This paper considers a diffusion-based molecular communication system, where the transmitter uses reaction shift keying (RSK) as the modulation scheme. We focus on the demodulation of RSK signal at the receiver. The receiver consists of a front-end molecular circuit and a back-end demodulator. The front-end molecular circuit is a set of chemical reactions consisting of multiple chemical species. The optimal demodulator computes the posteriori probability of the transmitted symbols given the history of the observation. The derivation of the optimal demodulator requires the solution to a specific Bayesian filtering problem. The solution to this Bayesian filtering problem had been derived for a few specific molecular circuits and specific choice(s) of observed chemical species. The derivation of such solution is also lengthy. The key contribution of this paper is to present a general solution to this Bayesian filtering problem, which can be applied to any molecular circuit and any choice of observed species.
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 survey, 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 survey ends with a technology readiness analysis of MC and future research directions. Nanotechnologies promise new solutions for several applications in biomedical, industrial and military fields. At nano-scale, a nano-machine can be considered as the most basic functional unit. Nano-machines are tiny components consisting of an arranged set of molecules, which are able to perform very simple tasks. Nanonetworks. i.e., the interconnection of nano-machines are expected to expand the capabilities of single nano-machines by allowing them to cooperate and share information. Traditional communication technologies are not suitable for nanonetworks mainly due to the size and power consumption of transceivers, receivers and other components. The use of molecules, instead of electromagnetic or acoustic waves, to encode and transmit the information represents a new communication paradigm that demands novel solutions such as molecular transceivers, channel models or protocols for nanonetworks. In this paper, first the state-of-the-art in nano-machines, including architectural aspects, expected features of future nano-machines, and current developments are presented for a better understanding of nanonetwork scenarios. Moreover, nanonetworks features and components are explained and compared with traditional communication networks. Also some interesting and important applications for nanonetworks are highlighted to motivate the communication needs between the nano-machines. Furthermore, nanonetworks for short-range communication based on calcium signaling and molecular motors as well as for long-range communication based on pheromones are explained in detail. Finally, open research challenges, such as the development of network components, molecular communication theory, and the development of new architectures and protocols, are presented which need to be solved in order to pave the way for the development and deployment of nanonetworks within the next couple of decades. The ability of engineered biological nanomachines to communicate with biological systems at the molecular level is anticipated to enable future applications such as monitoring the condition of a human body, regenerating biological tissues and organs, and interfacing artificial devices with neural systems. From the viewpoint of communication theory and engineering, molecular communication is proposed as a new paradigm for engineered biological nanomachines to communicate with the natural biological nanomachines which form a biological system. Distinct from the current telecommunication paradigm, molecular communication uses molecules as the carriers of information; sender biological nanomachines encode information on molecules and release the molecules in the environment, the molecules then propagate in the environment to receiver biological nanomachines, and the receiver biological nanomachines biochemically react with the molecules to decode information. Current molecular communication research is limited to small-scale networks of several biological nanomachines. Key challenges to bridge the gap between current research and practical applications include developing robust and scalable techniques to create a functional network from a large number of biological nanomachines. Developing networking mechanisms and communication protocols is anticipated to introduce new avenues into integrating engineered and natural biological nanomachines into a single networked system. In this paper, we present the state-of-the-art in the area of molecular communication by discussing its architecture, features, applications, design, engineering, and physical modeling. We then discuss challenges and opportunities in developing networking mechanisms and communication protocols to create a network from a large number of bio-nanomachines for future applications. Molecular communication is an emerging communication paradigm for biological nanomachines. It allows biological nanomachines to communicate through exchanging molecules in an aqueous environment and to perform collaborative tasks through integrating functionalities of individual biological nanomachines. This paper develops the layered architecture of molecular communication and describes research issues that molecular communication faces at each layer of the architecture. Specifically, this paper applies a layered architecture approach, traditionally used in communication networks, to molecular communication, decomposes complex molecular communication functionality into a set of manageable layers, identifies basic functionalities of each layer, and develops a descriptive model consisting of key components of the layer for each layer. This paper also discusses open research issues that need to be addressed at each layer. In addition, this paper provides an example design of targeted drug delivery, a nanomedical application, to illustrate how the layered architecture helps design an application of molecular communication. The primary contribution of this paper is to provide an in-depth architectural view of molecular communication. Establishing a layered architecture of molecular communication helps organize various research issues and design concerns into layers that are relatively independent of each other, and thus accelerates research in each layer and facilitates the design and development of applications of molecular communication. Abstract Molecular communication uses molecules (i.e., biochemical signals) as an information medium and allows biologically and artificially created nano- or microscale entities to communicate over a short distance. It is a new communication paradigm; it is different from the traditional communication paradigm, which uses electromagnetic waves (i.e., electronic and optical signals) as an information medium. Key research challenges in molecular communication include design of system components (i.e., a sender, a molecular propagation system, a receiver, and a molecular communication interface) and mathematical modeling of each system component as well as entire systems. We review all research activities in molecular communication to date, from its origin to recent experimental studies and theoretical approaches for each system component. As a model molecular communication system, we describe an integrated system that combines a molecular communication interface (using a lipid vesicle embedded with channel-forming proteins), a molecular propagation system (using microtubule motility on kinesin molecular motors and DNA hybridization), and a sender receiver (using giant lipid vesicles embedded with gemini-peptide lipids). We also present potential applications and the future outlook of molecular communication.