HLA based architecture for molecular communication simulation

Akkaya, Ali; Genc, Gaye; Tuǧcu, Tuna

doi:10.1016/j.simpat.2013.12.012

Cited by 18 publications

(9 citation statements)

References 22 publications

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“…In [236], distributed simulations based on high level architecture (HLA) were proposed and analyzed for MC. The authors mostly focused on confined space and parallelism gain, and did not consider the effect of consecutive symbols in their simulator, dMCS.…”

Section: E Simulation Toolsmentioning

confidence: 99%

A Comprehensive Survey of Recent Advancements in Molecular Communication

Farsad¹,

Yilmaz²,

Eckford³

et al. 2016

IEEE Commun. Surv. Tutorials

824

595

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With much advancement in the field of nanotechnology, bioengineering and synthetic biology over the past decade, microscales and nanoscales devices are becoming a reality. Yet the problem of engineering a reliable communication system between tiny devices is still an open problem. At the same time, despite the prevalence of radio communication, there are still areas where traditional electromagnetic waves find it difficult or expensive to reach. Points of interest in industry, cities, and medical applications often lie in embedded and entrenched areas, accessible only by ventricles at scales too small for conventional radio waves and microwaves, or they are located in such a way that directional high frequency systems are ineffective. Inspired by nature, one solution to these problems is molecular communication (MC), where chemical signals are used to transfer information. Although biologists have studied MC for decades, it has only been researched for roughly 10 year from a communication engineering lens. Significant number of papers have been published to date, but owing to the need for interdisciplinary work, much of the results are preliminary. In this paper, the recent advancements in the field of MC engineering are highlighted. First, the biological, chemical, and physical processes used by an MC system are discussed. This includes different components of the MC transmitter and receiver, as well as the propagation and transport mechanisms. Then, a comprehensive survey of some of the recent works on MC through a communication engineering lens is provided. The paper ends with a technology readiness analysis of MC and future research directions.Comment: Accepted for publication in IEEE Communications Surveys & Tutorial

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Section: E Simulation Toolsmentioning

confidence: 99%

A Comprehensive Survey of Recent Advancements in Molecular Communication

Farsad¹,

Yilmaz²,

Eckford³

et al. 2016

IEEE Commun. Surv. Tutorials

824

595

View full text Add to dashboard Cite

show abstract

“…Here, we highlight the features of simulators whose source code or executables are publicly available. Thus, we exclude simulators that have been described but not released, including NanoNS (Nanoscale Network Simulator) in [44], dMCS (Distributed Molecular Communication Simulator) in [45], and other tools developed internally by authors for their own research.…”

Section: Diffusive Molecular Communication Simulatorsmentioning

confidence: 99%

Simulating with AcCoRD: Actor-based Communication via Reaction–Diffusion

Noel

Cheung

Schober

et al. 2017

Nano Communication Networks

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This paper introduces AcCoRD (Actor-based Communication via Reaction-Diffusion) version 1.0. AcCoRD is a sandbox reaction-diffusion solver designed for the study of molecular communication systems. It uses a hybrid of microscopic and mesoscopic simulation models that enables scalability via user control of local accuracy. AcCoRD is developed in C as an open source command line tool and includes utilities to process simulation output in MATLAB. The latest code and links to user documentation can be found at https://github.com/adamjgnoel/AcCoRD/. This paper provides an overview of AcCoRD's design, including the motivation for developing a specialized reaction-diffusion solver. The corresponding algorithms are presented in detail, including the computational complexity of the microscopic and mesoscopic models. Other novel derivations include the transition rates between adjacent mesoscopic subvolumes of different sizes. Simulation results demonstrate the use of AcCoRD as both an accurate reaction-diffusion solver and one that is catered to the analysis of molecular communication systems. A link is included to videos that demonstrate many of the simulated scenarios. Additional insights from the simulation results include the selection of suitable hybrid model parameters, the impact of reactive surfaces that are in the proximity of a hybrid interface, and the size of a bounded environment that is necessary to assume that it is unbounded. The development of AcCoRD is ongoing, so its future direction is also discussed in order to highlight improvements that will expand its potential areas of application. New features that are being planned at the time of writing include a fluid flow model and more complex actor behavior.

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“…Computer architectures and control systems investigate how to speed up the simulation of large scale designs (e.g. VLSI (Very Large Scale Integration) design (Gonsiorowski, Carothers, & Tropper, 2012;Tsirogiannis & Theodoropoulos, 2013) and nanomachines (Akkaya, Genc, & Tugcu, 2014)), or the hybrid simulation of Cyber-physical systems or embedded system design with discrete and continuous components (Brito et al, 2016;Garraghan, McKee, Ouyang, Webster, & Xu, 2016;Pfeifer, Gerstlauer, & Valvano, 2013). Some authors address extremely large-scale supercomputer design that in turn uses DS on supercomputers (Liu, 2013;Mubarak, Carothers, Ross, & Carns, 2012).…”

Section: Distributed Simulation Applicationsmentioning

confidence: 99%

Distributed simulation: state-of-the-art and potential for operational research

Taylor

2019

European Journal of Operational Research

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HLA based architecture for molecular communication simulation

Cited by 18 publications

References 22 publications

A Comprehensive Survey of Recent Advancements in Molecular Communication

A Comprehensive Survey of Recent Advancements in Molecular Communication

Simulating with AcCoRD: Actor-based Communication via Reaction–Diffusion

Distributed simulation: state-of-the-art and potential for operational research

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