of DNA strand displacement and DNA strand algebra we have developed a method for logical inference which is not based on silicon-based computing. Essentially, it is a paradigm shift from silicon to carbon. In this paper, we have considered the inference mechanism, viz. modus ponens, to draw conclusion from any observed fact. Thus, the present approach to logical inference based on DNA strand algebra is basically an attempt to develop expert system design in the domain of DNA computing. We have illustrated our methodology with respect to the worked out example. Our methodology is very flexible for implementation of different expert system applications.

scholarly journals Implementing digital computing with DNA-based switching circuits

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Fei Wang ◽  
Hui Lv ◽  
Qian Li ◽  
Jiang Li ◽  
Xueli Zhang ◽  
...  
Keyword(s):  
Logic Gate ◽  
Scale Up ◽  
Full Adder ◽  
Switching Circuits ◽  
Dna Strand Displacement ◽  
Displacement Reactions ◽  
Dna Strands ◽  
Design Paradigm ◽  
Dna Strand ◽  
High Level

AbstractDNA strand displacement reactions (SDRs) provide a set of intelligent toolboxes for developing molecular computation. Whereas SDR-based logic gate circuits have achieved a high level of complexity, the scale-up for practical achievable computational tasks remains a hurdle. Switching circuits that were originally proposed by Shannon in 1938 and nowadays widely used in telecommunication represent an alternative and efficient means to realize fast-speed and high-bandwidth communication. Here we develop SDR-based DNA switching circuits (DSCs) for implementing digital computing. Using a routing strategy on a programmable DNA switch canvas, we show that arbitrary Boolean functions can be represented by DSCs and implemented with molecular switches with high computing speed. We further demonstrate the implementation of full-adder and square-rooting functions using DSCs, which only uses down to 1/4 DNA strands as compared with a dual-rail logic expression-based design. We expect that DSCs provide a design paradigm for digital computation with biomolecules.

Modeling and Synthesis of Supply Chain Networks Using High-Level Petri Nets

2016 ◽  
pp. 98-117
Author(s):  
Gen'ichi Yasuda
Keyword(s):  
Supply Chain ◽  
Petri Nets ◽  
Discrete Event ◽  
Formal Representation ◽  
Modeling And Control ◽  
Supply Chain Networks ◽  
Chain Processes ◽  
Event Dynamic ◽  
High Level ◽  
And Control

This chapter presents a systematic methodology for modeling and control of supply chain networks, especially focusing on formal representation and control synthesis aspects. A supply chain is represented as a discrete event dynamic system. The use of high-level Petri nets is proposed to formulate event related rules commonly seen in supply chains and analyze cause-effect relationships between events. Petri nets have been successfully introduced as an effective tool for describing control specifications and realizing the control in automated supply chain processes. The extended net representation of the productive task flows can provide more synthetic specifications for consistent management and control of supply chain systems by a top-down refinement methodology. Software implementation is described to simulate and control real supply chain processes.

Modeling and Synthesis of Supply Chain Networks Using High-Level Petri Nets

2020 ◽  
pp. 945-963
Author(s):  
Gen'ichi Yasuda
Keyword(s):  
Supply Chain ◽  
Petri Nets ◽  
Discrete Event ◽  
Formal Representation ◽  
Modeling And Control ◽  
Supply Chain Networks ◽  
Chain Processes ◽  
Event Dynamic ◽  
High Level ◽  
And Control

This chapter presents a systematic methodology for modeling and control of supply chain networks, especially focusing on formal representation and control synthesis aspects. A supply chain is represented as a discrete event dynamic system. The use of high-level Petri nets is proposed to formulate event related rules commonly seen in supply chains and analyze cause-effect relationships between events. Petri nets have been successfully introduced as an effective tool for describing control specifications and realizing the control in automated supply chain processes. The extended net representation of the productive task flows can provide more synthetic specifications for consistent management and control of supply chain systems by a top-down refinement methodology. Software implementation is described to simulate and control real supply chain processes.

scholarly journals Abstractions for DNA circuit design

2011 ◽  
Vol 9 (68) ◽  
pp. 470-486 ◽  
Author(s):  
Matthew R. Lakin ◽  
Simon Youssef ◽  
Luca Cardelli ◽  
Andrew Phillips
Keyword(s):  
Reaction Kinetics ◽  
Computational Cost ◽  
Logic Gates ◽  
Strand Displacement ◽  
Levels Of Detail ◽  
Molecular Detail ◽  
Dna Strand Displacement ◽  
Displacement System ◽  
Dna Strand ◽  
High Level

DNA strand displacement techniques have been used to implement a broad range of information processing devices, from logic gates, to chemical reaction networks, to architectures for universal computation. Strand displacement techniques enable computational devices to be implemented in DNA without the need for additional components, allowing computation to be programmed solely in terms of nucleotide sequences. A major challenge in the design of strand displacement devices has been to enable rapid analysis of high-level designs while also supporting detailed simulations that include known forms of interference. Another challenge has been to design devices capable of sustaining precise reaction kinetics over long periods, without relying on complex experimental equipment to continually replenish depleted species over time. In this paper, we present a programming language for designing DNA strand displacement devices, which supports progressively increasing levels of molecular detail. The language allows device designs to be programmed using a common syntax and then analysed at varying levels of detail, with or without interference, without needing to modify the program. This allows a trade-off to be made between the level of molecular detail and the computational cost of analysis. We use the language to design a buffered architecture for DNA devices, capable of maintaining precise reaction kinetics for a potentially unbounded period. We test the effectiveness of buffered gates to support long-running computation by designing a DNA strand displacement system capable of sustained oscillations.

A Behavior Based Approach to Cellular Self-Organizing Systems Design

2011 ◽  
Author(s):  
Chang Chen ◽  
Yan Jin
Keyword(s):  
Adaptive Systems ◽  
Systems Design ◽  
Functional Requirements ◽  
Multi Agent Systems ◽  
Multi Agent ◽  
Behavior Design ◽  
Behavior Based ◽  
High Level ◽  
And Control ◽  
Self Organizing

Multi-agent systems (MAS) have been considered a potential solution for developing adaptive systems. The design of MAS however is difficult because the global effect emerges from local actions and interactions that can be hard to specify and control. In order to achieve high level resilience and robustness of MAS and retain the capability of specifying desired global effects, we propose a cellular self-organizing (CSO) system framework and a biologically inspired behavior based design approach (BDA) and a field based regulative control mechanism (FBR). The BDA approach links global functional requirements with the local behavior design of a CSO system. FBR is a real-time, dynamical, distributed mechanism that regulates the emergence process for CSOs to self-organize and self-reconfigure in complex operation environments. BDA and FBR together extend the system adaptability without imposing global control over local agents. This paper describes the models of CSO, BDA and FBR and demonstrates their effectiveness by presenting simulation based case studies in which CSO agents explore an unknown environment and move an object to designated locations.

A Methodology to Analyze Multi-Agent Systems Modeled in High Level Petri Nets

2015 ◽  
Vol 25 (07) ◽  
pp. 1199-1235 ◽  
Author(s):  
Lily Chang ◽  
Xudong He
Keyword(s):  
Complex Systems ◽  
Petri Nets ◽  
Model Analysis ◽  
Tool Development ◽  
Multi Agent Systems ◽  
Agent Model ◽  
Agent Systems ◽  
Multi Agent ◽  
High Level

This paper presents a methodology for analyzing multi-agent systems modeled in nested predicate transition nets. The objective is to automate the model analysis for complex systems, and provide a foundation for tool development. We formally define the translation rules that translate the multi-agent model to an executable PROMELA model, and demonstrate the translation with an example.

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