A Survey of Biological Building Blocks for Synthetic Molecular Communication Systems

Söldner, Christian A.; Socher, Eileen; Jamali, Vahid; Wicke, Wayan; Ahmadzadeh, Arman; Breitinger, Hans‐Georg; Burkovski, Andreas; Castiglione, Kathrin; Schober, Robert; Sticht, Heinrich

doi:10.1109/comst.2020.3008819

Cited by 57 publications

(39 citation statements)

References 249 publications

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“…( 2) models a first-order reaction but can also be used to approximate higher order reactions, see, e.g., [27]- [29]. 2 Molecule harvesting units can be realized and integrated into practical MC transmitters, see, e.g., [25]. Examples of biological building blocks that can potentially realize the functionalities of a molecule harvesting unit include: a) light-driven inward proton pumps, capable of transporting protons (signaling molecules) from the surrounding medium into the interior of the transmitter, b) adenosine triphosphate (ATP)-driven and light-driven active calcium ion transporters, capable of harvesting calcium ions (signaling molecules), c) dopamine transporters capable of harvesting dopamine neurotransmitters in the synaptic cleft.…”

Section: System Modelmentioning

confidence: 99%

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Molecule Harvesting Transmitter Model for Molecular Communication Systems

Ahmadzadeh

Jamali

Schober

2022

IEEE Open J. Commun. Soc.

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This paper develops mathematical models for molecule harvesting transmitters in diffusive molecular communication (MC) systems. In particular, we consider a communication link consisting of a spherical transmitter nano-machine and a spherical receiver nano-machine suspended in a fluid environment. The transmitter and the receiver exchange information via signaling molecules. The transmitter is equipped with molecule harvesting units on its surface. Signaling molecules which come into contact with the harvesting units may be re-captured by the transmitter. For this system, we derive closed-form expressions for the channel impulse response and harvesting impulse response. Furthermore, we extend the harvesting transmitter model to the case of continuous signaling molecule release. In particular, we derive closed-form expressions for the average received signal at the receiver and the average harvested signal at the transmitter for different temporal release rates namely, constant, linearly increasing, and linearly decreasing release rates. Finally, we validate the accuracy of the derived mathematical expressions via particle-based simulations.

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Section: System Modelmentioning

confidence: 99%

“…where M is the total number of harvesting units on the surface of the transmitter. Specifically, k abs is substituted instead of k abs in ( 23), ( 24), (25), and (26).…”

Section: E Physical Properties Of Harvesting Unitsmentioning

confidence: 99%

Molecule Harvesting Transmitter Model for Molecular Communication Systems

Ahmadzadeh

Jamali

Schober

2022

IEEE Open J. Commun. Soc.

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“…General Survey [21] Applications in Medicine [22,23,24] Applications in Biology [11,10,25,26] Applications in Nanonetworking [27,28,29] Channel Models [30] Information Theoretic Limits [14,13] Modulation and Equalization [8,9,31] Synaptic Communication [32] The vast majority of the existing surveys have focused on applications. A key novel aspect of this survey is its focus on methodology.…”

Section: Topic Referencesmentioning

confidence: 99%

“…One advantage of this approach is that, under certain conditions, one can obtain explicit solutions, which are desirable for the design of modulation and detection schemes. Indeed, using the Wiener process model, there has been extensive work developing novel modulation and detection schemes, as well as parameter estimation and channel coding (e.g., [8,9,10,11]). Techniques from information theory have also provided insights into the fundamental performance limits of these schemes (e.g., [12,13,14]).…”

Section: Introductionmentioning

confidence: 99%

Stochastic reaction and diffusion systems in molecular communications: Recent results and open problems

Egan¹,

Akdeniz²,

Tang³

2022

Digital Signal Processing

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Chemical reactions and diffusion are two basic mechanisms governing the dynamics of molecules in a fluid.As such, they play a critical role in molecular communication for channel modeling, design of detection rules, implementation of molecular circuits for computation, and modeling interactions with external biochemical systems. For finite numbers of information-carrying molecules, stochastic models naturally arise with the simplest example given by the Wiener process, often known as Brownian motion. Nevertheless, the Wiener process fails to be accurate when external forces, friction, and chemical reactions are present. Recently, there have been several contributions that tailor molecular communication systems to these more challenging channel conditions. In this paper, we first overview a general family of stochastic models of reaction and diffusion systems, including both Langevin diffusion and the reaction-diffusion master equation. These models form a basis for the use of these models as molecular communication channels, from which modulation and detection schemes can be developed. We survey recent results on the design of these schemes, with a focus on a recently developed approach which is robust to a wide range of channel models, known as equilibrium signaling. We then turn to the implementation of these detection schemes and related parameter estimation problems via stochastic molecular circuits, based on stochastic chemical reaction networks. Finally, interactions between molecular communication systems and stochastic biological systems as well as open problems are discussed.Our overarching goal is to highlight how the consideration of general stochastic models of reaction and diffusion can be utilized in order to widen the application of molecular communications both within engineered systems, and also as motivation for advances in the mathematical characterization of these models.

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“…A frontier research can be envisaged, where nano-bio-info-cogno-devices are designed, built, and operated in an unprecedented manner. It is worth mentioning that there are already existing works in the literature that investigate MC using SB, as discussed in the recent surveys (Bi et al (2021); Söldner et al (2020)). In these works the biological components that can potentially serve as the main building blocks, i.e., transmitter, receiver, and signaling particles, for the design and implementation of synthetic MC systems are defined.…”

Section: Synthetic Biology and Molecular Communication: Two Growing And Potentially Converging Fieldsmentioning

confidence: 99%

Synthetic Cells Engaged in Molecular Communication: An Opportunity for Modelling Shannon- and Semantic-Information in the Chemical Domain

Magarini

Stano

2021

Front. Comms. Net.

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In this Perspective article we intend to focus on the opportunity of modelling Shannon information and/or “semantic” information in the field originated by the convergence of bottom-up synthetic biology (in particular, the construction of “synthetic cells”) and the engineering approaches to molecular communication. In particular we will argue that the emerging technology of synthetic cell fabrication will allow novel opportunities to study nano-scale communication and manipulation of information in unprecedented manner. More specifically, we will discuss the possibility of enquiring on the transfer and manipulation of information in the chemical domain, and interpreting such a dynamics according to Shannon or to MacKay-Bateson (“semantic” information).

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A Survey of Biological Building Blocks for Synthetic Molecular Communication Systems

Cited by 57 publications

References 249 publications

Molecule Harvesting Transmitter Model for Molecular Communication Systems

Molecule Harvesting Transmitter Model for Molecular Communication Systems

Stochastic reaction and diffusion systems in molecular communications: Recent results and open problems

Synthetic Cells Engaged in Molecular Communication: An Opportunity for Modelling Shannon- and Semantic-Information in the Chemical Domain

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